5500000@unknown@formal@none@1@S@New complexities in helper T Cell fate determination and the implications for autoimmune diseases@(((:tag . "JJ") (:stem . "new") (:form . "New") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "complexity") (:form . "complexities") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Cell") (:form . "Cell") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "fate") (:form . "fate") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "determination") (:form . "determination")\n  (:end . 52) (:start . 39) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "implication") (:form . "implications") (:end . 73)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 88)\n  (:start . 78) (:id . 54))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 97)\n  (:start . 89) (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.1) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5500001@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s1.2) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500002@unknown@formal@none@1@S@Recently, new complexities in cell fate decision for helper T cells have emerged.@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "complexity") (:form . "complexities") (:end . 26)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "fate") (:form . "fate") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "decision") (:form . "decision") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 59)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "emerge") (:form . "emerged") (:end . 80)\n  (:start . 73) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.3) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500003@unknown@formal@none@1@S@One new lineage, which has come to be called Th17 cells, selectively produces proinflammatory cytokines including interleukin-17 (IL-17, A and F), IL-21, and IL-22.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "come") (:form . "come") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 37) (:start . 35)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 44) (:start . 38)\n  (:id . 51))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 49) (:start . 45)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 55) (:start . 50)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 54))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 68)\n  (:start . 57) (:id . 55))\n ((:tag . "VBZ") (:stem . "produce") (:form . "produces") (:end . 77)\n  (:start . 69) (:id . 56))\n ((:tag . "JJ") (:stem . "proinflammatory") (:form . "proinflammatory")\n  (:end . 93) (:start . 78) (:id . 57))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 103)\n  (:start . 94) (:id . 58))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 113)\n  (:start . 104) (:id . 59))\n ((:tag . "NN") (:stem . "interleukin-17") (:form . "interleukin-17")\n  (:end . 128) (:start . 114) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 135)\n  (:start . 130) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 138) (:start . 137)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 144) (:start . 143)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "IL-21") (:form . "IL-21") (:end . 152)\n  (:start . 147) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 71))\n ((:tag . "NN") (:stem . "il-22") (:form . "IL-22") (:end . 163)\n  (:start . 158) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s1.4) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500004@unknown@formal@none@1@S@In conjunction with transforming growth factor ß-1 (TGFß-1), IL-6, IL-21, and IL-23, which activate the transcription factor, signal transducer, and activator of transcription 3 (Stat3), the expression of another transcription factor, retinoic acid-related orphan receptor-γt (RORγt) leads to the differentiation of Th17 cells in mice.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "conjunction") (:form . "conjunction") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "transform") (:form . "transforming") (:end . 32)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 39)\n  (:start . 33) (:id . 46))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 46)\n  (:start . 40) (:id . 47))\n ((:tag . "NNP") (:stem . "ß-1") (:form . 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"in") (:end . 329) (:start . 327)\n  (:id . 99))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 334)\n  (:start . 330) (:id . 100))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 335) (:start . 334)\n  (:id . 101)))@@@1@60@((:identifiers (:sid . :s1.5) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500005@unknown@formal@none@1@S@Other cytokines including IL-2, IL-4, interferon-γ (IFN-γ) and IL-27 inhibit Th17 differentiation.@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "il-2") (:form . "IL-2") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "interferon-γ") (:form . "interferon-γ") (:end . 50)\n  (:start . 38) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "il-27") (:form . "IL-27") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "inhibit") (:form . "inhibit") (:end . 76)\n  (:start . 69) (:id . 55))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 97) (:start . 82) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.6) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500006@unknown@formal@none@1@S@However, IL-2 acting with TGFß-1 induces differentiation of naive CD4+ T cells to become regulatory T cells (Tregs).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "il-2") (:form . "IL-2") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 20) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "tgfß-1") (:form . "TGFß-1") (:end . 32)\n  (:start . 26) (:id . 47))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 56) (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 70) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 72) (:start . 71)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 78) (:start . 73)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "VB") (:stem . "become") (:form . "become") (:end . 88)\n  (:start . 82) (:id . 56))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 99)\n  (:start . 89) (:id . 57))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 107)\n  (:start . 102) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 114)\n  (:start . 109) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.7) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500007@unknown@formal@none@1@S@Th17 cells are now known to play an important role not only in the pathogenesis of inflammation and autoimmune diseases, but also host defense against extracellular bacteria.@(((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 45)\n  (:start . 36) (:id . 50))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 59) (:start . 55)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 79)\n  (:start . 67) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 95)\n  (:start . 83) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 110)\n  (:start . 100) (:id . 60))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 119)\n  (:start . 111) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 62))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 124) (:start . 121)\n  (:id . 63))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 129) (:start . 125)\n  (:id . 64))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 134) (:start . 130)\n  (:id . 65))\n ((:tag . "NN") (:stem . "defense") (:form . "defense") (:end . 142)\n  (:start . 135) (:id . 66))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 150)\n  (:start . 143) (:id . 67))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 164) (:start . 151) (:id . 68))\n ((:tag . "NNS") (:stem . "bacteria") (:form . "bacteria") (:end . 173)\n  (:start . 165) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.8) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500008@unknown@formal@none@1@S@Conversely, extensive data substantiate the role of Tregs as essential in maintenance of peripheral tolerance.@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "substantiate") (:form . "substantiate") (:end . 39)\n  (:start . 27) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 70)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "NN") (:stem . "maintenance") (:form . "maintenance") (:end . 85)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "peripheral") (:form . "peripheral") (:end . 99)\n  (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "tolerance") (:form . "tolerance") (:end . 109)\n  (:start . 100) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.9) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500009@unknown@formal@none@1@S@Selectively targeting Tregs and Th17 cells are likely to be important strategies in the treatment of inflammatory and autoimmune diseases in humans.@(((:tag . "RB") (:stem . "selectively") (:form . "Selectively") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 21)\n  (:start . 12) (:id . 43))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 27) (:start . 22)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 31) (:start . 28)\n  (:id . 45))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 42) (:start . 37)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 69)\n  (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 80)\n  (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 83) (:start . 81)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 97)\n  (:start . 88) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 113)\n  (:start . 101) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 128)\n  (:start . 118) (:id . 60))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 137)\n  (:start . 129) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "human") (:form . "humans") (:end . 147)\n  (:start . 141) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x1.10.1) (:span 47 53)))\n (:hscopes ((:id . :x1.10.1) (:span 0 147)))\n (:identifiers (:sid . :s1.10) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500010@unknown@formal@none@1@S@Keywords: Th17 cells, autoimmune diseases, inflammation, IL-17, Rheumatoid arthritis@(((:tag . "NNPS") (:stem . "Keyword") (:form . "Keywords") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 32)\n  (:start . 22) (:id . 47))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 55)\n  (:start . 43) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "rheumatoid") (:form . "Rheumatoid") (:end . 74)\n  (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "arthritis") (:form . "arthritis") (:end . 84)\n  (:start . 75) (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.11) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500011@unknown@formal@none@1@S@Introduction@(((:tag . "NN") (:stem . "introduction") (:form . "Introduction") (:end . 12)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s1.12) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500012@unknown@formal@none@1@S@It is well-established that the innate immune response leads to activation of adaptive immunity, shaping the proper response, depending upon the pathogen eliciting the reaction.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "well-established") (:form . "well-established")\n  (:end . 22) (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "innate") (:form . "innate") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 60) (:start . 55)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 74)\n  (:start . 64) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "adaptive") (:form . "adaptive") (:end . 86)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "immunity") (:form . "immunity") (:end . 95)\n  (:start . 87) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "shape") (:form . "shaping") (:end . 104)\n  (:start . 97) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "proper") (:form . "proper") (:end . 115)\n  (:start . 109) (:id . 59))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 124)\n  (:start . 116) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "depend") (:form . "depending") (:end . 135)\n  (:start . 126) (:id . 62))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 140) (:start . 136)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 64))\n ((:tag . "NN") (:stem . "pathogen") (:form . "pathogen") (:end . 153)\n  (:start . 145) (:id . 65))\n ((:tag . "VBG") (:stem . "elicit") (:form . "eliciting") (:end . 163)\n  (:start . 154) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 67))\n ((:tag . "NN") (:stem . "reaction") (:form . "reaction") (:end . 176)\n  (:start . 168) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.13) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500013@unknown@formal@none@1@S@Conversely, though, it is also clear that adaptive immune response, especially, CD4+ or helper T cells orchestrate responses to effectively eliminate pathogens.@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "RB") (:stem . "though") (:form . "though") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 30) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 36) (:start . 31)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "adaptive") (:form . "adaptive") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 57)\n  (:start . 51) (:id . 52))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 66)\n  (:start . 58) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "RB") (:stem . "especially") (:form . "especially") (:end . 78)\n  (:start . 68) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 94)\n  (:start . 88) (:id . 59))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 102) (:start . 97)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "orchestrate") (:form . "orchestrate") (:end . 114)\n  (:start . 103) (:id . 62))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 124)\n  (:start . 115) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 127) (:start . 125)\n  (:id . 64))\n ((:tag . "RB") (:stem . "effectively") (:form . "effectively") (:end . 139)\n  (:start . 128) (:id . 65))\n ((:tag . "VB") (:stem . "eliminate") (:form . "eliminate") (:end . 149)\n  (:start . 140) (:id . 66))\n ((:tag . "NNS") (:stem . "pathogen") (:form . "pathogens") (:end . 159)\n  (:start . 150) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.14) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500014@unknown@formal@none@1@S@Classically, helper T cells were considered to differentiate into two lineages, T helper 1 (Th1) cells or Th2 cells (1).@(((:tag . "RB") (:stem . "classically") (:form . "Classically") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "VB") (:stem . "differentiate") (:form . "differentiate")\n  (:end . 60) (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "lineage") (:form . "lineages") (:end . 78)\n  (:start . 70) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 88)\n  (:start . 82) (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 102) (:start . 97)\n  (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 105) (:start . 103)\n  (:id . 62))\n ((:tag . "NN") (:stem . "th2") (:form . "Th2") (:end . 109) (:start . 106)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 115)\n  (:start . 110) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 65))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 118) (:start . 117)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.15) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500015@unknown@formal@none@1@S@In addition to ligation of the T-cell receptor (TCR) and co-stimulatory receptors, a suitable cytokine milieu is required for fate decision of helper T cells (1).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ligation") (:form . "ligation") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "t-cell") (:form . "T-cell") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 46)\n  (:start . 38) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "TCR") (:form . "TCR") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "co-stimulatory") (:form . "co-stimulatory")\n  (:end . 71) (:start . 57) (:id . 54))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 81)\n  (:start . 72) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "suitable") (:form . "suitable") (:end . 93)\n  (:start . 85) (:id . 58))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . "NN") (:stem . "milieu") (:form . "milieu") (:end . 109)\n  (:start . 103) (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 121)\n  (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . "NN") (:stem . "fate") (:form . "fate") (:end . 130) (:start . 126)\n  (:id . 64))\n ((:tag . "NN") (:stem . "decision") (:form . "decision") (:end . 139)\n  (:start . 131) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 66))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 149)\n  (:start . 143) (:id . 67))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 151) (:start . 150)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 157)\n  (:start . 152) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 70))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 160) (:start . 159)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s1.16) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500016@unknown@formal@none@1@S@In particular, interleukin-12 (IL-12), which is produced by activated antigen-presenting cells (APCs), promotes Th1 differentiation (2), whereas IL-4, produced by activated T cells and some innate immune cells, drives Th2 differentiation (1).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "interleukin-12") (:form . "interleukin-12")\n  (:end . 29) (:start . 15) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "il-12") (:form . "IL-12") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 44) (:start . 39)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 56)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 69)\n  (:start . 60) (:id . 54))\n ((:tag . "JJ") (:stem . "antigen-presenting") (:form . "antigen-presenting")\n  (:end . 88) (:start . 70) (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 94) (:start . 89)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "APC") (:form . "APCs") (:end . 100) (:start . 96)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 111)\n  (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 115) (:start . 112)\n  (:id . 62))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 131) (:start . 116) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 135) (:start . 134)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 67))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 144)\n  (:start . 137) (:id . 68))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 149) (:start . 145)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 159)\n  (:start . 151) (:id . 71))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 162) (:start . 160)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 172)\n  (:start . 163) (:id . 73))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 174) (:start . 173)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 180)\n  (:start . 175) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 184) (:start . 181)\n  (:id . 76))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 189) (:start . 185)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "innate") (:form . "innate") (:end . 196)\n  (:start . 190) (:id . 78))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 203)\n  (:start . 197) (:id . 79))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 209)\n  (:start . 204) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 210) (:start . 209)\n  (:id . 81))\n ((:tag . "VBZ") (:stem . "drive") (:form . "drives") (:end . 217)\n  (:start . 211) (:id . 82))\n ((:tag . "NN") (:stem . "th2") (:form . "Th2") (:end . 221) (:start . 218)\n  (:id . 83))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 237) (:start . 222) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 239) (:start . 238)\n  (:id . 85))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 240) (:start . 239)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 241) (:start . 240)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 242) (:start . 241)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s1.17) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500017@unknown@formal@none@1@S@While the Th1/Th2 paradigm provided invaluable insights for immunologists, its limitations were also clear.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "th1/th2") (:form . "Th1/Th2") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "paradigm") (:form . "paradigm") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "VBD") (:stem . "provide") (:form . "provided") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "JJ") (:stem . "invaluable") (:form . "invaluable") (:end . 46)\n  (:start . 36) (:id . 47))\n ((:tag . "NNS") (:stem . "insight") (:form . "insights") (:end . 55)\n  (:start . 47) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "immunologist") (:form . "immunologists")\n  (:end . 73) (:start . 60) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 51))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 78) (:start . 75)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "limitation") (:form . "limitations") (:end . 90)\n  (:start . 79) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 95) (:start . 91)\n  (:id . 54))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 100) (:start . 96)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 106)\n  (:start . 101) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.18) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500018@unknown@formal@none@1@S@What was the most obvious was the inability of this dichotomy to explain autoimmune diseases.@(((:tag . "WP") (:stem . "what") (:form . "What") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "inability") (:form . "inability") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "dichotomy") (:form . "dichotomy") (:end . 61)\n  (:start . 52) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "VB") (:stem . "explain") (:form . "explain") (:end . 72)\n  (:start . 65) (:id . 54))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 83)\n  (:start . 73) (:id . 55))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.19) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500019@unknown@formal@none@1@S@More recent studies have shown the existence of the additional subpopulations of T helper cells that are also important in immunoregulation and host defense.@(((:tag . "RBR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "existence") (:form . "existence") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 62)\n  (:start . 52) (:id . 51))\n ((:tag . "NNS") (:stem . "subpopulation") (:form . "subpopulations")\n  (:end . 77) (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 53))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 82) (:start . 81)\n  (:id . 54))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 89)\n  (:start . 83) (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 95) (:start . 90)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 100) (:start . 96)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 109) (:start . 105)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 119)\n  (:start . 110) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "NN") (:stem . "immunoregulation") (:form . "immunoregulation")\n  (:end . 139) (:start . 123) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 63))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 148) (:start . 144)\n  (:id . 64))\n ((:tag . "NN") (:stem . "defense") (:form . "defense") (:end . 156)\n  (:start . 149) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.20) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500020@unknown@formal@none@1@S@One important subset is CD4+CD25+, regulatory T cells (Tregs) (3, 4).@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "cd4+cd25+") (:form . "CD4+CD25+") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 45)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 54))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 64) (:start . 63)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 56))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 67) (:start . 66)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s1.21) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500021@unknown@formal@none@1@S@Tregs suppress the proliferation and function of effector T cells, and attenuate immune responses against self or nonself-antigens (3, 4).@(((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "suppress") (:form . "suppress") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 32) (:start . 19) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 59) (:start . 58)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "VB") (:stem . "attenuate") (:form . "attenuate") (:end . 80)\n  (:start . 71) (:id . 54))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 97)\n  (:start . 88) (:id . 56))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 105)\n  (:start . 98) (:id . 57))\n ((:tag . "NN") (:stem . "self") (:form . "self") (:end . 110) (:start . 106)\n  (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 113) (:start . 111)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "nonself-antigen") (:form . "nonself-antigens")\n  (:end . 130) (:start . 114) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 132) (:start . 131)\n  (:id . 61))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 133) (:start . 132)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 63))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.22) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500022@unknown@formal@none@1@S@Another recently identified new fate of T cells is Th17 cells that selectively produce IL-17 (A and F) (5, 6).@(((:tag . "DT") (:stem . "another") (:form . "Another") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 27)\n  (:start . 17) (:id . 44))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 31) (:start . 28)\n  (:id . 45))\n ((:tag . "NN") (:stem . "fate") (:form . "fate") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 61) (:start . 56)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 78)\n  (:start . 67) (:id . 54))\n ((:tag . "VBP") (:stem . "produce") (:form . "produce") (:end . 86)\n  (:start . 79) (:id . 55))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 92) (:start . 87)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 101) (:start . 100)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 105) (:start . 104)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 64))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 108) (:start . 107)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 109) (:start . 108)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s1.23) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500023@unknown@formal@none@1@S@In the past three years, discoveries pertaining to this newly identified T helper subset in humans and mice have accumulated with tremendous speed (7-10).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "past") (:form . "past") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "discovery") (:form . "discoveries") (:end . 36)\n  (:start . 25) (:id . 48))\n ((:tag . "VBG") (:stem . "pertain") (:form . "pertaining") (:end . 47)\n  (:start . 37) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "RB") (:stem . "newly") (:form . "newly") (:end . 61) (:start . 56)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 72)\n  (:start . 62) (:id . 53))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 81)\n  (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 88)\n  (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "human") (:form . "humans") (:end . 98)\n  (:start . 92) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 107)\n  (:start . 103) (:id . 60))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 112) (:start . 108)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "accumulate") (:form . "accumulated") (:end . 124)\n  (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 129) (:start . 125)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "tremendous") (:form . "tremendous") (:end . 140)\n  (:start . 130) (:id . 64))\n ((:tag . "NN") (:stem . "speed") (:form . "speed") (:end . 146)\n  (:start . 141) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 66))\n ((:tag . "CD") (:stem . "7-10") (:form . "7-10") (:end . 152) (:start . 148)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.24) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500024@unknown@formal@none@1@S@It is also clear that the notion of a single type of Th17 cell may not be correct, as there seems to be further complexity in terms of the cytokines produced by these cells.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 32)\n  (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 44)\n  (:start . 38) (:id . 51))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 49) (:start . 45)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 53))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 57) (:start . 53)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 62) (:start . 58)\n  (:id . 55))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 66) (:start . 63)\n  (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 70) (:start . 67)\n  (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 73) (:start . 71)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "correct") (:form . "correct") (:end . 81)\n  (:start . 74) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 85) (:start . 83)\n  (:id . 61))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 91) (:start . 86)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 97) (:start . 92)\n  (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 103) (:start . 101)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 111)\n  (:start . 104) (:id . 66))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 122)\n  (:start . 112) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 125) (:start . 123)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 131)\n  (:start . 126) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 148)\n  (:start . 139) (:id . 72))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 157)\n  (:start . 149) (:id . 73))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 160) (:start . 158)\n  (:id . 74))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 166)\n  (:start . 161) (:id . 75))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 172)\n  (:start . 167) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x1.25.1) (:span 92 97)) ((:id . :x1.25.2) (:span 63 66)))\n (:hscopes ((:id . :x1.25.1) (:span 86 172)) ((:id . :x1.25.2) (:span 63 81)))\n (:identifiers (:sid . :s1.25) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500025@unknown@formal@none@1@S@In this review, we will discuss the historical developments that led to a new understanding of the role of T cells in autoimmune diseases and recent advances that have led to even newer insights into T cell biology.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "review") (:form . "review") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 23) (:start . 19)\n  (:id . 47))\n ((:tag . "VB") (:stem . "discuss") (:form . "discuss") (:end . 31)\n  (:start . 24) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "historical") (:form . "historical") (:end . 46)\n  (:start . 36) (:id . 50))\n ((:tag . "NNS") (:stem . "development") (:form . "developments") (:end . 59)\n  (:start . 47) (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "lead") (:form . "led") (:end . 68) (:start . 65)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "understanding") (:form . "understanding")\n  (:end . 91) (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 103) (:start . 99)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 108) (:start . 107)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 114)\n  (:start . 109) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 128)\n  (:start . 118) (:id . 65))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 137)\n  (:start . 129) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 148)\n  (:start . 142) (:id . 68))\n ((:tag . "NNS") (:stem . "advance") (:form . "advances") (:end . 157)\n  (:start . 149) (:id . 69))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 162) (:start . 158)\n  (:id . 70))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 167) (:start . 163)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "lead") (:form . "led") (:end . 171) (:start . 168)\n  (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 174) (:start . 172)\n  (:id . 73))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 179) (:start . 175)\n  (:id . 74))\n ((:tag . "JJR") (:stem . "new") (:form . "newer") (:end . 185) (:start . 180)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "insight") (:form . "insights") (:end . 194)\n  (:start . 186) (:id . 76))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 199) (:start . 195)\n  (:id . 77))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 201) (:start . 200)\n  (:id . 78))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 206) (:start . 202)\n  (:id . 79))\n ((:tag . "NN") (:stem . "biology") (:form . "biology") (:end . 214)\n  (:start . 207) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s1.26) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500026@unknown@formal@none@1@S@Pathogenicity of IL-23, but not IL-12 in autoimmune diseases@(((:tag . "NNP") (:stem . "Pathogenicity") (:form . "Pathogenicity")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 22) (:start . 17)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "il-12") (:form . "IL-12") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 51)\n  (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 60)\n  (:start . 52) (:id . 51)))@@@1@10@((:identifiers (:sid . :s1.27) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500027@unknown@formal@none@1@S@Until a few years ago we thought we knew which subset of helper T cells was responsible for host defense or exacerbation of autoimmune diseases and we thought that answer fit well with the standard Th1/Th2 cells paradigm (11).@(((:tag . "IN") (:stem . "until") (:form . "Until") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "ago") (:form . "ago") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "think") (:form . "thought") (:end . 32)\n  (:start . 25) (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "know") (:form . "knew") (:end . 40) (:start . 36)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 46) (:start . 41)\n  (:id . 51))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 53)\n  (:start . 47) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 63)\n  (:start . 57) (:id . 54))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 71) (:start . 66)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 75) (:start . 72)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "responsible") (:form . "responsible") (:end . 87)\n  (:start . 76) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 96) (:start . 92)\n  (:id . 60))\n ((:tag . "NN") (:stem . "defense") (:form . "defense") (:end . 104)\n  (:start . 97) (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 107) (:start . 105)\n  (:id . 62))\n ((:tag . "NN") (:stem . "exacerbation") (:form . "exacerbation") (:end . 120)\n  (:start . 108) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 134)\n  (:start . 124) (:id . 65))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 143)\n  (:start . 135) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n  (:id . 67))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 150) (:start . 148)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "think") (:form . "thought") (:end . 158)\n  (:start . 151) (:id . 69))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 163) (:start . 159)\n  (:id . 70))\n ((:tag . "NN") (:stem . "answer") (:form . "answer") (:end . 170)\n  (:start . 164) (:id . 71))\n ((:tag . "VBP") (:stem . "fit") (:form . "fit") (:end . 174) (:start . 171)\n  (:id . 72))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 179) (:start . 175)\n  (:id . 73))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 184) (:start . 180)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 197)\n  (:start . 189) (:id . 76))\n ((:tag . "NN") (:stem . "th1/th2") (:form . "Th1/Th2") (:end . 205)\n  (:start . 198) (:id . 77))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 211)\n  (:start . 206) (:id . 78))\n ((:tag . "NN") (:stem . "paradigm") (:form . "paradigm") (:end . 220)\n  (:start . 212) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 222) (:start . 221)\n  (:id . 80))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 224) (:start . 222)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 225) (:start . 224)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x1.28.1) (:span 151 158)) ((:id . :x1.28.2) (:span 25 32)))\n (:hscopes ((:id . :x1.28.1) (:span 148 220))\n  ((:id . :x1.28.2) (:span 25 143)))\n (:identifiers (:sid . :s1.28) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500028@unknown@formal@none@1@S@Th1 cells produce interferon-γ (IFN-γ) and lymphotoxin, and are responsible for protection against intracellular pathogens such as viruses, mycobacteria, and protozoa (11).@(((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "produce") (:form . "produce") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "interferon-γ") (:form . "interferon-γ") (:end . 30)\n  (:start . 18) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "lymphotoxin") (:form . "lymphotoxin") (:end . 54)\n  (:start . 43) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "responsible") (:form . "responsible") (:end . 75)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "protection") (:form . "protection") (:end . 90)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 98)\n  (:start . 91) (:id . 57))\n ((:tag . "JJ") (:stem . "intracellular") (:form . "intracellular")\n  (:end . 112) (:start . 99) (:id . 58))\n ((:tag . "NNS") (:stem . "pathogen") (:form . "pathogens") (:end . 122)\n  (:start . 113) (:id . 59))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 127) (:start . 123)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 130) (:start . 128)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "virus") (:form . "viruses") (:end . 138)\n  (:start . 131) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "mycobacterium") (:form . "mycobacteria")\n  (:end . 152) (:start . 140) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 66))\n ((:tag . "NN") (:stem . "protozoa") (:form . "protozoa") (:end . 166)\n  (:start . 158) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 168) (:start . 167)\n  (:id . 68))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 170) (:start . 168)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 171) (:start . 170)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s1.29) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500029@unknown@formal@none@1@S@Produced by activated APCs, IL-12 activates the transcription factor, signal transducer, and activator of transcription 4 (Stat4) (2).@(((:tag . "VBN") (:stem . "produce") (:form . "Produced") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "apc") (:form . "APCs") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "il-12") (:form . "IL-12") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 61) (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 68)\n  (:start . 62) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 76)\n  (:start . 70) (:id . 53))\n ((:tag . "NN") (:stem . "transducer") (:form . "transducer") (:end . 87)\n  (:start . 77) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "NN") (:stem . "activator") (:form . "activator") (:end . 102)\n  (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 119) (:start . 106) (:id . 59))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 121) (:start . 120)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Stat4") (:form . "Stat4") (:end . 128)\n  (:start . 123) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 64))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 132) (:start . 131)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s1.30) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500030@unknown@formal@none@1@S@Stat4-dependent signaling in conjunction with TCR-dependent signals induces the expression of T-box-expressed-in-T-cells (T-bet), the so-called master regulator of Th1 differentiation (2).@(((:tag . "JJ") (:stem . "stat4-dependent") (:form . "Stat4-dependent")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 25)\n  (:start . 16) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 44))\n ((:tag . "NN") (:stem . "conjunction") (:form . "conjunction") (:end . 40)\n  (:start . 29) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "tcr-dependent") (:form . "TCR-dependent")\n  (:end . 59) (:start . 46) (:id . 47))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 67)\n  (:start . 60) (:id . 48))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 75)\n  (:start . 68) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 90)\n  (:start . 80) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "T-box-expressed-in-T-cell")\n  (:form . "T-box-expressed-in-T-cells") (:end . 120) (:start . 94)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "T-bet") (:form . "T-bet") (:end . 127)\n  (:start . 122) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "so-called") (:form . "so-called") (:end . 143)\n  (:start . 134) (:id . 59))\n ((:tag . "NN") (:stem . "master") (:form . "master") (:end . 150)\n  (:start . 144) (:id . 60))\n ((:tag . "NN") (:stem . "regulator") (:form . "regulator") (:end . 160)\n  (:start . 151) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 62))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 167) (:start . 164)\n  (:id . 63))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 183) (:start . 168) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 65))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 186) (:start . 185)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.31) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500031@unknown@formal@none@1@S@Recently, in humans, it has been shown that STAT4 polymorphisms are associated with rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) (12).@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "human") (:form . "humans") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 27) (:start . 24)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 32) (:start . 28)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 38) (:start . 33)\n  (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 43) (:start . 39)\n  (:id . 51))\n ((:tag . "NN") (:stem . "stat4") (:form . "STAT4") (:end . 49) (:start . 44)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "polymorphism") (:form . "polymorphisms")\n  (:end . 63) (:start . 50) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 78)\n  (:start . 68) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "rheumatoid") (:form . "rheumatoid") (:end . 94)\n  (:start . 84) (:id . 57))\n ((:tag . "NN") (:stem . "arthritis") (:form . "arthritis") (:end . 104)\n  (:start . 95) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 122)\n  (:start . 114) (:id . 63))\n ((:tag . "NN") (:stem . "lupus") (:form . "lupus") (:end . 128)\n  (:start . 123) (:id . 64))\n ((:tag . "NN") (:stem . "erythematosus") (:form . "erythematosus")\n  (:end . 142) (:start . 129) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 144) (:start . 143)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "SLE") (:form . "SLE") (:end . 147) (:start . 144)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 69))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 152) (:start . 150)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s1.32) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500032@unknown@formal@none@1@S@IFN-γ also activates Stat1 which further induces T-bet to form an autocrine feedback loop for IFN-γ production (2).@(((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "stat1") (:form . "Stat1") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "NN") (:stem . "t-bet") (:form . "T-bet") (:end . 54) (:start . 49)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "autocrine") (:form . "autocrine") (:end . 75)\n  (:start . 66) (:id . 53))\n ((:tag . "NN") (:stem . "feedback") (:form . "feedback") (:end . 84)\n  (:start . 76) (:id . 54))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 89) (:start . 85)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 93) (:start . 90)\n  (:id . 56))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 99) (:start . 94)\n  (:id . 57))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 110)\n  (:start . 100) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s1.33) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500033@unknown@formal@none@1@S@T-bet promotes not only IFN-γ production but also suppression of Th2 cytokines production by T cells (2).@(((:tag . "NNP") (:stem . "T-bet") (:form . "T-bet") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "suppression") (:form . "suppression") (:end . 61)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "th2") (:form . "Th2") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 89)\n  (:start . 79) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 92) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 94) (:start . 93)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 100) (:start . 95)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.34) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500034@unknown@formal@none@1@S@On the other hand, Th2 cells produce IL-4, IL-5, and IL-13 (1).@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "hand") (:form . "hand") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "th2") (:form . "Th2") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 28) (:start . 23)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "produce") (:form . "produce") (:end . 36)\n  (:start . 29) (:id . 49))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "IL-5") (:form . "IL-5") (:end . 47) (:start . 43)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 54))\n ((:tag . "NN") (:stem . "il-13") (:form . "IL-13") (:end . 58) (:start . 53)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 61) (:start . 60)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s1.35) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500035@unknown@formal@none@1@S@IL-4 activates Stat6, which up-regulates the expression of GATA-binding protein 3 (GATA-3) (1).@(((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "NNP") (:stem . "Stat6") (:form . "Stat6") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "up-regulate") (:form . "up-regulates") (:end . 40)\n  (:start . 28) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 55)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "gata-binding") (:form . "GATA-binding") (:end . 71)\n  (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 79)\n  (:start . 72) (:id . 52))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 81) (:start . 80)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "GATA-3") (:form . "GATA-3") (:end . 89)\n  (:start . 83) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.36) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500036@unknown@formal@none@1@S@Th2 cytokines are potent activators of B-cell Immunoglobulin E production, eosinophil recruitment, and mucosal expulsion mechanisms, and are essential for promoting host defense against helminths and other parasites (1).@(((:tag . "NN") (:stem . "th2") (:form . "Th2") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "potent") (:form . "potent") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "activator") (:form . "activators") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "B-cell") (:form . "B-cell") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "NNP") (:stem . "Immunoglobulin") (:form . "Immunoglobulin")\n  (:end . 60) (:start . 46) (:id . 49))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 62) (:start . 61)\n  (:id . 50))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 73)\n  (:start . 63) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "eosinophil") (:form . "eosinophil") (:end . 85)\n  (:start . 75) (:id . 53))\n ((:tag . "NN") (:stem . "recruitment") (:form . "recruitment") (:end . 97)\n  (:start . 86) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "mucosal") (:form . "mucosal") (:end . 110)\n  (:start . 103) (:id . 57))\n ((:tag . "NN") (:stem . "expulsion") (:form . "expulsion") (:end . 120)\n  (:start . 111) (:id . 58))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 131)\n  (:start . 121) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 140) (:start . 137)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 150)\n  (:start . 141) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 154) (:start . 151)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "promote") (:form . "promoting") (:end . 164)\n  (:start . 155) (:id . 65))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 169) (:start . 165)\n  (:id . 66))\n ((:tag . "NN") (:stem . "defense") (:form . "defense") (:end . 177)\n  (:start . 170) (:id . 67))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 185)\n  (:start . 178) (:id . 68))\n ((:tag . "NNS") (:stem . "helminth") (:form . "helminths") (:end . 195)\n  (:start . 186) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 199) (:start . 196)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 205)\n  (:start . 200) (:id . 71))\n ((:tag . "NNS") (:stem . "parasite") (:form . "parasites") (:end . 215)\n  (:start . 206) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 217) (:start . 216)\n  (:id . 73))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 218) (:start . 217)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 219) (:start . 218)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s1.37) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500037@unknown@formal@none@1@S@In addition, Th2 cells have been shown to mediate allergic diseases such as asthma, rhinitis, and atopic dermatitis (11).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "th2") (:form . "Th2") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 38) (:start . 33)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "VB") (:stem . "mediate") (:form . "mediate") (:end . 49)\n  (:start . 42) (:id . 51))\n ((:tag . "JJ") (:stem . "allergic") (:form . "allergic") (:end . 58)\n  (:start . 50) (:id . 52))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 67)\n  (:start . 59) (:id . 53))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "asthma") (:form . "asthma") (:end . 82)\n  (:start . 76) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "NN") (:stem . "rhinitis") (:form . "rhinitis") (:end . 92)\n  (:start . 84) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "atopic") (:form . "atopic") (:end . 104)\n  (:start . 98) (:id . 61))\n ((:tag . "NN") (:stem . "dermatitis") (:form . "dermatitis") (:end . 115)\n  (:start . 105) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 119) (:start . 117)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.38) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500038@unknown@formal@none@1@S@Traditionally, autoimmune diseases had been assumed to be associated with dysregulated Th1 responses (13).@(((:tag . "RB") (:stem . "traditionally") (:form . "Traditionally")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 34)\n  (:start . 26) (:id . 45))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "assume") (:form . "assumed") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 68)\n  (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "dysregulate") (:form . "dysregulated") (:end . 86)\n  (:start . 74) (:id . 53))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 90) (:start . 87)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 100)\n  (:start . 91) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 56))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 104) (:start . 102)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x1.39.1) (:span 44 51)))\n (:hscopes ((:id . :x1.39.1) (:span 15 100)))\n (:identifiers (:sid . :s1.39) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500039@unknown@formal@none@1@S@Because the treatment with anti-IL-12p40 antibody was effective in Crohn's disease (CD) and psoriasis (14, 15), it was further assumed that IL-12-mediated IFN-γ production and Th1 response were involved in the pathogenesis of autoimmunity.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "anti-il-12p40") (:form . "anti-IL-12p40")\n  (:end . 40) (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 49)\n  (:start . 41) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 53) (:start . 50)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 63)\n  (:start . 54) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Crohn") (:form . "Crohn") (:end . 72) (:start . 67)\n  (:id . 51))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 82)\n  (:start . 75) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "CD") (:form . "CD") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "psoriasis") (:form . "psoriasis") (:end . 101)\n  (:start . 92) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 105) (:start . 103)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 61))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 64))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 114) (:start . 112)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 118) (:start . 115)\n  (:id . 66))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 126)\n  (:start . 119) (:id . 67))\n ((:tag . "VBN") (:stem . "assume") (:form . "assumed") (:end . 134)\n  (:start . 127) (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 139) (:start . 135)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "il-12-mediated") (:form . "IL-12-mediated")\n  (:end . 154) (:start . 140) (:id . 70))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 160)\n  (:start . 155) (:id . 71))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 171)\n  (:start . 161) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n  (:id . 73))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 179) (:start . 176)\n  (:id . 74))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 188)\n  (:start . 180) (:id . 75))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 193) (:start . 189)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 202)\n  (:start . 194) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 205) (:start . 203)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n  (:id . 79))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 222)\n  (:start . 210) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 225) (:start . 223)\n  (:id . 81))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 238)\n  (:start . 226) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x1.40.1) (:span 127 134)))\n (:hscopes ((:id . :x1.40.1) (:span 112 238)))\n (:identifiers (:sid . :s1.40) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500040@unknown@formal@none@1@S@However, it was shown that IFN-γ deficiency exacerbated rather than ameliorated mouse models of autoimmune diseases such as experimental autoimmune encephalomyelitis (EAE) (16).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 21) (:start . 16)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "deficiency") (:form . "deficiency") (:end . 43)\n  (:start . 33) (:id . 49))\n ((:tag . "VBD") (:stem . "exacerbate") (:form . "exacerbated") (:end . 55)\n  (:start . 44) (:id . 50))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "ameliorate") (:form . "ameliorated") (:end . 79)\n  (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 85) (:start . 80)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 92)\n  (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 106)\n  (:start . 96) (:id . 57))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 115)\n  (:start . 107) (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 120) (:start . 116)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 123) (:start . 121)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 136)\n  (:start . 124) (:id . 61))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 147)\n  (:start . 137) (:id . 62))\n ((:tag . "NN") (:stem . "encephalomyelitis") (:form . "encephalomyelitis")\n  (:end . 165) (:start . 148) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "EAE") (:form . "EAE") (:end . 170) (:start . 167)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 171) (:start . 170)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 173) (:start . 172)\n  (:id . 67))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 175) (:start . 173)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.41) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500041@unknown@formal@none@1@S@Subsequently, a new cytokine, which consists of IL-23p19 and IL-12p40, was identified and termed IL-23 (17).@(((:tag . "RB") (:stem . "subsequently") (:form . "Subsequently") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "il-23p19") (:form . "IL-23p19") (:end . 56)\n  (:start . 48) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "IL-12p40") (:form . "IL-12p40") (:end . 69)\n  (:start . 61) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 85)\n  (:start . 75) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "term") (:form . "termed") (:end . 96) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "il-23") (:form . "IL-23") (:end . 102) (:start . 97)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.42) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500042@unknown@formal@none@1@S@Interestingly, the IL-23 receptor (IL-23R) forms dimers with the IL-12Rß1 chain shared by IL-12 and IL-23 (18).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "il-23") (:form . "IL-23") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "IL-23R") (:form . "IL-23R") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "form") (:form . "forms") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "dimer") (:form . "dimers") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "il-12rß1") (:form . "IL-12Rß1") (:end . 73)\n  (:start . 65) (:id . 54))\n ((:tag . "NN") (:stem . "chain") (:form . "chain") (:end . 79) (:start . 74)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "share") (:form . "shared") (:end . 86)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "NN") (:stem . "il-12") (:form . "IL-12") (:end . 95) (:start . 90)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "il-23") (:form . "IL-23") (:end . 105)\n  (:start . 100) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.43) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500043@unknown@formal@none@1@S@IL-23R is predominantly expressed on T and natural killer (NK) cells (18, 19).@(((:tag . "NNP") (:stem . "IL-23R") (:form . "IL-23R") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 33)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 38) (:start . 37)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "natural") (:form . "natural") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "killer") (:form . "killer") (:end . 57)\n  (:start . 51) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "NK") (:form . "NK") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 72) (:start . 70)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 76) (:start . 74)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.44) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500044@unknown@formal@none@1@S@IL-23 activates Janus kinase 2 (Jak2) and tyrosine kinase 2 (Tyk2), which in turn leads to activation of Stat1, Stat3, Stat4, and Stat5, among which Stat3 is the predominant factor phosphorylated by this cytokine (17, 18).@(((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "NNP") (:stem . "Janus") (:form . "Janus") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "jak2") (:form . "Jak2") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "tyrosine") (:form . "tyrosine") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 57)\n  (:start . 51) (:id . 52))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "tyk2") (:form . "Tyk2") (:end . 65) (:start . 61)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 73) (:start . 68)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 59))\n ((:tag . "NN") (:stem . "turn") (:form . "turn") (:end . 81) (:start . 77)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 87) (:start . 82)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 62))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 101)\n  (:start . 91) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Stat1") (:form . "Stat1") (:end . 110)\n  (:start . 105) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Stat3") (:form . "Stat3") (:end . 117)\n  (:start . 112) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Stat4") (:form . "Stat4") (:end . 124)\n  (:start . 119) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Stat5") (:form . "Stat5") (:end . 135)\n  (:start . 130) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 73))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 142)\n  (:start . 137) (:id . 74))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 148)\n  (:start . 143) (:id . 75))\n ((:tag . "NNP") (:stem . "Stat3") (:form . "Stat3") (:end . 154)\n  (:start . 149) (:id . 76))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 157) (:start . 155)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "predominant") (:form . "predominant") (:end . 173)\n  (:start . 162) (:id . 79))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 180)\n  (:start . 174) (:id . 80))\n ((:tag . "VBN") (:stem . "phosphorylate") (:form . "phosphorylated")\n  (:end . 195) (:start . 181) (:id . 81))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 198) (:start . 196)\n  (:id . 82))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 203) (:start . 199)\n  (:id . 83))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 212)\n  (:start . 204) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 214) (:start . 213)\n  (:id . 85))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 216) (:start . 214)\n  (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 217) (:start . 216)\n  (:id . 87))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 220) (:start . 218)\n  (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s1.45) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500045@unknown@formal@none@1@S@Of note, IL-23p19-deficient mice or IL-12p40-deficient (IL-12/IL-23-deficient) mice were resistant to collagen-induced arthritis (CIA) and EAE (20, 21).@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "note") (:form . "note") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "JJ") (:stem . "il-23p19-deficient") (:form . "IL-23p19-deficient")\n  (:end . 27) (:start . 9) (:id . 45))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "il-12p40-deficient") (:form . "IL-12p40-deficient")\n  (:end . 54) (:start . 36) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "il-12/il-23-deficient")\n  (:form . "IL-12/IL-23-deficient") (:end . 77) (:start . 56) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 83) (:start . 79)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 88) (:start . 84)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "resistant") (:form . "resistant") (:end . 98)\n  (:start . 89) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "collagen-induced") (:form . "collagen-induced")\n  (:end . 118) (:start . 102) (:id . 56))\n ((:tag . "NN") (:stem . "arthritis") (:form . "arthritis") (:end . 128)\n  (:start . 119) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "CIA") (:form . "CIA") (:end . 133) (:start . 130)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "EAE") (:form . "EAE") (:end . 142) (:start . 139)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 144) (:start . 143)\n  (:id . 63))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 146) (:start . 144)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 65))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 150) (:start . 148)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.46) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500046@unknown@formal@none@1@S@However, IL-12p35-deficient mice had increased susceptibility to CIA and EAE (20, 21).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "il-12p35-deficient") (:form . "IL-12p35-deficient")\n  (:end . 27) (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 32) (:start . 28)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 46)\n  (:start . 37) (:id . 47))\n ((:tag . "NN") (:stem . "susceptibility") (:form . "susceptibility")\n  (:end . 61) (:start . 47) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "CIA") (:form . "CIA") (:end . 68) (:start . 65)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "EAE") (:form . "EAE") (:end . 76) (:start . 73)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 53))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.47) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500047@unknown@formal@none@1@S@These studies directly negated the pathogenic role of the IL-12/IFN-γ axis in autoimmunity.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "negate") (:form . "negated") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "pathogenic") (:form . "pathogenic") (:end . 45)\n  (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 50) (:start . 46)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "il-12/ifn-γ") (:form . "IL-12/IFN-γ") (:end . 69)\n  (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 90)\n  (:start . 78) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.48) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500048@unknown@formal@none@1@S@This was an important piece of information that led to the unraveling of the Th1/Th2 paradigm as an explanation of autoimmunity.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "piece") (:form . "piece") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 42)\n  (:start . 31) (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "lead") (:form . "led") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "unraveling") (:form . "unraveling") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "th1/th2") (:form . "Th1/Th2") (:end . 84)\n  (:start . 77) (:id . 56))\n ((:tag . "NN") (:stem . "paradigm") (:form . "paradigm") (:end . 93)\n  (:start . 85) (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 99) (:start . 97)\n  (:id . 59))\n ((:tag . "NN") (:stem . "explanation") (:form . "explanation") (:end . 111)\n  (:start . 100) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 127)\n  (:start . 115) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.49) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500049@unknown@formal@none@1@S@Accordingly, additional studies on IL-23p19-deficient mice and the anti-IL-23p19 antibody revealed that IL-23, but not IL-12, was the culprit in autoimmunity, at least in mouse disease models (21-23).@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 31)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "il-23p19-deficient") (:form . "IL-23p19-deficient")\n  (:end . 53) (:start . 35) (:id . 47))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 58) (:start . 54)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "anti-il-23p19") (:form . "anti-IL-23p19")\n  (:end . 80) (:start . 67) (:id . 51))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 89)\n  (:start . 81) (:id . 52))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 98)\n  (:start . 90) (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 103) (:start . 99)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 109)\n  (:start . 104) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 56))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 114) (:start . 111)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "NN") (:stem . "il-12") (:form . "IL-12") (:end . 124)\n  (:start . 119) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 129) (:start . 126)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 62))\n ((:tag . "NN") (:stem . "culprit") (:form . "culprit") (:end . 141)\n  (:start . 134) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 157)\n  (:start . 145) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 66))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 161) (:start . 159)\n  (:id . 67))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 167)\n  (:start . 162) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 170) (:start . 168)\n  (:id . 69))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 176)\n  (:start . 171) (:id . 70))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 184)\n  (:start . 177) (:id . 71))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 191)\n  (:start . 185) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 193) (:start . 192)\n  (:id . 73))\n ((:tag . "CD") (:stem . "21-23") (:form . "21-23") (:end . 198)\n  (:start . 193) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s1.50) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500050@unknown@formal@none@1@S@The pathogenic role of IL-23 was also confirmed by the phenotype of IL-23p19 transgenic mice, in which premature death, systemic inflammation, anemia, and elevated serum levels of inflammatory cytokines and acute phase proteins were observed (22).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "pathogenic") (:form . "pathogenic") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 64)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "il-23p19") (:form . "IL-23p19") (:end . 76)\n  (:start . 68) (:id . 54))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 87)\n  (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 102)\n  (:start . 97) (:id . 59))\n ((:tag . "JJ") (:stem . "premature") (:form . "premature") (:end . 112)\n  (:start . 103) (:id . 60))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 118)\n  (:start . 113) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 128)\n  (:start . 120) (:id . 63))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 141)\n  (:start . 129) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 65))\n ((:tag . "NN") (:stem . "anemia") (:form . "anemia") (:end . 149)\n  (:start . 143) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "elevated") (:form . "elevated") (:end . 163)\n  (:start . 155) (:id . 69))\n ((:tag . "NN") (:stem . "serum") (:form . "serum") (:end . 169)\n  (:start . 164) (:id . 70))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 176)\n  (:start . 170) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 179) (:start . 177)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 192)\n  (:start . 180) (:id . 73))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 202)\n  (:start . 193) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 206) (:start . 203)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 212)\n  (:start . 207) (:id . 76))\n ((:tag . "NN") (:stem . "phase") (:form . "phase") (:end . 218)\n  (:start . 213) (:id . 77))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 227)\n  (:start . 219) (:id . 78))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 232) (:start . 228)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 241)\n  (:start . 233) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 243) (:start . 242)\n  (:id . 81))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 245) (:start . 243)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 246) (:start . 245)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 247) (:start . 246)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s1.51) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500051@unknown@formal@none@1@S@In human disease, the mRNA levels of both IL-23p19 and IL-12p40 were shown to be increased in skin lesions of psoriatic patients (24), suggesting that elevated IL-23 contributed to the pathogenesis of psoriasis.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "il-23p19") (:form . "IL-23p19") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "IL-12p40") (:form . "IL-12p40") (:end . 63)\n  (:start . 55) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 74) (:start . 69)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 90)\n  (:start . 81) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "NN") (:stem . "skin") (:form . "skin") (:end . 98) (:start . 94)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "lesion") (:form . "lesions") (:end . 106)\n  (:start . 99) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "psoriatic") (:form . "psoriatic") (:end . 119)\n  (:start . 110) (:id . 63))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 128)\n  (:start . 120) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 65))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 132) (:start . 130)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 145)\n  (:start . 135) (:id . 69))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 150) (:start . 146)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "elevated") (:form . "elevated") (:end . 159)\n  (:start . 151) (:id . 71))\n ((:tag . "NN") (:stem . "il-23") (:form . "IL-23") (:end . 165)\n  (:start . 160) (:id . 72))\n ((:tag . "VBD") (:stem . "contribute") (:form . "contributed") (:end . 177)\n  (:start . 166) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 180) (:start . 178)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 184) (:start . 181)\n  (:id . 75))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 197)\n  (:start . 185) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 200) (:start . 198)\n  (:id . 77))\n ((:tag . "NN") (:stem . "psoriasis") (:form . "psoriasis") (:end . 210)\n  (:start . 201) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x1.52.1) (:span 135 145)))\n (:hscopes ((:id . :x1.52.1) (:span 135 210)))\n (:identifiers (:sid . :s1.52) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500052@unknown@formal@none@1@S@Therefore, IL-23 began to attract attention as a factor crucial to inflammation and autoimmune diseases.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "begin") (:form . "began") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "VB") (:stem . "attract") (:form . "attract") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "attention") (:form . "attention") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 63)\n  (:start . 56) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 79)\n  (:start . 67) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 94)\n  (:start . 84) (:id . 56))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 103)\n  (:start . 95) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.53) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500053@unknown@formal@none@1@S@The IL-23/IL17 axis in inflammation@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "il-23/il17") (:form . "IL-23/IL17") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 35)\n  (:start . 23) (:id . 46)))@@@1@5@((:identifiers (:sid . :s1.54) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500054@unknown@formal@none@1@S@While it was becoming clear that IL-23 was the culprit in autoimmune and inflammatory diseases, the question remained, how was it acting?@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "become") (:form . "becoming") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "culprit") (:form . "culprit") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 68)\n  (:start . 58) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 85)\n  (:start . 73) (:id . 55))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 94)\n  (:start . 86) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "question") (:form . "question") (:end . 108)\n  (:start . 100) (:id . 59))\n ((:tag . "VBD") (:stem . "remain") (:form . "remained") (:end . 117)\n  (:start . 109) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 122) (:start . 119)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 126) (:start . 123)\n  (:id . 63))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 129) (:start . 127)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 136)\n  (:start . 130) (:id . 65))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 137) (:start . 136)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.55) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500055@unknown@formal@none@1@S@Another inflammatory cytokine, IL-17, was noted to be produced by activated purified T cells in the presence of LPS-stimulated dendritic cells (DCs) (5).@(((:tag . "DT") (:stem . "another") (:form . "Another") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 20)\n  (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 29)\n  (:start . 21) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 36) (:start . 31)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 62)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 75)\n  (:start . 66) (:id . 54))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 84)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 86) (:start . 85)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 108)\n  (:start . 100) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "lps-stimulated") (:form . "LPS-stimulated")\n  (:end . 126) (:start . 112) (:id . 62))\n ((:tag . "JJ") (:stem . "dendritic") (:form . "dendritic") (:end . 136)\n  (:start . 127) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 142)\n  (:start . 137) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 144) (:start . 143)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "DC") (:form . "DCs") (:end . 147) (:start . 144)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 68))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 151) (:start . 150)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s1.56) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500056@unknown@formal@none@1@S@It was also found that IL-23 promoted IL-17 production from memory T cells and this production was suppressed by treatment with anti-IL-12p40 antibody (5).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "il-23") (:form . "IL-23") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "promote") (:form . "promoted") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 66)\n  (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 94)\n  (:start . 84) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 98) (:start . 95)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "suppress") (:form . "suppressed") (:end . 109)\n  (:start . 99) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 122)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 127) (:start . 123)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "anti-il-12p40") (:form . "anti-IL-12p40")\n  (:end . 141) (:start . 128) (:id . 63))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 150)\n  (:start . 142) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 153) (:start . 152)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.57) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500057@unknown@formal@none@1@S@Now IL-17 is recognized as the founding member of a family of proinflammatory cytokines: IL-17 (IL-17A), IL-17B, IL-17C, IL-17D, IL-17E (known as IL-25), and IL-17F (6).@(((:tag . "RB") (:stem . "now") (:form . "Now") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "recognize") (:form . "recognized") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "found") (:form . "founding") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "member") (:form . "member") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 58)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "proinflammatory") (:form . "proinflammatory")\n  (:end . 77) (:start . 62) (:id . 54))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 87)\n  (:start . 78) (:id . 55))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 94) (:start . 89)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "IL-17A") (:form . "IL-17A") (:end . 102)\n  (:start . 96) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "IL-17B") (:form . "IL-17B") (:end . 111)\n  (:start . 105) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "IL-17C") (:form . "IL-17C") (:end . 119)\n  (:start . 113) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "IL-17D") (:form . "IL-17D") (:end . 127)\n  (:start . 121) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "IL-17E") (:form . "IL-17E") (:end . 135)\n  (:start . 129) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 142)\n  (:start . 137) (:id . 70))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 145) (:start . 143)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "IL-25") (:form . "IL-25") (:end . 151)\n  (:start . 146) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "IL-17F") (:form . "IL-17F") (:end . 164)\n  (:start . 158) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 166) (:start . 165)\n  (:id . 77))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 167) (:start . 166)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 168) (:start . 167)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s1.58) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500058@unknown@formal@none@1@S@IL-17A and IL-17F induce the production of various proinflammatory cytokines such as tumor necrosis factor-α (TNF- α), IL-1ß, and IL-6, and CXC chemokines from monocytes, airway epithelial cells, vein endothelial cells, and fibroblasts to mount defense against extracellular bacteria such as Klebsiella pneumonia, Bacteroides fragilis, and Mycobacterium tuberculosis (6, 25, 26).@(((:tag . "NNP") (:stem . "IL-17A") (:form . "IL-17A") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "IL-17F") (:form . "IL-17F") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "VBP") (:stem . "induce") (:form . "induce") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 39)\n  (:start . 29) (:id . 47))\n ((:tag . 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5500059@unknown@formal@none@1@S@These responses result in the recruitment, activation and migration of neutrophils to the sites of inflammation and infection (6).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "result") (:form . "result") (:end . 22)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "recruitment") (:form . "recruitment") (:end . 41)\n  (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 53)\n  (:start . 43) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "migration") (:form . "migration") (:end . 67)\n  (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "neutrophil") (:form . "neutrophils") (:end . 82)\n  (:start . 71) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 95) (:start . 90)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 111)\n  (:start . 99) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 59))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 125)\n  (:start . 116) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 61))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 128) (:start . 127)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.60) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500060@unknown@formal@none@1@S@CD4+ T cells are major producers of IL-17, but in addition CD8+ T cells, neutrophils, γδ T cells, and invariant natural killer T (NKT) cells also produce this cytokine (26-28).@(((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "producer") (:form . "producers") (:end . 32)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 52))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 58)\n  (:start . 50) (:id . 53))\n ((:tag . "JJ") (:stem . "cd8+") (:form . "CD8+") (:end . 63) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 71) (:start . 66)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "neutrophil") (:form . "neutrophils") (:end . 84)\n  (:start . 73) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 59))\n ((:tag . "NN") (:stem . "γδ") (:form . "γδ") (:end . 88) (:start . 86)\n  (:id . 60))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 90) (:start . 89)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 96) (:start . 91)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "invariant") (:form . "invariant") (:end . 111)\n  (:start . 102) (:id . 65))\n ((:tag . "JJ") (:stem . "natural") (:form . "natural") (:end . 119)\n  (:start . 112) (:id . 66))\n ((:tag . "NN") (:stem . "killer") (:form . "killer") (:end . 126)\n  (:start . 120) (:id . 67))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 128) (:start . 127)\n  (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "NKT") (:form . "NKT") (:end . 133) (:start . 130)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 140)\n  (:start . 135) (:id . 72))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 145) (:start . 141)\n  (:id . 73))\n ((:tag . "VBP") (:stem . "produce") (:form . "produce") (:end . 153)\n  (:start . 146) (:id . 74))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 158) (:start . 154)\n  (:id . 75))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 167)\n  (:start . 159) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n  (:id . 77))\n ((:tag . "CD") (:stem . "26-28") (:form . "26-28") (:end . 174)\n  (:start . 169) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 175) (:start . 174)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s1.61) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500061@unknown@formal@none@1@S@Various reports associated IL-23 with IL-17 production with the onset or exacerbation of inflammation (20-23, 29).@(((:tag . "JJ") (:stem . "various") (:form . "Various") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 26)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "il-23") (:form . "IL-23") (:end . 32) (:start . 27)\n  (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 43) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 54)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 59) (:start . 55)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . "NN") (:stem . "onset") (:form . "onset") (:end . 69) (:start . 64)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "exacerbation") (:form . "exacerbation") (:end . 85)\n  (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 101)\n  (:start . 89) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 56))\n ((:tag . "CD") (:stem . "20-23") (:form . "20-23") (:end . 108)\n  (:start . 103) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 58))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 112) (:start . 110)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.62) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500062@unknown@formal@none@1@S@For instance, IL-23p19-deficient mice showed reduced incidence of CIA, with fewer IL-17-producing CD4+ T cells (20).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "il-23p19-deficient") (:form . "IL-23p19-deficient")\n  (:end . 32) (:start . 14) (:id . 45))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 44) (:start . 38)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "NN") (:stem . "incidence") (:form . "incidence") (:end . 62)\n  (:start . 53) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "CIA") (:form . "CIA") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "il-17-producing") (:form . "IL-17-producing")\n  (:end . 97) (:start . 82) (:id . 55))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 102) (:start . 98)\n  (:id . 56))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 104) (:start . 103)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 110)\n  (:start . 105) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s1.63) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500063@unknown@formal@none@1@S@Consistent with this report, treatment with anti-IL-23p19 antibody reduced serum levels of IL-17 and inhibited development of EAE (29).@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 27)\n  (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "anti-il-23p19") (:form . "anti-IL-23p19")\n  (:end . 57) (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 66)\n  (:start . 58) (:id . 50))\n ((:tag . "VBD") (:stem . "reduce") (:form . "reduced") (:end . 74)\n  (:start . 67) (:id . 51))\n ((:tag . "NN") (:stem . "serum") (:form . "serum") (:end . 80) (:start . 75)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 87)\n  (:start . 81) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 96) (:start . 91)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 110)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 122)\n  (:start . 111) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "EAE") (:form . "EAE") (:end . 129) (:start . 126)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 61))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 133) (:start . 131)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.64) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500064@unknown@formal@none@1@S@Moreover, IL-23 was found to be essential for production of IL-17 and IL-6 in colitis mouse models (22, 23).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 41)\n  (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 56)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 74) (:start . 70)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "colitis") (:form . "colitis") (:end . 85)\n  (:start . 78) (:id . 57))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 91) (:start . 86)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 98)\n  (:start . 92) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 102) (:start . 100)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 62))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 106) (:start . 104)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.65) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500065@unknown@formal@none@1@S@Regardless of exactly how IL-23 works, these reports supported the idea that an IL-23/IL-17 axis, but not IL-12/IFN-γ axis, was a crucial pathway in the pathogenesis of various autoimmune diseases (21, 30).@(((:tag . "RB") (:stem . "regardless") (:form . "Regardless") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "RB") (:stem . "exactly") (:form . "exactly") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "il-23") (:form . "IL-23") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "work") (:form . "works") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "VBD") (:stem . "support") (:form . "supported") (:end . 62)\n  (:start . 53) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "il-23/il-17") (:form . "IL-23/IL-17") (:end . 91)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "il-12/ifn-γ") (:form . "IL-12/IFN-γ") (:end . 117)\n  (:start . 106) (:id . 61))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 122) (:start . 118)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 137)\n  (:start . 130) (:id . 66))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 145)\n  (:start . 138) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 69))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 165)\n  (:start . 153) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 176)\n  (:start . 169) (:id . 72))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 187)\n  (:start . 177) (:id . 73))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 196)\n  (:start . 188) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 198) (:start . 197)\n  (:id . 75))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 200) (:start . 198)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 201) (:start . 200)\n  (:id . 77))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 204) (:start . 202)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 205) (:start . 204)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s1.66) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500066@unknown@formal@none@1@S@Regulation of Th17 differentiation@(((:tag . "NNP") (:stem . "Regulation") (:form . "Regulation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Th17") (:form . "Th17") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 34) (:start . 19) (:id . 45)))@@@1@4@((:identifiers (:sid . :s1.67) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500067@unknown@formal@none@1@S@Although many results linked IL-23 with IL-17 production in CD4+ T cells, less was known about how Th17 cells arose from naive CD4+ T cells.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "link") (:form . "linked") (:end . 28) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "il-23") (:form . "IL-23") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 72) (:start . 67)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 78) (:start . 74)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 88) (:start . 83)\n  (:id . 57))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 94) (:start . 89)\n  (:id . 58))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 103) (:start . 99)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 109)\n  (:start . 104) (:id . 61))\n ((:tag . "VBD") (:stem . "arise") (:form . "arose") (:end . 115)\n  (:start . 110) (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 120) (:start . 116)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 126)\n  (:start . 121) (:id . 64))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 131) (:start . 127)\n  (:id . 65))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 133) (:start . 132)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 139)\n  (:start . 134) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.68) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500068@unknown@formal@none@1@S@It was very clear that development of IL-17-producing T cells was not dependent on the cytokines and the transcription factors required for Th1 or Th2 differentiation and then it was proposed that IL-17-producing CD4+ T cells represented a new subset of helper T cells (Th17 cells), which were crucial in mediating inflammatory responses (30-32).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 34)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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5500069@unknown@formal@none@1@S@While there was evidence that IL-23 stimulated CD4+ T cells to express various genes, including IL-17, and that IL-23-stimulated T cells were important in the pathogenesis of EAE (30), it was less clear whether IL-23 was the factor that drove naive CD4+ T cells to become IL-17 producers.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "il-23") (:form . "IL-23") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "stimulate") (:form . "stimulated") (:end . 46)\n  (:start . 36) (:id . 48))\n ((:tag . 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"cells") (:end . 261)\n  (:start . 256) (:id . 90))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 264) (:start . 262)\n  (:id . 91))\n ((:tag . "VB") (:stem . "become") (:form . "become") (:end . 271)\n  (:start . 265) (:id . 92))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 277)\n  (:start . 272) (:id . 93))\n ((:tag . "NNS") (:stem . "producer") (:form . "producers") (:end . 287)\n  (:start . 278) (:id . 94))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 288) (:start . 287)\n  (:id . 95)))@@@1@54@((:hcues ((:id . :x1.70.1) (:span 203 210)))\n (:hscopes ((:id . :x1.70.1) (:span 203 287)))\n (:identifiers (:sid . :s1.70) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500070@unknown@formal@none@1@S@It was especially puzzling that naive CD4+ T cells did not express IL-23R (18).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "especially") (:form . "especially") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "JJ") (:stem . "puzzling") (:form . "puzzling") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "VB") (:stem . "express") (:form . "express") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "NNP") (:stem . "IL-23R") (:form . "IL-23R") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.71) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500071@unknown@formal@none@1@S@In a search for optinum culture condition for Th17 differentiation it was recognized that naive CD4+ T cells cultured with activated DCs produced IL-17 (16).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 11) (:start . 5)\n  (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "optinum") (:form . "optinum") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "condition") (:form . "condition") (:end . 41)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 66) (:start . 51) (:id . 51))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "recognize") (:form . "recognized") (:end . 84)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 89) (:start . 85)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 95) (:start . 90)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 100) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 108)\n  (:start . 103) (:id . 59))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 117)\n  (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 122) (:start . 118)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 132)\n  (:start . 123) (:id . 62))\n ((:tag . "NNS") (:stem . "dc") (:form . "DCs") (:end . 136) (:start . 133)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 145)\n  (:start . 137) (:id . 64))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 151)\n  (:start . 146) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 66))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 155) (:start . 153)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.72) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500072@unknown@formal@none@1@S@It was then recognized that the combination of IL-6 and transforming growth factor ß-1 (TGFß-1), with appropriate stimulation of TCR, were the optinum stimuli inducing Th17 differentiation (Fig. 1a) (16).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "recognize") (:form . "recognized") (:end . 22)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 43)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "transform") (:form . "transforming") (:end . 68)\n  (:start . 56) (:id . 52))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 75)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 82)\n  (:start . 76) (:id . 54))\n ((:tag . "NNP") (:stem . "ß-1") (:form . "ß-1") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 94)\n  (:start . 88) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 101) (:start . 97)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 113)\n  (:start . 102) (:id . 61))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 125)\n  (:start . 114) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "TCR") (:form . "TCR") (:end . 132) (:start . 129)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 138) (:start . 134)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n  (:id . 67))\n ((:tag . "NN") (:stem . "optinum") (:form . "optinum") (:end . 150)\n  (:start . 143) (:id . 68))\n ((:tag . "NNS") (:stem . "stimulus") (:form . "stimuli") (:end . 158)\n  (:start . 151) (:id . 69))\n ((:tag . "VBG") (:stem . "induce") (:form . "inducing") (:end . 167)\n  (:start . 159) (:id . 70))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 172) (:start . 168)\n  (:id . 71))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 188) (:start . 173) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 190) (:start . 189)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 194) (:start . 190)\n  (:id . 74))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 197) (:start . 195)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 198) (:start . 197)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 200) (:start . 199)\n  (:id . 77))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 202) (:start . 200)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 203) (:start . 202)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s1.73) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500073@unknown@formal@none@1@S@Accordingly, TGFß-1-deficient mice showed impaired Th17 development, whereas addition of TGFß-1 rescued the number of Th17 cells (7, 33).@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "tgfß-1-deficient") (:form . "TGFß-1-deficient")\n  (:end . 29) (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 34) (:start . 30)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 41) (:start . 35)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "impaired") (:form . "impaired") (:end . 50)\n  (:start . 42) (:id . 47))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 55) (:start . 51)\n  (:id . 48))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 67)\n  (:start . 56) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 50))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 76)\n  (:start . 69) (:id . 51))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 85)\n  (:start . 77) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 95)\n  (:start . 89) (:id . 54))\n ((:tag . "VBD") (:stem . "rescue") (:form . "rescued") (:end . 103)\n  (:start . 96) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 56))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 114)\n  (:start . 108) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 58))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 122) (:start . 118)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 128)\n  (:start . 123) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 61))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 131) (:start . 130)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 63))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 135) (:start . 133)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.74) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5500075@unknown@formal@none@1@S@New T cell lineages in mice (a) and humans (c).@(((:tag . "JJ") (:stem . "new") (:form . "New") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "lineage") (:form . "lineages") (:end . 19)\n  (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 31) (:start . 30)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "human") (:form . "humans") (:end . 42)\n  (:start . 36) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 53))\n ((:tag . "NN") (:stem . "c") (:form . "c") (:end . 45) (:start . 44)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.76) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500076@unknown@formal@none@1@S@When stimulated by APCs such as DCs and macrophages, and cognate peptide, naive helper T cells differentiate into lineages determined by the cytokine milieu.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "apc") (:form . "APCs") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "dc") (:form . "DCs") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "macrophage") (:form . "macrophages") (:end . 51)\n  (:start . 40) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "cognate") (:form . "cognate") (:end . 64)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 72)\n  (:start . 65) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 79) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 86)\n  (:start . 80) (:id . 57))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 88) (:start . 87)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 94) (:start . 89)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "differentiate") (:form . "differentiate")\n  (:end . 108) (:start . 95) (:id . 60))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "lineage") (:form . "lineages") (:end . 122)\n  (:start . 114) (:id . 62))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 133)\n  (:start . 123) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 136) (:start . 134)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 65))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 149)\n  (:start . 141) (:id . 66))\n ((:tag . "NN") (:stem . "milieu") (:form . "milieu") (:end . 156)\n  (:start . 150) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.77) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500077@unknown@formal@none@1@S@TGFß-1 is a critical factor in the differentiation of new two lineages in mice T cells.@(((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 50) (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "lineage") (:form . "lineages") (:end . 70)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 78) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 80) (:start . 79)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 86) (:start . 81)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.78) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500078@unknown@formal@none@1@S@In conjunction with TCR stimulation, the combination of TGFß-1 and IL-2 (and other γc cytokines) induces the expression of Foxp3, leading to the differentiation of naive CD4+ T cells into anti-inflammatory Tregs (a).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "conjunction") (:form . "conjunction") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "TCR") (:form . "TCR") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 35)\n  (:start . 24) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 52)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "NN") (:stem . "tgfß-1") (:form . "TGFß-1") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "il-2") (:form . "IL-2") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 82) (:start . 77)\n  (:id . 56))\n ((:tag . "NN") (:stem . "γc") (:form . "γc") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 95)\n  (:start . 86) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 104)\n  (:start . 97) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 119)\n  (:start . 109) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Foxp3") (:form . "Foxp3") (:end . 128)\n  (:start . 123) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 137)\n  (:start . 130) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 140) (:start . 138)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 68))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 160) (:start . 145) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 169)\n  (:start . 164) (:id . 71))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 174) (:start . 170)\n  (:id . 72))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 176) (:start . 175)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 182)\n  (:start . 177) (:id . 74))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 187) (:start . 183)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "anti-inflammatory") (:form . "anti-inflammatory")\n  (:end . 205) (:start . 188) (:id . 76))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 211)\n  (:start . 206) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 213) (:start . 212)\n  (:id . 78))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 214) (:start . 213)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 215) (:start . 214)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s1.79) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500079@unknown@formal@none@1@S@However, in the presence of TGFß-1 with IL-6 or IL-21, which activates Stat3 and up-regulates RORγt, naive CD4+ T cells develop to become pro-inflammatory Th17 cells (a).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "tgfß-1") (:form . "TGFß-1") (:end . 34)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "IL-21") (:form . "IL-21") (:end . 53) (:start . 48)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 60) (:start . 55)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 70)\n  (:start . 61) (:id . 55))\n ((:tag . "NN") (:stem . "stat3") (:form . "Stat3") (:end . 76) (:start . 71)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "up-regulate") (:form . "up-regulates") (:end . 93)\n  (:start . 81) (:id . 58))\n ((:tag . "NN") (:stem . "rorγt") (:form . "RORγt") (:end . 99) (:start . 94)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 106)\n  (:start . 101) (:id . 61))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 111) (:start . 107)\n  (:id . 62))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 119)\n  (:start . 114) (:id . 64))\n ((:tag . "VBP") (:stem . "develop") (:form . "develop") (:end . 127)\n  (:start . 120) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n  (:id . 66))\n ((:tag . "VB") (:stem . "become") (:form . "become") (:end . 137)\n  (:start . 131) (:id . 67))\n ((:tag . "JJ") (:stem . "pro-inflammatory") (:form . "pro-inflammatory")\n  (:end . 154) (:start . 138) (:id . 68))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 159) (:start . 155)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 165)\n  (:start . 160) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 168) (:start . 167)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s1.80) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500080@unknown@formal@none@1@S@Th17 differentiation is suppressed by IFN-γ, IL-4, IL-2, IL-25, IL-27, and retinoic acid in mice (b).@(((:tag . "NNP") (:stem . "Th17") (:form . "Th17") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 20) (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "suppress") (:form . "suppressed") (:end . 34)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 43) (:start . 38)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "IL-2") (:form . "IL-2") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "IL-25") (:form . "IL-25") (:end . 62) (:start . 57)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "il-27") (:form . "IL-27") (:end . 69) (:start . 64)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "retinoic") (:form . "retinoic") (:end . 83)\n  (:start . 75) (:id . 58))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 88) (:start . 84)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 96) (:start . 92)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 62))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 99) (:start . 98)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.81) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500081@unknown@formal@none@1@S@Both Th17 cells and Tregs are also present in humans (c).@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "human") (:form . "humans") (:end . 52)\n  (:start . 46) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "c") (:form . "c") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 56) (:start . 55)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.82) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500082@unknown@formal@none@1@S@TGFß-1, IL-1ß, and IL-2 in combination with IL-6, IL-21 or IL-23 are necessary for human Th17 differentiation (c).@(((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "il-1ß") (:form . "IL-1ß") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "il-2") (:form . "IL-2") (:end . 23) (:start . 19)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n  (:id . 48))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 38)\n  (:start . 27) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 43) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 48) (:start . 44)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "IL-21") (:form . "IL-21") (:end . 55) (:start . 50)\n  (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 58) (:start . 56)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 64) (:start . 59)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 68) (:start . 65)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 78)\n  (:start . 69) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 88) (:start . 83)\n  (:id . 59))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 93) (:start . 89)\n  (:id . 60))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 109) (:start . 94) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 62))\n ((:tag . "NN") (:stem . "c") (:form . "c") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.83) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500083@unknown@formal@none@1@S@APCs, antigen-presenting cells; iTregs, inducible Tregs@(((:tag . "NNP") (:stem . "APC") (:form . "APCs") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "antigen-presenting") (:form . "antigen-presenting")\n  (:end . 24) (:start . 6) (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 30) (:start . 25)\n  (:id . 45))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "itreg") (:form . "iTregs") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "inducible") (:form . "inducible") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 55) (:start . 50)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s1.84) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500084@unknown@formal@none@1@S@Autocrine regulation of Th17 differentiation by IL-21@(((:tag . "NNP") (:stem . "Autocrine") (:form . "Autocrine") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 20)\n  (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 44) (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 47) (:start . 45)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "IL-21") (:form . "IL-21") (:end . 53) (:start . 48)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s1.85) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500085@unknown@formal@none@1@S@In the classic Th1/Th2 paradigm, T cell subsets produce factors that promote their differentiation and constrain the differentiation of the opposing lineage.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "classic") (:form . "classic") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "th1/th2") (:form . "Th1/Th2") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "paradigm") (:form . "paradigm") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "subset") (:form . "subsets") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "VBP") (:stem . "produce") (:form . "produce") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 63)\n  (:start . 56) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "promote") (:form . "promote") (:end . 76)\n  (:start . 69) (:id . 54))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 82)\n  (:start . 77) (:id . 55))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 98) (:start . 83) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "VB") (:stem . "constrain") (:form . "constrain") (:end . 112)\n  (:start . 103) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 59))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 132) (:start . 117) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "oppose") (:form . "opposing") (:end . 148)\n  (:start . 140) (:id . 63))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 156)\n  (:start . 149) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.86) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500086@unknown@formal@none@1@S@It was of interest in this regard that the Th17 cells were found to selectively produce IL-21 (35-38).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 18)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "regard") (:form . "regard") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 53) (:start . 48)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 58) (:start . 54)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 64) (:start . 59)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 55))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 79)\n  (:start . 68) (:id . 56))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 87)\n  (:start . 80) (:id . 57))\n ((:tag . "NN") (:stem . "il-21") (:form . "IL-21") (:end . 93) (:start . 88)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "CD") (:stem . "35-38") (:form . "35-38") (:end . 100) (:start . 95)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s1.87) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500087@unknown@formal@none@1@S@IL-21 has structural homology with IL-2 and IL-15, and the initial report showed the effects of IL-21 produced by CD4+ T cells and NKT cells on the proliferation and function of NK cells, B cells, and T cells (39, 40).@(((:tag . "NNP") (:stem . "IL-21") (:form . "IL-21") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "homology") (:form . "homology") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IL-2") (:form . "IL-2") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "IL-15") (:form . "IL-15") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 80) (:start . 74)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "il-21") (:form . "IL-21") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 110)\n  (:start . 102) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 118) (:start . 114)\n  (:id . 62))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 126)\n  (:start . 121) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 65))\n ((:tag . "NN") (:stem . "nkt") (:form . "NKT") (:end . 134) (:start . 131)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 140)\n  (:start . 135) (:id . 67))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 143) (:start . 141)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n  (:id . 69))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 161) (:start . 148) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 71))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 174)\n  (:start . 166) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "NK") (:form . "NK") (:end . 180) (:start . 178)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 186)\n  (:start . 181) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 187) (:start . 186)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 189) (:start . 188)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 195)\n  (:start . 190) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 200) (:start . 197)\n  (:id . 80))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 202) (:start . 201)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 208)\n  (:start . 203) (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 210) (:start . 209)\n  (:id . 83))\n ((:tag . "CD") (:stem . "39") (:form . "39") (:end . 212) (:start . 210)\n  (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 213) (:start . 212)\n  (:id . 85))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 216) (:start . 214)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 217) (:start . 216)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s1.88) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500088@unknown@formal@none@1@S@Recently though, it has also been found that the autocrine production of IL-21 by Th17 cells promotes Th17 differentiation while inhibiting IFN-γ production (35-38).@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "though") (:form . "though") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 39) (:start . 34)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "autocrine") (:form . "autocrine") (:end . 58)\n  (:start . 49) (:id . 52))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "il-21") (:form . "IL-21") (:end . 78) (:start . 73)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 92) (:start . 87)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 101)\n  (:start . 93) (:id . 59))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 122) (:start . 107) (:id . 61))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 128)\n  (:start . 123) (:id . 62))\n ((:tag . "VBG") (:stem . "inhibit") (:form . "inhibiting") (:end . 139)\n  (:start . 129) (:id . 63))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 145)\n  (:start . 140) (:id . 64))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 156)\n  (:start . 146) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 158) (:start . 157)\n  (:id . 66))\n ((:tag . "CD") (:stem . "35-38") (:form . "35-38") (:end . 163)\n  (:start . 158) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 164) (:start . 163)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.89) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500089@unknown@formal@none@1@S@Accordingly, the deficiency of IL-21 (or its receptor), or blocking of IL-21, attenuates the generation of Th17 cells (35-37).@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "deficiency") (:form . "deficiency") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IL-21") (:form . "IL-21") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 53)\n  (:start . 45) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 58) (:start . 56)\n  (:id . 54))\n ((:tag . "NN") (:stem . "blocking") (:form . "blocking") (:end . 67)\n  (:start . 59) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "IL-21") (:form . "IL-21") (:end . 76) (:start . 71)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "attenuate") (:form . "attenuates") (:end . 88)\n  (:start . 78) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 60))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 103)\n  (:start . 93) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 111) (:start . 107)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 117)\n  (:start . 112) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 119) (:start . 118)\n  (:id . 65))\n ((:tag . "CD") (:stem . "35-37") (:form . "35-37") (:end . 124)\n  (:start . 119) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.90) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500090@unknown@formal@none@1@S@Transcription factors for Th17 differentiation@(((:tag . "NN") (:stem . "transcription") (:form . "Transcription")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 21)\n  (:start . 14) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 25) (:start . 22)\n  (:id . 44))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 46) (:start . 31) (:id . 46)))@@@1@5@((:identifiers (:sid . :s1.91) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500091@unknown@formal@none@1@S@To precisely understand the molecular mechanisms of Th17 differentiation, it is important to define the transcription factors that directly regulate IL-17 production.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "precisely") (:form . "precisely") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "VB") (:stem . "understand") (:form . "understand") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 48)\n  (:start . 38) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 48))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 56) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 72) (:start . 57) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 76) (:start . 74)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 89)\n  (:start . 80) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n  (:id . 55))\n ((:tag . "VB") (:stem . "define") (:form . "define") (:end . 99)\n  (:start . 93) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 57))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 117) (:start . 104) (:id . 58))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 125)\n  (:start . 118) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 130) (:start . 126)\n  (:id . 60))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 139)\n  (:start . 131) (:id . 61))\n ((:tag . "VBP") (:stem . "regulate") (:form . "regulate") (:end . 148)\n  (:start . 140) (:id . 62))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 154)\n  (:start . 149) (:id . 63))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 165)\n  (:start . 155) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.92) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500092@unknown@formal@none@1@S@All of IL-6, IL-21, and IL-23 activate the transcription factor Stat3 in T cells (38, 41, 42); accordingly, Th17 differentiation is abrogated in Stat3-deficient T cells (38, 42-45).@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "IL-21") (:form . "IL-21") (:end . 18) (:start . 13)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 29) (:start . 24)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "activate") (:form . "activate") (:end . 38)\n  (:start . 30) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 51))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 56) (:start . 43) (:id . 52))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 63)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "stat3") (:form . "Stat3") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 80) (:start . 75)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 58))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 84) (:start . 82)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 60))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 88) (:start . 86)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 62))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 92) (:start . 90)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 64))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 94) (:start . 93)\n  (:id . 65))\n ((:tag . "RB") (:stem . "accordingly") (:form . "accordingly") (:end . 106)\n  (:start . 95) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 67))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 112) (:start . 108)\n  (:id . 68))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 128) (:start . 113) (:id . 69))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 131) (:start . 129)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "abrogate") (:form . "abrogated") (:end . 141)\n  (:start . 132) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "stat3-deficient") (:form . "Stat3-deficient")\n  (:end . 160) (:start . 145) (:id . 73))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 162) (:start . 161)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 168)\n  (:start . 163) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 170) (:start . 169)\n  (:id . 76))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 172) (:start . 170)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 78))\n ((:tag . "CD") (:stem . "42-45") (:form . "42-45") (:end . 179)\n  (:start . 174) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s1.93) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500093@unknown@formal@none@1@S@Moreover, conditional deletion of Stat3 in T cells also abrogates the development of autoimmune diseases such as EAE and autoimmune pneumonitis in mice (43).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "conditional") (:form . "conditional") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "stat3") (:form . "Stat3") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "abrogate") (:form . "abrogates") (:end . 65)\n  (:start . 56) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 81)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 95)\n  (:start . 85) (:id . 56))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 104)\n  (:start . 96) (:id . 57))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 109) (:start . 105)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 112) (:start . 110)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "EAE") (:form . "EAE") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 131)\n  (:start . 121) (:id . 62))\n ((:tag . "NN") (:stem . "pneumonitis") (:form . "pneumonitis") (:end . 143)\n  (:start . 132) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 151)\n  (:start . 147) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 66))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 155) (:start . 153)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.94) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500094@unknown@formal@none@1@S@The role of Stat3 in Th17 differentiation seems to be remarkably direct – i.e. Stat3 binds to the Il17 and Il21 loci, as detected by using chromatin immunoprecipitation (ChiP) assays (38, 41).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "stat3") (:form . "Stat3") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Th17") (:form . "Th17") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 41) (:start . 26) (:id . 48))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "RB") (:stem . "remarkably") (:form . "remarkably") (:end . 64)\n  (:start . 54) (:id . 52))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 71)\n  (:start . 65) (:id . 53))\n ((:tag . "FW") (:stem . "–") (:form . "–") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 78) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "stat3") (:form . "Stat3") (:end . 84) (:start . 79)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "bind") (:form . "binds") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "il17") (:form . "Il17") (:end . 102) (:start . 98)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "NN") (:stem . "il21") (:form . "Il21") (:end . 111) (:start . 107)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "locus") (:form . "loci") (:end . 116)\n  (:start . 112) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 120) (:start . 118)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 129)\n  (:start . 121) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 132) (:start . 130)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 138) (:start . 133)\n  (:id . 68))\n ((:tag . "NN") (:stem . "chromatin") (:form . "chromatin") (:end . 148)\n  (:start . 139) (:id . 69))\n ((:tag . "NN") (:stem . "immunoprecipitation")\n  (:form . "immunoprecipitation") (:end . 168) (:start . 149) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 170) (:start . 169)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "ChiP") (:form . "ChiP") (:end . 174) (:start . 170)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 175) (:start . 174)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 182)\n  (:start . 176) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 184) (:start . 183)\n  (:id . 75))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 186) (:start . 184)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 187) (:start . 186)\n  (:id . 77))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 190) (:start . 188)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 191) (:start . 190)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x1.95.1) (:span 42 47)))\n (:hscopes ((:id . :x1.95.1) (:span 0 71)))\n (:identifiers (:sid . :s1.95) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500095@unknown@formal@none@1@S@In addition, IL-6 and IL-23 promote IL-23R expression and this also is Stat3-dependent (10, 36, 37).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "promote") (:form . "promote") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "il-23r") (:form . "IL-23R") (:end . 42)\n  (:start . 36) (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 53)\n  (:start . 43) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "stat3-dependent") (:form . "Stat3-dependent")\n  (:end . 86) (:start . 71) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 58))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 94) (:start . 92)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 98) (:start . 96)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.96) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500096@unknown@formal@none@1@S@Recently, the importance of Stat3 in human Th17 differentiation has been documented (46).@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "stat3") (:form . "Stat3") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 63) (:start . 48) (:id . 51))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "document") (:form . "documented") (:end . 83)\n  (:start . 73) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 55))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.97) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500097@unknown@formal@none@1@S@Like other T cell subsets, Th17 cells also have a lineage-specific transcription factor, namely the retinoic acid-related orphan receptor-γt (RORγt) (8).@(((:tag . "IN") (:stem . "like") (:form . "Like") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "subset") (:form . "subsets") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "lineage-specific") (:form . "lineage-specific")\n  (:end . 66) (:start . 50) (:id . 53))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 80) (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "RB") (:stem . "namely") (:form . "namely") (:end . 95)\n  (:start . 89) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "retinoic") (:form . "retinoic") (:end . 108)\n  (:start . 100) (:id . 59))\n ((:tag . "JJ") (:stem . "acid-related") (:form . "acid-related") (:end . 121)\n  (:start . 109) (:id . 60))\n ((:tag . "NN") (:stem . "orphan") (:form . "orphan") (:end . 128)\n  (:start . 122) (:id . 61))\n ((:tag . "NN") (:stem . "receptor-γt") (:form . "receptor-γt") (:end . 140)\n  (:start . 129) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 147)\n  (:start . 142) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 151) (:start . 150)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.98) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500098@unknown@formal@none@1@S@Interestingly, RORγt-deficient T cells produce fewer Th17 cells, whereas overexpression of RORγt in T cells promotes IL-17 expression (8).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "rorγt-deficient") (:form . "RORγt-deficient")\n  (:end . 30) (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 32) (:start . 31)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 38) (:start . 33)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "produce") (:form . "produce") (:end . 46)\n  (:start . 39) (:id . 47))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 52) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 63) (:start . 58)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 51))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 72)\n  (:start . 65) (:id . 52))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 87) (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 96) (:start . 91)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 56))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 101) (:start . 100)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 107)\n  (:start . 102) (:id . 58))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 116)\n  (:start . 108) (:id . 59))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 122)\n  (:start . 117) (:id . 60))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 133)\n  (:start . 123) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 136) (:start . 135)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.99) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500099@unknown@formal@none@1@S@Furthermore, RORγt-deficient mice are less susceptible to EAE, suggesting that RORγt is a key regulator of Th17 differentiation (8).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "rorγt-deficient") (:form . "RORγt-deficient")\n  (:end . 28) (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 33) (:start . 29)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "susceptible") (:form . "susceptible") (:end . 54)\n  (:start . 43) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "EAE") (:form . "EAE") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 73)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 78) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 84) (:start . 79)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 89) (:start . 88)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "regulator") (:form . "regulator") (:end . 103)\n  (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 111) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 127) (:start . 112) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 62))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x1.100.1) (:span 63 73)))\n (:hscopes ((:id . :x1.100.1) (:span 63 127)))\n (:identifiers (:sid . :s1.100) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500100@unknown@formal@none@1@S@Recent studies have shown that RORγt expression is significantly reduced in Stat3-deficient T cells (43-45).@(((:tag . "JJ") (:stem . "recent") (:form . "Recent") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 25) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 64) (:start . 51) (:id . 50))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 72)\n  (:start . 65) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "stat3-deficient") (:form . "Stat3-deficient")\n  (:end . 91) (:start . 76) (:id . 53))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 93) (:start . 92)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 99) (:start . 94)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 56))\n ((:tag . "CD") (:stem . "43-45") (:form . "43-45") (:end . 106)\n  (:start . 101) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s1.101) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500101@unknown@formal@none@1@S@However, the precise molecular mechanisms of Stat3-mediated expression of RORγt are still unclear.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "precise") (:form . "precise") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "stat3-mediated") (:form . "Stat3-mediated")\n  (:end . 59) (:start . 45) (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 70)\n  (:start . 60) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 79) (:start . 74)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 83) (:start . 80)\n  (:id . 53))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 89) (:start . 84)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 97)\n  (:start . 90) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x1.102.1) (:span 90 97)))\n (:hscopes ((:id . :x1.102.1) (:span 9 97)))\n (:identifiers (:sid . :s1.102) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500102@unknown@formal@none@1@S@Even so, RORγt could be a good candidate to target in treating inflammatory diseases (discussed in further detail below).@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 14) (:start . 9)\n  (:id . 45))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 20) (:start . 15)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "good") (:form . "good") (:end . 30) (:start . 26)\n  (:id . 49))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 40)\n  (:start . 31) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n  (:id . 51))\n ((:tag . "VB") (:stem . "target") (:form . "target") (:end . 50)\n  (:start . 44) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "treat") (:form . "treating") (:end . 62)\n  (:start . 54) (:id . 54))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 75)\n  (:start . 63) (:id . 55))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 84)\n  (:start . 76) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "discuss") (:form . "discussed") (:end . 95)\n  (:start . 86) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 106)\n  (:start . 99) (:id . 60))\n ((:tag . "NN") (:stem . "detail") (:form . "detail") (:end . 113)\n  (:start . 107) (:id . 61))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 119)\n  (:start . 114) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x1.103.1) (:span 15 20)))\n (:hscopes ((:id . :x1.103.1) (:span 15 120)))\n (:identifiers (:sid . :s1.103) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500103@unknown@formal@none@1@S@Also, it has been shown that expression of another retinoic acid related nuclear receptor, RORα also induces Th17 differentiation (47).@(((:tag . "RB") (:stem . "also") (:form . "Also") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 12) (:start . 9)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 17) (:start . 13)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 23) (:start . 18)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 39)\n  (:start . 29) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 50)\n  (:start . 43) (:id . 51))\n ((:tag . "JJ") (:stem . "retinoic") (:form . "retinoic") (:end . 59)\n  (:start . 51) (:id . 52))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "related") (:form . "related") (:end . 72)\n  (:start . 65) (:id . 54))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 80)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "RORα") (:form . "RORα") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 108)\n  (:start . 101) (:id . 60))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 129) (:start . 114) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 133) (:start . 131)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.104) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500104@unknown@formal@none@1@S@RORα seems to synergize with RORγt to promote development of Th17 lineage (47).@(((:tag . "NNP") (:stem . "RORα") (:form . "RORα") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "VB") (:stem . "synergize") (:form . "synergize") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 57)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 73)\n  (:start . 66) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x1.105.1) (:span 5 10)))\n (:hscopes ((:id . :x1.105.1) (:span 0 73)))\n (:identifiers (:sid . :s1.105) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500105@unknown@formal@none@1@S@Counter-regulation of IL-17 and the Yin/Yang of Th17 cells and Tregs@(((:tag . "NN") (:stem . "counter-regulation") (:form . "Counter-regulation")\n  (:end . 18) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 27) (:start . 22)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 31) (:start . 28)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "NN") (:stem . "yin/yang") (:form . "Yin/Yang") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 58) (:start . 53)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 68) (:start . 63)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s1.106) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500106@unknown@formal@none@1@S@Because of their potential for inducing immune-mediated damage to the host, it is perhaps not surprising that multiple mechanisms exist to inhibit the production of Th17 cells (Fig. 1b).@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 16)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "induce") (:form . "inducing") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "JJ") (:stem . "immune-mediated") (:form . "immune-mediated")\n  (:end . 55) (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "damage") (:form . "damage") (:end . 62)\n  (:start . 56) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "surprising") (:form . "surprising") (:end . 104)\n  (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 109) (:start . 105)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 118)\n  (:start . 110) (:id . 60))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 129)\n  (:start . 119) (:id . 61))\n ((:tag . "VBP") (:stem . "exist") (:form . "exist") (:end . 135)\n  (:start . 130) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 138) (:start . 136)\n  (:id . 63))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 146)\n  (:start . 139) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n  (:id . 65))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 161)\n  (:start . 151) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 164) (:start . 162)\n  (:id . 67))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 169) (:start . 165)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 175)\n  (:start . 170) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 181) (:start . 177)\n  (:id . 71))\n ((:tag . "NN") (:stem . "1b") (:form . "1b") (:end . 184) (:start . 182)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 185) (:start . 184)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x1.107.1) (:span 82 89)))\n (:hscopes ((:id . :x1.107.1) (:span 82 175)))\n (:identifiers (:sid . :s1.107) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500107@unknown@formal@none@1@S@Indeed, it has been recognized that the Th1-related cytokine IFN-γ inhibits Th17 differentiation (31, 32).@(((:tag . "RB") (:stem . "indeed") (:form . "Indeed") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "recognize") (:form . "recognized") (:end . 30)\n  (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "th1-related") (:form . "Th1-related") (:end . 51)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 60)\n  (:start . 52) (:id . 51))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 75)\n  (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 96) (:start . 81) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 56))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 104) (:start . 102)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.108) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500108@unknown@formal@none@1@S@Consistent with this concept, T-bet-deficient mice show enhanced Th17 differentiation (48).@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "t-bet-deficient") (:form . "T-bet-deficient")\n  (:end . 45) (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 50) (:start . 46)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 55) (:start . 51)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 85) (:start . 70) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 53))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 89) (:start . 87)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.109) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500109@unknown@formal@none@1@S@Similarly, the Th2-related IL-4 is also shown to down-regulate Th17 differentiation (49).@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "th2-related") (:form . "Th2-related") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "VB") (:stem . "down-regulate") (:form . "down-regulate")\n  (:end . 62) (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 83) (:start . 68) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 54))\n ((:tag . "CD") (:stem . "49") (:form . "49") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.110) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500110@unknown@formal@none@1@S@However, how IFN-γ and IL-4 inhibit IL-17 production is not yet known.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "inhibit") (:form . "inhibit") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 55)))@@@1@14@((:hcues ((:id . :x1.111.1) (:span 56 69)))\n (:hscopes ((:id . :x1.111.1) (:span 9 69)))\n (:identifiers (:sid . :s1.111) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500111@unknown@formal@none@1@S@Interestingly, IL-27, an IL-12-related heterodimeric cytokine, also has anti-inflammatory effect by inhibiting the generation of Th17 lineage and leads to limitation of EAE (50).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "il-27") (:form . "IL-27") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "il-12-related") (:form . "IL-12-related")\n  (:end . 38) (:start . 25) (:id . 47))\n ((:tag . "JJ") (:stem . "heterodimeric") (:form . "heterodimeric")\n  (:end . 52) (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 61)\n  (:start . 53) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 50))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "anti-inflammatory") (:form . "anti-inflammatory")\n  (:end . 89) (:start . 72) (:id . 53))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 96)\n  (:start . 90) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 99) (:start . 97)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "inhibit") (:form . "inhibiting") (:end . 110)\n  (:start . 100) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 57))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 125)\n  (:start . 115) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n  (:id . 59))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 133) (:start . 129)\n  (:id . 60))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 141)\n  (:start . 134) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 151)\n  (:start . 146) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 154) (:start . 152)\n  (:id . 64))\n ((:tag . "NN") (:stem . "limitation") (:form . "limitation") (:end . 165)\n  (:start . 155) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "EAE") (:form . "EAE") (:end . 172) (:start . 169)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 68))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 176) (:start . 174)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 177) (:start . 176)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s1.112) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500112@unknown@formal@none@1@S@Like IFN-γ, IL-27 suppresses Th17 differentiation through a STAT1-dependent manner (51, 52).@(((:tag . "IN") (:stem . "like") (:form . "Like") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "il-27") (:form . "IL-27") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "suppress") (:form . "suppresses") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 49) (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 59) (:start . 58)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "stat1-dependent") (:form . "STAT1-dependent")\n  (:end . 75) (:start . 60) (:id . 51))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 82)\n  (:start . 76) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 53))\n ((:tag . "CD") (:stem . "51") (:form . "51") (:end . 86) (:start . 84)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "CD") (:stem . "52") (:form . "52") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s1.113) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500113@unknown@formal@none@1@S@IL-25 (IL-17E) was also shown to inhibit IL-17 production by promoting Th2 differentiation (53).@(((:tag . "NNP") (:stem . "IL-25") (:form . "IL-25") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "NNP") (:stem . "IL-17E") (:form . "IL-17E") (:end . 13)\n  (:start . 7) (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 23) (:start . 19)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 29) (:start . 24)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 32) (:start . 30)\n  (:id . 49))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 40)\n  (:start . 33) (:id . 50))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 46) (:start . 41)\n  (:id . 51))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 57)\n  (:start . 47) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "promote") (:form . "promoting") (:end . 70)\n  (:start . 61) (:id . 54))\n ((:tag . "NN") (:stem . "th2") (:form . "Th2") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 90) (:start . 75) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 57))\n ((:tag . "CD") (:stem . "53") (:form . "53") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.114) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500114@unknown@formal@none@1@S@These reports suggest a cross-regulatory relationship among Th1, Th2, and Th17 differentiation.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "cross-regulatory") (:form . "cross-regulatory")\n  (:end . 40) (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 53)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 59) (:start . 54)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Th1") (:form . "Th1") (:end . 63) (:start . 60)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Th2") (:form . "Th2") (:end . 68) (:start . 65)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 94) (:start . 79) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x1.115.1) (:span 14 21)))\n (:hscopes ((:id . :x1.115.1) (:span 14 94)))\n (:identifiers (:sid . :s1.115) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500115@unknown@formal@none@1@S@However, it still remains to be determined how Th1-related and Th2-related transcription factors negatively regulate IL-17 production.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 42)\n  (:start . 32) (:id . 49))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "th1-related") (:form . "Th1-related") (:end . 58)\n  (:start . 47) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "th2-related") (:form . "Th2-related") (:end . 74)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 88) (:start . 75) (:id . 54))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 96)\n  (:start . 89) (:id . 55))\n ((:tag . "RB") (:stem . "negatively") (:form . "negatively") (:end . 107)\n  (:start . 97) (:id . 56))\n ((:tag . "VBP") (:stem . "regulate") (:form . "regulate") (:end . 116)\n  (:start . 108) (:id . 57))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 122)\n  (:start . 117) (:id . 58))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 133)\n  (:start . 123) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x1.116.1) (:span 18 42)))\n (:hscopes ((:id . :x1.116.1) (:span 18 133)))\n (:identifiers (:sid . :s1.116) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500116@unknown@formal@none@1@S@Another new subset of helper T cells that provides considerable insight into the pathogenesis of autoimmunity is the CD4+CD25+ regulatory T cells (Tregs) (3, 4, 54).@(((:tag . "DT") (:stem . "another") (:form . "Another") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 50)\n  (:start . 42) (:id . 50))\n ((:tag . "JJ") (:stem . "considerable") (:form . "considerable") (:end . 63)\n  (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "insight") (:form . "insight") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 93)\n  (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 109)\n  (:start . 97) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "cd4+cd25+") (:form . "CD4+CD25+") (:end . 126)\n  (:start . 117) (:id . 60))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 137)\n  (:start . 127) (:id . 61))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 139) (:start . 138)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 145)\n  (:start . 140) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 152)\n  (:start . 147) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 67))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 156) (:start . 155)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n  (:id . 69))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 159) (:start . 158)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 71))\n ((:tag . "CD") (:stem . "54") (:form . "54") (:end . 163) (:start . 161)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 164) (:start . 163)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s1.117) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500117@unknown@formal@none@1@S@Tregs suppress proliferation of effector T cells and maintain self tolerance by down-regulating immune responses against self or nonself-antigens (3, 4, 54).@(((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "suppress") (:form . "suppress") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 28) (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 45))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 40)\n  (:start . 32) (:id . 46))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 42) (:start . 41)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "VB") (:stem . "maintain") (:form . "maintain") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "NN") (:stem . "self") (:form . "self") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tolerance") (:form . "tolerance") (:end . 76)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "down-regulate") (:form . "down-regulating")\n  (:end . 95) (:start . 80) (:id . 54))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 102)\n  (:start . 96) (:id . 55))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 112)\n  (:start . 103) (:id . 56))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 120)\n  (:start . 113) (:id . 57))\n ((:tag . "NN") (:stem . "self") (:form . "self") (:end . 125) (:start . 121)\n  (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 128) (:start . 126)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "nonself-antigen") (:form . "nonself-antigens")\n  (:end . 145) (:start . 129) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 61))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 148) (:start . 147)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 63))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 151) (:start . 150)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . "CD") (:stem . "54") (:form . "54") (:end . 155) (:start . 153)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.118) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500118@unknown@formal@none@1@S@The mechanism by which Tregs preserve peripheral tolerance is still not entirely clear; however, they preferentially express cytotoxic T-lymphocyte antigen 4 (CTLA-4), and immunosuppressive cytokines including TGFß-1 and IL-10 (55-57).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "preserve") (:form . "preserve") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "JJ") (:stem . "peripheral") (:form . "peripheral") (:end . 48)\n  (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "tolerance") (:form . "tolerance") (:end . 58)\n  (:start . 49) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 67) (:start . 62)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "RB") (:stem . "entirely") (:form . "entirely") (:end . 80)\n  (:start . 72) (:id . 53))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 86) (:start . 81)\n  (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 95)\n  (:start . 88) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "RB") (:stem . "preferentially") (:form . "preferentially")\n  (:end . 116) (:start . 102) (:id . 59))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 124)\n  (:start . 117) (:id . 60))\n ((:tag . "JJ") (:stem . "cytotoxic") (:form . "cytotoxic") (:end . 134)\n  (:start . 125) (:id . 61))\n ((:tag . "NNP") (:stem . "T-lymphocyte") (:form . "T-lymphocyte")\n  (:end . 147) (:start . 135) (:id . 62))\n ((:tag . "NN") (:stem . "antigen") (:form . "antigen") (:end . 155)\n  (:start . 148) (:id . 63))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 157) (:start . 156)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 65))\n ((:tag . "NN") (:stem . "ctla-4") (:form . "CTLA-4") (:end . 165)\n  (:start . 159) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "immunosuppressive") (:form . "immunosuppressive")\n  (:end . 189) (:start . 172) (:id . 70))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 199)\n  (:start . 190) (:id . 71))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 209)\n  (:start . 200) (:id . 72))\n ((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 216)\n  (:start . 210) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 220) (:start . 217)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 226)\n  (:start . 221) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 228) (:start . 227)\n  (:id . 76))\n ((:tag . "CD") (:stem . "55-57") (:form . "55-57") (:end . 233)\n  (:start . 228) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 234) (:start . 233)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 235) (:start . 234)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x1.119.1) (:span 68 86)))\n (:hscopes ((:id . :x1.119.1) (:span 0 86)))\n (:identifiers (:sid . :s1.119) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500119@unknown@formal@none@1@S@Naturally arising Tregs (nTregs) are generated in the thymus, whereas inducible Tregs (iTregs) arise from naive T cells after antigen exposure and cytokine stimulation in the periphery, especially in the gut (58).@(((:tag . "RB") (:stem . "naturally") (:form . "Naturally") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBG") (:stem . "arise") (:form . "arising") (:end . 17)\n  (:start . 10) (:id . 43))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "ntreg") (:form . "nTregs") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "thymus") (:form . "thymus") (:end . 60)\n  (:start . 54) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 69)\n  (:start . 62) (:id . 54))\n ((:tag . "JJ") (:stem . "inducible") (:form . "inducible") (:end . 79)\n  (:start . 70) (:id . 55))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "itreg") (:form . "iTregs") (:end . 93)\n  (:start . 87) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "arise") (:form . "arise") (:end . 100)\n  (:start . 95) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 105) (:start . 101)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 111)\n  (:start . 106) (:id . 62))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 119)\n  (:start . 114) (:id . 64))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 125)\n  (:start . 120) (:id . 65))\n ((:tag . "NN") (:stem . "antigen") (:form . "antigen") (:end . 133)\n  (:start . 126) (:id . 66))\n ((:tag . "NN") (:stem . "exposure") (:form . "exposure") (:end . 142)\n  (:start . 134) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 146) (:start . 143)\n  (:id . 68))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 155)\n  (:start . 147) (:id . 69))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 167)\n  (:start . 156) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 170) (:start . 168)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 174) (:start . 171)\n  (:id . 72))\n ((:tag . "NN") (:stem . "periphery") (:form . "periphery") (:end . 184)\n  (:start . 175) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 74))\n ((:tag . "RB") (:stem . "especially") (:form . "especially") (:end . 196)\n  (:start . 186) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 199) (:start . 197)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n  (:id . 77))\n ((:tag . "NN") (:stem . "gut") (:form . "gut") (:end . 207) (:start . 204)\n  (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 209) (:start . 208)\n  (:id . 79))\n ((:tag . "CD") (:stem . "58") (:form . "58") (:end . 211) (:start . 209)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 212) (:start . 211)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s1.120) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500120@unknown@formal@none@1@S@Recently, it has been shown that CD4+CD25+ T cells express the transcription factor, forkhead box protein 3 (Foxp3), which is necessary and sufficient for Tregs to develop and function (59, 60).@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "cd4+cd25+") (:form . "CD4+CD25+") (:end . 42)\n  (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 50) (:start . 45)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 58)\n  (:start . 51) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 76) (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 83)\n  (:start . 77) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "forkhead") (:form . "forkhead") (:end . 93)\n  (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "box") (:form . "box") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 105)\n  (:start . 98) (:id . 59))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Foxp3") (:form . "Foxp3") (:end . 114)\n  (:start . 109) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 122)\n  (:start . 117) (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 125) (:start . 123)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 135)\n  (:start . 126) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 150)\n  (:start . 140) (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 154) (:start . 151)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 160)\n  (:start . 155) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 163) (:start . 161)\n  (:id . 72))\n ((:tag . "VB") (:stem . "develop") (:form . "develop") (:end . 171)\n  (:start . 164) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n  (:id . 74))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 184)\n  (:start . 176) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 186) (:start . 185)\n  (:id . 76))\n ((:tag . "CD") (:stem . "59") (:form . "59") (:end . 188) (:start . 186)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 78))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 192) (:start . 190)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 193) (:start . 192)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s1.121) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500121@unknown@formal@none@1@S@In mice, IL-2 and TGFß-1 were able to differentiate CD4+CD25- naive T cells into CD4+ CD25+ Foxp3+ Tregs (61, 62).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "il-2") (:form . "IL-2") (:end . 13) (:start . 9)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 17) (:start . 14)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 24)\n  (:start . 18) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 34) (:start . 30)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 50))\n ((:tag . "VB") (:stem . "differentiate") (:form . "differentiate")\n  (:end . 51) (:start . 38) (:id . 51))\n ((:tag . "JJ") (:stem . "cd4+cd25-") (:form . "CD4+CD25-") (:end . 61)\n  (:start . 52) (:id . 52))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 75) (:start . 70)\n  (:id . 55))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "cd25+") (:form . "CD25+") (:end . 91) (:start . 86)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "foxp3+") (:form . "Foxp3+") (:end . 98)\n  (:start . 92) (:id . 59))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 104) (:start . 99)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 61))\n ((:tag . "CD") (:stem . "61") (:form . "61") (:end . 108) (:start . 106)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 63))\n ((:tag . "CD") (:stem . "62") (:form . "62") (:end . 112) (:start . 110)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.122) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500122@unknown@formal@none@1@S@Therefore, the importance of TGFß-1 for both Tregs and Th17 lineage led to the speculation that these lineages were related.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "tgfß-1") (:form . "TGFß-1") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "NNPS") (:stem . "Treg") (:form . "Tregs") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Th17") (:form . "Th17") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 67)\n  (:start . 60) (:id . 53))\n ((:tag . "VBD") (:stem . "lead") (:form . "led") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "speculation") (:form . "speculation") (:end . 90)\n  (:start . 79) (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "lineage") (:form . "lineages") (:end . 110)\n  (:start . 102) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 115) (:start . 111)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 123)\n  (:start . 116) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.123) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500123@unknown@formal@none@1@S@This putative relationship also led to investigation of the importance of IL-2 in Th17 differentiation (44).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 26)\n  (:start . 14) (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 31) (:start . 27)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "lead") (:form . "led") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "investigation") (:form . "investigation")\n  (:end . 52) (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 70)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "NN") (:stem . "il-2") (:form . "IL-2") (:end . 78) (:start . 74)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 86) (:start . 82)\n  (:id . 55))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 102) (:start . 87) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 57))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x1.124.1) (:span 5 13)))\n (:hscopes ((:id . :x1.124.1) (:span 5 26)))\n (:identifiers (:sid . :s1.124) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500124@unknown@formal@none@1@S@In fact, IL-2 was found to inhibit the expression of RORγt while the enhancing expression of Foxp3 (44).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "il-2") (:form . "IL-2") (:end . 13) (:start . 9)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 17) (:start . 14)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 23) (:start . 18)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 26) (:start . 24)\n  (:id . 48))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 34)\n  (:start . 27) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 49)\n  (:start . 39) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 58) (:start . 53)\n  (:id . 53))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 64) (:start . 59)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "enhance") (:form . "enhancing") (:end . 78)\n  (:start . 69) (:id . 56))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 89)\n  (:start . 79) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "CD") (:stem . "foxp3") (:form . "Foxp3") (:end . 98) (:start . 93)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 102) (:start . 100)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 103) (:start . 102)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.125) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500125@unknown@formal@none@1@S@Furthermore, blockade of IL-2 or deletion of Stat5 promoted Th17 differentiation, suggesting that IL-2 inhibited Th17 lineage by affecting the RORγt-Foxp3 balance (44).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "blockade") (:form . "blockade") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "il-2") (:form . "IL-2") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Stat5") (:form . "Stat5") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "promote") (:form . "promoted") (:end . 59)\n  (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 80) (:start . 65) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 92)\n  (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "il-2") (:form . "IL-2") (:end . 102) (:start . 98)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 112)\n  (:start . 103) (:id . 58))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 117) (:start . 113)\n  (:id . 59))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 125)\n  (:start . 118) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 128) (:start . 126)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "affect") (:form . "affecting") (:end . 138)\n  (:start . 129) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n  (:id . 63))\n ((:tag . "NN") (:stem . "rorγt-foxp3") (:form . "RORγt-Foxp3") (:end . 154)\n  (:start . 143) (:id . 64))\n ((:tag . "NN") (:stem . "balance") (:form . "balance") (:end . 162)\n  (:start . 155) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n  (:id . 66))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 166) (:start . 164)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x1.126.1) (:span 82 92)))\n (:hscopes ((:id . :x1.126.1) (:span 82 162)))\n (:identifiers (:sid . :s1.126) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500126@unknown@formal@none@1@S@Therefore, helper T cells seem to have a unique way of achieving a balance between Tregs and Th17 cells during ongoing immune responses.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "seem") (:form . "seem") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 47)\n  (:start . 41) (:id . 51))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "achieve") (:form . "achieving") (:end . 64)\n  (:start . 55) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . "NN") (:stem . "balance") (:form . "balance") (:end . 74)\n  (:start . 67) (:id . 56))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 82)\n  (:start . 75) (:id . 57))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 88) (:start . 83)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 59))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 97) (:start . 93)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 103) (:start . 98)\n  (:id . 61))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 110)\n  (:start . 104) (:id . 62))\n ((:tag . "VBG") (:stem . "ongoe") (:form . "ongoing") (:end . 118)\n  (:start . 111) (:id . 63))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 125)\n  (:start . 119) (:id . 64))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 135)\n  (:start . 126) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x1.127.1) (:span 26 30)))\n (:hscopes ((:id . :x1.127.1) (:span 11 135)))\n (:identifiers (:sid . :s1.127) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500127@unknown@formal@none@1@S@Recently, it has been reported that TGFß-1 can promote either Th17 or Tregs lineage differentiation, depending on its local concentration (63).@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "tgfß-1") (:form . "TGFß-1") (:end . 42)\n  (:start . 36) (:id . 49))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "NNP") (:stem . "Th17") (:form . "Th17") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "treg") (:form . "Tregs") (:end . 75) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 83)\n  (:start . 76) (:id . 56))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 99) (:start . 84) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "depend") (:form . "depending") (:end . 110)\n  (:start . 101) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 123)\n  (:start . 118) (:id . 62))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 137) (:start . 124) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 64))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 141) (:start . 139)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s1.128) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500128@unknown@formal@none@1@S@Interestingly, Foxp3 may inhibit RORγt activity on its target genes, at least in par,t through direct interaction with RORγt (63).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Foxp3") (:form . "Foxp3") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "rorγt") (:form . "RORγt") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 47)\n  (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 61)\n  (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "par,t") (:form . "par,t") (:end . 86) (:start . 81)\n  (:id . 57))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 94)\n  (:start . 87) (:id . 58))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 101)\n  (:start . 95) (:id . 59))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 113)\n  (:start . 102) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 118) (:start . 114)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 124)\n  (:start . 119) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 63))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 128) (:start . 126)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x1.129.1) (:span 21 24)))\n (:hscopes ((:id . :x1.129.1) (:span 21 124)))\n (:identifiers (:sid . :s1.129) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500129@unknown@formal@none@1@S@Further complexities of Th17 cells@(((:tag . "JJ") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "complexity") (:form . "complexities") (:end . 20)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 34) (:start . 29)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s1.130) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500130@unknown@formal@none@1@S@The roles of Th17 cells are complicated by the fact that these cells also have the ability to produce anti-inflammatory cytokines such as IL-10 (34).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "complicate") (:form . "complicated") (:end . 39)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 62) (:start . 57)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 73) (:start . 69)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 78) (:start . 74)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 90)\n  (:start . 83) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 101)\n  (:start . 94) (:id . 60))\n ((:tag . "JJ") (:stem . "anti-inflammatory") (:form . "anti-inflammatory")\n  (:end . 119) (:start . 102) (:id . 61))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 129)\n  (:start . 120) (:id . 62))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 134) (:start . 130)\n  (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 143)\n  (:start . 138) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 147) (:start . 145)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.131) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500131@unknown@formal@none@1@S@This cytokine has anti-inflammatory properties that suppress functions of DCs and macrophages (64).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "anti-inflammatory") (:form . "anti-inflammatory")\n  (:end . 35) (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 46)\n  (:start . 36) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 51) (:start . 47)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "suppress") (:form . "suppress") (:end . 60)\n  (:start . 52) (:id . 48))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 70)\n  (:start . 61) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "dc") (:form . "DCs") (:end . 77) (:start . 74)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "macrophage") (:form . "macrophages") (:end . 93)\n  (:start . 82) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 54))\n ((:tag . "CD") (:stem . "64") (:form . "64") (:end . 97) (:start . 95)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.132) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500132@unknown@formal@none@1@S@IL-10 can be produced by many cell types such as B cells, macrophages, DCs, Th2 cells, and distinct populations of Tregs (64).@(((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 50) (:start . 49)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 56) (:start . 51)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "macrophage") (:form . "macrophages") (:end . 69)\n  (:start . 58) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "DC") (:form . "DCs") (:end . 74) (:start . 71)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 58))\n ((:tag . "NN") (:stem . "th2") (:form . "Th2") (:end . 79) (:start . 76)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 85) (:start . 80)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 99)\n  (:start . 91) (:id . 63))\n ((:tag . "NNS") (:stem . "population") (:form . "populations") (:end . 111)\n  (:start . 100) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 120)\n  (:start . 115) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 67))\n ((:tag . "CD") (:stem . "64") (:form . "64") (:end . 124) (:start . 122)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.133) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500133@unknown@formal@none@1@S@Recently, it has been reported that de-novo generation of Th17 cells in the presence of IL-6 and TGFß-1 leads to the production of IL-10 with up-regulation of RORγt and IL-17 (34).@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "de-novo") (:form . "de-novo") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 84)\n  (:start . 76) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 103)\n  (:start . 97) (:id . 60))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 109)\n  (:start . 104) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 63))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 127)\n  (:start . 117) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 65))\n ((:tag . "NN") (:stem . "il-10") (:form . "IL-10") (:end . 136)\n  (:start . 131) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 141) (:start . 137)\n  (:id . 67))\n ((:tag . "NN") (:stem . "up-regulation") (:form . "up-regulation")\n  (:end . 155) (:start . 142) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 164)\n  (:start . 159) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 174)\n  (:start . 169) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n  (:id . 73))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 178) (:start . 176)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s1.134) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500134@unknown@formal@none@1@S@Furthermore, IL-1ß, but not IL-23, potentiates IL-10 production in Th17 cells along with IL-6 and TGFß-1 (34).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "il-1ß") (:form . "IL-1ß") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "il-23") (:form . "IL-23") (:end . 33) (:start . 28)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "potentiate") (:form . "potentiates") (:end . 46)\n  (:start . 35) (:id . 50))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 52) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 63)\n  (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 83) (:start . 78)\n  (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "tgfß-1") (:form . "TGFß-1") (:end . 104)\n  (:start . 98) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 61))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 108) (:start . 106)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 109) (:start . 108)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.135) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500135@unknown@formal@none@1@S@Paradoxically, IL-6 and TGFß-1 seem to drive initial Th17 lineage commitment but also restrain the pathogenic potential of Th17 cells by producing IL-10 also (34).@(((:tag . "RB") (:stem . "paradoxically") (:form . "Paradoxically")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "VBP") (:stem . "seem") (:form . "seem") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "VB") (:stem . "drive") (:form . "drive") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "commitment") (:form . "commitment") (:end . 76)\n  (:start . 66) (:id . 53))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "VB") (:stem . "restrain") (:form . "restrain") (:end . 94)\n  (:start . 86) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "pathogenic") (:form . "pathogenic") (:end . 109)\n  (:start . 99) (:id . 58))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 119)\n  (:start . 110) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 60))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 127) (:start . 123)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 133)\n  (:start . 128) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 136) (:start . 134)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 146)\n  (:start . 137) (:id . 64))\n ((:tag . "NN") (:stem . "il-10") (:form . "IL-10") (:end . 152)\n  (:start . 147) (:id . 65))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 157) (:start . 153)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 67))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 161) (:start . 159)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x1.136.1) (:span 31 35)))\n (:hscopes ((:id . :x1.136.1) (:span 15 157)))\n (:identifiers (:sid . :s1.136) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500136@unknown@formal@none@1@S@Another cytokine produced by Th17 cells is IL-22 (25, 65, 66).@(((:tag . "DT") (:stem . "another") (:form . "Another") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "il-22") (:form . "IL-22") (:end . 48) (:start . 43)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "CD") (:stem . "65") (:form . "65") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 54))\n ((:tag . "CD") (:stem . "66") (:form . "66") (:end . 60) (:start . 58)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.137) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500137@unknown@formal@none@1@S@IL-22 belongs to the IL-10 family of cytokines which include IL-19, IL-20, IL-24, and IL-26.@(((:tag . "NNP") (:stem . "IL-22") (:form . "IL-22") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "belong") (:form . "belongs") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "il-10") (:form . "IL-10") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 33)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "il-19") (:form . "IL-19") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "IL-20") (:form . "IL-20") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "IL-24") (:form . "IL-24") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "IL-26") (:form . "IL-26") (:end . 91) (:start . 86)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.138) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500138@unknown@formal@none@1@S@Expressed in activated T cells, Th1 cells and NK cells (67), IL-22 induces expression of various antimicrobial peptides such as ß-defensins in skin, respiratory, and digestive tissues, which express IL-22R (68).@(((:tag . "VBN") (:stem . "express") (:form . "Expressed") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "nk") (:form . "NK") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 54) (:start . 49)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "CD") (:stem . "67") (:form . "67") (:end . 58) (:start . 56)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 59) (:start . 58)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "IL-22") (:form . "IL-22") (:end . 66) (:start . 61)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 74)\n  (:start . 67) (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 85)\n  (:start . 75) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 96)\n  (:start . 89) (:id . 61))\n ((:tag . "JJ") (:stem . "antimicrobial") (:form . "antimicrobial")\n  (:end . 110) (:start . 97) (:id . 62))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 119)\n  (:start . 111) (:id . 63))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 124) (:start . 120)\n  (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 127) (:start . 125)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "ß-defensin") (:form . "ß-defensins") (:end . 139)\n  (:start . 128) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 142) (:start . 140)\n  (:id . 67))\n ((:tag . "NN") (:stem . "skin") (:form . "skin") (:end . 147) (:start . 143)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 69))\n ((:tag . "NN") (:stem . "respiratory") (:form . "respiratory") (:end . 160)\n  (:start . 149) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "digestive") (:form . "digestive") (:end . 175)\n  (:start . 166) (:id . 73))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 183)\n  (:start . 176) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 75))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 190)\n  (:start . 185) (:id . 76))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 198)\n  (:start . 191) (:id . 77))\n ((:tag . "NNP") (:stem . "IL-22R") (:form . "IL-22R") (:end . 205)\n  (:start . 199) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 207) (:start . 206)\n  (:id . 79))\n ((:tag . "CD") (:stem . "68") (:form . "68") (:end . 209) (:start . 207)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s1.139) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500139@unknown@formal@none@1@S@In fact, expression of IL-22 and ß-defensins is higher in skin from patients with psoriasis and atopic dermatitis than in that from healthy individuals (69).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 19)\n  (:start . 9) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IL-22") (:form . "IL-22") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "ß-defensin") (:form . "ß-defensins") (:end . 44)\n  (:start . 33) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 54) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "skin") (:form . "skin") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 76)\n  (:start . 68) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "NN") (:stem . "psoriasis") (:form . "psoriasis") (:end . 91)\n  (:start . 82) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "atopic") (:form . "atopic") (:end . 102)\n  (:start . 96) (:id . 59))\n ((:tag . "NN") (:stem . "dermatitis") (:form . "dermatitis") (:end . 113)\n  (:start . 103) (:id . 60))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 118) (:start . 114)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 126) (:start . 122)\n  (:id . 63))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 131) (:start . 127)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "healthy") (:form . "healthy") (:end . 139)\n  (:start . 132) (:id . 65))\n ((:tag . "NNS") (:stem . "individual") (:form . "individuals") (:end . 151)\n  (:start . 140) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 67))\n ((:tag . "CD") (:stem . "69") (:form . "69") (:end . 155) (:start . 153)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.140) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500140@unknown@formal@none@1@S@While it is clear that IL-22 and IL-17 can contribute to host defense and to pathogenesis of various autoimmune diseases (25), it is also notable that IL-22 also has important anti-inflammatory effects (70).@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IL-22") (:form . "IL-22") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 38) (:start . 33)\n  (:id . 49))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 53)\n  (:start . 43) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "defense") (:form . "defense") (:end . 69)\n  (:start . 62) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 89)\n  (:start . 77) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 100)\n  (:start . 93) (:id . 59))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 111)\n  (:start . 101) (:id . 60))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 120)\n  (:start . 112) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 65))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 129) (:start . 127)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 132) (:start . 130)\n  (:id . 67))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 137) (:start . 133)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "notable") (:form . "notable") (:end . 145)\n  (:start . 138) (:id . 69))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 150) (:start . 146)\n  (:id . 70))\n ((:tag . "NN") (:stem . "il-22") (:form . "IL-22") (:end . 156)\n  (:start . 151) (:id . 71))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 161) (:start . 157)\n  (:id . 72))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 165) (:start . 162)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 175)\n  (:start . 166) (:id . 74))\n ((:tag . "JJ") (:stem . "anti-inflammatory") (:form . "anti-inflammatory")\n  (:end . 193) (:start . 176) (:id . 75))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 201)\n  (:start . 194) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 203) (:start . 202)\n  (:id . 77))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 205) (:start . 203)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s1.141) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500141@unknown@formal@none@1@S@Specifically, IL-22-expressing Th17 cells provided protection in models of hepatitis (70).@(((:tag . "RB") (:stem . "specifically") (:form . "Specifically") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "il-22-expressing") (:form . "IL-22-expressing")\n  (:end . 30) (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 35) (:start . 31)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 41) (:start . 36)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "provide") (:form . "provided") (:end . 50)\n  (:start . 42) (:id . 47))\n ((:tag . "NN") (:stem . "protection") (:form . "protection") (:end . 61)\n  (:start . 51) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 71)\n  (:start . 65) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 51))\n ((:tag . "NN") (:stem . "hepatitis") (:form . "hepatitis") (:end . 84)\n  (:start . 75) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 53))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.142) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500142@unknown@formal@none@1@S@Recently, IL-22 also has been shown not to be required for the development of EAE in mice (71).@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "IL-22") (:form . "IL-22") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 45) (:start . 43)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 54)\n  (:start . 46) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 58) (:start . 55)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 74)\n  (:start . 63) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "eae") (:form . "EAE") (:end . 81) (:start . 78)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 89) (:start . 85)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 60))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 93) (:start . 91)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 94) (:start . 93)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.143) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500143@unknown@formal@none@1@S@These facts indicate the complexity of Th17 cells, which produce multiple cytokines and have diverse functions during inflammation.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "fact") (:form . "facts") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "produce") (:form . "produce") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 73)\n  (:start . 65) (:id . 53))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 83)\n  (:start . 74) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 100)\n  (:start . 93) (:id . 57))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 110)\n  (:start . 101) (:id . 58))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 117)\n  (:start . 111) (:id . 59))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 130)\n  (:start . 118) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.144) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500144@unknown@formal@none@1@S@As such, their relevance may vary among different autoimmune diseases.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 14) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "relevance") (:form . "relevance") (:end . 24)\n  (:start . 15) (:id . 46))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "VB") (:stem . "vary") (:form . "vary") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 39) (:start . 34)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 49)\n  (:start . 40) (:id . 50))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 60)\n  (:start . 50) (:id . 51))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 69)\n  (:start . 61) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 53)))@@@1@12@((:hcues ((:id . :x1.145.1) (:span 25 28)))\n (:hscopes ((:id . :x1.145.1) (:span 25 69)))\n (:identifiers (:sid . :s1.145) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500145@unknown@formal@none@1@S@Human Th17 differentiation@(((:tag . "JJ") (:stem . "human") (:form . "Human") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Th17") (:form . "Th17") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 26) (:start . 11) (:id . 44)))@@@1@3@((:identifiers (:sid . :s1.146) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500146@unknown@formal@none@1@S@While a large body of evidence has documented that the best recipe for generating Th17 cells from murine naive CD4+ T cells is the combination of TGFß-1 and IL-6 or IL-21, several groups initially reported that the regulation of human Th17 differentiation was quite distinct (Fig. 1c) (9, 10, 66, 72-74).@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . 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5500147@unknown@formal@none@1@S@Specifically, TGFß-1 was initially considered to have inhibitory effect on human IL-17 production; however, the role of TGFß-1 in human Th17 differentiation has recently become clearer.@(((:tag . "RB") (:stem . "specifically") (:form . "Specifically") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "RB") (:stem . "initially") (:form . "initially") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 45)\n  (:start . 35) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 53) (:start . 49)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 64)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 71)\n  (:start . 65) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 80) (:start . 75)\n  (:id . 53))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 86) (:start . 81)\n  (:id . 54))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 97)\n  (:start . 87) (:id . 55))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 98) (:start . 97)\n  (:id . 56))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 106)\n  (:start . 99) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 116) (:start . 112)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . "NN") (:stem . "tgfß-1") (:form . "TGFß-1") (:end . 126)\n  (:start . 120) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 135)\n  (:start . 130) (:id . 64))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 140) (:start . 136)\n  (:id . 65))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 156) (:start . 141) (:id . 66))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 160) (:start . 157)\n  (:id . 67))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 169)\n  (:start . 161) (:id . 68))\n ((:tag . "VBN") (:stem . "become") (:form . "become") (:end . 176)\n  (:start . 170) (:id . 69))\n ((:tag . "NN") (:stem . "clearer") (:form . "clearer") (:end . 184)\n  (:start . 177) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s1.148) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500148@unknown@formal@none@1@S@While TGFß-1 alone had an inhibitory effect on production of IL-17 by T cells, culturing human naive CD4+ T cells from cord blood in serum-free medium revealed a requirement of TGFß-1 for Th17 differentiation (72).@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 12)\n  (:start . 6) (:id . 43))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 36)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 57)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "culture") (:form . "culturing") (:end . 88)\n  (:start . 79) (:id . 57))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 94) (:start . 89)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 100) (:start . 95)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 105) (:start . 101)\n  (:id . 60))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 113)\n  (:start . 108) (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 118) (:start . 114)\n  (:id . 63))\n ((:tag . "NN") (:stem . "cord") (:form . "cord") (:end . 123) (:start . 119)\n  (:id . 64))\n ((:tag . "NN") (:stem . "blood") (:form . "blood") (:end . 129)\n  (:start . 124) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "serum-free") (:form . "serum-free") (:end . 143)\n  (:start . 133) (:id . 67))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 150)\n  (:start . 144) (:id . 68))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 159)\n  (:start . 151) (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 161) (:start . 160)\n  (:id . 70))\n ((:tag . "NN") (:stem . "requirement") (:form . "requirement") (:end . 173)\n  (:start . 162) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n  (:id . 72))\n ((:tag . "NN") (:stem . "tgfß-1") (:form . "TGFß-1") (:end . 183)\n  (:start . 177) (:id . 73))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 187) (:start . 184)\n  (:id . 74))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 192) (:start . 188)\n  (:id . 75))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 208) (:start . 193) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 210) (:start . 209)\n  (:id . 77))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 212) (:start . 210)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s1.149) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500149@unknown@formal@none@1@S@TGFß-1 seems to have dual effects on human Th17 differentiation in a dose-dependent manner.@(((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "dual") (:form . "dual") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 63) (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "dose-dependent") (:form . "dose-dependent")\n  (:end . 83) (:start . 69) (:id . 54))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 90)\n  (:start . 84) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x1.150.1) (:span 7 12)))\n (:hscopes ((:id . :x1.150.1) (:span 0 90)))\n (:identifiers (:sid . :s1.150) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500150@unknown@formal@none@1@S@While TGFß-1 is required for the expression of RORγt in human naive CD4+ T cells from cord blood, TGFß-1 can inhibit the function of RORγt at high doses (72).@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "tgfß-1") (:form . "TGFß-1") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 61) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cord") (:form . "cord") (:end . 90) (:start . 86)\n  (:id . 58))\n ((:tag . "NN") (:stem . "blood") (:form . "blood") (:end . 96) (:start . 91)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 104)\n  (:start . 98) (:id . 61))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 108) (:start . 105)\n  (:id . 62))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 116)\n  (:start . 109) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 64))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 129)\n  (:start . 121) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 138)\n  (:start . 133) (:id . 67))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 141) (:start . 139)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 146) (:start . 142)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "dose") (:form . "doses") (:end . 152)\n  (:start . 147) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 71))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 156) (:start . 154)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s1.151) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500151@unknown@formal@none@1@S@However, inflammatory cytokines (IL-1ß, IL-6, and IL-21 or IL-23) relieve the latter effect of TGFß-1 (72).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 21)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 33) (:start . 32)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IL-1ß") (:form . "IL-1ß") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "IL-21") (:form . "IL-21") (:end . 55) (:start . 50)\n  (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 64) (:start . 59)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "relieve") (:form . "relieve") (:end . 73)\n  (:start . 66) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 84)\n  (:start . 78) (:id . 58))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 91)\n  (:start . 85) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 60))\n ((:tag . "NN") (:stem . "tgfß-1") (:form . "TGFß-1") (:end . 101)\n  (:start . 95) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 62))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 105) (:start . 103)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s1.152) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500152@unknown@formal@none@1@S@By using serum-free medium it has thus been clarified that the optimum conditions for human Th17 differentiation are TGFß-1, IL-1ß, and IL-2 in combination with IL-6, IL-21 or IL-23 (72-74).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "serum-free") (:form . "serum-free") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "clarify") (:form . "clarified") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "optimum") (:form . "optimum") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 81)\n  (:start . 71) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 91) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 112) (:start . 97) (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 116) (:start . 113)\n  (:id . 59))\n ((:tag . "NN") (:stem . "tgfß-1") (:form . "TGFß-1") (:end . 123)\n  (:start . 117) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 61))\n ((:tag . "NN") (:stem . "il-1ß") (:form . "IL-1ß") (:end . 130)\n  (:start . 125) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 64))\n ((:tag . "NN") (:stem . "il-2") (:form . "IL-2") (:end . 140) (:start . 136)\n  (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 143) (:start . 141)\n  (:id . 66))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 155)\n  (:start . 144) (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 160) (:start . 156)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 165) (:start . 161)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "IL-21") (:form . "IL-21") (:end . 172)\n  (:start . 167) (:id . 71))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 175) (:start . 173)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 181)\n  (:start . 176) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 183) (:start . 182)\n  (:id . 74))\n ((:tag . "CD") (:stem . "72-74") (:form . "72-74") (:end . 188)\n  (:start . 183) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s1.153) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500153@unknown@formal@none@1@S@Of these latter cytokines, IL-23 seems to be the most effective (10, 66, 72, 73).@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 63)\n  (:start . 54) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 67) (:start . 65)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 56))\n ((:tag . "CD") (:stem . "66") (:form . "66") (:end . 71) (:start . 69)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 58))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 75) (:start . 73)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 60))\n ((:tag . "CD") (:stem . "73") (:form . "73") (:end . 79) (:start . 77)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x1.154.1) (:span 33 38)))\n (:hscopes ((:id . :x1.154.1) (:span 27 63)))\n (:identifiers (:sid . :s1.154) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500154@unknown@formal@none@1@S@A key aspect of Th17 regulation is the regulation of IL-23R (10).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 5) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "aspect") (:form . "aspect") (:end . 12) (:start . 6)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 31)\n  (:start . 21) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 49)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "IL-23R") (:form . "IL-23R") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 64) (:start . 63)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.155) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500155@unknown@formal@none@1@S@Naive CD4+ T cells express low levels of this receptor, but the combination of TGFß-1, IL-1ß, and IL-23 can strongly induce this receptor (10, 72).@(((:tag . "JJ") (:stem . "naive") (:form . "Naive") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 75)\n  (:start . 64) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "TGFß-1") (:form . "TGFß-1") (:end . 85)\n  (:start . 79) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 58))\n ((:tag . "NN") (:stem . "il-1ß") (:form . "IL-1ß") (:end . 92) (:start . 87)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 103)\n  (:start . 98) (:id . 62))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 107) (:start . 104)\n  (:id . 63))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 116)\n  (:start . 108) (:id . 64))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 123)\n  (:start . 117) (:id . 65))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 128) (:start . 124)\n  (:id . 66))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 137)\n  (:start . 129) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 68))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 141) (:start . 139)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 70))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 145) (:start . 143)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s1.156) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500156@unknown@formal@none@1@S@Thus, IL-23 promotes expression of its own receptor, allowing it to be an effective inducer of IL-17.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 51)\n  (:start . 43) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "allow") (:form . "allowing") (:end . 61)\n  (:start . 53) (:id . 52))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 83)\n  (:start . 74) (:id . 57))\n ((:tag . "NN") (:stem . "inducer") (:form . "inducer") (:end . 91)\n  (:start . 84) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 100)\n  (:start . 95) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.157) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500157@unknown@formal@none@1@S@It is of note is that CCR6+IL-23R+ human memory CD4+ T cells are major producers of IL-17 (75, 76).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "note") (:form . "note") (:end . 13) (:start . 9)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "ccr6+il-23r+") (:form . "CCR6+IL-23R+") (:end . 34)\n  (:start . 22) (:id . 48))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 47)\n  (:start . 41) (:id . 50))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 60) (:start . 55)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 70) (:start . 65)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "producer") (:form . "producers") (:end . 80)\n  (:start . 71) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 89) (:start . 84)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "CD") (:stem . "75") (:form . "75") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 61))\n ((:tag . "CD") (:stem . "76") (:form . "76") (:end . 97) (:start . 95)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s1.158) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500158@unknown@formal@none@1@S@Because CCR6+CD4+ T cells, but not CCR6-CD4+ T cells, secrete IL-17 and expression of IL-23R, CCR6, and RORγt is up-regulated during Th17 differentiation (72), these factors seem to be essential for development of human Th17 lineage.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "ccr6+cd4+") (:form . "CCR6+CD4+") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 19) (:start . 18)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 25) (:start . 20)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "ccr6-cd4+") (:form . "CCR6-CD4+") (:end . 44)\n  (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 52) (:start . 47)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "secrete") (:form . "secrete") (:end . 61)\n  (:start . 54) (:id . 53))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 82)\n  (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "IL-23R") (:form . "IL-23R") (:end . 92)\n  (:start . 86) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "CCR6") (:form . "CCR6") (:end . 98) (:start . 94)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 109)\n  (:start . 104) (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 112) (:start . 110)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "up-regulate") (:form . "up-regulated") (:end . 125)\n  (:start . 113) (:id . 65))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 132)\n  (:start . 126) (:id . 66))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 137) (:start . 133)\n  (:id . 67))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 153) (:start . 138) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 69))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 157) (:start . 155)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n  (:id . 72))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 165)\n  (:start . 160) (:id . 73))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 173)\n  (:start . 166) (:id . 74))\n ((:tag . "VBP") (:stem . "seem") (:form . "seem") (:end . 178) (:start . 174)\n  (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 181) (:start . 179)\n  (:id . 76))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 184) (:start . 182)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 194)\n  (:start . 185) (:id . 78))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 198) (:start . 195)\n  (:id . 79))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 210)\n  (:start . 199) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 213) (:start . 211)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 219)\n  (:start . 214) (:id . 82))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 224) (:start . 220)\n  (:id . 83))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 232)\n  (:start . 225) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 233) (:start . 232)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x1.159.1) (:span 174 178)))\n (:hscopes ((:id . :x1.159.1) (:span 160 232)))\n (:identifiers (:sid . :s1.159) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500159@unknown@formal@none@1@S@Importantly, it has been shown that mutations presumed to underlie hyper-IgE syndrome (HIES, “Job's syndrome”) are identified in the STAT3 gene (46).@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 45)\n  (:start . 36) (:id . 49))\n ((:tag . "VBN") (:stem . "presume") (:form . "presumed") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "VB") (:stem . "underlie") (:form . "underlie") (:end . 66)\n  (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "hyper-ige") (:form . "hyper-IgE") (:end . 76)\n  (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "syndrome") (:form . "syndrome") (:end . 85)\n  (:start . 77) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "HIES") (:form . "HIES") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 57))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Job") (:form . "Job") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 99) (:start . 97)\n  (:id . 60))\n ((:tag . "NN") (:stem . "syndrome") (:form . "syndrome") (:end . 108)\n  (:start . 100) (:id . 61))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 114) (:start . 111)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 125)\n  (:start . 115) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 67))\n ((:tag . "NN") (:stem . "stat3") (:form . "STAT3") (:end . 138)\n  (:start . 133) (:id . 68))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 143) (:start . 139)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 70))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 147) (:start . 145)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x1.160.1) (:span 46 54)))\n (:hscopes ((:id . :x1.160.1) (:span 46 110)))\n (:identifiers (:sid . :s1.160) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500160@unknown@formal@none@1@S@Purified naive CD4+ T cells from HIES individuals can not differentiate into Th17 cells in vitro and have lower expression of RORγt (46), suggesting that Stat3 signaling is also a crucial factor for the generation of human Th17 cells.@(((:tag . "VBN") (:stem . "purify") (:form . "Purified") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "HIES") (:form . "HIES") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "individual") (:form . "individuals") (:end . 49)\n  (:start . 38) (:id . 49))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "VB") (:stem . "differentiate") (:form . "differentiate")\n  (:end . 71) (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 81) (:start . 77)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 87) (:start . 82)\n  (:id . 55))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 111) (:start . 106)\n  (:id . 60))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 122)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "RORγt") (:form . "RORγt") (:end . 131)\n  (:start . 126) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 148)\n  (:start . 138) (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 153) (:start . 149)\n  (:id . 69))\n ((:tag . "NN") (:stem . "stat3") (:form . "Stat3") (:end . 159)\n  (:start . 154) (:id . 70))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 169)\n  (:start . 160) (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 172) (:start . 170)\n  (:id . 72))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 177) (:start . 173)\n  (:id . 73))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 179) (:start . 178)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 187)\n  (:start . 180) (:id . 75))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 194)\n  (:start . 188) (:id . 76))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 198) (:start . 195)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 202) (:start . 199)\n  (:id . 78))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 213)\n  (:start . 203) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 216) (:start . 214)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 222)\n  (:start . 217) (:id . 81))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 227) (:start . 223)\n  (:id . 82))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 233)\n  (:start . 228) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x1.161.1) (:span 138 148)))\n (:hscopes ((:id . :x1.161.1) (:span 138 233)))\n (:identifiers (:sid . :s1.161) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500161@unknown@formal@none@1@S@Th17 cells in autoimmune diseases@(((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 33)\n  (:start . 25) (:id . 46)))@@@1@5@((:identifiers (:sid . :s1.162) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500162@unknown@formal@none@1@S@Although Th17 cells are important and essential subsets participating in host defense against extracellular antigens, evidence implicating Th17 cells as a causal factor of autoimmune diseases is also mounting (25).@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "subset") (:form . "subsets") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "VBG") (:stem . "participate") (:form . "participating") (:end . 69)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 77) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "defense") (:form . "defense") (:end . 85)\n  (:start . 78) (:id . 53))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 93)\n  (:start . 86) (:id . 54))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 107) (:start . 94) (:id . 55))\n ((:tag . "NNS") (:stem . "antigen") (:form . "antigens") (:end . 116)\n  (:start . 108) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 57))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 126)\n  (:start . 118) (:id . 58))\n ((:tag . "VBG") (:stem . "implicate") (:form . "implicating") (:end . 138)\n  (:start . 127) (:id . 59))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 143) (:start . 139)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 149)\n  (:start . 144) (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 152) (:start . 150)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 154) (:start . 153)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "causal") (:form . "causal") (:end . 161)\n  (:start . 155) (:id . 64))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 168)\n  (:start . 162) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 182)\n  (:start . 172) (:id . 67))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 191)\n  (:start . 183) (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 194) (:start . 192)\n  (:id . 69))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 199) (:start . 195)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "mount") (:form . "mounting") (:end . 208)\n  (:start . 200) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 210) (:start . 209)\n  (:id . 72))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 212) (:start . 210)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x1.163.1) (:span 127 138)))\n (:hscopes ((:id . :x1.163.1) (:span 127 191)))\n (:identifiers (:sid . :s1.163) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500163@unknown@formal@none@1@S@Following extensive analysis of mouse disease models such as EAE, CIA, and IBD, it has also become evident that IL-17 is a contributing factor in human autoimmune diseases.@(((:tag . "VBG") (:stem . "follow") (:form . "Following") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 19)\n  (:start . 10) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 28)\n  (:start . 20) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 37) (:start . 32)\n  (:id . 46))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 52)\n  (:start . 46) (:id . 48))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "EAE") (:form . "EAE") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "CIA") (:form . "CIA") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "IBD") (:form . "IBD") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 82) (:start . 80)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 86) (:start . 83)\n  (:id . 59))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 91) (:start . 87)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "become") (:form . "become") (:end . 98)\n  (:start . 92) (:id . 61))\n ((:tag . "JJ") (:stem . "evident") (:form . "evident") (:end . 106)\n  (:start . 99) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 111) (:start . 107)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 117)\n  (:start . 112) (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 120) (:start . 118)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 122) (:start . 121)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "contribute") (:form . "contributing") (:end . 135)\n  (:start . 123) (:id . 67))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 142)\n  (:start . 136) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 145) (:start . 143)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 151)\n  (:start . 146) (:id . 70))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 162)\n  (:start . 152) (:id . 71))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 171)\n  (:start . 163) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s1.164) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500164@unknown@formal@none@1@S@For instance, perivascular IL-17-producing T cells are present in brain lesions of active MS patients and these cells are reduced in quiescent MS patients (77).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "perivascular") (:form . "perivascular") (:end . 26)\n  (:start . 14) (:id . 45))\n ((:tag . "JJ") (:stem . "il-17-producing") (:form . "IL-17-producing")\n  (:end . 42) (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 44) (:start . 43)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 50) (:start . 45)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 62)\n  (:start . 55) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 71) (:start . 66)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "lesion") (:form . "lesions") (:end . 79)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 89)\n  (:start . 83) (:id . 55))\n ((:tag . "NNP") (:stem . "MS") (:form . "MS") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 101)\n  (:start . 93) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 58))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 111)\n  (:start . 106) (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 117)\n  (:start . 112) (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 121) (:start . 118)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 129)\n  (:start . 122) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "quiescent") (:form . "quiescent") (:end . 142)\n  (:start . 133) (:id . 64))\n ((:tag . "NNP") (:stem . "MS") (:form . "MS") (:end . 145) (:start . 143)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 154)\n  (:start . 146) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 67))\n ((:tag . "CD") (:stem . "77") (:form . "77") (:end . 158) (:start . 156)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.165) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500165@unknown@formal@none@1@S@Moreover, DCs from MS patients secrete more IL-23 than healthy controls, and T cells from MS patients secrete more IL-17 than healthy controls (78).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "DC") (:form . "DCs") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "MS") (:form . "MS") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "VBP") (:stem . "secrete") (:form . "secrete") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "il-23") (:form . "IL-23") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "healthy") (:form . "healthy") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 71)\n  (:start . 63) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 78) (:start . 77)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 84) (:start . 79)\n  (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 89) (:start . 85)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "MS") (:form . "MS") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 101)\n  (:start . 93) (:id . 60))\n ((:tag . "VBP") (:stem . "secrete") (:form . "secrete") (:end . 109)\n  (:start . 102) (:id . 61))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 114) (:start . 110)\n  (:id . 62))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 120)\n  (:start . 115) (:id . 63))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 125) (:start . 121)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "healthy") (:form . "healthy") (:end . 133)\n  (:start . 126) (:id . 65))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 142)\n  (:start . 134) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 144) (:start . 143)\n  (:id . 67))\n ((:tag . "CD") (:stem . "78") (:form . "78") (:end . 146) (:start . 144)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.166) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500166@unknown@formal@none@1@S@Also, elevated levels of IL-17 have been noted in the sera and in tissues of patients with RA, IBD, and psoriasis (25).@(((:tag . "RB") (:stem . "also") (:form . "Also") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "elevated") (:form . "elevated") (:end . 14)\n  (:start . 6) (:id . 44))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "serum") (:form . "sera") (:end . 58) (:start . 54)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 73)\n  (:start . 66) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 85)\n  (:start . 77) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "IBD") (:form . "IBD") (:end . 98) (:start . 95)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 64))\n ((:tag . "NN") (:stem . "psoriasis") (:form . "psoriasis") (:end . 113)\n  (:start . 104) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 66))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 117) (:start . 115)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.167) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500167@unknown@formal@none@1@S@We will see more evidence confirming the roles of IL-17 in human diseases and inflammation in the future.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "VBG") (:stem . "confirm") (:form . "confirming") (:end . 36)\n  (:start . 26) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 55) (:start . 50)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 64) (:start . 59)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 73)\n  (:start . 65) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 90)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "future") (:form . "future") (:end . 104)\n  (:start . 98) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.168) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500168@unknown@formal@none@1@S@Recent genetic data has linked polymorphisms of the Il23r gene to various human diseases such as ankylosing spondylitis, CD, and psoriasis (79-81).@(((:tag . "JJ") (:stem . "recent") (:form . "Recent") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "data") (:form . "data") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "link") (:form . "linked") (:end . 30) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "polymorphism") (:form . "polymorphisms")\n  (:end . 44) (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Il23r") (:form . "Il23r") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 73)\n  (:start . 66) (:id . 53))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 88)\n  (:start . 80) (:id . 55))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "ankylose") (:form . "ankylosing") (:end . 107)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "spondylitis") (:form . "spondylitis") (:end . 119)\n  (:start . 108) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "CD") (:form . "CD") (:end . 123) (:start . 121)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 63))\n ((:tag . "NN") (:stem . "psoriasis") (:form . "psoriasis") (:end . 138)\n  (:start . 129) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 65))\n ((:tag . "CD") (:stem . "79-81") (:form . "79-81") (:end . 145)\n  (:start . 140) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.169) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500169@unknown@formal@none@1@S@Accordingly treating CD and psoriasis patients with anti-IL-12p40 antibody has resulted in some success (14, 15).@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "VBG") (:stem . "treat") (:form . "treating") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "NN") (:stem . "cd") (:form . "CD") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "psoriasis") (:form . "psoriasis") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 46)\n  (:start . 38) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "anti-il-12p40") (:form . "anti-IL-12p40")\n  (:end . 65) (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 74)\n  (:start . 66) (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 78) (:start . 75)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "result") (:form . "resulted") (:end . 87)\n  (:start . 79) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 53))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 95) (:start . 91)\n  (:id . 54))\n ((:tag . "NN") (:stem . "success") (:form . "success") (:end . 103)\n  (:start . 96) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n  (:id . 56))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 107) (:start . 105)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.170) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500170@unknown@formal@none@1@S@These results argue strongly for a role of the IL-23/IL-17 axis in human autoimmune diseases.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "argue") (:form . "argue") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "il-23/il-17") (:form . "IL-23/IL-17") (:end . 58)\n  (:start . 47) (:id . 51))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 83)\n  (:start . 73) (:id . 55))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x1.171.1) (:span 14 28)))\n (:hscopes ((:id . :x1.171.1) (:span 14 92)))\n (:identifiers (:sid . :s1.171) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500171@unknown@formal@none@1@S@Th17 cells in rheumatoid arthritis@(((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "rheumatoid") (:form . "rheumatoid") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "arthritis") (:form . "arthritis") (:end . 34)\n  (:start . 25) (:id . 46)))@@@1@5@((:identifiers (:sid . :s1.172) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500172@unknown@formal@none@1@S@It is of particular interest to evaluate the contribution of Th17 cells to the pathogenesis of RA, because targeting pathogenetic Th17 might be a reasonable strategy for treating RA.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 19)\n  (:start . 9) (:id . 45))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "contribution") (:form . "contribution") (:end . 57)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 91)\n  (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 106)\n  (:start . 99) (:id . 60))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 116)\n  (:start . 107) (:id . 61))\n ((:tag . "JJ") (:stem . "pathogenetic") (:form . "pathogenetic") (:end . 129)\n  (:start . 117) (:id . 62))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 134) (:start . 130)\n  (:id . 63))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 140)\n  (:start . 135) (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 143) (:start . 141)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "reasonable") (:form . "reasonable") (:end . 156)\n  (:start . 146) (:id . 67))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 165)\n  (:start . 157) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 169) (:start . 166)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "treat") (:form . "treating") (:end . 178)\n  (:start . 170) (:id . 70))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 181) (:start . 179)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x1.173.1) (:span 135 140)))\n (:hscopes ((:id . :x1.173.1) (:span 135 181)))\n (:identifiers (:sid . :s1.173) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500173@unknown@formal@none@1@S@First, IL-17-deficient mice fail to develop CIA when challenged (82).@(((:tag . "RB") (:stem . "first") (:form . "First") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "il-17-deficient") (:form . "IL-17-deficient")\n  (:end . 22) (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "fail") (:form . "fail") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "VB") (:stem . "develop") (:form . "develop") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "NNP") (:stem . "CIA") (:form . "CIA") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "challenge") (:form . "challenged") (:end . 63)\n  (:start . 53) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "CD") (:stem . "82") (:form . "82") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s1.174) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500174@unknown@formal@none@1@S@Consistent with this, treatment with neutralizing IL-17 monoclonal antibody ameliorates joint inflammation in CIA models (83).@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "neutralize") (:form . "neutralizing") (:end . 49)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "monoclonal") (:form . "monoclonal") (:end . 66)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 75)\n  (:start . 67) (:id . 51))\n ((:tag . "VBZ") (:stem . "ameliorate") (:form . "ameliorates") (:end . 87)\n  (:start . 76) (:id . 52))\n ((:tag . "JJ") (:stem . "joint") (:form . "joint") (:end . 93) (:start . 88)\n  (:id . 53))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 106)\n  (:start . 94) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 109) (:start . 107)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "CIA") (:form . "CIA") (:end . 113) (:start . 110)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 120)\n  (:start . 114) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 58))\n ((:tag . "CD") (:stem . "83") (:form . "83") (:end . 124) (:start . 122)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.175) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500175@unknown@formal@none@1@S@Furthermore, it has been reported that active immunization using virus-like particles conjugated with recombinant IL-17 leads to high levels of anti-IL-17 antibodies in mice and reduces scores of disease severity in CIA (84).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "immunization") (:form . "immunization") (:end . 58)\n  (:start . 46) (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 64) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "virus-like") (:form . "virus-like") (:end . 75)\n  (:start . 65) (:id . 52))\n ((:tag . "NNS") (:stem . "particle") (:form . "particles") (:end . 85)\n  (:start . 76) (:id . 53))\n ((:tag . "VBN") (:stem . "conjugate") (:form . "conjugated") (:end . 96)\n  (:start . 86) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 101) (:start . 97)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "recombinant") (:form . "recombinant") (:end . 113)\n  (:start . 102) (:id . 56))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 119)\n  (:start . 114) (:id . 57))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 125)\n  (:start . 120) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 128) (:start . 126)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 133) (:start . 129)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 140)\n  (:start . 134) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "anti-il-17") (:form . "anti-IL-17") (:end . 154)\n  (:start . 144) (:id . 63))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 165)\n  (:start . 155) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 168) (:start . 166)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 173)\n  (:start . 169) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 177) (:start . 174)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "reduce") (:form . "reduces") (:end . 185)\n  (:start . 178) (:id . 68))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 192)\n  (:start . 186) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 195) (:start . 193)\n  (:id . 70))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 203)\n  (:start . 196) (:id . 71))\n ((:tag . "NN") (:stem . "severity") (:form . "severity") (:end . 212)\n  (:start . 204) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 215) (:start . 213)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "CIA") (:form . "CIA") (:end . 219) (:start . 216)\n  (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 221) (:start . 220)\n  (:id . 75))\n ((:tag . "CD") (:stem . "84") (:form . "84") (:end . 223) (:start . 221)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 224) (:start . 223)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s1.176) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500176@unknown@formal@none@1@S@These results highlight the role of IL-17 as an exacerbation factor in rodent arthritis models.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "highlight") (:form . "highlight") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "exacerbation") (:form . "exacerbation") (:end . 60)\n  (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 67)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "NN") (:stem . "rodent") (:form . "rodent") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "NN") (:stem . "arthritis") (:form . "arthritis") (:end . 87)\n  (:start . 78) (:id . 55))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 94)\n  (:start . 88) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s1.177) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500177@unknown@formal@none@1@S@Because the expression of IL-17 and IL-23p19 was observed in the synovial fluid and serum of RA patients, these factors were presumed to be pathogenic (85).@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "IL-23p19") (:form . "IL-23p19") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 57)\n  (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "synovial") (:form . "synovial") (:end . 73)\n  (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "fluid") (:form . "fluid") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "serum") (:form . "serum") (:end . 89) (:start . 84)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 104)\n  (:start . 96) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 111)\n  (:start . 106) (:id . 61))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 119)\n  (:start . 112) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 124) (:start . 120)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "presume") (:form . "presumed") (:end . 133)\n  (:start . 125) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 136) (:start . 134)\n  (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 139) (:start . 137)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "pathogenic") (:form . "pathogenic") (:end . 150)\n  (:start . 140) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 152) (:start . 151)\n  (:id . 68))\n ((:tag . "CD") (:stem . "85") (:form . "85") (:end . 154) (:start . 152)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x1.178.1) (:span 125 133)))\n (:hscopes ((:id . :x1.178.1) (:span 106 150)))\n (:identifiers (:sid . :s1.178) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500178@unknown@formal@none@1@S@In particular, IL-17 up-regulates the production of IL-1ß and TNF-α from APCs in arthritic joints (86, 87).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "up-regulate") (:form . "up-regulates") (:end . 33)\n  (:start . 21) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 48)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "IL-1ß") (:form . "IL-1ß") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "apc") (:form . "APCs") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "arthritic") (:form . "arthritic") (:end . 90)\n  (:start . 81) (:id . 56))\n ((:tag . "NNS") (:stem . "joint") (:form . "joints") (:end . 97)\n  (:start . 91) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n  (:id . 58))\n ((:tag . "CD") (:stem . "86") (:form . "86") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "CD") (:stem . "87") (:form . "87") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.179) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500179@unknown@formal@none@1@S@Moreover, IL-17 induces IL-6, IL-8, and IL-23 from RA synovial fibroblasts and chemokines such as CCL20/MIP3α from synoviocytes to induce migration of T cells and DCs into inflammatory lesions (86, 87).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "il-8") (:form . "IL-8") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "IL-23") (:form . "IL-23") (:end . 45) (:start . 40)\n  (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 50) (:start . 46)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 53) (:start . 51)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "synovial") (:form . "synovial") (:end . 62)\n  (:start . 54) (:id . 54))\n ((:tag . "NNS") (:stem . "fibroblast") (:form . "fibroblasts") (:end . 74)\n  (:start . 63) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "chemokine") (:form . "chemokines") (:end . 89)\n  (:start . 79) (:id . 57))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 94) (:start . 90)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "ccl20/mip3α") (:form . "CCL20/MIP3α") (:end . 109)\n  (:start . 98) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 114) (:start . 110)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "synoviocyte") (:form . "synoviocytes") (:end . 127)\n  (:start . 115) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n  (:id . 63))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 137)\n  (:start . 131) (:id . 64))\n ((:tag . "NN") (:stem . "migration") (:form . "migration") (:end . 147)\n  (:start . 138) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 66))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 152) (:start . 151)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 158)\n  (:start . 153) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "dc") (:form . "DCs") (:end . 166) (:start . 163)\n  (:id . 70))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 171) (:start . 167)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 184)\n  (:start . 172) (:id . 72))\n ((:tag . "NNS") (:stem . "lesion") (:form . "lesions") (:end . 192)\n  (:start . 185) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 194) (:start . 193)\n  (:id . 74))\n ((:tag . "CD") (:stem . "86") (:form . "86") (:end . 196) (:start . 194)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 76))\n ((:tag . "CD") (:stem . "87") (:form . "87") (:end . 200) (:start . 198)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 201) (:start . 200)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s1.180) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500180@unknown@formal@none@1@S@IL-17 also promotes cartilage breakdown by inducing matrix metalloproteinases-1 (MMP-1) from RA synovium (86, 87).@(((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "cartilage") (:form . "cartilage") (:end . 29)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "breakdown") (:form . "breakdown") (:end . 39)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "induce") (:form . "inducing") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 58)\n  (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "metalloproteinases-1")\n  (:form . "metalloproteinases-1") (:end . 79) (:start . 59) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 51))\n ((:tag . "NN") (:stem . "mmp-1") (:form . "MMP-1") (:end . 86) (:start . 81)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 92) (:start . 88)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 95) (:start . 93)\n  (:id . 55))\n ((:tag . "NN") (:stem . "synovium") (:form . "synovium") (:end . 104)\n  (:start . 96) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 57))\n ((:tag . "CD") (:stem . "86") (:form . "86") (:end . 108) (:start . 106)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "CD") (:stem . "87") (:form . "87") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s1.181) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500181@unknown@formal@none@1@S@Additionally, IL-17 induces cyclooxygenase-2 (COX-2)-dependent prostaglandin E2 (PGE2) synthesis by osteoblasts and it then induces expression of receptor activator of NF-κB ligand (RANKL) to differentiate osteoclast progenitors into mature osteoclasts (86, 87).@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "cyclooxygenase-2") (:form . "cyclooxygenase-2")\n  (:end . 44) (:start . 28) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "COX-2)-dependent") (:form . "COX-2)-dependent")\n  (:end . 62) (:start . 46) (:id . 48))\n ((:tag . "NN") (:stem . "prostaglandin") (:form . "prostaglandin")\n  (:end . 76) (:start . 63) (:id . 49))\n ((:tag . "NN") (:stem . "e2") (:form . "E2") (:end . 79) (:start . 77)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 51))\n ((:tag . "NN") (:stem . "pge2") (:form . "PGE2") (:end . 85) (:start . 81)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 53))\n ((:tag . "NN") (:stem . "synthesis") (:form . "synthesis") (:end . 96)\n  (:start . 87) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 99) (:start . 97)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "osteoblast") (:form . "osteoblasts") (:end . 111)\n  (:start . 100) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 118) (:start . 116)\n  (:id . 58))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 123) (:start . 119)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 131)\n  (:start . 124) (:id . 60))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 142)\n  (:start . 132) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n  (:id . 62))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 154)\n  (:start . 146) (:id . 63))\n ((:tag . "NN") (:stem . "activator") (:form . "activator") (:end . 164)\n  (:start . 155) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 167) (:start . 165)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 173)\n  (:start . 168) (:id . 66))\n ((:tag . "NN") (:stem . "ligand") (:form . "ligand") (:end . 180)\n  (:start . 174) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 182) (:start . 181)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "RANKL") (:form . "RANKL") (:end . 187)\n  (:start . 182) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 191) (:start . 189)\n  (:id . 71))\n ((:tag . "VB") (:stem . "differentiate") (:form . "differentiate")\n  (:end . 205) (:start . 192) (:id . 72))\n ((:tag . "JJ") (:stem . "osteoclast") (:form . "osteoclast") (:end . 216)\n  (:start . 206) (:id . 73))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 228)\n  (:start . 217) (:id . 74))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 233) (:start . 229)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "mature") (:form . "mature") (:end . 240)\n  (:start . 234) (:id . 76))\n ((:tag . "NNS") (:stem . "osteoclast") (:form . "osteoclasts") (:end . 252)\n  (:start . 241) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 254) (:start . 253)\n  (:id . 78))\n ((:tag . "CD") (:stem . "86") (:form . "86") (:end . 256) (:start . 254)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 257) (:start . 256)\n  (:id . 80))\n ((:tag . "CD") (:stem . "87") (:form . "87") (:end . 260) (:start . 258)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 261) (:start . 260)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 262) (:start . 261)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s1.182) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500182@unknown@formal@none@1@S@Pro-oxidants such as nitric oxide are also produced by chondrocytes and osteoblasts in response to IL-17 (86, 87).@(((:tag . "NNS") (:stem . "pro-oxidant") (:form . "Pro-oxidants") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 17) (:start . 13)\n  (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "nitric") (:form . "nitric") (:end . 27)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "oxide") (:form . "oxide") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "chondrocyte") (:form . "chondrocytes") (:end . 67)\n  (:start . 55) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "osteoblast") (:form . "osteoblasts") (:end . 83)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 54))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 95)\n  (:start . 87) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 104)\n  (:start . 99) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 58))\n ((:tag . "CD") (:stem . "86") (:form . "86") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 60))\n ((:tag . "CD") (:stem . "87") (:form . "87") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.183) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500183@unknown@formal@none@1@S@Taken together, these multiple factors induced by IL-17 seem to promote bone resorption, extracellular matrix degradation, synovium proliferation, angiogenesis, and recruitment and activation of immune cells for bone erosion and articular destruction in RA joints.@(((:tag . "VBN") (:stem . "take") (:form . "Taken") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "seem") (:form . "seem") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 71)\n  (:start . 64) (:id . 53))\n ((:tag . "NN") (:stem . "bone") (:form . "bone") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "resorption") (:form . "resorption") (:end . 87)\n  (:start . 77) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 102) (:start . 89) (:id . 57))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 109)\n  (:start . 103) (:id . 58))\n ((:tag . "NN") (:stem . "degradation") (:form . "degradation") (:end . 121)\n  (:start . 110) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 60))\n ((:tag . "NN") (:stem . "synovium") (:form . "synovium") (:end . 131)\n  (:start . 123) (:id . 61))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 145) (:start . 132) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 63))\n ((:tag . "NN") (:stem . "angiogenesis") (:form . "angiogenesis") (:end . 159)\n  (:start . 147) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n  (:id . 66))\n ((:tag . "NN") (:stem . "recruitment") (:form . "recruitment") (:end . 176)\n  (:start . 165) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 180) (:start . 177)\n  (:id . 68))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 191)\n  (:start . 181) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 194) (:start . 192)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 201)\n  (:start . 195) (:id . 71))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 207)\n  (:start . 202) (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 211) (:start . 208)\n  (:id . 73))\n ((:tag . "NN") (:stem . "bone") (:form . "bone") (:end . 216) (:start . 212)\n  (:id . 74))\n ((:tag . "NN") (:stem . "erosion") (:form . "erosion") (:end . 224)\n  (:start . 217) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 228) (:start . 225)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "articular") (:form . "articular") (:end . 238)\n  (:start . 229) (:id . 77))\n ((:tag . "NN") (:stem . "destruction") (:form . "destruction") (:end . 250)\n  (:start . 239) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 253) (:start . 251)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 256) (:start . 254)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "joint") (:form . "joints") (:end . 263)\n  (:start . 257) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 264) (:start . 263)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x1.184.1) (:span 56 60)))\n (:hscopes ((:id . :x1.184.1) (:span 16 263)))\n (:identifiers (:sid . :s1.184) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500184@unknown@formal@none@1@S@This being said, there is little evidence of T cell proliferation in RA and we still do not know for certain the cellular source of IL-17 in RA synovium (88).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "say") (:form . "said") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "little") (:form . "little") (:end . 32)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 51) (:start . 47)\n  (:id . 52))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 65) (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 78) (:start . 76)\n  (:id . 57))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 84) (:start . 79)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 91) (:start . 88)\n  (:id . 60))\n ((:tag . "VB") (:stem . "know") (:form . "know") (:end . 96) (:start . 92)\n  (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 100) (:start . 97)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 108)\n  (:start . 101) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 121)\n  (:start . 113) (:id . 65))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 128)\n  (:start . 122) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 137)\n  (:start . 132) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 143) (:start . 141)\n  (:id . 70))\n ((:tag . "NN") (:stem . "synovium") (:form . "synovium") (:end . 152)\n  (:start . 144) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 72))\n ((:tag . "CD") (:stem . "88") (:form . "88") (:end . 156) (:start . 154)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x1.185.1) (:span 88 108)))\n (:hscopes ((:id . :x1.185.1) (:span 88 152)))\n (:identifiers (:sid . :s1.185) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500185@unknown@formal@none@1@S@For these reasons, IL-17 seems to be a rational target in the treatment of RA, and Phase I/II clinical trials of anti-IL-17 monoclonal antibody (AIN457) have commenced (http://www.clinicaltrials.gov/).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "reason") (:form . "reasons") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "rational") (:form . "rational") (:end . 47)\n  (:start . 39) (:id . 51))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 54))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 71)\n  (:start . 62) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 77) (:start . 75)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 59))\n ((:tag . "NN") (:stem . "phase") (:form . "Phase") (:end . 88) (:start . 83)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "I/II") (:form . "I/II") (:end . 93) (:start . 89)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 102)\n  (:start . 94) (:id . 62))\n ((:tag . "NNS") (:stem . "trial") (:form . "trials") (:end . 109)\n  (:start . 103) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "anti-il-17") (:form . "anti-IL-17") (:end . 123)\n  (:start . 113) (:id . 65))\n ((:tag . "JJ") (:stem . "monoclonal") (:form . "monoclonal") (:end . 134)\n  (:start . 124) (:id . 66))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 143)\n  (:start . 135) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "AIN457") (:form . "AIN457") (:end . 151)\n  (:start . 145) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 70))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 157) (:start . 153)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "commence") (:form . "commenced") (:end . 167)\n  (:start . 158) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n  (:id . 73))\n ((:tag . "NN") (:stem . "http://www.clinicaltrials.gov/")\n  (:form . "http://www.clinicaltrials.gov/") (:end . 199) (:start . 169)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 200) (:start . 199)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x1.186.1) (:span 25 30)))\n (:hscopes ((:id . :x1.186.1) (:span 19 77)))\n (:identifiers (:sid . :s1.186) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500186@unknown@formal@none@1@S@It has been reported that combining inhibitors to block TNF-α and IL-17 has the synergistic effect of suppressing IL-6 production and collagen degradation in the synovium and bone of RA patients (89).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "combine") (:form . "combining") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "inhibitor") (:form . "inhibitors") (:end . 46)\n  (:start . 36) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "VB") (:stem . "block") (:form . "block") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "synergistic") (:form . "synergistic") (:end . 91)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 98)\n  (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "suppress") (:form . "suppressing") (:end . 113)\n  (:start . 102) (:id . 59))\n ((:tag . "NN") (:stem . "il-6") (:form . "IL-6") (:end . 118) (:start . 114)\n  (:id . 60))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 129)\n  (:start . 119) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 62))\n ((:tag . "NN") (:stem . "collagen") (:form . "collagen") (:end . 142)\n  (:start . 134) (:id . 63))\n ((:tag . "NN") (:stem . "degradation") (:form . "degradation") (:end . 154)\n  (:start . 143) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 157) (:start . 155)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 66))\n ((:tag . "NN") (:stem . "synovium") (:form . "synovium") (:end . 170)\n  (:start . 162) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 174) (:start . 171)\n  (:id . 68))\n ((:tag . "NN") (:stem . "bone") (:form . "bone") (:end . 179) (:start . 175)\n  (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 182) (:start . 180)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 185) (:start . 183)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 194)\n  (:start . 186) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 196) (:start . 195)\n  (:id . 73))\n ((:tag . "CD") (:stem . "89") (:form . "89") (:end . 198) (:start . 196)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s1.187) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500187@unknown@formal@none@1@S@Therefore, anti-IL-17 therapy may become an alternative for treating patients unresponsive to conventional anti-TNF therapy.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "anti-il-17") (:form . "anti-IL-17") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "therapy") (:form . "therapy") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "VB") (:stem . "become") (:form . "become") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "alternative") (:form . "alternative") (:end . 55)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "treat") (:form . "treating") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 77)\n  (:start . 69) (:id . 52))\n ((:tag . "JJ") (:stem . "unresponsive") (:form . "unresponsive") (:end . 90)\n  (:start . 78) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "conventional") (:form . "conventional") (:end . 106)\n  (:start . 94) (:id . 55))\n ((:tag . "JJ") (:stem . "anti-tnf") (:form . "anti-TNF") (:end . 115)\n  (:start . 107) (:id . 56))\n ((:tag . "NN") (:stem . "therapy") (:form . "therapy") (:end . 123)\n  (:start . 116) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x1.188.1) (:span 30 33)))\n (:hscopes ((:id . :x1.188.1) (:span 30 123)))\n (:identifiers (:sid . :s1.188) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500188@unknown@formal@none@1@S@It still remains to be seen whether blocking IL-17 will affect other proinflammatory cytokines for example IL-6, IL-1, and IL-22 in RA patients.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "VBG") (:stem . "block") (:form . "blocking") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "proinflammatory") (:form . "proinflammatory")\n  (:end . 84) (:start . 69) (:id . 54))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 94)\n  (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 98) (:start . 95)\n  (:id . 56))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 106)\n  (:start . 99) (:id . 57))\n ((:tag . "NN") (:stem . "il-6") (:form . "IL-6") (:end . 111) (:start . 107)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "IL-1") (:form . "IL-1") (:end . 117) (:start . 113)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 62))\n ((:tag . "NN") (:stem . "il-22") (:form . "IL-22") (:end . 128)\n  (:start . 123) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 131) (:start . 129)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 134) (:start . 132)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 143)\n  (:start . 135) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x1.189.1) (:span 28 35)))\n (:hscopes ((:id . :x1.189.1) (:span 28 143)))\n (:identifiers (:sid . :s1.189) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500189@unknown@formal@none@1@S@More studies will shed light on the validity of anti-IL-17 therapy.@(((:tag . "JJR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VB") (:stem . "shed") (:form . "shed") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "light") (:form . "light") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "validity") (:form . "validity") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "anti-il-17") (:form . "anti-IL-17") (:end . 58)\n  (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "therapy") (:form . "therapy") (:end . 66)\n  (:start . 59) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s1.190) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500190@unknown@formal@none@1@S@While the role of IL-6 in regulating IL-17 production has only recently been appreciated, the role of IL-6 as a proinflammatory cytokine has long been recognized.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "il-6") (:form . "IL-6") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "regulate") (:form . "regulating") (:end . 36)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 53)\n  (:start . 43) (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 71)\n  (:start . 63) (:id . 53))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "appreciate") (:form . "appreciated") (:end . 88)\n  (:start . 77) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "NN") (:stem . "il-6") (:form . "IL-6") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 109) (:start . 107)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 111) (:start . 110)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "proinflammatory") (:form . "proinflammatory")\n  (:end . 127) (:start . 112) (:id . 63))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 136)\n  (:start . 128) (:id . 64))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 140) (:start . 137)\n  (:id . 65))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 145) (:start . 141)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 150) (:start . 146)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "recognize") (:form . "recognized") (:end . 161)\n  (:start . 151) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s1.191) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500191@unknown@formal@none@1@S@For this reason, targeting IL-6 in RA has been considered for some time.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "reason") (:form . "reason") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "il-6") (:form . "IL-6") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 46) (:start . 42)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 57)\n  (:start . 47) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 71) (:start . 67)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s1.192) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500192@unknown@formal@none@1@S@Indeed the efficacy of humanized anti IL-6R monoclonal antibodies (tocilizumab/atlizumab) in the treatment of adults and children with arthritis has recently been reported (90).@(((:tag . "RB") (:stem . "indeed") (:form . "Indeed") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "efficacy") (:form . "efficacy") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "humanized") (:form . "humanized") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "JJ") (:stem . "anti") (:form . "anti") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "il-6r") (:form . "IL-6R") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "monoclonal") (:form . "monoclonal") (:end . 54)\n  (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 65)\n  (:start . 55) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tocilizumab/atlizumab")\n  (:form . "tocilizumab/atlizumab") (:end . 88) (:start . 67) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 55))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 106)\n  (:start . 97) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 116)\n  (:start . 110) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 129)\n  (:start . 121) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 134) (:start . 130)\n  (:id . 61))\n ((:tag . "NN") (:stem . "arthritis") (:form . "arthritis") (:end . 144)\n  (:start . 135) (:id . 62))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 148) (:start . 145)\n  (:id . 63))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 157)\n  (:start . 149) (:id . 64))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 162) (:start . 158)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 171)\n  (:start . 163) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 173) (:start . 172)\n  (:id . 67))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 175) (:start . 173)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.193) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500193@unknown@formal@none@1@S@Also, in April 2008 tocilizumab was been approved in Japan for treatment of RA in Japan, and Phase III trials have been completed in the US (http://www.clinicaltrials.gov/).@(((:tag . "RB") (:stem . "also") (:form . "Also") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "April") (:form . "April") (:end . 14) (:start . 9)\n  (:id . 45))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "tocilizumab") (:form . "tocilizumab") (:end . 31)\n  (:start . 20) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "approve") (:form . "approved") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Japan") (:form . "Japan") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 72)\n  (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Japan") (:form . "Japan") (:end . 87) (:start . 82)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 60))\n ((:tag . "NN") (:stem . "phase") (:form . "Phase") (:end . 98) (:start . 93)\n  (:id . 61))\n ((:tag . "CD") (:stem . "iii") (:form . "III") (:end . 102) (:start . 99)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "trial") (:form . "trials") (:end . 109)\n  (:start . 103) (:id . 63))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 114) (:start . 110)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 119) (:start . 115)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "complete") (:form . "completed") (:end . 129)\n  (:start . 120) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "US") (:form . "US") (:end . 139) (:start . 137)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "http://www.clinicaltrials.gov/")\n  (:form . "http://www.clinicaltrials.gov/") (:end . 171) (:start . 141)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s1.194) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500194@unknown@formal@none@1@S@To what extent their efficacy relates to inhibition of IL-17 will be important to ascertain.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "WP") (:stem . "what") (:form . "what") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 20)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "efficacy") (:form . "efficacy") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "VBZ") (:stem . "relate") (:form . "relates") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 51)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 60) (:start . 55)\n  (:id . 51))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 78)\n  (:start . 69) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "VB") (:stem . "ascertain") (:form . "ascertain") (:end . 91)\n  (:start . 82) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x1.195.1) (:span 69 91)))\n (:hscopes ((:id . :x1.195.1) (:span 0 91)))\n (:identifiers (:sid . :s1.195) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500195@unknown@formal@none@1@S@Similarly, in the US, recombinant human anti-IL-1Rα antagonist (anakinra) has been approved for use in the treatment of RA (91).@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "US") (:form . "US") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "recombinant") (:form . "recombinant") (:end . 33)\n  (:start . 22) (:id . 48))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 39) (:start . 34)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "anti-il-1rα") (:form . "anti-IL-1Rα") (:end . 51)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "antagonist") (:form . "antagonist") (:end . 62)\n  (:start . 52) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "anakinra") (:form . "anakinra") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 82) (:start . 78)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "approve") (:form . "approved") (:end . 91)\n  (:start . 83) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 116)\n  (:start . 107) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 122) (:start . 120)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n  (:id . 65))\n ((:tag . "CD") (:stem . "91") (:form . "91") (:end . 126) (:start . 124)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 127) (:start . 126)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s1.196) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500196@unknown@formal@none@1@S@Recently, more IL-1-targeting therapies for RA patients are in Phase II studies including anti-IL-1ß monoclonal antibody (ACZ885), human monoclonal antibody to IL-1R (AMG108), and IL-1 Trap/rilonacept (http://www.clinicaltrials.gov/).@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "il-1-targeting") (:form . "IL-1-targeting")\n  (:end . 29) (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "therapy") (:form . "therapies") (:end . 39)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 46) (:start . 44)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "phase") (:form . "Phase") (:end . 68) (:start . 63)\n  (:id . 52))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 89)\n  (:start . 80) (:id . 55))\n ((:tag . "JJ") (:stem . "anti-il-1ß") (:form . "anti-IL-1ß") (:end . 100)\n  (:start . 90) (:id . 56))\n ((:tag . "JJ") (:stem . "monoclonal") (:form . "monoclonal") (:end . 111)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 120)\n  (:start . 112) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "ACZ885") (:form . "ACZ885") (:end . 128)\n  (:start . 122) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 136)\n  (:start . 131) (:id . 63))\n ((:tag . "JJ") (:stem . "monoclonal") (:form . "monoclonal") (:end . 147)\n  (:start . 137) (:id . 64))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 156)\n  (:start . 148) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 159) (:start . 157)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "IL-1R") (:form . "IL-1R") (:end . 165)\n  (:start . 160) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "AMG108") (:form . "AMG108") (:end . 173)\n  (:start . 167) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 174) (:start . 173)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "IL-1") (:form . "IL-1") (:end . 184) (:start . 180)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Trap/rilonacept") (:form . "Trap/rilonacept")\n  (:end . 200) (:start . 185) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 202) (:start . 201)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "http://www.clinicaltrials.gov/")\n  (:form . "http://www.clinicaltrials.gov/") (:end . 232) (:start . 202)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 233) (:start . 232)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s1.197) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500197@unknown@formal@none@1@S@Although IL-1 has been reported to contribute to Th17 differentiation in mouse and man, it remains to be determined whether therapeutic targeting of IL-1 will substantially affect IL-17 in RA.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "il-1") (:form . "IL-1") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 45)\n  (:start . 35) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 69) (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 78) (:start . 73)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "man") (:form . "man") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 98)\n  (:start . 91) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 115)\n  (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 123)\n  (:start . 116) (:id . 62))\n ((:tag . "JJ") (:stem . "therapeutic") (:form . "therapeutic") (:end . 135)\n  (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 145)\n  (:start . 136) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "IL-1") (:form . "IL-1") (:end . 153) (:start . 149)\n  (:id . 66))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 158) (:start . 154)\n  (:id . 67))\n ((:tag . "RB") (:stem . "substantially") (:form . "substantially")\n  (:end . 172) (:start . 159) (:id . 68))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 179)\n  (:start . 173) (:id . 69))\n ((:tag . "NN") (:stem . "il-17") (:form . "IL-17") (:end . 185)\n  (:start . 180) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 188) (:start . 186)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 191) (:start . 189)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x1.198.1) (:span 116 123)))\n (:hscopes ((:id . :x1.198.1) (:span 116 191)))\n (:identifiers (:sid . :s1.198) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500198@unknown@formal@none@1@S@On the basis of the efficacy of anti-IL-12p40 therapy in human autoimmune diseases (14, 15), a humanized monoclonal anti-IL-12p40 antibody (ABT-874) was tested in RA (92).@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "efficacy") (:form . "efficacy") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "anti-il-12p40") (:form . "anti-IL-12p40")\n  (:end . 45) (:start . 32) (:id . 49))\n ((:tag . "NN") (:stem . "therapy") (:form . "therapy") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 73)\n  (:start . 63) (:id . 53))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "humanized") (:form . "humanized") (:end . 104)\n  (:start . 95) (:id . 62))\n ((:tag . "JJ") (:stem . "monoclonal") (:form . "monoclonal") (:end . 115)\n  (:start . 105) (:id . 63))\n ((:tag . "JJ") (:stem . "anti-il-12p40") (:form . "anti-IL-12p40")\n  (:end . 129) (:start . 116) (:id . 64))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 138)\n  (:start . 130) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 66))\n ((:tag . "NN") (:stem . "abt-874") (:form . "ABT-874") (:end . 147)\n  (:start . 140) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 152) (:start . 149)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 159)\n  (:start . 153) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 162) (:start . 160)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 165) (:start . 163)\n  (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 73))\n ((:tag . "CD") (:stem . "92") (:form . "92") (:end . 169) (:start . 167)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s1.199) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500199@unknown@formal@none@1@S@However this antibody was not shown to be effective because of the trial design (92).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 59)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "trial") (:form . "trial") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "design") (:form . "design") (:end . 79)\n  (:start . 73) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "CD") (:stem . "92") (:form . "92") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s1.200) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500200@unknown@formal@none@1@S@Another strategy for targeting IL-12/IL-23 is apilimod mesylate (STA-5326), an oral inhibitor of IL-12p35/p40, which has been tested in a Phase II study for RA (http://www.clinicaltrials.gov/).@(((:tag . "DT") (:stem . "another") (:form . "Another") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "il-12/il-23") (:form . "IL-12/IL-23") (:end . 42)\n  (:start . 31) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 45) (:start . 43)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "apilimod") (:form . "apilimod") (:end . 54)\n  (:start . 46) (:id . 48))\n ((:tag . "NN") (:stem . "mesylate") (:form . "mesylate") (:end . 63)\n  (:start . 55) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "STA-5326") (:form . "STA-5326") (:end . 73)\n  (:start . 65) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "oral") (:form . "oral") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "inhibitor") (:form . "inhibitor") (:end . 93)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "IL-12p35/p40") (:form . "IL-12p35/p40")\n  (:end . 109) (:start . 97) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 116)\n  (:start . 111) (:id . 60))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 125) (:start . 121)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 132)\n  (:start . 126) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 137) (:start . 136)\n  (:id . 65))\n ((:tag . "NN") (:stem . "phase") (:form . "Phase") (:end . 143)\n  (:start . 138) (:id . 66))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 146) (:start . 144)\n  (:id . 67))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 152)\n  (:start . 147) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 156) (:start . 153)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 159) (:start . 157)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 161) (:start . 160)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "http://www.clinicaltrials.gov/")\n  (:form . "http://www.clinicaltrials.gov/") (:end . 191) (:start . 161)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 192) (:start . 191)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s1.201) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500201@unknown@formal@none@1@S@Whether selectively targeting IL-23p19 will be more efficacious or have a better safety profile remains to be determined.@(((:tag . "IN") (:stem . "whether") (:form . "Whether") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 19)\n  (:start . 8) (:id . 43))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 29)\n  (:start . 20) (:id . 44))\n ((:tag . "NN") (:stem . "il-23p19") (:form . "IL-23p19") (:end . 38)\n  (:start . 30) (:id . 45))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 43) (:start . 39)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 46) (:start . 44)\n  (:id . 47))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "efficacious") (:form . "efficacious") (:end . 63)\n  (:start . 52) (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 66) (:start . 64)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 71) (:start . 67)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 52))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 80) (:start . 74)\n  (:id . 53))\n ((:tag . "NN") (:stem . "safety") (:form . "safety") (:end . 87)\n  (:start . 81) (:id . 54))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 95)\n  (:start . 88) (:id . 55))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 103)\n  (:start . 96) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 106) (:start . 104)\n  (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 109) (:start . 107)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 120)\n  (:start . 110) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x1.202.1) (:span 64 66)) ((:id . :x1.202.2) (:span 0 7)))\n (:hscopes ((:id . :x1.202.1) (:span 44 95)) ((:id . :x1.202.2) (:span 0 95)))\n (:identifiers (:sid . :s1.202) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500202@unknown@formal@none@1@S@In principle, targeting IL-21 might also be efficacious in treating RA in which IL-17 is involved in immune-mediated damage.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "principle") (:form . "principle") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "il-21") (:form . "IL-21") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "efficacious") (:form . "efficacious") (:end . 55)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "treat") (:form . "treating") (:end . 67)\n  (:start . 59) (:id . 52))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 79) (:start . 74)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 97)\n  (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "immune-mediated") (:form . "immune-mediated")\n  (:end . 116) (:start . 101) (:id . 60))\n ((:tag . "NN") (:stem . "damage") (:form . "damage") (:end . 123)\n  (:start . 117) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x1.203.1) (:span 30 35)))\n (:hscopes ((:id . :x1.203.1) (:span 30 123)))\n (:identifiers (:sid . :s1.203) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500203@unknown@formal@none@1@S@Importantly, the common gamma chain and JAK3 play a pivotal role in the signal transduction of IL-21 (25).@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "gamma") (:form . "gamma") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "chain") (:form . "chain") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "jak3") (:form . "JAK3") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "play") (:form . "play") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "pivotal") (:form . "pivotal") (:end . 59)\n  (:start . 52) (:id . 52))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 78)\n  (:start . 72) (:id . 56))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 91)\n  (:start . 79) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "IL-21") (:form . "IL-21") (:end . 100)\n  (:start . 95) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 104) (:start . 102)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s1.204) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500204@unknown@formal@none@1@S@In fact, a JAK3 inhibitor (CP-690550) is about to be tested in RA (Phase II trial) (http://www.clinicaltrials.gov/).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "jak3") (:form . "JAK3") (:end . 15) (:start . 11)\n  (:id . 46))\n ((:tag . "NN") (:stem . "inhibitor") (:form . "inhibitor") (:end . 25)\n  (:start . 16) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "CP-690550") (:form . "CP-690550") (:end . 36)\n  (:start . 27) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n  (:id . 51))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 46) (:start . 41)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 52) (:start . 50)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 59) (:start . 53)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "RA") (:form . "RA") (:end . 65) (:start . 63)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 58))\n ((:tag . "NN") (:stem . "phase") (:form . "Phase") (:end . 72) (:start . 67)\n  (:id . 59))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 75) (:start . 73)\n  (:id . 60))\n ((:tag . "NN") (:stem . "trial") (:form . "trial") (:end . 81) (:start . 76)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "http://www.clinicaltrials.gov/")\n  (:form . "http://www.clinicaltrials.gov/") (:end . 114) (:start . 84)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.205) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500205@unknown@formal@none@1@S@It will be important to know whether the efficacy of this drug is related to inhibition of IL-17.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 20)\n  (:start . 11) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "know") (:form . "know") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "efficacy") (:form . "efficacy") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "drug") (:form . "drug") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 73)\n  (:start . 66) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 87)\n  (:start . 77) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 96) (:start . 91)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x1.206.1) (:span 29 36)))\n (:hscopes ((:id . :x1.206.1) (:span 29 96)))\n (:identifiers (:sid . :s1.206) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500206@unknown@formal@none@1@S@Concluding remarks@(((:tag . "VBG") (:stem . "conclude") (:form . "Concluding") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "remark") (:form . "remarks") (:end . 18)\n  (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s1.207) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500207@unknown@formal@none@1@S@The past four years have witnessed major revisions of our views on the lineage commitment of helper T cells.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "past") (:form . "past") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "witness") (:form . "witnessed") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "revision") (:form . "revisions") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "view") (:form . "views") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 78)\n  (:start . 71) (:id . 55))\n ((:tag . "NN") (:stem . "commitment") (:form . "commitment") (:end . 89)\n  (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 99)\n  (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 107)\n  (:start . 102) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s1.208) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500208@unknown@formal@none@1@S@The conventional Th1/Th2 dichotomy has been replaced by more complex multi-lineage models which do a much better job of explaining the pathogenesis of autoimmunity (Fig. 1).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "conventional") (:form . "conventional") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "th1/th2") (:form . "Th1/Th2") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "NN") (:stem . "dichotomy") (:form . "dichotomy") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "replace") (:form . "replaced") (:end . 52)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 55) (:start . 53)\n  (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 68)\n  (:start . 61) (:id . 51))\n ((:tag . "JJ") (:stem . "multi-lineage") (:form . "multi-lineage")\n  (:end . 82) (:start . 69) (:id . 52))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 89)\n  (:start . 83) (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 95) (:start . 90)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 98) (:start . 96)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n  (:id . 56))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 105) (:start . 101)\n  (:id . 57))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 112)\n  (:start . 106) (:id . 58))\n ((:tag . "NN") (:stem . "job") (:form . "job") (:end . 116) (:start . 113)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "explain") (:form . "explaining") (:end . 130)\n  (:start . 120) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n  (:id . 62))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 147)\n  (:start . 135) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 64))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 163)\n  (:start . 151) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 165) (:start . 164)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 169) (:start . 165)\n  (:id . 67))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 171) (:start . 170)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.209) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500209@unknown@formal@none@1@S@It now seems that Th17 cells are one of the more important villains in the pathogenesis of autoimmune diseases.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 48) (:start . 44)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 58)\n  (:start . 49) (:id . 53))\n ((:tag . "NNS") (:stem . "villain") (:form . "villains") (:end . 67)\n  (:start . 59) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 56))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 87)\n  (:start . 75) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 101)\n  (:start . 91) (:id . 59))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 110)\n  (:start . 102) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x1.210.1) (:span 7 12)))\n (:hscopes ((:id . :x1.210.1) (:span 7 110)))\n (:identifiers (:sid . :s1.210) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500210@unknown@formal@none@1@S@However, it is of note that they are also essential for host defense against extracellular bacteria.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "note") (:form . "note") (:end . 22) (:start . 18)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 32) (:start . 28)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n  (:id . 50))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 41) (:start . 37)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 51)\n  (:start . 42) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 55) (:start . 52)\n  (:id . 53))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 60) (:start . 56)\n  (:id . 54))\n ((:tag . "NN") (:stem . "defense") (:form . "defense") (:end . 68)\n  (:start . 61) (:id . 55))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 76)\n  (:start . 69) (:id . 56))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 90) (:start . 77) (:id . 57))\n ((:tag . "NNS") (:stem . "bacteria") (:form . "bacteria") (:end . 99)\n  (:start . 91) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s1.211) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500211@unknown@formal@none@1@S@Therefore, the challenge will be to keep Th17 function in check to control autoimmunity, while maintaining host defense at the same time.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "challenge") (:form . "challenge") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "VB") (:stem . "keep") (:form . "keep") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "check") (:form . "check") (:end . 63) (:start . 58)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 74)\n  (:start . 67) (:id . 55))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 87)\n  (:start . 75) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 57))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 94) (:start . 89)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "maintain") (:form . "maintaining") (:end . 106)\n  (:start . 95) (:id . 59))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 111) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "defense") (:form . "defense") (:end . 119)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 131) (:start . 127)\n  (:id . 64))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 136) (:start . 132)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s1.212) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500212@unknown@formal@none@1@S@In this regard, we still need to learn what are the most critical factors for Th17 differentiation.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "regard") (:form . "regard") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 24) (:start . 19)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "need") (:form . "need") (:end . 29) (:start . 25)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 32) (:start . 30)\n  (:id . 49))\n ((:tag . "VB") (:stem . "learn") (:form . "learn") (:end . 38) (:start . 33)\n  (:id . 50))\n ((:tag . "WP") (:stem . "what") (:form . "what") (:end . 43) (:start . 39)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 53))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 56) (:start . 52)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 65)\n  (:start . 57) (:id . 55))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 73)\n  (:start . 66) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "NN") (:stem . "th17") (:form . "Th17") (:end . 82) (:start . 78)\n  (:id . 58))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 98) (:start . 83) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s1.213) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500213@unknown@formal@none@1@S@We also need to better understand which human autoimmune diseases are truly mediated by IL-17 and, by extension, which diseases will benefit most from anti-IL-17 therapy.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "need") (:form . "need") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "RBR") (:stem . "well") (:form . "better") (:end . 22) (:start . 16)\n  (:id . 46))\n ((:tag . "VB") (:stem . "understand") (:form . "understand") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 65)\n  (:start . 57) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "RB") (:stem . "truly") (:form . "truly") (:end . 75) (:start . 70)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 84)\n  (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 93) (:start . 88)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "NN") (:stem . "extension") (:form . "extension") (:end . 111)\n  (:start . 102) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 118)\n  (:start . 113) (:id . 62))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 127)\n  (:start . 119) (:id . 63))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 132) (:start . 128)\n  (:id . 64))\n ((:tag . "VB") (:stem . "benefit") (:form . "benefit") (:end . 140)\n  (:start . 133) (:id . 65))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 145) (:start . 141)\n  (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 150) (:start . 146)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "anti-il-17") (:form . "anti-IL-17") (:end . 161)\n  (:start . 151) (:id . 68))\n ((:tag . "NN") (:stem . "therapy") (:form . "therapy") (:end . 169)\n  (:start . 162) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s1.214) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500214@unknown@formal@none@1@S@With the current pace of investigations on Th17, this field has a great potential for advances.@(((:tag . "IN") (:stem . "with") (:form . "With") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "pace") (:form . "pace") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "investigation") (:form . "investigations")\n  (:end . 39) (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Th17") (:form . "Th17") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "great") (:form . "great") (:end . 71) (:start . 66)\n  (:id . 55))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 81)\n  (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 85) (:start . 82)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "advance") (:form . "advances") (:end . 94)\n  (:start . 86) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s1.215) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500215@unknown@formal@none@1@S@There is no doubt that IL-17 and the other proinflammatory cytokines are likely to be relevant therapeutic targets in the treatment of human autoimmune diseases.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "doubt") (:form . "doubt") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IL-17") (:form . "IL-17") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 42) (:start . 37)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "proinflammatory") (:form . "proinflammatory")\n  (:end . 58) (:start . 43) (:id . 51))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 79)\n  (:start . 73) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 94)\n  (:start . 86) (:id . 57))\n ((:tag . "JJ") (:stem . "therapeutic") (:form . "therapeutic") (:end . 106)\n  (:start . 95) (:id . 58))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 114)\n  (:start . 107) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 61))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 131)\n  (:start . 122) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 140)\n  (:start . 135) (:id . 64))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 151)\n  (:start . 141) (:id . 65))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 160)\n  (:start . 152) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x1.216.1) (:span 73 79)))\n (:hscopes ((:id . :x1.216.1) (:span 23 160)))\n (:identifiers (:sid . :s1.216) (:did . :pmc2596867) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500216@unknown@formal@none@1@S@Estrogen directly activates AID transcription and function@(((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 27)\n  (:start . 18) (:id . 44))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 31) (:start . 28)\n  (:id . 45))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 45) (:start . 32) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 47))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 58)\n  (:start . 50) (:id . 48)))@@@1@7@((:identifiers (:sid . :s2.1) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5500217@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s2.2) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500218@unknown@formal@none@1@S@The immunological targets of estrogen at the molecular, humoral, and cellular level have been well documented, as has estrogen's role in establishing a gender bias in autoimmunity and cancer.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "immunological") (:form . "immunological")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 25)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 54)\n  (:start . 45) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "humoral") (:form . "humoral") (:end . 63)\n  (:start . 56) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 77)\n  (:start . 69) (:id . 54))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 93) (:start . 89)\n  (:id . 57))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "document") (:form . "documented") (:end . 109)\n  (:start . 99) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 126)\n  (:start . 118) (:id . 63))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 128) (:start . 126)\n  (:id . 64))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 133) (:start . 129)\n  (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "establish") (:form . "establishing") (:end . 149)\n  (:start . 137) (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 151) (:start . 150)\n  (:id . 68))\n ((:tag . "NN") (:stem . "gender") (:form . "gender") (:end . 158)\n  (:start . 152) (:id . 69))\n ((:tag . "NN") (:stem . "bias") (:form . "bias") (:end . 163) (:start . 159)\n  (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 166) (:start . 164)\n  (:id . 71))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 179)\n  (:start . 167) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 183) (:start . 180)\n  (:id . 73))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 190)\n  (:start . 184) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s2.3) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500219@unknown@formal@none@1@S@During a healthy immune response, activation-induced deaminase (AID) deaminates cytosines at immunoglobulin (Ig) loci, initiating somatic hypermutation (SHM) and class switch recombination (CSR).@(((:tag . "IN") (:stem . "during") (:form . "During") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "healthy") (:form . "healthy") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "activation-induced") (:form . "activation-induced")\n  (:end . 52) (:start . 34) (:id . 48))\n ((:tag . "NNP") (:stem . "deaminase") (:form . "deaminase") (:end . 62)\n  (:start . 53) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 67) (:start . 64)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "deaminate") (:form . "deaminates") (:end . 79)\n  (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "cytosine") (:form . "cytosines") (:end . 89)\n  (:start . 80) (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 92) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "immunoglobulin") (:form . "immunoglobulin")\n  (:end . 107) (:start . 93) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Ig") (:form . "Ig") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "locus") (:form . "loci") (:end . 117)\n  (:start . 113) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "initiate") (:form . "initiating") (:end . 129)\n  (:start . 119) (:id . 62))\n ((:tag . "JJ") (:stem . "somatic") (:form . "somatic") (:end . 137)\n  (:start . 130) (:id . 63))\n ((:tag . "NN") (:stem . "hypermutation") (:form . "hypermutation")\n  (:end . 151) (:start . 138) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 156) (:start . 153)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 68))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 167)\n  (:start . 162) (:id . 69))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 174)\n  (:start . 168) (:id . 70))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n  (:end . 188) (:start . 175) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 190) (:start . 189)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "CSR") (:form . "CSR") (:end . 193) (:start . 190)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s2.4) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500220@unknown@formal@none@1@S@Protein levels of nuclear AID are tightly controlled, as unregulated expression can lead to alterations in the immune response.@(((:tag . "NN") (:stem . "protein") (:form . "Protein") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "RB") (:stem . "tightly") (:form . "tightly") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "VBN") (:stem . "control") (:form . "controlled") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "unregulated") (:form . "unregulated") (:end . 68)\n  (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 79)\n  (:start . 69) (:id . 53))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "VB") (:stem . "lead") (:form . "lead") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "alteration") (:form . "alterations") (:end . 103)\n  (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 117)\n  (:start . 111) (:id . 60))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 126)\n  (:start . 118) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x2.5.1) (:span 80 83)))\n (:hscopes ((:id . :x2.5.1) (:span 80 126)))\n (:identifiers (:sid . :s2.5) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500221@unknown@formal@none@1@S@Furthermore, hyperactivation of AID outside the immune system leads to oncogenesis.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "hyperactivation") (:form . "hyperactivation")\n  (:end . 28) (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "IN") (:stem . "outside") (:form . "outside") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 54)\n  (:start . 48) (:id . 49))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 61)\n  (:start . 55) (:id . 50))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 67) (:start . 62)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 70) (:start . 68)\n  (:id . 52))\n ((:tag . "NN") (:stem . "oncogenesis") (:form . "oncogenesis") (:end . 82)\n  (:start . 71) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s2.6) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500222@unknown@formal@none@1@S@Here, we demonstrate that the estrogen–estrogen receptor complex binds to the AID promoter, enhancing AID messenger RNA expression, leading to a direct increase in AID protein production and alterations in SHM and CSR at the Ig locus.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 20)\n  (:start . 9) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen–estrogen") (:form . "estrogen–estrogen")\n  (:end . 47) (:start . 30) (:id . 48))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 56)\n  (:start . 48) (:id . 49))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 64)\n  (:start . 57) (:id . 50))\n ((:tag . "VBZ") (:stem . "bind") (:form . "binds") (:end . 70) (:start . 65)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 90)\n  (:start . 82) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "enhance") (:form . "enhancing") (:end . 101)\n  (:start . 92) (:id . 57))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 105) (:start . 102)\n  (:id . 58))\n ((:tag . "NN") (:stem . "messenger") (:form . "messenger") (:end . 115)\n  (:start . 106) (:id . 59))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 130)\n  (:start . 120) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 139)\n  (:start . 132) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 144) (:start . 143)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 151)\n  (:start . 145) (:id . 66))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 160)\n  (:start . 152) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 163) (:start . 161)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 167) (:start . 164)\n  (:id . 69))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 175)\n  (:start . 168) (:id . 70))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 186)\n  (:start . 176) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 190) (:start . 187)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "alteration") (:form . "alterations") (:end . 202)\n  (:start . 191) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 205) (:start . 203)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 209) (:start . 206)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 213) (:start . 210)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "CSR") (:form . "CSR") (:end . 217) (:start . 214)\n  (:id . 77))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 220) (:start . 218)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 224) (:start . 221)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Ig") (:form . "Ig") (:end . 227) (:start . 225)\n  (:id . 80))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 233)\n  (:start . 228) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s2.7) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500223@unknown@formal@none@1@S@Enhanced translocations of the c-myc oncogene showed that the genotoxicity of estrogen via AID production was not limited to the Ig locus.@(((:tag . "VBN") (:stem . "enhance") (:form . "Enhanced") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 23) (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "NN") (:stem . "c-myc") (:form . "c-myc") (:end . 36) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "oncogene") (:form . "oncogene") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 52) (:start . 46)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "NN") (:stem . "genotoxicity") (:form . "genotoxicity") (:end . 74)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 52))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 86)\n  (:start . 78) (:id . 53))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 90) (:start . 87)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 94) (:start . 91)\n  (:id . 55))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 105)\n  (:start . 95) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 109) (:start . 106)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 113) (:start . 110)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 121)\n  (:start . 114) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 124) (:start . 122)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Ig") (:form . "Ig") (:end . 131) (:start . 129)\n  (:id . 62))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 137)\n  (:start . 132) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.8) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500224@unknown@formal@none@1@S@Outside of the immune system (e.g., breast and ovaries), estrogen induced AID expression by >20-fold.@(((:tag . "IN") (:stem . "outside") (:form . "Outside") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "breast") (:form . "breast") (:end . 42)\n  (:start . 36) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "ovary") (:form . "ovaries") (:end . 54)\n  (:start . 47) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 54))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 65)\n  (:start . 57) (:id . 55))\n ((:tag . "VBD") (:stem . "induce") (:form . "induced") (:end . 73)\n  (:start . 66) (:id . 56))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 88)\n  (:start . 78) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "JJ") (:stem . ">20-fold") (:form . ">20-fold") (:end . 100)\n  (:start . 92) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.9) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500225@unknown@formal@none@1@S@The estrogen response was also partially conserved within the DNA deaminase family (APOBEC3B, -3F, and -3G), and could be inhibited by tamoxifen, an estrogen antagonist.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 40)\n  (:start . 31) (:id . 47))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 50)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 57)\n  (:start . 51) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "deaminase") (:form . "deaminase") (:end . 75)\n  (:start . 66) (:id . 52))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 82)\n  (:start . 76) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "APOBEC3B") (:form . "APOBEC3B") (:end . 92)\n  (:start . 84) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 56))\n ((:tag . "NN") (:stem . "-3f") (:form . "-3F") (:end . 97) (:start . 94)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 59))\n ((:tag . "NN") (:stem . "-3g") (:form . "-3G") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 63))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 118)\n  (:start . 113) (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 121) (:start . 119)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "inhibit") (:form . "inhibited") (:end . 131)\n  (:start . 122) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 134) (:start . 132)\n  (:id . 67))\n ((:tag . "NN") (:stem . "tamoxifen") (:form . "tamoxifen") (:end . 144)\n  (:start . 135) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 69))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 148) (:start . 146)\n  (:id . 70))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 157)\n  (:start . 149) (:id . 71))\n ((:tag . "NN") (:stem . "antagonist") (:form . "antagonist") (:end . 168)\n  (:start . 158) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.10) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500226@unknown@formal@none@1@S@We therefore suggest that estrogen-induced autoimmunity and oncogenesis may be derived through AID-dependent DNA instability.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "estrogen-induced") (:form . "estrogen-induced")\n  (:end . 42) (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 55)\n  (:start . 43) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 48))\n ((:tag . "NN") (:stem . "oncogenesis") (:form . "oncogenesis") (:end . 71)\n  (:start . 60) (:id . 49))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 75) (:start . 72)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 78) (:start . 76)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 86)\n  (:start . 79) (:id . 52))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 94)\n  (:start . 87) (:id . 53))\n ((:tag . "JJ") (:stem . "aid-dependent") (:form . "AID-dependent")\n  (:end . 108) (:start . 95) (:id . 54))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 112) (:start . 109)\n  (:id . 55))\n ((:tag . "NN") (:stem . "instability") (:form . "instability") (:end . 124)\n  (:start . 113) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x2.11.1) (:span 72 75)) ((:id . :x2.11.2) (:span 13 20)))\n (:hscopes ((:id . :x2.11.1) (:span 26 124)) ((:id . :x2.11.2) (:span 13 124)))\n (:identifiers (:sid . :s2.11) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500227@unknown@formal@none@1@S@ @(((:tag . "LS") (:stem . " ") (:form . " ") (:end . 1) (:start . 0)\n  (:id . 42)))@@@1@1@((:identifiers (:sid . :s2.12) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500228@unknown@formal@none@1@S@Humoral immune responses triggered by foreign antigens require B cell activation.@(((:tag . "JJ") (:stem . "humoral") (:form . "Humoral") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "VBN") (:stem . "trigger") (:form . "triggered") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "foreign") (:form . "foreign") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . "NNS") (:stem . "antigen") (:form . "antigens") (:end . 54)\n  (:start . 46) (:id . 48))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 62)\n  (:start . 55) (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 64) (:start . 63)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 80)\n  (:start . 70) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.13) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500229@unknown@formal@none@1@S@The activated B cell undergoes antibody affinity maturation, which in higher vertebrates includes somatic hypermutation (SHM), gene conversion of antigen-binding V regions, and class switching (1); all of these processes require activation-induced deaminase (AID) (2–5).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "undergo") (:form . "undergoes") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . 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"VBP") (:stem . "require") (:form . "require") (:end . 228)\n  (:start . 221) (:id . 80))\n ((:tag . "JJ") (:stem . "activation-induced") (:form . "activation-induced")\n  (:end . 247) (:start . 229) (:id . 81))\n ((:tag . "NNP") (:stem . "deaminase") (:form . "deaminase") (:end . 257)\n  (:start . 248) (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 259) (:start . 258)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 262) (:start . 259)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 263) (:start . 262)\n  (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 265) (:start . 264)\n  (:id . 86))\n ((:tag . "CD") (:stem . "2–5") (:form . "2–5") (:end . 268) (:start . 265)\n  (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 269) (:start . 268)\n  (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") 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5500230@unknown@formal@none@1@S@AID initiates these events by deaminating deoxycytosine to deoxyuracil in DNA (for review see reference [6–8]).@(((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "initiate") (:form . "initiates") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "deaminate") (:form . "deaminating") (:end . 41)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "deoxycytosine") (:form . "deoxycytosine")\n  (:end . 55) (:start . 42) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 49))\n ((:tag . "NN") (:stem . "deoxyuracil") (:form . "deoxyuracil") (:end . 70)\n  (:start . 59) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 77) (:start . 74)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "review") (:form . "review") (:end . 89)\n  (:start . 83) (:id . 55))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 93) (:start . 90)\n  (:id . 56))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 103)\n  (:start . 94) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "CD") (:stem . "6–8") (:form . "6–8") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 109) (:start . 108)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.15) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500231@unknown@formal@none@1@S@The resulting dU:dG lesion can be recognized by several different DNA repair pathways to create the aforementioned antibody diversifications.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "dU:dG") (:form . "dU:dG") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "lesion") (:form . "lesion") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "recognize") (:form . "recognized") (:end . 44)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 65)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "repair") (:form . "repair") (:end . 76)\n  (:start . 70) (:id . 53))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 85)\n  (:start . 77) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "VB") (:stem . "create") (:form . "create") (:end . 95)\n  (:start . 89) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "aforementioned") (:form . "aforementioned")\n  (:end . 114) (:start . 100) (:id . 58))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 123)\n  (:start . 115) (:id . 59))\n ((:tag . "NNS") (:stem . "diversification") (:form . "diversifications")\n  (:end . 140) (:start . 124) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.16) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500232@unknown@formal@none@1@S@This necessity for immune diversification and sufficiency for genome instability also highlights AID as an important pathogenic regulator.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "necessity") (:form . "necessity") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "diversification") (:form . "diversification")\n  (:end . 41) (:start . 26) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sufficiency") (:form . "sufficiency") (:end . 57)\n  (:start . 46) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n  (:id . 49))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 68)\n  (:start . 62) (:id . 50))\n ((:tag . "NN") (:stem . "instability") (:form . "instability") (:end . 80)\n  (:start . 69) (:id . 51))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 85) (:start . 81)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "highlight") (:form . "highlights") (:end . 96)\n  (:start . 86) (:id . 53))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 100) (:start . 97)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 103) (:start . 101)\n  (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 106) (:start . 104)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 116)\n  (:start . 107) (:id . 57))\n ((:tag . "JJ") (:stem . "pathogenic") (:form . "pathogenic") (:end . 127)\n  (:start . 117) (:id . 58))\n ((:tag . "NN") (:stem . "regulator") (:form . "regulator") (:end . 137)\n  (:start . 128) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.17) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500233@unknown@formal@none@1@S@In the immune system, hyper- or hypoexpression of AID can alter autoimmune pathologies (9–11).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "hyper-") (:form . "hyper-") (:end . 28)\n  (:start . 22) (:id . 47))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "hypoexpression") (:form . "hypoexpression")\n  (:end . 46) (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "VB") (:stem . "alter") (:form . "alter") (:end . 63) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 74)\n  (:start . 64) (:id . 54))\n ((:tag . "NNS") (:stem . "pathology") (:form . "pathologies") (:end . 86)\n  (:start . 75) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "CD") (:stem . "9–11") (:form . "9–11") (:end . 92) (:start . 88)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.18) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500234@unknown@formal@none@1@S@Furthermore, SHM, by way of AID, may contribute to lymphomagenesis by mutating (proto-)oncogenes and tumor suppressor genes, or by promoting chromosomal translocations (12–14).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 31) (:start . 28)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 50))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 36) (:start . 33)\n  (:id . 51))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 47)\n  (:start . 37) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 53))\n ((:tag . "NN") (:stem . "lymphomagenesis") (:form . "lymphomagenesis")\n  (:end . 66) (:start . 51) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 69) (:start . 67)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "mutate") (:form . "mutating") (:end . 78)\n  (:start . 70) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "proto-)oncogenes") (:form . "proto-)oncogenes")\n  (:end . 96) (:start . 80) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 59))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . "NN") (:stem . "suppressor") (:form . "suppressor") (:end . 117)\n  (:start . 107) (:id . 61))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 123)\n  (:start . 118) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 127) (:start . 125)\n  (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 130) (:start . 128)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "promote") (:form . "promoting") (:end . 140)\n  (:start . 131) (:id . 66))\n ((:tag . "JJ") (:stem . "chromosomal") (:form . "chromosomal") (:end . 152)\n  (:start . 141) (:id . 67))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 167) (:start . 153) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n  (:id . 69))\n ((:tag . "CD") (:stem . "12–14") (:form . "12–14") (:end . 174)\n  (:start . 169) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 175) (:start . 174)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x2.19.1) (:span 33 36)))\n (:hscopes ((:id . :x2.19.1) (:span 33 167)))\n (:identifiers (:sid . :s2.19) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500235@unknown@formal@none@1@S@There is strong evidence that AID is required for c-myc translocation, leading to tumorgenesis in a murine model for Burkitt's lymphoma (15, 16).@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 45)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "c-myc") (:form . "c-myc") (:end . 55) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "translocation") (:form . "translocation")\n  (:end . 69) (:start . 56) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 78)\n  (:start . 71) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "tumorgenesis") (:form . "tumorgenesis") (:end . 94)\n  (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "murine") (:form . "murine") (:end . 106)\n  (:start . 100) (:id . 59))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 112)\n  (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Burkitt") (:form . "Burkitt") (:end . 124)\n  (:start . 117) (:id . 62))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 126) (:start . 124)\n  (:id . 63))\n ((:tag . "NN") (:stem . "lymphoma") (:form . "lymphoma") (:end . 135)\n  (:start . 127) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 65))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 139) (:start . 137)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 67))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 143) (:start . 141)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.20) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500236@unknown@formal@none@1@S@Other nonphysiological AID targets include BCL6, CD95/Fas, RHO/TTF, PAX-5, and PIM1 (12, 17–19).@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "nonphysiological") (:form . "nonphysiological")\n  (:end . 22) (:start . 6) (:id . 43))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 26) (:start . 23)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 34)\n  (:start . 27) (:id . 45))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 42)\n  (:start . 35) (:id . 46))\n ((:tag . "NNP") (:stem . "BCL6") (:form . "BCL6") (:end . 47) (:start . 43)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "CD95/Fas") (:form . "CD95/Fas") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "RHO/TTF") (:form . "RHO/TTF") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "PAX-5") (:form . "PAX-5") (:end . 73) (:start . 68)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "pim1") (:form . "PIM1") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 57))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 59))\n ((:tag . "CD") (:stem . "17–19") (:form . "17–19") (:end . 94) (:start . 89)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.21) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500237@unknown@formal@none@1@S@Outside the immune system, there are indications that systemic hyperexpression of AID can induce non–B cell cancers from lung (20), lymphatic (20), and liver (21) tissues.@(((:tag . "IN") (:stem . "outside") (:form . "Outside") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "indication") (:form . "indications") (:end . 48)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . "NN") (:stem . "hyperexpression") (:form . "hyperexpression")\n  (:end . 78) (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 89) (:start . 86)\n  (:id . 55))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 96)\n  (:start . 90) (:id . 56))\n ((:tag . "NN") (:stem . "non–b") (:form . "non–B") (:end . 102) (:start . 97)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 107) (:start . 103)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "cancer") (:form . "cancers") (:end . 115)\n  (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 120) (:start . 116)\n  (:id . 60))\n ((:tag . "NN") (:stem . "lung") (:form . "lung") (:end . 125) (:start . 121)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 62))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "lymphatic") (:form . "lymphatic") (:end . 141)\n  (:start . 132) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 145) (:start . 143)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 151) (:start . 148)\n  (:id . 71))\n ((:tag . "NN") (:stem . "liver") (:form . "liver") (:end . 157)\n  (:start . 152) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 73))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 161) (:start . 159)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 170)\n  (:start . 163) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x2.22.1) (:span 37 48)))\n (:hscopes ((:id . :x2.22.1) (:span 37 170)))\n (:identifiers (:sid . :s2.22) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500238@unknown@formal@none@1@S@AID has also been implicated as a developmental epigenetic reprogramming factor, and its expression levels in oocytes is almost equivalent to that in lymph nodes (22), suggesting that AID could be regulated by pathways other than B cell activation pathways (e.g., E-box proteins [23], NF-κB [24], and Pax5 [25]), with hormones being plausible candidates.@(((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . 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5500239@unknown@formal@none@1@S@Several clinical and epidemiological studies have indicated that females can have stronger and more rapid immune responses upon antigen encounter (26, 27).@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "epidemiological") (:form . "epidemiological")\n  (:end . 36) (:start . 21) (:id . 45))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 44)\n  (:start . 37) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 49) (:start . 45)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 59)\n  (:start . 50) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 64) (:start . 60)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "female") (:form . "females") (:end . 72)\n  (:start . 65) (:id . 50))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 76) (:start . 73)\n  (:id . 51))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 81) (:start . 77)\n  (:id . 52))\n ((:tag . "JJR") (:stem . "strong") (:form . "stronger") (:end . 90)\n  (:start . 82) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 54))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 99) (:start . 95)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 105)\n  (:start . 100) (:id . 56))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 112)\n  (:start . 106) (:id . 57))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 122)\n  (:start . 113) (:id . 58))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 127) (:start . 123)\n  (:id . 59))\n ((:tag . "NN") (:stem . "antigen") (:form . "antigen") (:end . 135)\n  (:start . 128) (:id . 60))\n ((:tag . "NN") (:stem . "encounter") (:form . "encounter") (:end . 145)\n  (:start . 136) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 62))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 149) (:start . 147)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 64))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 153) (:start . 151)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x2.24.1) (:span 73 76)) ((:id . :x2.24.2) (:span 50 64)))\n (:hscopes ((:id . :x2.24.1) (:span 73 145)) ((:id . :x2.24.2) (:span 50 145)))\n (:identifiers (:sid . :s2.24) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500240@unknown@formal@none@1@S@This gender bias is also reflected in the occurrence of pathogenic immune responses, as found in asthma and other autoimmune diseases (28–31).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "gender") (:form . "gender") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "bias") (:form . "bias") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "reflect") (:form . "reflected") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "pathogenic") (:form . "pathogenic") (:end . 66)\n  (:start . 56) (:id . 52))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 83)\n  (:start . 74) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "asthma") (:form . "asthma") (:end . 103)\n  (:start . 97) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 113)\n  (:start . 108) (:id . 61))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 124)\n  (:start . 114) (:id . 62))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 133)\n  (:start . 125) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 64))\n ((:tag . "CD") (:stem . "28–31") (:form . "28–31") (:end . 140)\n  (:start . 135) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.25) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500241@unknown@formal@none@1@S@Several nonimmune pathologies are also strongly influenced by the activity of sex hormones, most notably certain types of cancer.@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "nonimmune") (:form . "nonimmune") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "pathology") (:form . "pathologies") (:end . 29)\n  (:start . 18) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 33) (:start . 30)\n  (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 47)\n  (:start . 39) (:id . 47))\n ((:tag . "VBN") (:stem . "influence") (:form . "influenced") (:end . 58)\n  (:start . 48) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 61) (:start . 59)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 50))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 74)\n  (:start . 66) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 52))\n ((:tag . "NN") (:stem . "sex") (:form . "sex") (:end . 81) (:start . 78)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "hormone") (:form . "hormones") (:end . 90)\n  (:start . 82) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 55))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 96) (:start . 92)\n  (:id . 56))\n ((:tag . "RB") (:stem . "notably") (:form . "notably") (:end . 104)\n  (:start . 97) (:id . 57))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 112)\n  (:start . 105) (:id . 58))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 118)\n  (:start . 113) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 60))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 128)\n  (:start . 122) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.26) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500242@unknown@formal@none@1@S@Estrogen and its biological and synthetic derivatives are thought to be oncogenic for breast and ovarian tissue (32, 33), most often being associated with their growth-promoting and differentiating capacity.@(((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "synthetic") (:form . "synthetic") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "derivative") (:form . "derivatives") (:end . 53)\n  (:start . 42) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 57) (:start . 54)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 65)\n  (:start . 58) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "oncogenic") (:form . "oncogenic") (:end . 81)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "NN") (:stem . "breast") (:form . "breast") (:end . 92)\n  (:start . 86) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "ovarian") (:form . "ovarian") (:end . 104)\n  (:start . 97) (:id . 57))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 111)\n  (:start . 105) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 119) (:start . 117)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 126) (:start . 122)\n  (:id . 65))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 132)\n  (:start . 127) (:id . 66))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 138) (:start . 133)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 149)\n  (:start . 139) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 154) (:start . 150)\n  (:id . 69))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 160)\n  (:start . 155) (:id . 70))\n ((:tag . "JJ") (:stem . "growth-promoting") (:form . "growth-promoting")\n  (:end . 177) (:start . 161) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 181) (:start . 178)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "differentiate") (:form . "differentiating")\n  (:end . 197) (:start . 182) (:id . 73))\n ((:tag . "NN") (:stem . "capacity") (:form . "capacity") (:end . 206)\n  (:start . 198) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x2.27.1) (:span 58 65)))\n (:hscopes ((:id . :x2.27.1) (:span 0 206)))\n (:identifiers (:sid . :s2.27) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500243@unknown@formal@none@1@S@To further elucidate how AID can be regulated, both within and outside the immune system, and to determine which signaling pathways could use DNA deaminases as DNA instability factors, we analyzed the effect of estrogen on AID's expression and on downstream pathways such as SHM and class switch recombination (CSR).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "VB") (:stem . "elucidate") (:form . "elucidate") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . 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"estrogen") (:end . 219)\n  (:start . 211) (:id . 79))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 222) (:start . 220)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 226) (:start . 223)\n  (:id . 81))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 228) (:start . 226)\n  (:id . 82))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 239)\n  (:start . 229) (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 243) (:start . 240)\n  (:id . 84))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 246) (:start . 244)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "downstream") (:form . "downstream") (:end . 257)\n  (:start . 247) (:id . 86))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 266)\n  (:start . 258) (:id . 87))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 271) (:start . 267)\n  (:id . 88))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 274) (:start . 272)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 278) (:start . 275)\n  (:id . 90))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 282) (:start . 279)\n  (:id . 91))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 288)\n  (:start . 283) (:id . 92))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 295)\n  (:start . 289) (:id . 93))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n  (:end . 309) (:start . 296) (:id . 94))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 311) (:start . 310)\n  (:id . 95))\n ((:tag . "NNP") (:stem . "CSR") (:form . "CSR") (:end . 314) (:start . 311)\n  (:id . 96))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 315) (:start . 314)\n  (:id . 97))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 316) (:start . 315)\n  (:id . 98)))@@@1@57@((:identifiers (:sid . :s2.28) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500244@unknown@formal@none@1@S@We show that AID can be up-regulated by estrogen, whereas tamoxifen (Tam) can inhibit this stimulation.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "up-regulate") (:form . "up-regulated") (:end . 36)\n  (:start . 24) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . "NN") (:stem . "tamoxifen") (:form . "tamoxifen") (:end . 67)\n  (:start . 58) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 85)\n  (:start . 78) (:id . 58))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 90) (:start . 86)\n  (:id . 59))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 102)\n  (:start . 91) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.29) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500245@unknown@formal@none@1@S@This effect was most pronounced, but not limited to regulation at the level of transcription.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "pronounced") (:form . "pronounced") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 62)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 75) (:start . 70)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 92) (:start . 79) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.30) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500246@unknown@formal@none@1@S@Treatment with estrogen increased AID protein expression, enhanced CSR, augmented mutation frequency in Ig and non-Ig genes, and increased the translocation frequency of c-myc.@(((:tag . "NNP") (:stem . "Treatment") (:form . "Treatment") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 33)\n  (:start . 24) (:id . 45))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 56)\n  (:start . 46) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 66)\n  (:start . 58) (:id . 50))\n ((:tag . "NNP") (:stem . "CSR") (:form . "CSR") (:end . 70) (:start . 67)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "augment") (:form . "augmented") (:end . 81)\n  (:start . 72) (:id . 53))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 90)\n  (:start . 82) (:id . 54))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 100)\n  (:start . 91) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 56))\n ((:tag . "NN") (:stem . "ig") (:form . "Ig") (:end . 106) (:start . 104)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "non-ig") (:form . "non-Ig") (:end . 117)\n  (:start . 111) (:id . 59))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 123)\n  (:start . 118) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 138)\n  (:start . 129) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n  (:id . 64))\n ((:tag . "NN") (:stem . "translocation") (:form . "translocation")\n  (:end . 156) (:start . 143) (:id . 65))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 166)\n  (:start . 157) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 169) (:start . 167)\n  (:id . 67))\n ((:tag . "NN") (:stem . "c-myc") (:form . "c-myc") (:end . 175)\n  (:start . 170) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.31) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500247@unknown@formal@none@1@S@Estrogen-induced AID messenger RNA (mRNA) production was independent of other B cell stimulatory pathways and could be observed outside immune tissue.@(((:tag . "JJ") (:stem . "estrogen-induced") (:form . "Estrogen-induced")\n  (:end . 16) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 20) (:start . 17)\n  (:id . 43))\n ((:tag . "NN") (:stem . "messenger") (:form . "messenger") (:end . 30)\n  (:start . 21) (:id . 44))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 34) (:start . 31)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 68)\n  (:start . 57) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 77) (:start . 72)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "stimulatory") (:form . "stimulatory") (:end . 96)\n  (:start . 85) (:id . 56))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 105)\n  (:start . 97) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 58))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 115)\n  (:start . 110) (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 118) (:start . 116)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 127)\n  (:start . 119) (:id . 61))\n ((:tag . "IN") (:stem . "outside") (:form . "outside") (:end . 135)\n  (:start . 128) (:id . 62))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 142)\n  (:start . 136) (:id . 63))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 149)\n  (:start . 143) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.32) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500248@unknown@formal@none@1@S@We were able to identify two potential estrogen response elements (EREs) near the AID promoter, and determined enhanced ERα binding to the promoter after estrogen treatment in vitro and in vivo.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 38)\n  (:start . 29) (:id . 48))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 47)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 65)\n  (:start . 57) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "ERE") (:form . "EREs") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "IN") (:stem . "near") (:form . "near") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 85) (:start . 82)\n  (:id . 57))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 94)\n  (:start . 86) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 110)\n  (:start . 100) (:id . 61))\n ((:tag . "VBD") (:stem . "enhance") (:form . "enhanced") (:end . 119)\n  (:start . 111) (:id . 62))\n ((:tag . "NN") (:stem . "erα") (:form . "ERα") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 131)\n  (:start . 124) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 134) (:start . 132)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 66))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 147)\n  (:start . 139) (:id . 67))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 153)\n  (:start . 148) (:id . 68))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 162)\n  (:start . 154) (:id . 69))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 172)\n  (:start . 163) (:id . 70))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 181)\n  (:start . 176) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n  (:id . 73))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 188) (:start . 186)\n  (:id . 74))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 193) (:start . 189)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s2.33) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500249@unknown@formal@none@1@S@APOBEC3, the evolutionarily related DNA deaminases (34), were also responsive to estrogen treatment in different tissues and cell types.@(((:tag . "NNP") (:stem . "APOBEC3") (:form . "APOBEC3") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "evolutionarily") (:form . "evolutionarily")\n  (:end . 27) (:start . 13) (:id . 45))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "deaminas") (:form . "deaminases") (:end . 50)\n  (:start . 40) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "responsive") (:form . "responsive") (:end . 77)\n  (:start . 67) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 89)\n  (:start . 81) (:id . 57))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 99)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 112)\n  (:start . 103) (:id . 60))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 120)\n  (:start . 113) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 62))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 129) (:start . 125)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 135)\n  (:start . 130) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.34) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500250@unknown@formal@none@1@S@Our data indicate that the mutagenic DNA deaminases are potentially an important target for hormonal regulation.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mutagenic") (:form . "mutagenic") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "deaminas") (:form . "deaminases") (:end . 51)\n  (:start . 41) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "RB") (:stem . "potentially") (:form . "potentially") (:end . 67)\n  (:start . 56) (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 70) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 80)\n  (:start . 71) (:id . 53))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 87)\n  (:start . 81) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "hormonal") (:form . "hormonal") (:end . 100)\n  (:start . 92) (:id . 56))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 111)\n  (:start . 101) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x2.35.1) (:span 56 67)) ((:id . :x2.35.2) (:span 9 22)))\n (:hscopes ((:id . :x2.35.1) (:span 23 111)) ((:id . :x2.35.2) (:span 9 111)))\n (:identifiers (:sid . :s2.35) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500251@unknown@formal@none@1@S@RESULTS@(((:tag . "NNS") (:stem . "results") (:form . "RESULTS") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s2.36) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500252@unknown@formal@none@1@S@Differential effect of sex hormones on AID mRNA@(((:tag . "JJ") (:stem . "differential") (:form . "Differential") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 19)\n  (:start . 13) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sex") (:form . "sex") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "hormone") (:form . "hormones") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 47) (:start . 43)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s2.37) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500253@unknown@formal@none@1@S@Hormones such as estrogen and progesterone exert their biological effects through binding to their intracellular receptors and, upon entering the nucleus, act as transcription factors (35).@(((:tag . "NNS") (:stem . "hormone") (:form . "Hormones") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "progesterone") (:form . "progesterone") (:end . 42)\n  (:start . 30) (:id . 47))\n ((:tag . "VBP") (:stem . "exert") (:form . "exert") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 54)\n  (:start . 49) (:id . 49))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 65)\n  (:start . 55) (:id . 50))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 73)\n  (:start . 66) (:id . 51))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 81)\n  (:start . 74) (:id . 52))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 89)\n  (:start . 82) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n  (:id . 54))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 98)\n  (:start . 93) (:id . 55))\n ((:tag . "JJ") (:stem . "intracellular") (:form . "intracellular")\n  (:end . 112) (:start . 99) (:id . 56))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 122)\n  (:start . 113) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 59))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 132) (:start . 128)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "enter") (:form . "entering") (:end . 141)\n  (:start . 133) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 62))\n ((:tag . "NN") (:stem . "nucleus") (:form . "nucleus") (:end . 153)\n  (:start . 146) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "act") (:form . "act") (:end . 158) (:start . 155)\n  (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 161) (:start . 159)\n  (:id . 66))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 175) (:start . 162) (:id . 67))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 183)\n  (:start . 176) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 69))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 187) (:start . 185)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s2.38) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500254@unknown@formal@none@1@S@To determine the effects of hormones on AID expression, we stimulated isolated murine splenic B cells with IL-4 and LPS, which are known to induce AID (24), while adding physiological amounts of progesterone and estrogen.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "hormone") (:form . "hormones") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "stimulate") (:form . "stimulated") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "JJ") (:stem . "murine") (:form . "murine") (:end . 85)\n  (:start . 79) (:id . 55))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 93)\n  (:start . 86) (:id . 56))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 101) (:start . 96)\n  (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 111) (:start . 107)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 119) (:start . 116)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 126)\n  (:start . 121) (:id . 64))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 130) (:start . 127)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 136)\n  (:start . 131) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n  (:id . 67))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 146)\n  (:start . 140) (:id . 68))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 150) (:start . 147)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 152) (:start . 151)\n  (:id . 70))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 154) (:start . 152)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 73))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 162)\n  (:start . 157) (:id . 74))\n ((:tag . "VBG") (:stem . "add") (:form . "adding") (:end . 169)\n  (:start . 163) (:id . 75))\n ((:tag . "JJ") (:stem . "physiological") (:form . "physiological")\n  (:end . 183) (:start . 170) (:id . 76))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 191)\n  (:start . 184) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 194) (:start . 192)\n  (:id . 78))\n ((:tag . "NN") (:stem . "progesterone") (:form . "progesterone") (:end . 207)\n  (:start . 195) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 211) (:start . 208)\n  (:id . 80))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 220)\n  (:start . 212) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 221) (:start . 220)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s2.39) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500255@unknown@formal@none@1@S@Progesterone addition reduced AID mRNA levels by fivefold, as revealed by quantitative real-time PCR (qRT-PCR; Fig. 1 A).@(((:tag . "NNP") (:stem . "Progesterone") (:form . "Progesterone") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 21)\n  (:start . 13) (:id . 43))\n ((:tag . "VBD") (:stem . "reduce") (:form . "reduced") (:end . 29)\n  (:start . 22) (:id . 44))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 33) (:start . 30)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 45)\n  (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "RB") (:stem . "fivefold") (:form . "fivefold") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "reveal") (:form . "revealed") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 86)\n  (:start . 74) (:id . 54))\n ((:tag . "JJ") (:stem . "real-time") (:form . "real-time") (:end . 96)\n  (:start . 87) (:id . 55))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 100) (:start . 97)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 109)\n  (:start . 102) (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 110) (:start . 109)\n  (:id . 59))\n ((:tag . "CD") (:stem . "fig.") (:form . "Fig.") (:end . 115) (:start . 111)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 119) (:start . 118)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.40) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500256@unknown@formal@none@1@S@This and all subsequent qRT-PCR analyses were normalized to GAPDH expression, and all enhancements or repressions were analyzed as relative changes to DMSO.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "normalize") (:form . "normalized") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "gapdh") (:form . "GAPDH") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 76)\n  (:start . 66) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "enhancement") (:form . "enhancements") (:end . 98)\n  (:start . 86) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 101) (:start . 99)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "repression") (:form . "repressions") (:end . 113)\n  (:start . 102) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 118) (:start . 114)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 127)\n  (:start . 119) (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 130) (:start . 128)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 139)\n  (:start . 131) (:id . 62))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 147)\n  (:start . 140) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 150) (:start . 148)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "DMSO") (:form . "DMSO") (:end . 155) (:start . 151)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.41) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500257@unknown@formal@none@1@S@To observe a stimulatory effect of estrogen, cells were only treated for a short time period (8 h) rather than the usual 24–48 h.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "observe") (:form . "observe") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "stimulatory") (:form . "stimulatory") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "period") (:form . "period") (:end . 92)\n  (:start . 86) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 62))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 105)\n  (:start . 99) (:id . 63))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 110) (:start . 106)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "usual") (:form . "usual") (:end . 120)\n  (:start . 115) (:id . 66))\n ((:tag . "CD") (:stem . "24–48") (:form . "24–48") (:end . 126)\n  (:start . 121) (:id . 67))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 128) (:start . 127)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.42) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500258@unknown@formal@none@1@S@This was done to avoid a possible maximal induction of LPS/IL-4 caused by longer treatment.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "do") (:form . "done") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "VB") (:stem . "avoid") (:form . "avoid") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 33)\n  (:start . 25) (:id . 48))\n ((:tag . "JJ") (:stem . "maximal") (:form . "maximal") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "induction") (:form . "induction") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "lps/il-4") (:form . "LPS/IL-4") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 70)\n  (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "JJR") (:stem . "long") (:form . "longer") (:end . 80) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 90)\n  (:start . 81) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x2.43.1) (:span 25 33)))\n (:hscopes ((:id . :x2.43.1) (:span 25 90)))\n (:identifiers (:sid . :s2.43) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500259@unknown@formal@none@1@S@In contrast to progesterone, physiological amounts of estrogen were able to enhance AID expression threefold in these cells (Fig. 1 A).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "progesterone") (:form . "progesterone") (:end . 27)\n  (:start . 15) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "physiological") (:form . "physiological")\n  (:end . 42) (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 83)\n  (:start . 76) (:id . 54))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 98)\n  (:start . 88) (:id . 56))\n ((:tag . "RB") (:stem . "threefold") (:form . "threefold") (:end . 108)\n  (:start . 99) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 117)\n  (:start . 112) (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 123)\n  (:start . 118) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 129) (:start . 125)\n  (:id . 62))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.44) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500260@unknown@formal@none@1@S@This antithetical effect of estrogen and progesterone indicated that AID gene regulation is embedded within a systemic sex hormone pathway.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "antithetical") (:form . "antithetical") (:end . 17)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 24)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 36)\n  (:start . 28) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "progesterone") (:form . "progesterone") (:end . 53)\n  (:start . 41) (:id . 48))\n ((:tag . "VBD") (:stem . "indicate") (:form . "indicated") (:end . 63)\n  (:start . 54) (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 68) (:start . 64)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 77) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 88)\n  (:start . 78) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 91) (:start . 89)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "embed") (:form . "embedded") (:end . 100)\n  (:start . 92) (:id . 55))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 107)\n  (:start . 101) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 109) (:start . 108)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 118)\n  (:start . 110) (:id . 58))\n ((:tag . "NN") (:stem . "sex") (:form . "sex") (:end . 122) (:start . 119)\n  (:id . 59))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 130)\n  (:start . 123) (:id . 60))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 138)\n  (:start . 131) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x2.45.1) (:span 54 68)))\n (:hscopes ((:id . :x2.45.1) (:span 54 138)))\n (:identifiers (:sid . :s2.45) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500261@unknown@formal@none@1@S@The effects of estrogen and progesterone on AID mRNA in murine splenic B-cells.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "progesterone") (:form . "progesterone") (:end . 40)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "murine") (:form . "murine") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "NNS") (:stem . "b-cell") (:form . "B-cells") (:end . 78)\n  (:start . 71) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.46) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500262@unknown@formal@none@1@S@(A) AID mRNA in response to estrogen and progesterone treatment in stimulated B cells.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 12) (:start . 8)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 47))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 24)\n  (:start . 16) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 36)\n  (:start . 28) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 51))\n ((:tag . "NN") (:stem . "progesterone") (:form . "progesterone") (:end . 53)\n  (:start . 41) (:id . 52))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 63)\n  (:start . 54) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 77)\n  (:start . 67) (:id . 55))\n ((:tag . "NN") (:stem . "b") (:form . "B") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 85) (:start . 80)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.47) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500263@unknown@formal@none@1@S@Isolated mouse spleen B cells were stimulated with LPS and IL-4 and treated with different physiological concentrations of estrogen for 8 h or progesterone for 24 h.@(((:tag . "VBN") (:stem . "isolate") (:form . "Isolated") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "spleen") (:form . "spleen") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 45)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "lps") (:form . "LPS") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 75)\n  (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 90)\n  (:start . 81) (:id . 56))\n ((:tag . "JJ") (:stem . "physiological") (:form . "physiological")\n  (:end . 104) (:start . 91) (:id . 57))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 119) (:start . 105) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 59))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 131)\n  (:start . 123) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 135) (:start . 132)\n  (:id . 61))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 137) (:start . 136)\n  (:id . 62))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 139) (:start . 138)\n  (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . "NN") (:stem . "progesterone") (:form . "progesterone") (:end . 155)\n  (:start . 143) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 159) (:start . 156)\n  (:id . 66))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 162) (:start . 160)\n  (:id . 67))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 164) (:start . 163)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.48) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500264@unknown@formal@none@1@S@Unless indicated, DMSO is set to 1, and treatments are represented as relative change to DMSO.@(((:tag . "IN") (:stem . "unless") (:form . "Unless") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 16)\n  (:start . 7) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dmso") (:form . "DMSO") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 50)\n  (:start . 40) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 54) (:start . 51)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 66)\n  (:start . 55) (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 69) (:start . 67)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 78)\n  (:start . 70) (:id . 56))\n ((:tag . "NN") (:stem . "change") (:form . "change") (:end . 85)\n  (:start . 79) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "DMSO") (:form . "DMSO") (:end . 93) (:start . 89)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.49) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500265@unknown@formal@none@1@S@(B) AID mRNA in response to estrogen treatment in unstimulated B cells after 8 h treatment with physiological concentrations of estrogen.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 12) (:start . 8)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 47))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 24)\n  (:start . 16) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 36)\n  (:start . 28) (:id . 50))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 46)\n  (:start . 37) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "unstimulated") (:form . "unstimulated") (:end . 62)\n  (:start . 50) (:id . 53))\n ((:tag . "NN") (:stem . "b") (:form . "B") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 70) (:start . 65)\n  (:id . 55))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 76) (:start . 71)\n  (:id . 56))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 78) (:start . 77)\n  (:id . 57))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 90)\n  (:start . 81) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 95) (:start . 91)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "physiological") (:form . "physiological")\n  (:end . 109) (:start . 96) (:id . 61))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 124) (:start . 110) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 136)\n  (:start . 128) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.50) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500266@unknown@formal@none@1@S@(C) AID mRNA induction upon different treatment.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 12) (:start . 8)\n  (:id . 46))\n ((:tag . "NN") (:stem . "induction") (:form . "induction") (:end . 22)\n  (:start . 13) (:id . 47))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 27) (:start . 23)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 37)\n  (:start . 28) (:id . 49))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 47)\n  (:start . 38) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 48) (:start . 47)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.51) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500267@unknown@formal@none@1@S@Cells were treated with 1 nM estrogen and/or 50 nM Tam (Tam) for up to 8 h.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "nM") (:form . "nM") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 59) (:start . 56)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 64) (:start . 61)\n  (:id . 56))\n ((:tag . "RB") (:stem . "up") (:form . "up") (:end . 67) (:start . 65)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 70) (:start . 68)\n  (:id . 58))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 72) (:start . 71)\n  (:id . 59))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 74) (:start . 73)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.52) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500268@unknown@formal@none@1@S@DMSO at 0 h is set to 1.@(((:tag . "NNP") (:stem . "DMSO") (:form . "DMSO") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 9) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 18) (:start . 15)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 21) (:start . 19)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 23) (:start . 22)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 24) (:start . 23)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s2.53) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500269@unknown@formal@none@1@S@All qRT-PCR data are representative of three independent experiments, and error bars indicate standard deviations from the mean.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 35) (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 56)\n  (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 68)\n  (:start . 57) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 79) (:start . 74)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 84) (:start . 80)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 93)\n  (:start . 85) (:id . 55))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 102)\n  (:start . 94) (:id . 56))\n ((:tag . "NNS") (:stem . "deviation") (:form . "deviations") (:end . 113)\n  (:start . 103) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 118) (:start . 114)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 59))\n ((:tag . "NN") (:stem . "mean") (:form . "mean") (:end . 127) (:start . 123)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.54) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500270@unknown@formal@none@1@S@Timelines of cell treatments are indicated next to the graphs.@(((:tag . "NNS") (:stem . "timeline") (:form . "Timelines") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "graph") (:form . "graphs") (:end . 61)\n  (:start . 55) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.55) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500271@unknown@formal@none@1@S@NT, not treated.@(((:tag . "NN") (:stem . "nt") (:form . "NT") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 3) (:start . 2) (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 7) (:start . 4)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 15)\n  (:start . 8) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 16) (:start . 15)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s2.56) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500272@unknown@formal@none@1@S@For A and B, absolute values as compared with GAPDH mRNA are shown in Fig. S10, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "absolute") (:form . "absolute") (:end . 21)\n  (:start . 13) (:id . 47))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 28)\n  (:start . 22) (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 31) (:start . 29)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 40)\n  (:start . 32) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 51) (:start . 46)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 56) (:start . 52)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 66) (:start . 61)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 74) (:start . 70)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "S10") (:form . "S10") (:end . 78) (:start . 75)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 89)\n  (:start . 80) (:id . 60))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 92) (:start . 90)\n  (:id . 61))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 145) (:start . 93) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s2.57) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500273@unknown@formal@none@1@S@We focused our subsequent experiments on the verification that the estrogen-induced stimulation on AID was analogous to another known estrogen response gene.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "focus") (:form . "focused") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 37)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "verification") (:form . "verification") (:end . 57)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "estrogen-induced") (:form . "estrogen-induced")\n  (:end . 83) (:start . 67) (:id . 52))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 95)\n  (:start . 84) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 98) (:start . 96)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 102) (:start . 99)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 106) (:start . 103)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "analogous") (:form . "analogous") (:end . 116)\n  (:start . 107) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 119) (:start . 117)\n  (:id . 58))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 127)\n  (:start . 120) (:id . 59))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 133)\n  (:start . 128) (:id . 60))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 142)\n  (:start . 134) (:id . 61))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 151)\n  (:start . 143) (:id . 62))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 156) (:start . 152)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.58) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500274@unknown@formal@none@1@S@Because we could determine that the expression of gene regulated in breast cancer 1 (a known estrogen response gene) (36) had a similar stimulation profile in B cells (unpublished data), it seemed likely that the AID gene could also be activated in uninduced B cells with estrogen.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 46)\n  (:start . 36) (:id . 48))\n ((:tag . 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(:end . 281) (:start . 280)\n  (:id . 96)))@@@1@55@((:hcues ((:id . :x2.59.1) (:span 222 227)) ((:id . :x2.59.2) (:span 197 203))\n  ((:id . :x2.59.3) (:span 190 196)))\n (:hscopes ((:id . :x2.59.1) (:span 209 280))\n  ((:id . :x2.59.2) (:span 197 280)) ((:id . :x2.59.3) (:span 187 280)))\n (:identifiers (:sid . :s2.59) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500275@unknown@formal@none@1@S@Stimulation of isolated splenic B cells with physiological amounts of estrogen produced a sevenfold increase in AID mRNA (Fig. 1 B).@(((:tag . "NN") (:stem . "stimulation") (:form . "Stimulation") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 31)\n  (:start . 24) (:id . 45))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 33) (:start . 32)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "physiological") (:form . "physiological")\n  (:end . 58) (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 66)\n  (:start . 59) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 78)\n  (:start . 70) (:id . 52))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 87)\n  (:start . 79) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 89) (:start . 88)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "sevenfold") (:form . "sevenfold") (:end . 99)\n  (:start . 90) (:id . 55))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 108)\n  (:start . 100) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 115) (:start . 112)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 120) (:start . 116)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 126) (:start . 122)\n  (:id . 61))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 128) (:start . 127)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.60) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500276@unknown@formal@none@1@S@This induction began to plateau at 4 h, with the earliest indication of an increase detectable at ~2 h (Fig. 1 C).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "induction") (:form . "induction") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "begin") (:form . "began") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "VB") (:stem . "plateau") (:form . "plateau") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 44) (:start . 40)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 52))\n ((:tag . "JJS") (:stem . "early") (:form . "earliest") (:end . 57)\n  (:start . 49) (:id . 53))\n ((:tag . "NN") (:stem . "indication") (:form . "indication") (:end . 68)\n  (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 83)\n  (:start . 75) (:id . 57))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 94)\n  (:start . 84) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "CD") (:stem . "~2") (:form . "~2") (:end . 100) (:start . 98)\n  (:id . 60))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 108) (:start . 104)\n  (:id . 63))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 110) (:start . 109)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 112) (:start . 111)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.61) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500277@unknown@formal@none@1@S@In most systems, the synthetic hormone Tam acts as an antagonist to estrogen stimulation, presumably by binding to the estrogen receptor (ER) and altering its DNA binding capacity (37).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "synthetic") (:form . "synthetic") (:end . 30)\n  (:start . 21) (:id . 47))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "act") (:form . "acts") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "antagonist") (:form . "antagonist") (:end . 64)\n  (:start . 54) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 76)\n  (:start . 68) (:id . 55))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 88)\n  (:start . 77) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "RB") (:stem . "presumably") (:form . "presumably") (:end . 100)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 111)\n  (:start . 104) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 62))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 127)\n  (:start . 119) (:id . 63))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 136)\n  (:start . 128) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "ER") (:form . "ER") (:end . 140) (:start . 138)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "alter") (:form . "altering") (:end . 154)\n  (:start . 146) (:id . 69))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 158) (:start . 155)\n  (:id . 70))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 162) (:start . 159)\n  (:id . 71))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 170)\n  (:start . 163) (:id . 72))\n ((:tag . "NN") (:stem . "capacity") (:form . "capacity") (:end . 179)\n  (:start . 171) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 181) (:start . 180)\n  (:id . 74))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 183) (:start . 181)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x2.62.1) (:span 90 100)))\n (:hscopes ((:id . :x2.62.1) (:span 90 179)))\n (:identifiers (:sid . :s2.62) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500278@unknown@formal@none@1@S@The presence of Tam during the estrogen treatment of isolated splenic B cells inhibited the stimulatory activity, whereas Tam on its own had only a limited effect on AID mRNA expression at the concentration used (Fig. 1 C, Estrogen 1 nM/Tam and Tam, respectively).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "treatment") (:form . 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5500279@unknown@formal@none@1@S@Interestingly, at very low concentrations, Tam can have a stimulatory effect on AID mRNA (Fig. S1 A, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1), which may reflect Tam's agonistic activity (see Discussion).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 41) (:start . 27) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "stimulatory") (:form . "stimulatory") (:end . 69)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 76)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 94) (:start . 90)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 97) (:start . 95)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 99) (:start . 98)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 110)\n  (:start . 101) (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 113) (:start . 111)\n  (:id . 64))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 166) (:start . 114) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 67))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 174)\n  (:start . 169) (:id . 68))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 178) (:start . 175)\n  (:id . 69))\n ((:tag . "VB") (:stem . "reflect") (:form . "reflect") (:end . 186)\n  (:start . 179) (:id . 70))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 190) (:start . 187)\n  (:id . 71))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 192) (:start . 190)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "agonistic") (:form . "agonistic") (:end . 202)\n  (:start . 193) (:id . 73))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 211)\n  (:start . 203) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 213) (:start . 212)\n  (:id . 75))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 216) (:start . 213)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Discussion") (:form . "Discussion") (:end . 227)\n  (:start . 217) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 228) (:start . 227)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x2.64.1) (:span 175 178)) ((:id . :x2.64.2) (:span 47 50)))\n (:hscopes ((:id . :x2.64.1) (:span 175 211)) ((:id . :x2.64.2) (:span 47 88)))\n (:identifiers (:sid . :s2.64) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500280@unknown@formal@none@1@S@Hormonal regulation of AID mRNA is predominantly via transcription@(((:tag . "JJ") (:stem . "hormonal") (:form . "Hormonal") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 19)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 48) (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 66) (:start . 53) (:id . 50)))@@@1@9@((:identifiers (:sid . :s2.65) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500281@unknown@formal@none@1@S@Although we were able to observe an increase in AID mRNA at 2 h (Fig. 1), we needed to determine if this regulation was direct or indirect.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "VB") (:stem . "observe") (:form . "observe") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 61) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 69) (:start . 65)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 71) (:start . 70)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 76) (:start . 74)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "need") (:form . "needed") (:end . 83) (:start . 77)\n  (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 86) (:start . 84)\n  (:id . 63))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 96)\n  (:start . 87) (:id . 64))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 99) (:start . 97)\n  (:id . 65))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 104) (:start . 100)\n  (:id . 66))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 115)\n  (:start . 105) (:id . 67))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 119) (:start . 116)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 126)\n  (:start . 120) (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 129) (:start . 127)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "indirect") (:form . "indirect") (:end . 138)\n  (:start . 130) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x2.66.1) (:span 127 129)) ((:id . :x2.66.2) (:span 97 99)))\n (:hscopes ((:id . :x2.66.1) (:span 120 138))\n  ((:id . :x2.66.2) (:span 97 138)))\n (:identifiers (:sid . :s2.66) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5500283@unknown@formal@none@1@S@This suggested that the effect of estrogen was directly mediated on AID's mRNA synthesis.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "suggest") (:form . "suggested") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 64)\n  (:start . 56) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 78) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "synthesis") (:form . "synthesis") (:end . 88)\n  (:start . 79) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x2.68.1) (:span 5 14)))\n (:hscopes ((:id . :x2.68.1) (:span 5 88)))\n (:identifiers (:sid . :s2.68) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500284@unknown@formal@none@1@S@Because qRT-PCR of cDNA is a readout of steady-state mRNA, we also tested if the increase by estrogen was caused by transcription or mRNA metabolism.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "cDNA") (:form . "cDNA") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "readout") (:form . "readout") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "steady-state") (:form . "steady-state") (:end . 52)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 73) (:start . 67)\n  (:id . 55))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 89)\n  (:start . 81) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 101)\n  (:start . 93) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 105) (:start . 102)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 112)\n  (:start . 106) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 115) (:start . 113)\n  (:id . 63))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 129) (:start . 116) (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 137) (:start . 133)\n  (:id . 66))\n ((:tag . "NN") (:stem . "metabolism") (:form . "metabolism") (:end . 148)\n  (:start . 138) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x2.69.1) (:span 130 132)) ((:id . :x2.69.2) (:span 74 76)))\n (:hscopes ((:id . :x2.69.1) (:span 116 148))\n  ((:id . :x2.69.2) (:span 74 148)))\n (:identifiers (:sid . :s2.69) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500285@unknown@formal@none@1@S@Treatment of cells with transcription inhibitors (actinomycin D [ACT] and α-amanitin [AMA]) abrogated the effect of estrogen, indicating that this alteration in AID's mRNA was not caused by message stability (Fig. S1 B).@(((:tag . "NNP") (:stem . "Treatment") (:form . "Treatment") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 37) (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "inhibitor") (:form . "inhibitors") (:end . 48)\n  (:start . 38) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 48))\n ((:tag . "NN") (:stem . "actinomycin") (:form . "actinomycin") (:end . 61)\n  (:start . 50) (:id . 49))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 63) (:start . 62)\n  (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 65) (:start . 64)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "ACT") (:form . "ACT") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "α-amanitin") (:form . "α-amanitin") (:end . 84)\n  (:start . 74) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 86) (:start . 85)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "AMA") (:form . "AMA") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "abrogate") (:form . "abrogated") (:end . 101)\n  (:start . 92) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 61))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 112)\n  (:start . 106) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 63))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 124)\n  (:start . 116) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 136)\n  (:start . 126) (:id . 66))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 141) (:start . 137)\n  (:id . 67))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 146) (:start . 142)\n  (:id . 68))\n ((:tag . "NN") (:stem . "alteration") (:form . "alteration") (:end . 157)\n  (:start . 147) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 160) (:start . 158)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 164) (:start . 161)\n  (:id . 71))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 166) (:start . 164)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 171) (:start . 167)\n  (:id . 73))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 175) (:start . 172)\n  (:id . 74))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 179) (:start . 176)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 186)\n  (:start . 180) (:id . 76))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 189) (:start . 187)\n  (:id . 77))\n ((:tag . "NN") (:stem . "message") (:form . "message") (:end . 197)\n  (:start . 190) (:id . 78))\n ((:tag . "NN") (:stem . "stability") (:form . "stability") (:end . 207)\n  (:start . 198) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 209) (:start . 208)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 213) (:start . 209)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 216) (:start . 214)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 218) (:start . 217)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 219) (:start . 218)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x2.70.1) (:span 126 141)))\n (:hscopes ((:id . :x2.70.1) (:span 126 207)))\n (:identifiers (:sid . :s2.70) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500286@unknown@formal@none@1@S@As estrogen can affect pre-mRNA to mRNA processing (38), we designed qRT-PCR primers to span the complete transcription unit of AID (Fig. S2 A, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "pre-mrna") (:form . "pre-mRNA") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 50)\n  (:start . 40) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 59) (:start . 57)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "design") (:form . "designed") (:end . 68)\n  (:start . 60) (:id . 55))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 76)\n  (:start . 69) (:id . 56))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 84)\n  (:start . 77) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "VB") (:stem . "span") (:form . "span") (:end . 92) (:start . 88)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 105)\n  (:start . 97) (:id . 61))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 119) (:start . 106) (:id . 62))\n ((:tag . "NN") (:stem . "unit") (:form . "unit") (:end . 124) (:start . 120)\n  (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 131) (:start . 128)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 137) (:start . 133)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 140) (:start . 138)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 142) (:start . 141)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 153)\n  (:start . 144) (:id . 71))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 156) (:start . 154)\n  (:id . 72))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 209) (:start . 157) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s2.71) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500287@unknown@formal@none@1@S@When we compared the relative change in expression of the various pre-mRNA's exons and introns to that of the mature mRNA, we found only a minor effect caused by estrogen treatment (the 5'-most PCR unit, <100 bp away from the start of AID gene, was up-regulated to almost the same extent as the mature mRNA [Fig. S2 B]).@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "compare") (:form . "compared") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "change") (:form . "change") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . 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5500289@unknown@formal@none@1@S@Because the relative change did not significantly alter the overall effect, we did not pursue this analysis further, although recent data suggests that alternative splicing may influence AID expression (39).@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "change") (:form . "change") (:end . 27)\n  (:start . 21) (:id . 45))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 49) (:start . 36) (:id . 48))\n ((:tag . "VB") (:stem . "alter") (:form . "alter") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 67)\n  (:start . 60) (:id . 51))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 74)\n  (:start . 68) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 86) (:start . 83)\n  (:id . 56))\n ((:tag . "VB") (:stem . "pursue") (:form . "pursue") (:end . 93)\n  (:start . 87) (:id . 57))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 107)\n  (:start . 99) (:id . 59))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 115)\n  (:start . 108) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 125)\n  (:start . 117) (:id . 62))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 132)\n  (:start . 126) (:id . 63))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 137)\n  (:start . 133) (:id . 64))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 146)\n  (:start . 138) (:id . 65))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 151) (:start . 147)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 163)\n  (:start . 152) (:id . 67))\n ((:tag . "NN") (:stem . "splicing") (:form . "splicing") (:end . 172)\n  (:start . 164) (:id . 68))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 176) (:start . 173)\n  (:id . 69))\n ((:tag . "VB") (:stem . "influence") (:form . "influence") (:end . 186)\n  (:start . 177) (:id . 70))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 190) (:start . 187)\n  (:id . 71))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 201)\n  (:start . 191) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 203) (:start . 202)\n  (:id . 73))\n ((:tag . "CD") (:stem . "39") (:form . "39") (:end . 205) (:start . 203)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x2.74.1) (:span 173 176)) ((:id . :x2.74.2) (:span 138 146)))\n (:hscopes ((:id . :x2.74.1) (:span 173 201))\n  ((:id . :x2.74.2) (:span 138 201)))\n (:identifiers (:sid . :s2.74) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500290@unknown@formal@none@1@S@The experiments substantiate the notion that estrogen's main mode of action on AID is through transcriptional regulation and not mRNA metabolism.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "substantiate") (:form . "substantiate") (:end . 28)\n  (:start . 16) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 45))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 39)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 44) (:start . 40)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 53)\n  (:start . 45) (:id . 48))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 55) (:start . 53)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "main") (:form . "main") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "mode") (:form . "mode") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "action") (:form . "action") (:end . 75)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 93)\n  (:start . 86) (:id . 57))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 109) (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 120)\n  (:start . 110) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 60))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 128) (:start . 125)\n  (:id . 61))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 133) (:start . 129)\n  (:id . 62))\n ((:tag . "NN") (:stem . "metabolism") (:form . "metabolism") (:end . 144)\n  (:start . 134) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.75) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500291@unknown@formal@none@1@S@Identification of hormone response elements in the AID promoter regions@(((:tag . "NN") (:stem . "identification") (:form . "Identification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 25)\n  (:start . 18) (:id . 44))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 34)\n  (:start . 26) (:id . 45))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 43)\n  (:start . 35) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 63)\n  (:start . 55) (:id . 50))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 71)\n  (:start . 64) (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.76) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500292@unknown@formal@none@1@S@The rapid effect of the hormones on AID message via transcription suggested that the AID gene is a direct target for hormonal regulation.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "hormone") (:form . "hormones") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "message") (:form . "message") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 65) (:start . 52) (:id . 52))\n ((:tag . "VBD") (:stem . "suggest") (:form . "suggested") (:end . 75)\n  (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 93) (:start . 89)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 105)\n  (:start . 99) (:id . 60))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 112)\n  (:start . 106) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "hormonal") (:form . "hormonal") (:end . 125)\n  (:start . 117) (:id . 63))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 136)\n  (:start . 126) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x2.77.1) (:span 66 75)))\n (:hscopes ((:id . :x2.77.1) (:span 66 136)))\n (:identifiers (:sid . :s2.77) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500293@unknown@formal@none@1@S@Using bioinformatic analysis (Fig. 2 A), we were able to identify putative EREs in the context of other response elements, such as NF-κB.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "bioinformatic") (:form . "bioinformatic")\n  (:end . 19) (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 28)\n  (:start . 20) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 43) (:start . 41)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 48) (:start . 44)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 53) (:start . 49)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 54))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 65)\n  (:start . 57) (:id . 55))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 74)\n  (:start . 66) (:id . 56))\n ((:tag . "NNS") (:stem . "ere") (:form . "EREs") (:end . 79) (:start . 75)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 59))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 94)\n  (:start . 87) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 103) (:start . 98)\n  (:id . 62))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 112)\n  (:start . 104) (:id . 63))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 121)\n  (:start . 113) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 127) (:start . 123)\n  (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 130) (:start . 128)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 136)\n  (:start . 131) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.78) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500294@unknown@formal@none@1@S@We dissected the 1.5 kb upstream and the 2 kb downstream of the ATG regions for hormone-responsive elements in a heterologous transcription assay.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "dissect") (:form . "dissected") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "CD") (:stem . "1.5") (:form . "1.5") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 45) (:start . 43)\n  (:id . 51))\n ((:tag . "RB") (:stem . "downstream") (:form . "downstream") (:end . 56)\n  (:start . 46) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "ATG") (:form . "ATG") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 75)\n  (:start . 68) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "hormone-responsive") (:form . "hormone-responsive")\n  (:end . 98) (:start . 80) (:id . 58))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 107)\n  (:start . 99) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "heterologous") (:form . "heterologous") (:end . 125)\n  (:start . 113) (:id . 62))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 139) (:start . 126) (:id . 63))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 145)\n  (:start . 140) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.79) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500295@unknown@formal@none@1@S@The potential response regions were placed into a luciferase reporter construct and transfected into human SiHa cells, followed by treatment with the indicated hormone (or cotransfected with expression plasmids), and then analyzed for luciferase activity.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "place") (:form . "placed") (:end . 42)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 69)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 79)\n  (:start . 70) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 95)\n  (:start . 84) (:id . 54))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 100) (:start . 96)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 106)\n  (:start . 101) (:id . 56))\n ((:tag . "NNP") (:stem . "SiHa") (:form . "SiHa") (:end . 111) (:start . 107)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 117)\n  (:start . 112) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 127)\n  (:start . 119) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 130) (:start . 128)\n  (:id . 61))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 140)\n  (:start . 131) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 145) (:start . 141)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 149) (:start . 146)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 159)\n  (:start . 150) (:id . 65))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 167)\n  (:start . 160) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n  (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 171) (:start . 169)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "cotransfecte") (:form . "cotransfected")\n  (:end . 185) (:start . 172) (:id . 69))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 190) (:start . 186)\n  (:id . 70))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 201)\n  (:start . 191) (:id . 71))\n ((:tag . "NNS") (:stem . "plasmid") (:form . "plasmids") (:end . 210)\n  (:start . 202) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 211) (:start . 210)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 212) (:start . 211)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 216) (:start . 213)\n  (:id . 75))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 221) (:start . 217)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 230)\n  (:start . 222) (:id . 77))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 234) (:start . 231)\n  (:id . 78))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 245)\n  (:start . 235) (:id . 79))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 254)\n  (:start . 246) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 255) (:start . 254)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x2.80.1) (:span 4 13)))\n (:hscopes ((:id . :x2.80.1) (:span 4 30)))\n (:identifiers (:sid . :s2.80) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500296@unknown@formal@none@1@S@As we were primarily interested in the effect of hormones on expression, we used relative change as a readout rather than absolute values, which provided a more direct evaluation of the hormone treatment but potentially obscured the individual effect of the various DNA elements.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "RB") (:stem . "primarily") (:form . "primarily") (:end . 20)\n  (:start . 11) (:id . 45))\n ((:tag . "JJ") (:stem . "interested") (:form . "interested") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "hormone") (:form . "hormones") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 71)\n  (:start . 61) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 89)\n  (:start . 81) (:id . 57))\n ((:tag . "NN") (:stem . "change") (:form . "change") (:end . 96)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . 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"a") (:end . 155) (:start . 154)\n  (:id . 69))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 160) (:start . 156)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 167)\n  (:start . 161) (:id . 71))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 178)\n  (:start . 168) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 181) (:start . 179)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n  (:id . 74))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 193)\n  (:start . 186) (:id . 75))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 203)\n  (:start . 194) (:id . 76))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 207) (:start . 204)\n  (:id . 77))\n ((:tag . "RB") (:stem . "potentially") (:form . "potentially") (:end . 219)\n  (:start . 208) (:id . 78))\n ((:tag . "VBD") (:stem . "obscure") (:form . "obscured") (:end . 228)\n  (:start . 220) (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 232) (:start . 229)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 243)\n  (:start . 233) (:id . 81))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 250)\n  (:start . 244) (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 253) (:start . 251)\n  (:id . 83))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 257) (:start . 254)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 265)\n  (:start . 258) (:id . 85))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 269) (:start . 266)\n  (:id . 86))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 278)\n  (:start . 270) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 279) (:start . 278)\n  (:id . 88)))@@@1@47@((:hcues ((:id . :x2.81.1) (:span 208 219)))\n (:hscopes ((:id . :x2.81.1) (:span 208 278)))\n (:identifiers (:sid . :s2.81) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500297@unknown@formal@none@1@S@When compared with DMSO treatment, estrogen responsiveness was most significant with Fragment C, indicating that this contained the predominant estrogen-responsive DNA element.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "DMSO") (:form . "DMSO") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "responsiveness") (:form . "responsiveness")\n  (:end . 58) (:start . 44) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 79)\n  (:start . 68) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 84) (:start . 80)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Fragment") (:form . "Fragment") (:end . 93)\n  (:start . 85) (:id . 54))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 95) (:start . 94)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 107)\n  (:start . 97) (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 112) (:start . 108)\n  (:id . 58))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 117) (:start . 113)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 127)\n  (:start . 118) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "predominant") (:form . "predominant") (:end . 143)\n  (:start . 132) (:id . 62))\n ((:tag . "JJ") (:stem . "estrogen-responsive")\n  (:form . "estrogen-responsive") (:end . 163) (:start . 144) (:id . 63))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 167) (:start . 164)\n  (:id . 64))\n ((:tag . "NN") (:stem . "element") (:form . "element") (:end . 175)\n  (:start . 168) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x2.82.1) (:span 97 112)))\n (:hscopes ((:id . :x2.82.1) (:span 97 175)))\n (:identifiers (:sid . :s2.82) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500298@unknown@formal@none@1@S@Comparable to the mRNA production of AID in B cells, Fragment C also responded in a dose-dependent manner to estrogen (Fig. 2 C).@(((:tag . "JJ") (:stem . "comparable") (:form . "Comparable") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 33)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Fragment") (:form . "Fragment") (:end . 61)\n  (:start . 53) (:id . 53))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 63) (:start . 62)\n  (:id . 54))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "respond") (:form . "responded") (:end . 78)\n  (:start . 69) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 83) (:start . 82)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "dose-dependent") (:form . "dose-dependent")\n  (:end . 98) (:start . 84) (:id . 59))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 105)\n  (:start . 99) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 61))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 117)\n  (:start . 109) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 119) (:start . 118)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 123) (:start . 119)\n  (:id . 64))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 125) (:start . 124)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 127) (:start . 126)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s2.83) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500299@unknown@formal@none@1@S@Aside from the putative ERE, Fragment C also harbored the two published NF-κB binding sites (24).@(((:tag . "RB") (:stem . "aside") (:form . "Aside") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "ere") (:form . "ERE") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Fragment") (:form . "Fragment") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "harbor") (:form . "harbored") (:end . 53)\n  (:start . 45) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "publish") (:form . "published") (:end . 71)\n  (:start . 62) (:id . 54))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 85)\n  (:start . 78) (:id . 56))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 91) (:start . 86)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.84) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500300@unknown@formal@none@1@S@As indicated by the qRT-PCR analysis in Fig. 1 A, estrogen and the LPS/IL-4–induced NF-κB stress-response pathway could act synergistically on AID mRNA production.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 58)\n  (:start . 50) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "lps/il-4–induced") (:form . "LPS/IL-4–induced")\n  (:end . 83) (:start . 67) (:id . 56))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 89) (:start . 84)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "stress-response") (:form . "stress-response")\n  (:end . 105) (:start . 90) (:id . 58))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 113)\n  (:start . 106) (:id . 59))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 119)\n  (:start . 114) (:id . 60))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 123) (:start . 120)\n  (:id . 61))\n ((:tag . "RB") (:stem . "synergistically") (:form . "synergistically")\n  (:end . 139) (:start . 124) (:id . 62))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 142) (:start . 140)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 146) (:start . 143)\n  (:id . 64))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 151) (:start . 147)\n  (:id . 65))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 162)\n  (:start . 152) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x2.85.1) (:span 114 119)))\n (:hscopes ((:id . :x2.85.1) (:span 114 162)))\n (:identifiers (:sid . :s2.85) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500301@unknown@formal@none@1@S@To more directly stimulate the NF-κB pathway in SiHa cells, we used the cell-autonomous activator TNF-α (Fig. 2 C).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "VB") (:stem . "stimulate") (:form . "stimulate") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "SiHa") (:form . "SiHa") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 58) (:start . 53)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "cell-autonomous") (:form . "cell-autonomous")\n  (:end . 87) (:start . 72) (:id . 56))\n ((:tag . "NN") (:stem . "activator") (:form . "activator") (:end . 97)\n  (:start . 88) (:id . 57))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 103)\n  (:start . 98) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 111) (:start . 110)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.86) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500302@unknown@formal@none@1@S@Interestingly, aside from the synergy (e.g., 10-9 M), the two maxima of the dose response were offset (TNF-γ treated, 10-9 M; untreated, 10-7 M), indicating a higher complexity of the two interacting pathways.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "RB") (:stem . "aside") (:form . "aside") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "synergy") (:form . "synergy") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "CD") (:stem . "10-9") (:form . "10-9") (:end . 49) (:start . 45)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 55))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 61) (:start . 58)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "maximum") (:form . "maxima") (:end . 68)\n  (:start . 62) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 59))\n ((:tag . "NN") (:stem . "dose") (:form . "dose") (:end . 80) (:start . 76)\n  (:id . 60))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 89)\n  (:start . 81) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 94) (:start . 90)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "offset") (:form . "offset") (:end . 101)\n  (:start . 95) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "TNF-γ") (:form . "TNF-γ") (:end . 108)\n  (:start . 103) (:id . 65))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 116)\n  (:start . 109) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 67))\n ((:tag . "CD") (:stem . "10-9") (:form . "10-9") (:end . 122) (:start . 118)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 124) (:start . 123)\n  (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 125) (:start . 124)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 135)\n  (:start . 126) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 72))\n ((:tag . "CD") (:stem . "10-7") (:form . "10-7") (:end . 141) (:start . 137)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 143) (:start . 142)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 76))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 156)\n  (:start . 146) (:id . 77))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 158) (:start . 157)\n  (:id . 78))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 165)\n  (:start . 159) (:id . 79))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 176)\n  (:start . 166) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 179) (:start . 177)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n  (:id . 82))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 187) (:start . 184)\n  (:id . 83))\n ((:tag . "NN") (:stem . "interacting") (:form . "interacting") (:end . 199)\n  (:start . 188) (:id . 84))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 208)\n  (:start . 200) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s2.87) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500303@unknown@formal@none@1@S@To demonstrate independence of the two pathways, we analyzed the response of Fragment C to treatment with TNF-α and estrogen upon cotransfection of the dominant-negative mutant of IκBα (IκBα S32A/S36A dominant mutant [IκBα-mt]), which is known to inhibit the release of NF-κB from the cytoplasm into the nucleus after stimulation.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "demonstrate") (:form . "demonstrate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "independence") (:form . "independence") (:end . 27)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 47)\n  (:start . 39) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "analyze") (:form . "analyzed") (:end . 60)\n  (:start . 52) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 73)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Fragment") (:form . "Fragment") (:end . 85)\n  (:start . 77) (:id . 55))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 100)\n  (:start . 91) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 111)\n  (:start . 106) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 61))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 129) (:start . 125)\n  (:id . 63))\n ((:tag . "NN") (:stem . "cotransfection") (:form . "cotransfection")\n  (:end . 144) (:start . 130) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "dominant-negative") (:form . "dominant-negative")\n  (:end . 169) (:start . 152) (:id . 67))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 176)\n  (:start . 170) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 179) (:start . 177)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "IκBα") (:form . "IκBα") (:end . 184) (:start . 180)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 186) (:start . 185)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "IκBα") (:form . "IκBα") (:end . 190) (:start . 186)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "S32A/S36A") (:form . "S32A/S36A") (:end . 200)\n  (:start . 191) (:id . 73))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 209)\n  (:start . 201) (:id . 74))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 216)\n  (:start . 210) (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 218) (:start . 217)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "IκBα-mt") (:form . "IκBα-mt") (:end . 225)\n  (:start . 218) (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 226) (:start . 225)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 227) (:start . 226)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 228) (:start . 227)\n  (:id . 80))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 234)\n  (:start . 229) (:id . 81))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 237) (:start . 235)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 243)\n  (:start . 238) (:id . 83))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 246) (:start . 244)\n  (:id . 84))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 254)\n  (:start . 247) (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 258) (:start . 255)\n  (:id . 86))\n ((:tag . "NN") (:stem . "release") (:form . "release") (:end . 266)\n  (:start . 259) (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 269) (:start . 267)\n  (:id . 88))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 275)\n  (:start . 270) (:id . 89))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 280) (:start . 276)\n  (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 284) (:start . 281)\n  (:id . 91))\n ((:tag . "NN") (:stem . "cytoplasm") (:form . "cytoplasm") (:end . 294)\n  (:start . 285) (:id . 92))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 299) (:start . 295)\n  (:id . 93))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 303) (:start . 300)\n  (:id . 94))\n ((:tag . "NN") (:stem . "nucleus") (:form . "nucleus") (:end . 311)\n  (:start . 304) (:id . 95))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 317)\n  (:start . 312) (:id . 96))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 329)\n  (:start . 318) (:id . 97))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 330) (:start . 329)\n  (:id . 98)))@@@1@57@((:identifiers (:sid . :s2.88) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500304@unknown@formal@none@1@S@As shown in Fig. 2 D, the TNF-α activation was inhibited in the presence of IκBα-mt, yet estrogen was able to independently activate the transcription.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 49))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 31) (:start . 26)\n  (:id . 50))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 42)\n  (:start . 32) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 46) (:start . 43)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "inhibit") (:form . "inhibited") (:end . 56)\n  (:start . 47) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 55))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 72)\n  (:start . 64) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "IκBα-mt") (:form . "IκBα-mt") (:end . 83)\n  (:start . 76) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 59))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 88) (:start . 85)\n  (:id . 60))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 97)\n  (:start . 89) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 101) (:start . 98)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 106) (:start . 102)\n  (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 109) (:start . 107)\n  (:id . 64))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n  (:end . 123) (:start . 110) (:id . 65))\n ((:tag . "VB") (:stem . "activate") (:form . "activate") (:end . 132)\n  (:start . 124) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 67))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 150) (:start . 137) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.89) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500305@unknown@formal@none@1@S@This indicated that in the AID promoter, the NF-κB site and its proximal ERE could act independently as well as synergistically.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "indicate") (:form . "indicated") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 50) (:start . 45)\n  (:id . 51))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "proximal") (:form . "proximal") (:end . 72)\n  (:start . 64) (:id . 55))\n ((:tag . "NN") (:stem . "ere") (:form . "ERE") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 82) (:start . 77)\n  (:id . 57))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n  (:end . 100) (:start . 87) (:id . 59))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 103) (:start . 101)\n  (:id . 60))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 108) (:start . 104)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 111) (:start . 109)\n  (:id . 62))\n ((:tag . "RB") (:stem . "synergistically") (:form . "synergistically")\n  (:end . 127) (:start . 112) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x2.90.1) (:span 5 19)))\n (:hscopes ((:id . :x2.90.1) (:span 0 127)))\n (:identifiers (:sid . :s2.90) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500306@unknown@formal@none@1@S@Human AID promoter analysis for hormone response elements.@(((:tag . "JJ") (:stem . "human") (:form . "Human") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s2.91) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500307@unknown@formal@none@1@S@(A) Schematic representation of potential EREs (square) and NF-κB sites (circle) and their respective locations in the human promoter.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "representation") (:form . "representation")\n  (:end . 28) (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 41)\n  (:start . 32) (:id . 48))\n ((:tag . "NNS") (:stem . "ere") (:form . "EREs") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "square") (:form . "square") (:end . 54)\n  (:start . 48) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 71) (:start . 66)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . "NN") (:stem . "circle") (:form . "circle") (:end . 79)\n  (:start . 73) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 90)\n  (:start . 85) (:id . 60))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 101)\n  (:start . 91) (:id . 61))\n ((:tag . "NNS") (:stem . "location") (:form . "locations") (:end . 111)\n  (:start . 102) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 124)\n  (:start . 119) (:id . 65))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 133)\n  (:start . 125) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.92) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500308@unknown@formal@none@1@S@The indicated promoter regions (marked A–E) were inserted into a luciferase reporter construct with a minimal promoter.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "marked") (:form . "marked") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "NNP") (:stem . "A–E") (:form . "A–E") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 75)\n  (:start . 65) (:id . 54))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 84)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 99) (:start . 95)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "minimal") (:form . "minimal") (:end . 109)\n  (:start . 102) (:id . 59))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 118)\n  (:start . 110) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.93) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500309@unknown@formal@none@1@S@The vectors were transfected into SiHa cells, incubated for 24 h, treated for 4 h with hormones or TNF-α, and analyzed for luciferase activity.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "vector") (:form . "vectors") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 28)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "SiHa") (:form . "SiHa") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 73)\n  (:start . 66) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 79) (:start . 78)\n  (:id . 57))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 81) (:start . 80)\n  (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 86) (:start . 82)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "hormone") (:form . "hormones") (:end . 95)\n  (:start . 87) (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 98) (:start . 96)\n  (:id . 61))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 104) (:start . 99)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 118)\n  (:start . 110) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 122) (:start . 119)\n  (:id . 66))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 133)\n  (:start . 123) (:id . 67))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 142)\n  (:start . 134) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.94) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500310@unknown@formal@none@1@S@(B) Relative luciferase activity after estrogen treatment.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "relative") (:form . "Relative") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 23)\n  (:start . 13) (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 47)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.95) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500311@unknown@formal@none@1@S@Cells were transfected with constructs containing AID promoter fragments and treated with estrogen for 4 h.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 49)\n  (:start . 39) (:id . 47))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 53) (:start . 50)\n  (:id . 48))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 62)\n  (:start . 54) (:id . 49))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 72)\n  (:start . 63) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 84)\n  (:start . 77) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 89) (:start . 85)\n  (:id . 53))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 98)\n  (:start . 90) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 102) (:start . 99)\n  (:id . 55))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 104) (:start . 103)\n  (:id . 56))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 106) (:start . 105)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.96) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500312@unknown@formal@none@1@S@(C) Effect of TNF-α and estrogen on the human AID promoter.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "effect") (:form . "Effect") (:end . 10) (:start . 4)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 46))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 19) (:start . 14)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 48))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 32)\n  (:start . 24) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 35) (:start . 33)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 45) (:start . 40)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 49) (:start . 46)\n  (:id . 53))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 58)\n  (:start . 50) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.97) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500313@unknown@formal@none@1@S@Expression construct with an AID promoter region containing NF-κB sites and putative ERE (Fragment C) were transfected into cells, followed by TNF-α and/or estrogen treatment for 4 h.@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 20)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n  (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 48)\n  (:start . 42) (:id . 48))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 59)\n  (:start . 49) (:id . 49))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 65) (:start . 60)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 71) (:start . 66)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 84)\n  (:start . 76) (:id . 53))\n ((:tag . "NNP") (:stem . "ERE") (:form . "ERE") (:end . 88) (:start . 85)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Fragment") (:form . "Fragment") (:end . 98)\n  (:start . 90) (:id . 56))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 118)\n  (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 129)\n  (:start . 124) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 139)\n  (:start . 131) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 142) (:start . 140)\n  (:id . 65))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 148)\n  (:start . 143) (:id . 66))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 155)\n  (:start . 149) (:id . 67))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 164)\n  (:start . 156) (:id . 68))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 174)\n  (:start . 165) (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 178) (:start . 175)\n  (:id . 70))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 180) (:start . 179)\n  (:id . 71))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 182) (:start . 181)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.98) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500314@unknown@formal@none@1@S@(D) Estrogen can act independently from NF-κB.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 20) (:start . 17)\n  (:id . 47))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n  (:end . 34) (:start . 21) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.99) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500315@unknown@formal@none@1@S@Cells were cotransfected with Fragment C and an IκBα-mt expression vector.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "cotransfecte") (:form . "cotransfected")\n  (:end . 24) (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Fragment") (:form . "Fragment") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 40) (:start . 39)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "iκbα-mt") (:form . "IκBα-mt") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 66)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 73)\n  (:start . 67) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.100) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500316@unknown@formal@none@1@S@After 24 h, cells were treated with TNF-α and/or 100 nM estrogen for 4 h.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 17) (:start . 12)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 30)\n  (:start . 23) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 35) (:start . 31)\n  (:id . 49))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 41) (:start . 36)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 48)\n  (:start . 42) (:id . 51))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 55) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 64)\n  (:start . 56) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 72) (:start . 71)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.101) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500317@unknown@formal@none@1@S@Timelines of cell treatments are indicated below the graphs.@(((:tag . "NNS") (:stem . "timeline") (:form . "Timelines") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "graph") (:form . "graphs") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.102) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500318@unknown@formal@none@1@S@NT, not treated.@(((:tag . "NN") (:stem . "nt") (:form . "NT") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 3) (:start . 2) (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 7) (:start . 4)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 15)\n  (:start . 8) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 16) (:start . 15)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s2.103) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500319@unknown@formal@none@1@S@ERE binding in B cell extracts@(((:tag . "NN") (:stem . "ere") (:form . "ERE") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "extract") (:form . "extracts") (:end . 30)\n  (:start . 22) (:id . 47)))@@@1@6@((:identifiers (:sid . :s2.104) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500320@unknown@formal@none@1@S@The transient transfection assay indicated that a predicted ERE was subject to estrogen regulation.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "transient") (:form . "transient") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 26)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 32) (:start . 27)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "indicate") (:form . "indicated") (:end . 42)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 47) (:start . 43)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 59)\n  (:start . 50) (:id . 49))\n ((:tag . "NN") (:stem . "ere") (:form . "ERE") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 67) (:start . 64)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "subject") (:form . "subject") (:end . 75)\n  (:start . 68) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 98)\n  (:start . 88) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x2.105.1) (:span 33 47)))\n (:hscopes ((:id . :x2.105.1) (:span 33 98)))\n (:identifiers (:sid . :s2.105) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500321@unknown@formal@none@1@S@Thus, we analyzed ER binding to the AID promoter and focused on the more widely expressed receptor subtype ERα.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "analyze") (:form . "analyzed") (:end . 17)\n  (:start . 9) (:id . 45))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 28)\n  (:start . 21) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 48)\n  (:start . 40) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "focus") (:form . "focused") (:end . 60)\n  (:start . 53) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 72) (:start . 68)\n  (:id . 56))\n ((:tag . "RB") (:stem . "widely") (:form . "widely") (:end . 79)\n  (:start . 73) (:id . 57))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 89)\n  (:start . 80) (:id . 58))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 98)\n  (:start . 90) (:id . 59))\n ((:tag . "NN") (:stem . "subtype") (:form . "subtype") (:end . 106)\n  (:start . 99) (:id . 60))\n ((:tag . "NN") (:stem . "erα") (:form . "ERα") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.106) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500322@unknown@formal@none@1@S@To analyze the binding of ER to parts of the AID promoter in vitro, we prepared nuclear extracts from treated and untreated cells and performed electromobility shift assays (EMSA).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "analyze") (:form . "analyze") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 48) (:start . 45)\n  (:id . 52))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 57)\n  (:start . 49) (:id . 53))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 54))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 66) (:start . 61)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 70) (:start . 68)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "prepare") (:form . "prepared") (:end . 79)\n  (:start . 71) (:id . 58))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 87)\n  (:start . 80) (:id . 59))\n ((:tag . "NNS") (:stem . "extract") (:form . "extracts") (:end . 96)\n  (:start . 88) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 101) (:start . 97)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 109)\n  (:start . 102) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 123)\n  (:start . 114) (:id . 64))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 129)\n  (:start . 124) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 143)\n  (:start . 134) (:id . 67))\n ((:tag . "NN") (:stem . "electromobility") (:form . "electromobility")\n  (:end . 159) (:start . 144) (:id . 68))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 165)\n  (:start . 160) (:id . 69))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 172)\n  (:start . 166) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "EMSA") (:form . "EMSA") (:end . 178) (:start . 174)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s2.107) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500323@unknown@formal@none@1@S@For the biochemical analysis of the ER binding to the ERE, we focused on NF-κB proximal ERE of Fragment C.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "biochemical") (:form . "biochemical") (:end . 19)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "ere") (:form . "ERE") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 61) (:start . 59)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "focus") (:form . "focused") (:end . 69)\n  (:start . 62) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 72) (:start . 70)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 78) (:start . 73)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "proximal") (:form . "proximal") (:end . 87)\n  (:start . 79) (:id . 58))\n ((:tag . "NN") (:stem . "ere") (:form . "ERE") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Fragment") (:form . "Fragment") (:end . 103)\n  (:start . 95) (:id . 61))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 105) (:start . 104)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s2.108) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500324@unknown@formal@none@1@S@A 34-bp fragment containing the 5'-most proposed ER binding site was incubated with untreated and treated extract (Fig. 3 B, lanes 2 and 3).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "34-bp") (:form . "34-bp") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "5'-most") (:form . "5’-most") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 93)\n  (:start . 84) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 105)\n  (:start . 98) (:id . 57))\n ((:tag . "NN") (:stem . "extract") (:form . "extract") (:end . 113)\n  (:start . 106) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 119) (:start . 115)\n  (:id . 60))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 121) (:start . 120)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 123) (:start . 122)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 130)\n  (:start . 125) (:id . 64))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 132) (:start . 131)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n  (:id . 66))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 138) (:start . 137)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.109) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500325@unknown@formal@none@1@S@The estrogen treatment clearly induced a protein that could bind the fragment (arrow), which was not induced when treating the B cells with TNF-α before extract preparation (lane 4).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "VBD") (:stem . "induce") (:form . "induced") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n  (:id . 49))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "VB") (:stem . "bind") (:form . "bind") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "NN") (:stem . "arrow") (:form . "arrow") (:end . 84) (:start . 79)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 92) (:start . 87)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 108)\n  (:start . 101) (:id . 61))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 113) (:start . 109)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "treat") (:form . "treating") (:end . 122)\n  (:start . 114) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 128) (:start . 127)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 134)\n  (:start . 129) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 139) (:start . 135)\n  (:id . 67))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 145)\n  (:start . 140) (:id . 68))\n ((:tag . "IN") (:stem . "before") (:form . "before") (:end . 152)\n  (:start . 146) (:id . 69))\n ((:tag . "NN") (:stem . "extract") (:form . "extract") (:end . 160)\n  (:start . 153) (:id . 70))\n ((:tag . "NN") (:stem . "preparation") (:form . "preparation") (:end . 172)\n  (:start . 161) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 72))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 178) (:start . 174)\n  (:id . 73))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 180) (:start . 179)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 181) (:start . 180)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s2.110) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500326@unknown@formal@none@1@S@Cotreatment with estrogen and TNF-α had the same effect as estrogen alone (Fig. 3 B, lane 5), indicating that the two pathways act through different nuclear proteins.@(((:tag . "NNP") (:stem . "Cotreatment") (:form . "Cotreatment") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 16) (:start . 12)\n  (:id . 43))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 67)\n  (:start . 59) (:id . 52))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 73) (:start . 68)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 58))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 89) (:start . 85)\n  (:id . 59))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 91) (:start . 90)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 104)\n  (:start . 94) (:id . 63))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 109) (:start . 105)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 65))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 117) (:start . 114)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 126)\n  (:start . 118) (:id . 67))\n ((:tag . "VBP") (:stem . "act") (:form . "act") (:end . 130) (:start . 127)\n  (:id . 68))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 138)\n  (:start . 131) (:id . 69))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 148)\n  (:start . 139) (:id . 70))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 156)\n  (:start . 149) (:id . 71))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 165)\n  (:start . 157) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x2.111.1) (:span 94 109)))\n (:hscopes ((:id . :x2.111.1) (:span 94 165)))\n (:identifiers (:sid . :s2.111) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500327@unknown@formal@none@1@S@Competition experiments with the ER binding site (Fig. 3 B, lanes 6–8) or a mutation of the proposed ER site (Fig. 3 B, lanes 9–11) showed a specific competition, indicating ER-like binding kinetics.@(((:tag . "NN") (:stem . "competition") (:form . "Competition") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 23)\n  (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 28) (:start . 24)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 45))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . "CD") (:stem . "6–8") (:form . "6–8") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 73) (:start . 71)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 75) (:start . 74)\n  (:id . 58))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 84)\n  (:start . 76) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 100)\n  (:start . 92) (:id . 62))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 103) (:start . 101)\n  (:id . 63))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 108) (:start . 104)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 114) (:start . 110)\n  (:id . 66))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 116) (:start . 115)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 118) (:start . 117)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 125)\n  (:start . 120) (:id . 70))\n ((:tag . "CD") (:stem . "9–11") (:form . "9–11") (:end . 130) (:start . 126)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 72))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 138)\n  (:start . 132) (:id . 73))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 140) (:start . 139)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 149)\n  (:start . 141) (:id . 75))\n ((:tag . "NN") (:stem . "competition") (:form . "competition") (:end . 161)\n  (:start . 150) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 77))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 173)\n  (:start . 163) (:id . 78))\n ((:tag . "JJ") (:stem . "er-like") (:form . "ER-like") (:end . 181)\n  (:start . 174) (:id . 79))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 189)\n  (:start . 182) (:id . 80))\n ((:tag . "NNS") (:stem . "kinetic") (:form . "kinetics") (:end . 198)\n  (:start . 190) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s2.112) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500328@unknown@formal@none@1@S@Using antibodies to the DNA-binding domain of ERα strongly inhibited the formation of the estrogen-induced band (Fig. 3 C, lanes 2 vs. 3–5), but the shift was unaffected by a control antibody (Fig. 3 C, lanes 2 vs. 6–8, arrow).@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "dna-binding") (:form . "DNA-binding") (:end . 35)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 42)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "ERα") (:form . "ERα") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 58)\n  (:start . 50) (:id . 50))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 68)\n  (:start . 59) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "estrogen-induced") (:form . "estrogen-induced")\n  (:end . 106) (:start . 90) (:id . 56))\n ((:tag . "NN") (:stem . "band") (:form . "band") (:end . 111) (:start . 107)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 117) (:start . 113)\n  (:id . 59))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 121) (:start . 120)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 128)\n  (:start . 123) (:id . 63))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . "CC") (:stem . "vs.") (:form . "vs.") (:end . 134) (:start . 131)\n  (:id . 65))\n ((:tag . "CD") (:stem . "3–5") (:form . "3–5") (:end . 138) (:start . 135)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 68))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 144) (:start . 141)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 70))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 154)\n  (:start . 149) (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 158) (:start . 155)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "unaffected") (:form . "unaffected") (:end . 169)\n  (:start . 159) (:id . 73))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 172) (:start . 170)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 174) (:start . 173)\n  (:id . 75))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 182)\n  (:start . 175) (:id . 76))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 191)\n  (:start . 183) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 193) (:start . 192)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 197) (:start . 193)\n  (:id . 79))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 199) (:start . 198)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 201) (:start . 200)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 202) (:start . 201)\n  (:id . 82))\n ((:tag . "VBZ") (:stem . "lane") (:form . "lanes") (:end . 208)\n  (:start . 203) (:id . 83))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 210) (:start . 209)\n  (:id . 84))\n ((:tag . "IN") (:stem . "vs.") (:form . "vs.") (:end . 214) (:start . 211)\n  (:id . 85))\n ((:tag . "CD") (:stem . "6–8") (:form . "6–8") (:end . 218) (:start . 215)\n  (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 219) (:start . 218)\n  (:id . 87))\n ((:tag . "NN") (:stem . "arrow") (:form . "arrow") (:end . 225)\n  (:start . 220) (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 226) (:start . 225)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s2.113) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500329@unknown@formal@none@1@S@The anti-ERα antibody did induce the appearance of a high molecular weight complex (Fig. 3 C, triangle in lanes 4 and 5), which could be caused by either the supershift of a dimerized ERα or heterodimer ERα/ERß; however, this needs to be analyzed further.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "anti-erα") (:form . "anti-ERα") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "appearance") (:form . "appearance") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . 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5500330@unknown@formal@none@1@S@Identification of ER binding to human AID promoter by EMSA and ChIP.@(((:tag . "NN") (:stem . "identification") (:form . "Identification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "ER") (:form . "ER") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 50)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "EMSA") (:form . "EMSA") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "ChIP") (:form . "ChIP") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s2.115) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500331@unknown@formal@none@1@S@(A) Schematic representation of human AID promoter region (as in Fig. 2 A).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "representation") (:form . "representation")\n  (:end . 28) (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 50)\n  (:start . 42) (:id . 50))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 57)\n  (:start . 51) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 69) (:start . 65)\n  (:id . 55))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.116) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500332@unknown@formal@none@1@S@The position of the oligonucleotide used for EMSA and the region amplified by qRT-PCR for ChIP are marked as a black line and a dashed line, respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "oligonucleotide") (:form . "oligonucleotide")\n  (:end . 35) (:start . 20) (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "EMSA") (:form . "EMSA") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 64)\n  (:start . 58) (:id . 52))\n ((:tag . "VBN") (:stem . "amplify") (:form . "amplified") (:end . 74)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 85)\n  (:start . 78) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "ChIP") (:form . "ChIP") (:end . 94) (:start . 90)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 98) (:start . 95)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 105)\n  (:start . 99) (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 116)\n  (:start . 111) (:id . 62))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 121) (:start . 117)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 127) (:start . 126)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "dashed") (:form . "dashed") (:end . 134)\n  (:start . 128) (:id . 66))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 139) (:start . 135)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 68))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 153)\n  (:start . 141) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.117) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500333@unknown@formal@none@1@S@(B) Estrogen (denoted as E) -induced oligonucleotide shift (marked with an arrow) in Ramos nuclear extracts.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "denote") (:form . "denoted") (:end . 21)\n  (:start . 14) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 24) (:start . 22)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 26) (:start . 25)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "-induced") (:form . "-induced") (:end . 36)\n  (:start . 28) (:id . 51))\n ((:tag . "NN") (:stem . "oligonucleotide") (:form . "oligonucleotide")\n  (:end . 52) (:start . 37) (:id . 52))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 58) (:start . 53)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 66) (:start . 60)\n  (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 71) (:start . 67)\n  (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 74) (:start . 72)\n  (:id . 57))\n ((:tag . "NN") (:stem . "arrow") (:form . "arrow") (:end . 80) (:start . 75)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 90) (:start . 85)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 98)\n  (:start . 91) (:id . 62))\n ((:tag . "NNS") (:stem . "extract") (:form . "extracts") (:end . 107)\n  (:start . 99) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.118) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500334@unknown@formal@none@1@S@Cells were treated for 72 h in hormone-depleted serum, followed by 4-h treatment with 10 nM estrogen (lanes 3 and 5–11) and/or TNF-α (lanes 4 and 5), and nuclear extract preparation.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "hormone-depleted") (:form . "hormone-depleted")\n  (:end . 47) (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "serum") (:form . "serum") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "4-h") (:form . "4-h") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 80)\n  (:start . 71) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 100)\n  (:start . 92) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 107)\n  (:start . 102) (:id . 61))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 63))\n ((:tag . "CD") (:stem . "5–11") (:form . "5–11") (:end . 118) (:start . 114)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 126)\n  (:start . 120) (:id . 66))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 132)\n  (:start . 127) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 139)\n  (:start . 134) (:id . 69))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 141) (:start . 140)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 71))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 147) (:start . 146)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 153) (:start . 150)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 161)\n  (:start . 154) (:id . 76))\n ((:tag . "NN") (:stem . "extract") (:form . "extract") (:end . 169)\n  (:start . 162) (:id . 77))\n ((:tag . "NN") (:stem . "preparation") (:form . "preparation") (:end . 181)\n  (:start . 170) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s2.119) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500335@unknown@formal@none@1@S@Different concentrations of unlabeled competitors ER (lanes 6–8) and mutated ER mut (lanes 9–11) were added to the binding reaction.@(((:tag . "JJ") (:stem . "different") (:form . "Different") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 24) (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "unlabeled") (:form . "unlabeled") (:end . 37)\n  (:start . 28) (:id . 45))\n ((:tag . "NNS") (:stem . "competitor") (:form . "competitors") (:end . 49)\n  (:start . 38) (:id . 46))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 52) (:start . 50)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 59) (:start . 54)\n  (:id . 49))\n ((:tag . "CD") (:stem . "6–8") (:form . "6–8") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 64) (:start . 63)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "mut") (:form . "mut") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "CD") (:stem . "9–11") (:form . "9–11") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 101) (:start . 97)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 107) (:start . 102)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 63))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 122)\n  (:start . 115) (:id . 64))\n ((:tag . "NN") (:stem . "reaction") (:form . "reaction") (:end . 131)\n  (:start . 123) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.120) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500336@unknown@formal@none@1@S@Open triangle, nonspecific DNA binding band.@(((:tag . "JJ") (:stem . "open") (:form . "Open") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "triangle") (:form . "triangle") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "nonspecific") (:form . "nonspecific") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "band") (:form . "band") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 44) (:start . 43)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s2.121) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500337@unknown@formal@none@1@S@(C) EMSA with anti-ERα antibodies.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "EMSA") (:form . "EMSA") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 13) (:start . 9)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "anti-erα") (:form . "anti-ERα") (:end . 22)\n  (:start . 14) (:id . 47))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 33)\n  (:start . 23) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 34) (:start . 33)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s2.122) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500338@unknown@formal@none@1@S@Increasing concentrations of anti-ERα antibody and a nonspecific antibody were added to the binding reaction (see Materials and methods).@(((:tag . "VBG") (:stem . "increase") (:form . "Increasing") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 25) (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "anti-erα") (:form . "anti-ERα") (:end . 37)\n  (:start . 29) (:id . 45))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 46)\n  (:start . 38) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "nonspecific") (:form . "nonspecific") (:end . 64)\n  (:start . 53) (:id . 49))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 73)\n  (:start . 65) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 78) (:start . 74)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 84) (:start . 79)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 54))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 99)\n  (:start . 92) (:id . 55))\n ((:tag . "NN") (:stem . "reaction") (:form . "reaction") (:end . 108)\n  (:start . 100) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 57))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 113) (:start . 110)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "material") (:form . "Materials") (:end . 123)\n  (:start . 114) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 135)\n  (:start . 128) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s2.123) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500339@unknown@formal@none@1@S@The estrogen-induced band is marked with an arrow, and a super-shifted band appearing upon anti-ERα antibody addition is marked with a closed triangle.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "estrogen-induced") (:form . "estrogen-induced")\n  (:end . 20) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "band") (:form . "band") (:end . 25) (:start . 21)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 35) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "arrow") (:form . "arrow") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "super-shifted") (:form . "super-shifted")\n  (:end . 70) (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "band") (:form . "band") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "appear") (:form . "appearing") (:end . 85)\n  (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 90) (:start . 86)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "anti-erα") (:form . "anti-ERα") (:end . 99)\n  (:start . 91) (:id . 57))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 108)\n  (:start . 100) (:id . 58))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 117)\n  (:start . 109) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 120) (:start . 118)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 127)\n  (:start . 121) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 132) (:start . 128)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 134) (:start . 133)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "closed") (:form . "closed") (:end . 141)\n  (:start . 135) (:id . 64))\n ((:tag . "NN") (:stem . "triangle") (:form . "triangle") (:end . 150)\n  (:start . 142) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.124) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500340@unknown@formal@none@1@S@Open triangle, nonspecific DNA-binding band.@(((:tag . "JJ") (:stem . "open") (:form . "Open") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "triangle") (:form . "triangle") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "nonspecific") (:form . "nonspecific") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "JJ") (:stem . "dna-binding") (:form . "DNA-binding") (:end . 38)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "band") (:form . "band") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 44) (:start . 43)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s2.125) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500341@unknown@formal@none@1@S@(D) ERα binds to upstream region of human AID promoter.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "ERα") (:form . "ERα") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "bind") (:form . "binds") (:end . 13) (:start . 8)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 16) (:start . 14)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 25)\n  (:start . 17) (:id . 48))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 32)\n  (:start . 26) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 41) (:start . 36)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 45) (:start . 42)\n  (:id . 52))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 54)\n  (:start . 46) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s2.126) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500342@unknown@formal@none@1@S@Cells were treated as in B.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 27) (:start . 26)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s2.127) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500343@unknown@formal@none@1@S@Data are representative of three independent experiments and error bars indicate standard deviations from the mean.@(((:tag . "NNPS") (:stem . "Datum") (:form . "Data") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 23) (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 44)\n  (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 56)\n  (:start . 45) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 49))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 66) (:start . 61)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 71) (:start . 67)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 80)\n  (:start . 72) (:id . 52))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 89)\n  (:start . 81) (:id . 53))\n ((:tag . "NNS") (:stem . "deviation") (:form . "deviations") (:end . 100)\n  (:start . 90) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 105) (:start . 101)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 56))\n ((:tag . "NN") (:stem . "mean") (:form . "mean") (:end . 114) (:start . 110)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.128) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500344@unknown@formal@none@1@S@ChIP was performed using anti-ERα or control antibodies, and the bound DNA was subjected to qRT-PCR.@(((:tag . "NN") (:stem . "chip") (:form . "ChIP") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "anti-erα") (:form . "anti-ERα") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 55)\n  (:start . 45) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "bind") (:form . "bound") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "subject") (:form . "subjected") (:end . 88)\n  (:start . 79) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 99)\n  (:start . 92) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.129) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500345@unknown@formal@none@1@S@Estrogen and Tam treatments are marked with E1 (estrogen 1 nM), E10 (estrogen 10 nM), and Tam, respectively.@(((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 38) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "E1") (:form . "E1") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 56)\n  (:start . 48) (:id . 51))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "nM") (:form . "nM") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "E10") (:form . "E10") (:end . 67) (:start . 64)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 57))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 77)\n  (:start . 69) (:id . 58))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 80) (:start . 78)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "nM") (:form . "nM") (:end . 83) (:start . 81)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 93) (:start . 90)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 65))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 107)\n  (:start . 95) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.130) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500346@unknown@formal@none@1@S@(E) Estrogen can cooperate with TNF-α in recruiting NF-κB to AID promoter.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . "VB") (:stem . "cooperate") (:form . "cooperate") (:end . 26)\n  (:start . 17) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "recruit") (:form . "recruiting") (:end . 51)\n  (:start . 41) (:id . 51))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 57) (:start . 52)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 73)\n  (:start . 65) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.131) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500347@unknown@formal@none@1@S@ChIP is as in D, using anti–NF-κB or control antibodies.@(((:tag . "NNP") (:stem . "ChIP") (:form . "ChIP") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 22) (:start . 17)\n  (:id . 48))\n ((:tag . "NN") (:stem . "anti–nf-κb") (:form . "anti–NF-κB") (:end . 33)\n  (:start . 23) (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 36) (:start . 34)\n  (:id . 50))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 44)\n  (:start . 37) (:id . 51))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 55)\n  (:start . 45) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.132) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500348@unknown@formal@none@1@S@NT, not treated.@(((:tag . "NN") (:stem . "nt") (:form . "NT") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 3) (:start . 2) (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 7) (:start . 4)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 15)\n  (:start . 8) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 16) (:start . 15)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s2.133) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500349@unknown@formal@none@1@S@Because estrogen and TNF-α co-stimulation did not alter ER binding to the ERE, we wanted to determine if the reciprocal of NF-κB binding to the NF-κB site, after the combined treatment, was also unaffected.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "co-stimulation") (:form . "co-stimulation")\n  (:end . 41) (:start . 27) (:id . 46))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 45) (:start . 42)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "VB") (:stem . "alter") (:form . "alter") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "ere") (:form . "ERE") (:end . 77) (:start . 74)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "want") (:form . "wanted") (:end . 88) (:start . 82)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 101)\n  (:start . 92) (:id . 59))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "NN") (:stem . "reciprocal") (:form . "reciprocal") (:end . 119)\n  (:start . 109) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 128)\n  (:start . 123) (:id . 64))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 136)\n  (:start . 129) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 149)\n  (:start . 144) (:id . 68))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 154) (:start . 150)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n  (:id . 70))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 161)\n  (:start . 156) (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "combined") (:form . "combined") (:end . 174)\n  (:start . 166) (:id . 73))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 184)\n  (:start . 175) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 75))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 189) (:start . 186)\n  (:id . 76))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 194) (:start . 190)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "unaffected") (:form . "unaffected") (:end . 205)\n  (:start . 195) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x2.134.1) (:span 102 104)))\n (:hscopes ((:id . :x2.134.1) (:span 102 205)))\n (:identifiers (:sid . :s2.134) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500350@unknown@formal@none@1@S@To that end, we probed the published NF-κB site (24) with our extracts.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "probe") (:form . "probed") (:end . 22)\n  (:start . 16) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "publish") (:form . "published") (:end . 36)\n  (:start . 27) (:id . 49))\n ((:tag . "NN") (:stem . "nf-κb") (:form . "NF-κB") (:end . 42) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 51) (:start . 49)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 57) (:start . 53)\n  (:id . 55))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 61) (:start . 58)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "extract") (:form . "extracts") (:end . 70)\n  (:start . 62) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.135) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500351@unknown@formal@none@1@S@Using cold competitors (Fig. S3 B, lane 4 vs. 6–11, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1), as well as anti–NF-κB antibodies (Fig. S3 C), we could demonstrate the specificity of the NF-κB binding site.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "cold") (:form . "cold") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "competitor") (:form . "competitors") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 39) (:start . 35)\n  (:id . 50))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 41) (:start . 40)\n  (:id . 51))\n ((:tag . "IN") (:stem . "vs.") (:form . "vs.") (:end . 45) (:start . 42)\n  (:id . 52))\n ((:tag . "CD") (:stem . "6–11") (:form . "6–11") (:end . 50) (:start . 46)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 61)\n  (:start . 52) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 64) (:start . 62)\n  (:id . 56))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 117) (:start . 65) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 59))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 122) (:start . 120)\n  (:id . 60))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 127) (:start . 123)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "anti–nf-κb") (:form . "anti–NF-κB") (:end . 141)\n  (:start . 131) (:id . 63))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 152)\n  (:start . 142) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 158) (:start . 154)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 161) (:start . 159)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 163) (:start . 162)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 164) (:start . 163)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 70))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 168) (:start . 166)\n  (:id . 71))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 174)\n  (:start . 169) (:id . 72))\n ((:tag . "VB") (:stem . "demonstrate") (:form . "demonstrate") (:end . 186)\n  (:start . 175) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 190) (:start . 187)\n  (:id . 74))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 202)\n  (:start . 191) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 215)\n  (:start . 210) (:id . 78))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 223)\n  (:start . 216) (:id . 79))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 228) (:start . 224)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s2.136) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500352@unknown@formal@none@1@S@As with the ER binding site, NF-κB binding was not altered by cotreatment with estrogen and TNF-α (Fig. S3 B, lanes 4 vs. 5).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 22)\n  (:start . 15) (:id . 46))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 34) (:start . 29)\n  (:id . 49))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 42)\n  (:start . 35) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 50) (:start . 47)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "alter") (:form . "altered") (:end . 58)\n  (:start . 51) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 61) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cotreatment") (:form . "cotreatment") (:end . 73)\n  (:start . 62) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 78) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 87)\n  (:start . 79) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 97) (:start . 92)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 103) (:start . 99)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 108) (:start . 107)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 115)\n  (:start . 110) (:id . 65))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 117) (:start . 116)\n  (:id . 66))\n ((:tag . "CC") (:stem . "vs.") (:form . "vs.") (:end . 121) (:start . 118)\n  (:id . 67))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 123) (:start . 122)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.137) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500353@unknown@formal@none@1@S@This indicated that the respective treatments did not alter the general DNA-binding properties of ER or NF-κB proteins.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "indicate") (:form . "indicated") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 45)\n  (:start . 35) (:id . 47))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "VB") (:stem . "alter") (:form . "alter") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "JJ") (:stem . "dna-binding") (:form . "DNA-binding") (:end . 83)\n  (:start . 72) (:id . 53))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 94)\n  (:start . 84) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "ER") (:form . "ER") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 109)\n  (:start . 104) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 118)\n  (:start . 110) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x2.138.1) (:span 5 19)))\n (:hscopes ((:id . :x2.138.1) (:span 5 118)))\n (:identifiers (:sid . :s2.138) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500354@unknown@formal@none@1@S@Because the distance, on the AID promoter, between the ER and NF-κB sites was larger than our EMSA probes (i.e., neither probe contained both binding sites), we could not study the effect of cooperative binding.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 50)\n  (:start . 43) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "ER") (:form . "ER") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 67) (:start . 62)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 73) (:start . 68)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 84)\n  (:start . 78) (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 89) (:start . 85)\n  (:id . 59))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 93) (:start . 90)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "EMSA") (:form . "EMSA") (:end . 98) (:start . 94)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "probe") (:form . "probes") (:end . 105)\n  (:start . 99) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 63))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 111) (:start . 107)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 65))\n ((:tag . "DT") (:stem . "neither") (:form . "neither") (:end . 120)\n  (:start . 113) (:id . 66))\n ((:tag . "NN") (:stem . "probe") (:form . "probe") (:end . 126)\n  (:start . 121) (:id . 67))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 136)\n  (:start . 127) (:id . 68))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 141) (:start . 137)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 149)\n  (:start . 142) (:id . 70))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 155)\n  (:start . 150) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n  (:id . 73))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 160) (:start . 158)\n  (:id . 74))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 166)\n  (:start . 161) (:id . 75))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 170) (:start . 167)\n  (:id . 76))\n ((:tag . "VB") (:stem . "study") (:form . "study") (:end . 176)\n  (:start . 171) (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 180) (:start . 177)\n  (:id . 78))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 187)\n  (:start . 181) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 190) (:start . 188)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "cooperative") (:form . "cooperative") (:end . 202)\n  (:start . 191) (:id . 81))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 210)\n  (:start . 203) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s2.139) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500355@unknown@formal@none@1@S@ER binding to AID promoter in vivo@(((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 34) (:start . 30)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s2.140) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500356@unknown@formal@none@1@S@Although the in vitro binding of the ER to the AID promoter indicated a direct binding, we also wanted to probe this interaction in vivo.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 50) (:start . 47)\n  (:id . 52))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 59)\n  (:start . 51) (:id . 53))\n ((:tag . "VBD") (:stem . "indicate") (:form . "indicated") (:end . 69)\n  (:start . 60) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 78)\n  (:start . 72) (:id . 56))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 86)\n  (:start . 79) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 95) (:start . 91)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "want") (:form . "wanted") (:end . 102)\n  (:start . 96) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n  (:id . 62))\n ((:tag . "VB") (:stem . "probe") (:form . "probe") (:end . 111)\n  (:start . 106) (:id . 63))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 116) (:start . 112)\n  (:id . 64))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 128)\n  (:start . 117) (:id . 65))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 131) (:start . 129)\n  (:id . 66))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 136) (:start . 132)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x2.141.1) (:span 60 69)))\n (:hscopes ((:id . :x2.141.1) (:span 60 86)))\n (:identifiers (:sid . :s2.141) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500357@unknown@formal@none@1@S@To this end, we used the constitutive AID-expressing and mutating Burkitt lymphoma Ramos cells and performed chromatin immunoprecipitation (ChIP) assay, followed by qRT-PCR.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 20) (:start . 16)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 37)\n  (:start . 25) (:id . 49))\n ((:tag . "NN") (:stem . "aid-expressing") (:form . "AID-expressing")\n  (:end . 52) (:start . 38) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "mutate") (:form . "mutating") (:end . 65)\n  (:start . 57) (:id . 52))\n ((:tag . "NNP") (:stem . "Burkitt") (:form . "Burkitt") (:end . 73)\n  (:start . 66) (:id . 53))\n ((:tag . "NN") (:stem . "lymphoma") (:form . "lymphoma") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 88) (:start . 83)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 94) (:start . 89)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 108)\n  (:start . 99) (:id . 58))\n ((:tag . "NN") (:stem . "chromatin") (:form . "chromatin") (:end . 118)\n  (:start . 109) (:id . 59))\n ((:tag . "NN") (:stem . "immunoprecipitation")\n  (:form . "immunoprecipitation") (:end . 138) (:start . 119) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "ChIP") (:form . "ChIP") (:end . 144) (:start . 140)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 63))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 151)\n  (:start . 146) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 161)\n  (:start . 153) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 164) (:start . 162)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 172)\n  (:start . 165) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.142) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500358@unknown@formal@none@1@S@Treated cells were fixed, lysed, DNA sheared, and ERα or NF-κB immunoprecipitated, and the DNA was released for PCR.@(((:tag . "VBN") (:stem . "treat") (:form . "Treated") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "lyse") (:form . "lysed") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "shear") (:form . "sheared") (:end . 44)\n  (:start . 37) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "ERα") (:form . "ERα") (:end . 53) (:start . 50)\n  (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 56) (:start . 54)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 62) (:start . 57)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "immunoprecipitate") (:form . "immunoprecipitated")\n  (:end . 81) (:start . 63) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 59))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 94) (:start . 91)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 98) (:start . 95)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "release") (:form . "released") (:end . 107)\n  (:start . 99) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 111) (:start . 108)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 115) (:start . 112)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.143) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500359@unknown@formal@none@1@S@As shown in Fig. 3 D, the anti-ER antibody specifically immunoprecipitated the AID promoter upon estrogen stimulation in a dose-dependent manner.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "anti-er") (:form . "anti-ER") (:end . 33)\n  (:start . 26) (:id . 50))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 42)\n  (:start . 34) (:id . 51))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 55)\n  (:start . 43) (:id . 52))\n ((:tag . "VBD") (:stem . "immunoprecipitate") (:form . "immunoprecipitated")\n  (:end . 74) (:start . 56) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 91)\n  (:start . 83) (:id . 56))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 105)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 117)\n  (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 122) (:start . 121)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "dose-dependent") (:form . "dose-dependent")\n  (:end . 137) (:start . 123) (:id . 62))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 144)\n  (:start . 138) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.144) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500360@unknown@formal@none@1@S@A control antibody was unable to precipitate this region.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "unable") (:form . "unable") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "VB") (:stem . "precipitate") (:form . "precipitate") (:end . 44)\n  (:start . 33) (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.145) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500361@unknown@formal@none@1@S@Analogous to the EMSA assay, we did not detect a significant increase in ER binding to AID promoter when we co-stimulated with TNF-α, just as TNF-α treatment alone did not enhance ER binding.@(((:tag . "JJ") (:stem . "analogous") (:form . "Analogous") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "EMSA") (:form . "EMSA") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 46)\n  (:start . 40) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 60)\n  (:start . 49) (:id . 53))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 69)\n  (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "ER") (:form . "ER") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 83)\n  (:start . 76) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 86) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 90) (:start . 87)\n  (:id . 59))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 99)\n  (:start . 91) (:id . 60))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 104) (:start . 100)\n  (:id . 61))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 107) (:start . 105)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "co-stimulate") (:form . "co-stimulated")\n  (:end . 121) (:start . 108) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 126) (:start . 122)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 132)\n  (:start . 127) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 66))\n ((:tag . "RB") (:stem . "just") (:form . "just") (:end . 138) (:start . 134)\n  (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 141) (:start . 139)\n  (:id . 68))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 147)\n  (:start . 142) (:id . 69))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 157)\n  (:start . 148) (:id . 70))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 163)\n  (:start . 158) (:id . 71))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 167) (:start . 164)\n  (:id . 72))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 171) (:start . 168)\n  (:id . 73))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 179)\n  (:start . 172) (:id . 74))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 182) (:start . 180)\n  (:id . 75))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 190)\n  (:start . 183) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s2.146) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500362@unknown@formal@none@1@S@Again, cotreatment of cells with Tam and estrogen before ChIP did reduce the binding of ERα to the AID promoter, whereas Tam on its own did not significantly alter ERα binding (Fig. 3 D, E 10/Tam and Tam, respectively), providing further evidence for a direct binding of ERα to the AID promoter.@(((:tag . "RB") (:stem . "again") (:form . "Again") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "cotreatment") (:form . "cotreatment") (:end . 18)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "CC") (:stem . 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5500363@unknown@formal@none@1@S@Treatment of the cells with TNF-α increased the binding of NF-κB to the AID promoter by more than sevenfold (Fig. 3 E).@(((:tag . "NNP") (:stem . "Treatment") (:form . "Treatment") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 64) (:start . 59)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 84)\n  (:start . 76) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 97) (:start . 93)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "sevenfold") (:form . "sevenfold") (:end . 107)\n  (:start . 98) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 113) (:start . 109)\n  (:id . 62))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 115) (:start . 114)\n  (:id . 63))\n ((:tag . "NN") (:stem . "e") (:form . "E") (:end . 117) (:start . 116)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.148) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500364@unknown@formal@none@1@S@Interestingly, co-stimulation of the cells with TNF-α and estrogen had a synergistic effect on the NF-κB binding; the binding increased to >30-fold above unstimulated treatment (4.5-fold above TNF-α alone).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "co-stimulation") (:form . "co-stimulation")\n  (:end . 29) (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 42) (:start . 37)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 66)\n  (:start . 58) (:id . 51))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "synergistic") (:form . "synergistic") (:end . 84)\n  (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 91)\n  (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 104)\n  (:start . 99) (:id . 58))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 112)\n  (:start . 105) (:id . 59))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 125)\n  (:start . 118) (:id . 62))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 135)\n  (:start . 126) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 138) (:start . 136)\n  (:id . 64))\n ((:tag . "VB") (:stem . ">30-fold") (:form . ">30-fold") (:end . 147)\n  (:start . 139) (:id . 65))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 153)\n  (:start . 148) (:id . 66))\n ((:tag . "JJ") (:stem . "unstimulated") (:form . "unstimulated") (:end . 166)\n  (:start . 154) (:id . 67))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 176)\n  (:start . 167) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 178) (:start . 177)\n  (:id . 69))\n ((:tag . "RB") (:stem . "4.5-fold") (:form . "4.5-fold") (:end . 186)\n  (:start . 178) (:id . 70))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 192)\n  (:start . 187) (:id . 71))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 198)\n  (:start . 193) (:id . 72))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 204)\n  (:start . 199) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 205) (:start . 204)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s2.149) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500365@unknown@formal@none@1@S@Estrogen up-regulates AID protein production@(((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "up-regulate") (:form . "up-regulates") (:end . 21)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 25) (:start . 22)\n  (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 33)\n  (:start . 26) (:id . 45))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 44)\n  (:start . 34) (:id . 46)))@@@1@5@((:identifiers (:sid . :s2.150) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500366@unknown@formal@none@1@S@For us to determine if the effect of estrogen on AID would also extend to the protein level, we developed a quantitative approach for measuring AID protein.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 19)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 45)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 58) (:start . 53)\n  (:id . 53))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 63) (:start . 59)\n  (:id . 54))\n ((:tag . "VB") (:stem . "extend") (:form . "extend") (:end . 70)\n  (:start . 64) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 85)\n  (:start . 78) (:id . 58))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 91) (:start . 86)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 95) (:start . 93)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "develop") (:form . "developed") (:end . 105)\n  (:start . 96) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 107) (:start . 106)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 120)\n  (:start . 108) (:id . 64))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 129)\n  (:start . 121) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "measure") (:form . "measuring") (:end . 143)\n  (:start . 134) (:id . 67))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 147) (:start . 144)\n  (:id . 68))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 155)\n  (:start . 148) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x2.151.1) (:span 53 58)) ((:id . :x2.151.2) (:span 20 22)))\n (:hscopes ((:id . :x2.151.1) (:span 53 91)) ((:id . :x2.151.2) (:span 20 91)))\n (:identifiers (:sid . :s2.151) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500367@unknown@formal@none@1@S@We generated a DT40 cell line (a cell line derived from a chicken B cell lymphoma that constitutively expresses AID and undergoes Ig diversification) to express a double tag (3xFLAG-2xTEV-3xc-Myc) fused to the C terminal exon of endogenous AID (AID FLAG-Myc–tagged AID protein [AID-FM]; Fig. S4, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dt40") (:form . "DT40") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 37) (:start . 33)\n  (:id . 50))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 42) (:start . 38)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 50)\n  (:start . 43) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 54))\n ((:tag . "NN") (:stem . "chicken") (:form . "chicken") (:end . 65)\n  (:start . 58) (:id . 55))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 67) (:start . 66)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 72) (:start . 68)\n  (:id . 57))\n ((:tag . "NN") (:stem . "lymphoma") (:form . "lymphoma") (:end . 81)\n  (:start . 73) (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 86) (:start . 82)\n  (:id . 59))\n ((:tag . "RB") (:stem . "constitutively") (:form . "constitutively")\n  (:end . 101) (:start . 87) (:id . 60))\n ((:tag . "VBZ") (:stem . "express") (:form . "expresses") (:end . 111)\n  (:start . 102) (:id . 61))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 115) (:start . 112)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "undergo") (:form . "undergoes") (:end . 129)\n  (:start . 120) (:id . 64))\n ((:tag . "NN") (:stem . "ig") (:form . "Ig") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "NN") (:stem . "diversification") (:form . "diversification")\n  (:end . 148) (:start . 133) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 152) (:start . 150)\n  (:id . 68))\n ((:tag . "VB") (:stem . "express") (:form . "express") (:end . 160)\n  (:start . 153) (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 162) (:start . 161)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 169)\n  (:start . 163) (:id . 71))\n ((:tag . "NN") (:stem . "tag") (:form . "tag") (:end . 173) (:start . 170)\n  (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 175) (:start . 174)\n  (:id . 73))\n ((:tag . "NN") (:stem . "3xflag-2xtev-3xc-myc")\n  (:form . "3xFLAG-2xTEV-3xc-Myc") (:end . 195) (:start . 175) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 196) (:start . 195)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "fuse") (:form . "fused") (:end . 202)\n  (:start . 197) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 205) (:start . 203)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 211) (:start . 210)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 220)\n  (:start . 212) (:id . 80))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 225) (:start . 221)\n  (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 228) (:start . 226)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 239)\n  (:start . 229) (:id . 83))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 243) (:start . 240)\n  (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 245) (:start . 244)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 248) (:start . 245)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "flag-myc–tagged") (:form . "FLAG-Myc–tagged")\n  (:end . 264) (:start . 249) (:id . 87))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 268) (:start . 265)\n  (:id . 88))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 276)\n  (:start . 269) (:id . 89))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 278) (:start . 277)\n  (:id . 90))\n ((:tag . "NNP") (:stem . "AID-FM") (:form . "AID-FM") (:end . 284)\n  (:start . 278) (:id . 91))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 285) (:start . 284)\n  (:id . 92))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 286) (:start . 285)\n  (:id . 93))\n ((:tag . "CD") (:stem . "fig.") (:form . "Fig.") (:end . 291) (:start . 287)\n  (:id . 94))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 294) (:start . 292)\n  (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 295) (:start . 294)\n  (:id . 96))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 305)\n  (:start . 296) (:id . 97))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 308) (:start . 306)\n  (:id . 98))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 361) (:start . 309) (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 362) (:start . 361)\n  (:id . 100))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 363) (:start . 362)\n  (:id . 101)))@@@1@60@((:identifiers (:sid . :s2.152) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500368@unknown@formal@none@1@S@The modified DT40 express a WT AID protein and an AID-FM fusion protein, both transcribed from the endogenous AID locus.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "modify") (:form . "modified") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "dt40") (:form . "DT40") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "wt") (:form . "WT") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "aid-fm") (:form . "AID-FM") (:end . 56)\n  (:start . 50) (:id . 52))\n ((:tag . "NN") (:stem . "fusion") (:form . "fusion") (:end . 63)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 71)\n  (:start . 64) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 77) (:start . 73)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "transcribe") (:form . "transcribed") (:end . 89)\n  (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 94) (:start . 90)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 109)\n  (:start . 99) (:id . 60))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 113) (:start . 110)\n  (:id . 61))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 119)\n  (:start . 114) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s2.153) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500369@unknown@formal@none@1@S@Comparing the qRT-PCR induction kinetics with that of the AID-FM expression, we determined that the steady-state levels of AID protein correlated to those of the mRNA (Fig. 4, A and B).@(((:tag . "VBG") (:stem . "compare") (:form . "Comparing") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "induction") (:form . "induction") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "NNS") (:stem . "kinetic") (:form . "kinetics") (:end . 40)\n  (:start . 32) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 47))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 50) (:start . 46)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "aid-fm") (:form . "AID-FM") (:end . 64)\n  (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 75)\n  (:start . 65) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "determine") (:form . "determined") (:end . 90)\n  (:start . 80) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 95) (:start . 91)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "steady-state") (:form . "steady-state") (:end . 112)\n  (:start . 100) (:id . 58))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 119)\n  (:start . 113) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 134)\n  (:start . 127) (:id . 62))\n ((:tag . "VBD") (:stem . "correlate") (:form . "correlated") (:end . 145)\n  (:start . 135) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 64))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 154)\n  (:start . 149) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 157) (:start . 155)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 166) (:start . 162)\n  (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 168) (:start . 167)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 172) (:start . 168)\n  (:id . 70))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 174) (:start . 173)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 177) (:start . 176)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 181) (:start . 178)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 183) (:start . 182)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s2.154) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500370@unknown@formal@none@1@S@Using the translation inhibitor CHX (Fig. 4 C), we showed that estrogen was not able to increase AID-FM expression in the absence of translation.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "inhibitor") (:form . "inhibitor") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "NNP") (:stem . "CHX") (:form . "CHX") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 50) (:start . 48)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 57) (:start . 51)\n  (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 55))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 71)\n  (:start . 63) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 75) (:start . 72)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 79) (:start . 76)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 84) (:start . 80)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n  (:id . 60))\n ((:tag . "VB") (:stem . "increase") (:form . "increase") (:end . 96)\n  (:start . 88) (:id . 61))\n ((:tag . "JJ") (:stem . "aid-fm") (:form . "AID-FM") (:end . 103)\n  (:start . 97) (:id . 62))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 114)\n  (:start . 104) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 65))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 129)\n  (:start . 122) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 67))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 144)\n  (:start . 133) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.155) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500371@unknown@formal@none@1@S@In the presence of the proteasome inhibitor MG-132 (Fig. 4 C), estrogen increased AID-FM production above that of the MG-132 alone, indicating that estrogen was not acting on the proteasome to increase AID-FM activity.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 15)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "proteasome") (:form . "proteasome") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "inhibitor") (:form . "inhibitor") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "NNP") (:stem . "MG-132") (:form . "MG-132") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 71)\n  (:start . 63) (:id . 56))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 81)\n  (:start . 72) (:id . 57))\n ((:tag . "JJ") (:stem . "aid-fm") (:form . "AID-FM") (:end . 88)\n  (:start . 82) (:id . 58))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 99)\n  (:start . 89) (:id . 59))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 105)\n  (:start . 100) (:id . 60))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 110) (:start . 106)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 63))\n ((:tag . "NN") (:stem . "mg-132") (:form . "MG-132") (:end . 124)\n  (:start . 118) (:id . 64))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 130)\n  (:start . 125) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 142)\n  (:start . 132) (:id . 67))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 147) (:start . 143)\n  (:id . 68))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 156)\n  (:start . 148) (:id . 69))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 160) (:start . 157)\n  (:id . 70))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 164) (:start . 161)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 171)\n  (:start . 165) (:id . 72))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 174) (:start . 172)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 74))\n ((:tag . "NN") (:stem . "proteasome") (:form . "proteasome") (:end . 189)\n  (:start . 179) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 192) (:start . 190)\n  (:id . 76))\n ((:tag . "VB") (:stem . "increase") (:form . "increase") (:end . 201)\n  (:start . 193) (:id . 77))\n ((:tag . "NNP") (:stem . "AID-FM") (:form . "AID-FM") (:end . 208)\n  (:start . 202) (:id . 78))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 217)\n  (:start . 209) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x2.156.1) (:span 132 147)))\n (:hscopes ((:id . :x2.156.1) (:span 132 217)))\n (:identifiers (:sid . :s2.156) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500372@unknown@formal@none@1@S@The aforementioned co-stimulatory effects of TNF-α were also observed at the level of protein production (Fig. 4, E 10/TNF-α).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "aforementioned") (:form . "aforementioned")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "co-stimulatory") (:form . "co-stimulatory")\n  (:end . 33) (:start . 19) (:id . 44))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 41)\n  (:start . 34) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 50) (:start . 45)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 55) (:start . 51)\n  (:id . 48))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 60) (:start . 56)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 69)\n  (:start . 61) (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 82) (:start . 77)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 54))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 104)\n  (:start . 94) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 110) (:start . 106)\n  (:id . 58))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "10/TNF-α") (:form . "10/TNF-α") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.157) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500373@unknown@formal@none@1@S@The effects of estrogen on AID protein in DT40.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "DT40") (:form . "DT40") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.158) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500374@unknown@formal@none@1@S@(A) Estrogen induces AID mRNA expression.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 20)\n  (:start . 13) (:id . 46))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 29) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 40)\n  (:start . 30) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 41) (:start . 40)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s2.159) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500375@unknown@formal@none@1@S@AID-FM–tagged DT40 cells were treated with DMSO, 100 nM estrogen, and 10 nM estrogen with TNF-α, lysed, and analyzed for AID mRNA expression with pRT-PCR at various time-points.@(((:tag . "JJ") (:stem . "aid-fm–tagged") (:form . "AID-FM–tagged")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "dt40") (:form . "DT40") (:end . 18) (:start . 14)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 24) (:start . 19)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "DMSO") (:form . "DMSO") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 84)\n  (:start . 76) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 89) (:start . 85)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 95) (:start . 90)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "lyse") (:form . "lysed") (:end . 102) (:start . 97)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 116)\n  (:start . 108) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 120) (:start . 117)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 124) (:start . 121)\n  (:id . 66))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 129) (:start . 125)\n  (:id . 67))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 140)\n  (:start . 130) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 145) (:start . 141)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "pRT-PCR") (:form . "pRT-PCR") (:end . 153)\n  (:start . 146) (:id . 70))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 156) (:start . 154)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 164)\n  (:start . 157) (:id . 72))\n ((:tag . "NNS") (:stem . "time-point") (:form . "time-points") (:end . 176)\n  (:start . 165) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s2.160) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500376@unknown@formal@none@1@S@(B) Estrogen induces AID-FM fusion protein expression.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 20)\n  (:start . 13) (:id . 46))\n ((:tag . "JJ") (:stem . "aid-fm") (:form . "AID-FM") (:end . 27)\n  (:start . 21) (:id . 47))\n ((:tag . "NN") (:stem . "fusion") (:form . "fusion") (:end . 34)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 53)\n  (:start . 43) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.161) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500377@unknown@formal@none@1@S@Treatment as in A, but lysates were analyzed by quantitative Western blot.@(((:tag . "NNP") (:stem . "Treatment") (:form . "Treatment") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "lysate") (:form . "lysates") (:end . 30)\n  (:start . 23) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 44)\n  (:start . 36) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 60)\n  (:start . 48) (:id . 52))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.162) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500378@unknown@formal@none@1@S@For each sample, FLAG and Tubulin expression was quantitated.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "FLAG") (:form . "FLAG") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Tubulin") (:form . "Tubulin") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 44)\n  (:start . 34) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "quantitate") (:form . "quantitated") (:end . 60)\n  (:start . 49) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.163) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500379@unknown@formal@none@1@S@The graph is derived from correlating the FLAG expression to Tubulin expression, and then determining the ratio of estrogen-induced FLAG expression to untreated DMSO samples.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "graph") (:form . "graph") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "correlate") (:form . "correlating") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "FLAG") (:form . "FLAG") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 57)\n  (:start . 47) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Tubulin") (:form . "Tubulin") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 79)\n  (:start . 69) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "determine") (:form . "determining") (:end . 101)\n  (:start . 90) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 58))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 111)\n  (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "estrogen-induced") (:form . "estrogen-induced")\n  (:end . 131) (:start . 115) (:id . 61))\n ((:tag . "NNP") (:stem . "FLAG") (:form . "FLAG") (:end . 136) (:start . 132)\n  (:id . 62))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 147)\n  (:start . 137) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 150) (:start . 148)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 160)\n  (:start . 151) (:id . 65))\n ((:tag . "NN") (:stem . "dmso") (:form . "DMSO") (:end . 165) (:start . 161)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 173)\n  (:start . 166) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s2.164) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500380@unknown@formal@none@1@S@(C) Estrogen does not affect AID-FM fusion protein stability.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 17) (:start . 13)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 28)\n  (:start . 22) (:id . 48))\n ((:tag . "JJ") (:stem . "aid-fm") (:form . "AID-FM") (:end . 35)\n  (:start . 29) (:id . 49))\n ((:tag . "NN") (:stem . "fusion") (:form . "fusion") (:end . 42)\n  (:start . 36) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 50)\n  (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "stability") (:form . "stability") (:end . 60)\n  (:start . 51) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.165) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500381@unknown@formal@none@1@S@Cells were incubated with CHX or MG-132 for 2 h, followed by estrogen treatment for 4 h.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "CHX") (:form . "CHX") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "MG-132") (:form . "MG-132") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 47) (:start . 46)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 57)\n  (:start . 49) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 60) (:start . 58)\n  (:id . 54))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 69)\n  (:start . 61) (:id . 55))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 79)\n  (:start . 70) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 87) (:start . 86)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.166) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500382@unknown@formal@none@1@S@Protein levels were determined by quantitative Western blot.@(((:tag . "NN") (:stem . "protein") (:form . "Protein") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 46)\n  (:start . 34) (:id . 47))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 54)\n  (:start . 47) (:id . 48))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 59) (:start . 55)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s2.167) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500383@unknown@formal@none@1@S@For all experiments, cells were grown in hormone depleted media for 48 h.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 19)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "grow") (:form . "grown") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "VBN") (:stem . "deplete") (:form . "depleted") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "medium") (:form . "media") (:end . 63)\n  (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.168) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500384@unknown@formal@none@1@S@Results are normalized to control treatments as indicated on each graph.@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "normalize") (:form . "normalized") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "VB") (:stem . "control") (:form . "control") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 44)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "graph") (:form . "graph") (:end . 71) (:start . 66)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.169) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500385@unknown@formal@none@1@S@Timelines of cell treatments are indicated below the graphs.@(((:tag . "NNS") (:stem . "timeline") (:form . "Timelines") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "graph") (:form . "graphs") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.170) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500386@unknown@formal@none@1@S@Hormonal regulation of CSR and SHM@(((:tag . "JJ") (:stem . "hormonal") (:form . "Hormonal") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 19)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "CSR") (:form . "CSR") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 34) (:start . 31)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s2.171) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500387@unknown@formal@none@1@S@On the molecular level, CSR requires AID, yet regulation can be achieved on multiple levels, some of which may be hormonally influenced.@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "CSR") (:form . "CSR") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 45) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 56)\n  (:start . 46) (:id . 52))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 72)\n  (:start . 64) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 84)\n  (:start . 76) (:id . 57))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 91)\n  (:start . 85) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 97) (:start . 93)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 106)\n  (:start . 101) (:id . 62))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 113) (:start . 111)\n  (:id . 64))\n ((:tag . "RB") (:stem . "hormonally") (:form . "hormonally") (:end . 124)\n  (:start . 114) (:id . 65))\n ((:tag . "VBN") (:stem . "influence") (:form . "influenced") (:end . 135)\n  (:start . 125) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x2.172.1) (:span 107 110)))\n (:hscopes ((:id . :x2.172.1) (:span 93 135)))\n (:identifiers (:sid . :s2.172) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500388@unknown@formal@none@1@S@To analyze CSR, isolated mouse splenic B cells were treated with different combinations of cytokines and hormones.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "analyze") (:form . "analyze") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "CSR") (:form . "CSR") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 59)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 74)\n  (:start . 65) (:id . 54))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 87)\n  (:start . 75) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 100)\n  (:start . 91) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "hormone") (:form . "hormones") (:end . 113)\n  (:start . 105) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.173) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500389@unknown@formal@none@1@S@B cell stimulation with LPS, LPS and IL-4, LPS and IFN-γ, or LPS and TGF-ß results in switching to IgG3, IgG1, IgG2a, or IgG2b/IgA, respectively.@(((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 18)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 46) (:start . 43)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 56) (:start . 51)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 60) (:start . 58)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 64) (:start . 61)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 58))\n ((:tag . "NN") (:stem . "tgf-ß") (:form . "TGF-ß") (:end . 74) (:start . 69)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 82)\n  (:start . 75) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "switch") (:form . "switching") (:end . 95)\n  (:start . 86) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "IgG3") (:form . "IgG3") (:end . 103) (:start . 99)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "IgG1") (:form . "IgG1") (:end . 109) (:start . 105)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "IgG2a") (:form . "IgG2a") (:end . 116)\n  (:start . 111) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 120) (:start . 118)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "IgG2b/IgA") (:form . "IgG2b/IgA") (:end . 130)\n  (:start . 121) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 72))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 144)\n  (:start . 132) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s2.174) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500390@unknown@formal@none@1@S@To ensure we could correlate AID activity precisely, and to avoid possible proliferative and antiapoptotic effects of estrogen on stimulated B cells, we monitored the early molecular events of class switching.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "VB") (:stem . "correlate") (:form . "correlate") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "RB") (:stem . "precisely") (:form . "precisely") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "VB") (:stem . "avoid") (:form . "avoid") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 74)\n  (:start . 66) (:id . 54))\n ((:tag . "JJ") (:stem . "proliferative") (:form . "proliferative")\n  (:end . 88) (:start . 75) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "antiapoptotic") (:form . "antiapoptotic")\n  (:end . 106) (:start . 93) (:id . 57))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 114)\n  (:start . 107) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 59))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 126)\n  (:start . 118) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 129) (:start . 127)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 140)\n  (:start . 130) (:id . 62))\n ((:tag . "NN") (:stem . "b") (:form . "B") (:end . 142) (:start . 141)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 148)\n  (:start . 143) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 65))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 152) (:start . 150)\n  (:id . 66))\n ((:tag . "VBD") (:stem . "monitor") (:form . "monitored") (:end . 162)\n  (:start . 153) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 172)\n  (:start . 167) (:id . 69))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 182)\n  (:start . 173) (:id . 70))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 189)\n  (:start . 183) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 192) (:start . 190)\n  (:id . 72))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 198)\n  (:start . 193) (:id . 73))\n ((:tag . "NN") (:stem . "switching") (:form . "switching") (:end . 208)\n  (:start . 199) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x2.175.1) (:span 66 74)))\n (:hscopes ((:id . :x2.175.1) (:span 66 148)))\n (:identifiers (:sid . :s2.175) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500391@unknown@formal@none@1@S@One of the molecular intermediates during class switching is the generation of a looped-out circular DNA called a switch circle (Fig. S5, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1).@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 20)\n  (:start . 11) (:id . 45))\n ((:tag . "NNS") (:stem . "intermediate") (:form . "intermediates")\n  (:end . 34) (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 41)\n  (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 47) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "switching") (:form . "switching") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 75)\n  (:start . 65) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 80) (:start . 79)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "looped-out") (:form . "looped-out") (:end . 91)\n  (:start . 81) (:id . 55))\n ((:tag . "JJ") (:stem . "circular") (:form . "circular") (:end . 100)\n  (:start . 92) (:id . 56))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 104) (:start . 101)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "call") (:form . "called") (:end . 111)\n  (:start . 105) (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 120)\n  (:start . 114) (:id . 60))\n ((:tag . "NN") (:stem . "circle") (:form . "circle") (:end . 127)\n  (:start . 121) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 133) (:start . 129)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 136) (:start . 134)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 147)\n  (:start . 138) (:id . 66))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 150) (:start . 148)\n  (:id . 67))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 203) (:start . 151) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 204) (:start . 203)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.176) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500392@unknown@formal@none@1@S@The circular DNA contains a recombined transcription unit that produces switch circle transcripts; it is generated from the promoter of the downstream switch region and the Igµ switch region.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "circular") (:form . "circular") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "recombined") (:form . "recombined") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 52) (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "unit") (:form . "unit") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "produce") (:form . "produces") (:end . 71)\n  (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 78)\n  (:start . 72) (:id . 52))\n ((:tag . "NN") (:stem . "circle") (:form . "circle") (:end . 85)\n  (:start . 79) (:id . 53))\n ((:tag . "NNS") (:stem . "transcript") (:form . "transcripts") (:end . 97)\n  (:start . 86) (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 98) (:start . 97)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 101) (:start . 99)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 104) (:start . 102)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 114)\n  (:start . 105) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 119) (:start . 115)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 60))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 132)\n  (:start . 124) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "downstream") (:form . "downstream") (:end . 150)\n  (:start . 140) (:id . 64))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 157)\n  (:start . 151) (:id . 65))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 164)\n  (:start . 158) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 172) (:start . 169)\n  (:id . 68))\n ((:tag . "NN") (:stem . "igµ") (:form . "Igµ") (:end . 176) (:start . 173)\n  (:id . 69))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 183)\n  (:start . 177) (:id . 70))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 190)\n  (:start . 184) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s2.177) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500393@unknown@formal@none@1@S@Using a previously described qRT-PCR approach (40), we were able to show enhanced switching to IgG1, IgG3, IgA, or IgE after hormone treatment of splenic B cells (Fig. 5 A).@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 47) (:start . 46)\n  (:id . 48))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 59) (:start . 55)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 64) (:start . 60)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 55))\n ((:tag . "VB") (:stem . "show") (:form . "show") (:end . 72) (:start . 68)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "enhanced") (:form . "enhanced") (:end . 81)\n  (:start . 73) (:id . 57))\n ((:tag . "NN") (:stem . "switching") (:form . "switching") (:end . 91)\n  (:start . 82) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "IgG1") (:form . "IgG1") (:end . 99) (:start . 95)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "IgG3") (:form . "IgG3") (:end . 105) (:start . 101)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "IgA") (:form . "IgA") (:end . 110) (:start . 107)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 65))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 114) (:start . 112)\n  (:id . 66))\n ((:tag . "NN") (:stem . "ige") (:form . "IgE") (:end . 118) (:start . 115)\n  (:id . 67))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 124)\n  (:start . 119) (:id . 68))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 132)\n  (:start . 125) (:id . 69))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 142)\n  (:start . 133) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 153)\n  (:start . 146) (:id . 72))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 155) (:start . 154)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 161)\n  (:start . 156) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 163) (:start . 162)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 167) (:start . 163)\n  (:id . 76))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 169) (:start . 168)\n  (:id . 77))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 171) (:start . 170)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s2.178) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500394@unknown@formal@none@1@S@Presumably through the increased production of AID, estrogen was able to enhance switch circle formation for all subclasses tested.@(((:tag . "RB") (:stem . "presumably") (:form . "Presumably") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 18)\n  (:start . 11) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 43)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 60)\n  (:start . 52) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 69) (:start . 65)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 80)\n  (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . "NN") (:stem . "circle") (:form . "circle") (:end . 94)\n  (:start . 88) (:id . 56))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 104)\n  (:start . 95) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 108) (:start . 105)\n  (:id . 58))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "subclass") (:form . "subclasses") (:end . 123)\n  (:start . 113) (:id . 60))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 130)\n  (:start . 124) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x2.179.1) (:span 0 10)))\n (:hscopes ((:id . :x2.179.1) (:span 0 50)))\n (:identifiers (:sid . :s2.179) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500395@unknown@formal@none@1@S@As with the AID production, this link was perturbed with the addition of Tam during estrogen treatment (Fig. 5 A, Estrogen 10 nM/Tam and Tam).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 26)\n  (:start . 16) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "link") (:form . "link") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "perturb") (:form . "perturbed") (:end . 51)\n  (:start . 42) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 69)\n  (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 83)\n  (:start . 77) (:id . 57))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 92)\n  (:start . 84) (:id . 58))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 102)\n  (:start . 93) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 108) (:start . 104)\n  (:id . 61))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 110) (:start . 109)\n  (:id . 62))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 122)\n  (:start . 114) (:id . 65))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 125) (:start . 123)\n  (:id . 66))\n ((:tag . "NN") (:stem . "nm/tam") (:form . "nM/Tam") (:end . 132)\n  (:start . 126) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 140) (:start . 137)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s2.180) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500396@unknown@formal@none@1@S@Hormonal effects on Ig class switching, hypermutation, and translocation.@(((:tag . "JJ") (:stem . "hormonal") (:form . "Hormonal") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ig") (:form . "Ig") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "switching") (:form . "switching") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "hypermutation") (:form . "hypermutation")\n  (:end . 53) (:start . 40) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "translocation") (:form . "translocation")\n  (:end . 72) (:start . 59) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.181) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500397@unknown@formal@none@1@S@(A) Estrogen induces isotype switching.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 20)\n  (:start . 13) (:id . 46))\n ((:tag . "NN") (:stem . "isotype") (:form . "isotype") (:end . 28)\n  (:start . 21) (:id . 47))\n ((:tag . "NN") (:stem . "switching") (:form . "switching") (:end . 38)\n  (:start . 29) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 39) (:start . 38)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s2.182) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500398@unknown@formal@none@1@S@Isolated mouse splenic B cells were stimulated for 48 h with LPS + IL-4 for switching to IgG1 and IgE, LPS + TGF-ß for switching to IgA, and LPS for switching to IgG3.@(((:tag . "VBN") (:stem . "isolate") (:form . "Isolated") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 46)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "CC") (:stem . "+") (:form . "+") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 71) (:start . 67)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "switch") (:form . "switching") (:end . 85)\n  (:start . 76) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "IgG1") (:form . "IgG1") (:end . 93) (:start . 89)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "IgE") (:form . "IgE") (:end . 101) (:start . 98)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 106) (:start . 103)\n  (:id . 63))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 108) (:start . 107)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "TGF-ß") (:form . "TGF-ß") (:end . 114)\n  (:start . 109) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 118) (:start . 115)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "switch") (:form . "switching") (:end . 128)\n  (:start . 119) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 131) (:start . 129)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "IgA") (:form . "IgA") (:end . 135) (:start . 132)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 71))\n ((:tag . "NN") (:stem . "lps") (:form . "LPS") (:end . 144) (:start . 141)\n  (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 148) (:start . 145)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "switch") (:form . "switching") (:end . 158)\n  (:start . 149) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 161) (:start . 159)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "IgG3") (:form . "IgG3") (:end . 166) (:start . 162)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s2.183) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500399@unknown@formal@none@1@S@Indicated amounts of estrogen and/or Tam were added to the cells together with cytokines.@(((:tag . "VBN") (:stem . "indicate") (:form . "Indicated") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 17)\n  (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 36)\n  (:start . 30) (:id . 46))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 51) (:start . 46)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 64) (:start . 59)\n  (:id . 52))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 73)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 88)\n  (:start . 79) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.184) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500400@unknown@formal@none@1@S@Relative efficiency of class switching was determined by detecting circle transcripts with qRT-PCR, and data are normalized to the control treatment with DMSO from three independent experiments (error bars indicate standard deviations).@(((:tag . "JJ") (:stem . "relative") (:form . "Relative") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "efficiency") (:form . "efficiency") (:end . 19)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "switching") (:form . "switching") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 53)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 56) (:start . 54)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "detect") (:form . "detecting") (:end . 66)\n  (:start . 57) (:id . 50))\n ((:tag . "NN") (:stem . "circle") (:form . "circle") (:end . 73)\n  (:start . 67) (:id . 51))\n ((:tag . "NNS") (:stem . "transcript") (:form . "transcripts") (:end . 85)\n  (:start . 74) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 98)\n  (:start . 91) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 108)\n  (:start . 104) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 112) (:start . 109)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "normalize") (:form . "normalized") (:end . 123)\n  (:start . 113) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 126) (:start . 124)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 61))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 138)\n  (:start . 131) (:id . 62))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 148)\n  (:start . 139) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 153) (:start . 149)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "DMSO") (:form . "DMSO") (:end . 158) (:start . 154)\n  (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 163) (:start . 159)\n  (:id . 66))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 169)\n  (:start . 164) (:id . 67))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 181)\n  (:start . 170) (:id . 68))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 193)\n  (:start . 182) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 195) (:start . 194)\n  (:id . 70))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 200)\n  (:start . 195) (:id . 71))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 205) (:start . 201)\n  (:id . 72))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 214)\n  (:start . 206) (:id . 73))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 223)\n  (:start . 215) (:id . 74))\n ((:tag . "NNS") (:stem . "deviation") (:form . "deviations") (:end . 234)\n  (:start . 224) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 235) (:start . 234)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 236) (:start . 235)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s2.185) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500401@unknown@formal@none@1@S@(B) Estrogen increases the mutation frequency in VH and CD95/Fas loci of Ramos, and in Sγ3 of splenic mouse cells.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 22)\n  (:start . 13) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 35)\n  (:start . 27) (:id . 48))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 45)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "VH") (:form . "VH") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "CD95/Fas") (:form . "CD95/Fas") (:end . 64)\n  (:start . 56) (:id . 53))\n ((:tag . "NNS") (:stem . "locus") (:form . "loci") (:end . 69) (:start . 65)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 78) (:start . 73)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 59))\n ((:tag . "NN") (:stem . "sγ3") (:form . "Sγ3") (:end . 90) (:start . 87)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 101)\n  (:start . 94) (:id . 62))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 107)\n  (:start . 102) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 113)\n  (:start . 108) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.186) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500402@unknown@formal@none@1@S@Ramos cells were grown in the presence of 100 nM estrogen for ~20 doublings, followed by sequencing of 341 bp from human VH or 750 bp from human CD95/Fas locus.@(((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "grow") (:form . "grown") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 38)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 57)\n  (:start . 49) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "CD") (:stem . "~20") (:form . "~20") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "doubling") (:form . "doublings") (:end . 75)\n  (:start . 66) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 85)\n  (:start . 77) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 99)\n  (:start . 89) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . "CD") (:stem . "341") (:form . "341") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 114) (:start . 110)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 120)\n  (:start . 115) (:id . 64))\n ((:tag . "NN") (:stem . "vh") (:form . "VH") (:end . 123) (:start . 121)\n  (:id . 65))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 126) (:start . 124)\n  (:id . 66))\n ((:tag . "CD") (:stem . "750") (:form . "750") (:end . 130) (:start . 127)\n  (:id . 67))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 133) (:start . 131)\n  (:id . 68))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 138) (:start . 134)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 144)\n  (:start . 139) (:id . 70))\n ((:tag . "NN") (:stem . "cd95/fas") (:form . "CD95/Fas") (:end . 153)\n  (:start . 145) (:id . 71))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 159)\n  (:start . 154) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.187) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500403@unknown@formal@none@1@S@Splenic mouse cells were treated for 6 d with LPS and 10 nM estrogen, and switch gamma3 loci amplified and sequenced (Fig. S7).@(((:tag . "JJ") (:stem . "splenic") (:form . "Splenic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "d") (:form . "d") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "lps") (:form . "LPS") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 59) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 68)\n  (:start . 60) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 57))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 80)\n  (:start . 74) (:id . 58))\n ((:tag . "NN") (:stem . "gamma3") (:form . "gamma3") (:end . 87)\n  (:start . 81) (:id . 59))\n ((:tag . "NNS") (:stem . "locus") (:form . "loci") (:end . 92) (:start . 88)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "amplify") (:form . "amplified") (:end . 102)\n  (:start . 93) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 116)\n  (:start . 107) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 122) (:start . 118)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 125) (:start . 123)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s2.188) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500404@unknown@formal@none@1@S@Mutation frequencies are normalized to the control treatments with DMSO.@(((:tag . "NN") (:stem . "mutation") (:form . "Mutation") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "frequency") (:form . "frequencies") (:end . 20)\n  (:start . 9) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 24) (:start . 21)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "normalize") (:form . "normalized") (:end . 35)\n  (:start . 25) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 61)\n  (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "DMSO") (:form . "DMSO") (:end . 71) (:start . 67)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.189) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500405@unknown@formal@none@1@S@A standard unpaired two-tailed Student's t test showed a significant difference in mutation frequency in the Sγ3 loci of DMSO- and estrogen-treated spleen cells.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "JJ") (:stem . "unpaired") (:form . "unpaired") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "JJ") (:stem . "two-tailed") (:form . "two-tailed") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "t") (:form . "t") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 54) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 68)\n  (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 79)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 91)\n  (:start . 83) (:id . 55))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 101)\n  (:start . 92) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 58))\n ((:tag . "NN") (:stem . "sγ3") (:form . "Sγ3") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "locus") (:form . "loci") (:end . 117)\n  (:start . 113) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 61))\n ((:tag . "NN") (:stem . "dmso-") (:form . "DMSO-") (:end . 126)\n  (:start . 121) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "estrogen-treated") (:form . "estrogen-treated")\n  (:end . 147) (:start . 131) (:id . 64))\n ((:tag . "NN") (:stem . "spleen") (:form . "spleen") (:end . 154)\n  (:start . 148) (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 160)\n  (:start . 155) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.190) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500406@unknown@formal@none@1@S@(C) Estrogen enhances the c-myc/IgH translocations in splenic B cells from p53+/- mice.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "VBZ") (:stem . "enhance") (:form . "enhances") (:end . 21)\n  (:start . 13) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "c-myc/igh") (:form . "c-myc/IgH") (:end . 35)\n  (:start . 26) (:id . 48))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 50) (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "p53+/-") (:form . "p53+/-") (:end . 81)\n  (:start . 75) (:id . 55))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s2.191) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500407@unknown@formal@none@1@S@In each experiment, 2 spleens per sample were treated with or without 50 nM estrogen in the presence of LPS for 72 h.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "spleen") (:form . "spleens") (:end . 29)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 40)\n  (:start . 34) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 53)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 69)\n  (:start . 62) (:id . 54))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 84)\n  (:start . 76) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 100)\n  (:start . 92) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 61))\n ((:tag . "NN") (:stem . "lps") (:form . "LPS") (:end . 107) (:start . 104)\n  (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 111) (:start . 108)\n  (:id . 63))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 114) (:start . 112)\n  (:id . 64))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x2.192.1) (:span 59 61)))\n (:hscopes ((:id . :x2.192.1) (:span 54 69)))\n (:identifiers (:sid . :s2.192) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500408@unknown@formal@none@1@S@More than 7 × 107 cells were analyzed by long-range PCR (5 × 104 cells/PCR; Fig. S8 and Supplemental materials and methods).@(((:tag . "JJR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "HYPH") (:stem . "×") (:form . "×") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "CD") (:stem . "107") (:form . "107") (:end . 17) (:start . 14)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 23) (:start . 18)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 37)\n  (:start . 29) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "long-range") (:form . "long-range") (:end . 51)\n  (:start . 41) (:id . 51))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 58) (:start . 57)\n  (:id . 54))\n ((:tag . "SYM") (:stem . "×") (:form . "×") (:end . 60) (:start . 59)\n  (:id . 55))\n ((:tag . "CD") (:stem . "104") (:form . "104") (:end . 64) (:start . 61)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "cells/PCR") (:form . "cells/PCR") (:end . 74)\n  (:start . 65) (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 75) (:start . 74)\n  (:id . 58))\n ((:tag . "FW") (:stem . "fig.") (:form . "Fig.") (:end . 80) (:start . 76)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "S8") (:form . "S8") (:end . 83) (:start . 81)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 100)\n  (:start . 88) (:id . 62))\n ((:tag . "NNS") (:stem . "material") (:form . "materials") (:end . 110)\n  (:start . 101) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 122)\n  (:start . 115) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.193) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500409@unknown@formal@none@1@S@Frequency was determined as c-myc/IgH translocation events per cell number analyzed.@(((:tag . "NN") (:stem . "frequency") (:form . "Frequency") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "c-myc/igh") (:form . "c-myc/IgH") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "NN") (:stem . "translocation") (:form . "translocation")\n  (:end . 51) (:start . 38) (:id . 47))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 58)\n  (:start . 52) (:id . 48))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 62) (:start . 59)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 67) (:start . 63)\n  (:id . 50))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 74)\n  (:start . 68) (:id . 51))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 83)\n  (:start . 75) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.194) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500410@unknown@formal@none@1@S@Statistics was performed on the results of the pooled experiments (two-tailed, unpaired Student's t test: P = 0.026).@(((:tag . "NNP") (:stem . "Statistic") (:form . "Statistics") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "pool") (:form . "pooled") (:end . 53) (:start . 47)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 65)\n  (:start . 54) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "two-tailed") (:form . "two-tailed") (:end . 77)\n  (:start . 67) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "unpaired") (:form . "unpaired") (:end . 87)\n  (:start . 79) (:id . 55))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 95)\n  (:start . 88) (:id . 56))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "t") (:form . "t") (:end . 99) (:start . 98)\n  (:id . 58))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 104) (:start . 100)\n  (:id . 59))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . "CD") (:stem . "0.026") (:form . "0.026") (:end . 115)\n  (:start . 110) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.195) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500411@unknown@formal@none@1@S@Fig. S7, Fig. S8, and Supplemental materials and methods are available at http://www.jem.org/cgi/content/full/jem.20080521/DC1.@(((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 13) (:start . 9)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "S8") (:form . "S8") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 34)\n  (:start . 22) (:id . 49))\n ((:tag . "NNS") (:stem . "material") (:form . "materials") (:end . 44)\n  (:start . 35) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 56)\n  (:start . 49) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 70)\n  (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 126) (:start . 74) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s2.196) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500412@unknown@formal@none@1@S@To determine the effect of estrogen-induced AID on SHM, we sequenced the VH region of in vitro–cultured Ramos cells, as well as the switch region of γ3 from ex vivo–stimulated splenic B cells.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "estrogen-induced") (:form . "estrogen-induced")\n  (:end . 43) (:start . 27) (:id . 47))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "sequence") (:form . "sequenced") (:end . 68)\n  (:start . 59) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "VH") (:form . "VH") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 82)\n  (:start . 76) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "vitro–culture") (:form . "vitro–cultured")\n  (:end . 103) (:start . 89) (:id . 59))\n ((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 109)\n  (:start . 104) (:id . 60))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 115)\n  (:start . 110) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 62))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 119) (:start . 117)\n  (:id . 63))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 124) (:start . 120)\n  (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 127) (:start . 125)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 66))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 138)\n  (:start . 132) (:id . 67))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 145)\n  (:start . 139) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n  (:id . 69))\n ((:tag . "NN") (:stem . "γ3") (:form . "γ3") (:end . 151) (:start . 149)\n  (:id . 70))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 156) (:start . 152)\n  (:id . 71))\n ((:tag . "NN") (:stem . "ex") (:form . "ex") (:end . 159) (:start . 157)\n  (:id . 72))\n ((:tag . "VBD") (:stem . "vivo–stimulate") (:form . "vivo–stimulated")\n  (:end . 175) (:start . 160) (:id . 73))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 183)\n  (:start . 176) (:id . 74))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 185) (:start . 184)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 191)\n  (:start . 186) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s2.197) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500413@unknown@formal@none@1@S@A 3-wk estrogen treatment of Ramos HS13 (41), which possesses a premature stop codon embedded within the AID target motif WRC, showed enhanced surface Ig expression and VH SHM (Fig. 5 B and Fig. S6, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "3-wk") (:form . "3-wk") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 15)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "HS13") (:form . "HS13") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 43) (:start . 41)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 51) (:start . 46)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "possess") (:form . "possesses") (:end . 61)\n  (:start . 52) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "premature") (:form . "premature") (:end . 73)\n  (:start . 64) (:id . 56))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 78) (:start . 74)\n  (:id . 57))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 84) (:start . 79)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "embed") (:form . "embedded") (:end . 93)\n  (:start . 85) (:id . 59))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 100)\n  (:start . 94) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 108) (:start . 105)\n  (:id . 62))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 115)\n  (:start . 109) (:id . 63))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 121)\n  (:start . 116) (:id . 64))\n ((:tag . "NNP") (:stem . "WRC") (:form . "WRC") (:end . 125) (:start . 122)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 66))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 133)\n  (:start . 127) (:id . 67))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 142)\n  (:start . 134) (:id . 68))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 150)\n  (:start . 143) (:id . 69))\n ((:tag . "NN") (:stem . "ig") (:form . "Ig") (:end . 153) (:start . 151)\n  (:id . 70))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 164)\n  (:start . 154) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "VH") (:form . "VH") (:end . 171) (:start . 169)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 175) (:start . 172)\n  (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 181) (:start . 177)\n  (:id . 76))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 183) (:start . 182)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 185) (:start . 184)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 189) (:start . 186)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 194) (:start . 190)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "S6") (:form . "S6") (:end . 197) (:start . 195)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 198) (:start . 197)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 208)\n  (:start . 199) (:id . 83))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 211) (:start . 209)\n  (:id . 84))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 264) (:start . 212) (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 265) (:start . 264)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 266) (:start . 265)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s2.198) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500414@unknown@formal@none@1@S@Because Ramos expresses constitutive amounts of AID, estrogen treatment did not enhance AID production substantially; thus, we used the ex vivo treatment of spleens as a means to detect mutations in the switch region (42).@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "express") (:form . "expresses") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 36)\n  (:start . 24) (:id . 45))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 44)\n  (:start . 37) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 51) (:start . 48)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 71)\n  (:start . 62) (:id . 51))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 79) (:start . 76)\n  (:id . 53))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 87)\n  (:start . 80) (:id . 54))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 102)\n  (:start . 92) (:id . 56))\n ((:tag . "RB") (:stem . "substantially") (:form . "substantially")\n  (:end . 116) (:start . 103) (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 117) (:start . 116)\n  (:id . 58))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 122) (:start . 118)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 126) (:start . 124)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 131) (:start . 127)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 135) (:start . 132)\n  (:id . 63))\n ((:tag . "FW") (:stem . "ex") (:form . "ex") (:end . 138) (:start . 136)\n  (:id . 64))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 143) (:start . 139)\n  (:id . 65))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 153)\n  (:start . 144) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 156) (:start . 154)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "spleen") (:form . "spleens") (:end . 164)\n  (:start . 157) (:id . 68))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 167) (:start . 165)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 169) (:start . 168)\n  (:id . 70))\n ((:tag . "NN") (:stem . "means") (:form . "means") (:end . 175)\n  (:start . 170) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 178) (:start . 176)\n  (:id . 72))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 185)\n  (:start . 179) (:id . 73))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 195)\n  (:start . 186) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 198) (:start . 196)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 202) (:start . 199)\n  (:id . 76))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 209)\n  (:start . 203) (:id . 77))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 216)\n  (:start . 210) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 218) (:start . 217)\n  (:id . 79))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 220) (:start . 218)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s2.199) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500415@unknown@formal@none@1@S@To this end, we treated LPS-activated splenic B cells with 10 nM estrogen for 6 d and sequenced the Sγ3 region.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "treat") (:form . "treated") (:end . 23)\n  (:start . 16) (:id . 47))\n ((:tag . "JJ") (:stem . "lps-activated") (:form . "LPS-activated")\n  (:end . 37) (:start . 24) (:id . 48))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 73)\n  (:start . 65) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 79) (:start . 78)\n  (:id . 57))\n ((:tag . "NN") (:stem . "d") (:form . "d") (:end . 81) (:start . 80)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "sequence") (:form . "sequenced") (:end . 95)\n  (:start . 86) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 61))\n ((:tag . "NN") (:stem . "sγ3") (:form . "Sγ3") (:end . 103) (:start . 100)\n  (:id . 62))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 110)\n  (:start . 104) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.200) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500416@unknown@formal@none@1@S@Because AID+/- mice show a haploinsufficiency effect (43, 44), we used F1 spleens from an AID-/- and BALB/c cross for analysis, hypothesizing that the estrogen effect would be more pronounced.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "aid+/-") (:form . "AID+/-") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "haploinsufficiency") (:form . "haploinsufficiency")\n  (:end . 45) (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 52)\n  (:start . 46) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 70) (:start . 66)\n  (:id . 56))\n ((:tag . "NN") (:stem . "f1") (:form . "F1") (:end . 73) (:start . 71)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "spleen") (:form . "spleens") (:end . 81)\n  (:start . 74) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 86) (:start . 82)\n  (:id . 59))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 89) (:start . 87)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "aid-/-") (:form . "AID-/-") (:end . 96)\n  (:start . 90) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "BALB/c") (:form . "BALB/c") (:end . 107)\n  (:start . 101) (:id . 63))\n ((:tag . "RB") (:stem . "cross") (:form . "cross") (:end . 113)\n  (:start . 108) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 117) (:start . 114)\n  (:id . 65))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 126)\n  (:start . 118) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "hypothesize") (:form . "hypothesizing")\n  (:end . 141) (:start . 128) (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 146) (:start . 142)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n  (:id . 70))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 159)\n  (:start . 151) (:id . 71))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 166)\n  (:start . 160) (:id . 72))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 172)\n  (:start . 167) (:id . 73))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 175) (:start . 173)\n  (:id . 74))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 180) (:start . 176)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "pronounced") (:form . "pronounced") (:end . 191)\n  (:start . 181) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x2.201.1) (:span 167 172))\n  ((:id . :x2.201.2) (:span 128 141)))\n (:hscopes ((:id . :x2.201.1) (:span 147 191))\n  ((:id . :x2.201.2) (:span 128 191)))\n (:identifiers (:sid . :s2.201) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500417@unknown@formal@none@1@S@As can be seen in Fig. 5 B and Fig. S7, there was a significant (P < 0.02) enhancement of mutation frequency in the switch region after estrogen treatment.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 14) (:start . 10)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 22) (:start . 18)\n  (:id . 47))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 24) (:start . 23)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 26) (:start . 25)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 35) (:start . 31)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 38) (:start . 36)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 53))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 45) (:start . 40)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 49) (:start . 46)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 63)\n  (:start . 52) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 58))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 66) (:start . 65)\n  (:id . 59))\n ((:tag . "JJR") (:stem . "<") (:form . "<") (:end . 68) (:start . 67)\n  (:id . 60))\n ((:tag . "CD") (:stem . "0.02") (:form . "0.02") (:end . 73) (:start . 69)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n  (:id . 62))\n ((:tag . "NN") (:stem . "enhancement") (:form . "enhancement") (:end . 86)\n  (:start . 75) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 64))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 98)\n  (:start . 90) (:id . 65))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 108)\n  (:start . 99) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 68))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 122)\n  (:start . 116) (:id . 69))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 129)\n  (:start . 123) (:id . 70))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 135)\n  (:start . 130) (:id . 71))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 144)\n  (:start . 136) (:id . 72))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 154)\n  (:start . 145) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s2.202) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500418@unknown@formal@none@1@S@Enhanced non-Ig loci targeting of AID@(((:tag . "VBN") (:stem . "enhance") (:form . "Enhanced") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "non-ig") (:form . "non-Ig") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "locus") (:form . "loci") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 37) (:start . 34)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s2.203) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500419@unknown@formal@none@1@S@It is known that AID can be mistargeted to non-Ig genes (12, 17–19).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "mistargete") (:form . "mistargeted") (:end . 39)\n  (:start . 28) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "non-ig") (:form . "non-Ig") (:end . 49)\n  (:start . 43) (:id . 51))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 55) (:start . 50)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 59) (:start . 57)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 55))\n ((:tag . "CD") (:stem . "17–19") (:form . "17–19") (:end . 66) (:start . 61)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.204) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500420@unknown@formal@none@1@S@The effect of aberrant AID targeting can lead to somatic mutations or even translocations of protooncogenes or tumor suppressors, and subsequently to oncogenesis (16).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "VB") (:stem . "lead") (:form . "lead") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "somatic") (:form . "somatic") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 66)\n  (:start . 57) (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 89) (:start . 75) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "protooncogene") (:form . "protooncogenes")\n  (:end . 107) (:start . 93) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 110) (:start . 108)\n  (:id . 58))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 116)\n  (:start . 111) (:id . 59))\n ((:tag . "NNS") (:stem . "suppressor") (:form . "suppressors") (:end . 128)\n  (:start . 117) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 62))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 146)\n  (:start . 134) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n  (:id . 64))\n ((:tag . "NN") (:stem . "oncogenesis") (:form . "oncogenesis") (:end . 161)\n  (:start . 150) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 163) (:start . 162)\n  (:id . 66))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 165) (:start . 163)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x2.205.1) (:span 108 110)) ((:id . :x2.205.2) (:span 67 69))\n  ((:id . :x2.205.3) (:span 37 40)))\n (:hscopes ((:id . :x2.205.1) (:span 93 128))\n  ((:id . :x2.205.2) (:span 49 128)) ((:id . :x2.205.3) (:span 37 161)))\n (:identifiers (:sid . :s2.205) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500421@unknown@formal@none@1@S@To determine if the activity of hormones via AID can also lead to an alteration in non-Ig loci, we chose to look at the proapoptotic tumor suppressor CD95/Fas.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "hormone") (:form . "hormones") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "VB") (:stem . "lead") (:form . "lead") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 68) (:start . 66)\n  (:id . 55))\n ((:tag . "NN") (:stem . "alteration") (:form . "alteration") (:end . 79)\n  (:start . 69) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "non-ig") (:form . "non-Ig") (:end . 89)\n  (:start . 83) (:id . 58))\n ((:tag . "NNS") (:stem . "locus") (:form . "loci") (:end . 94) (:start . 90)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 98) (:start . 96)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 104)\n  (:start . 99) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 107) (:start . 105)\n  (:id . 63))\n ((:tag . "VB") (:stem . "look") (:form . "look") (:end . 112) (:start . 108)\n  (:id . 64))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 115) (:start . 113)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "proapoptotic") (:form . "proapoptotic") (:end . 132)\n  (:start . 120) (:id . 67))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 138)\n  (:start . 133) (:id . 68))\n ((:tag . "NN") (:stem . "suppressor") (:form . "suppressor") (:end . 149)\n  (:start . 139) (:id . 69))\n ((:tag . "NN") (:stem . "cd95/fas") (:form . "CD95/Fas") (:end . 158)\n  (:start . 150) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x2.206.1) (:span 13 15)))\n (:hscopes ((:id . :x2.206.1) (:span 13 94)))\n (:identifiers (:sid . :s2.206) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500422@unknown@formal@none@1@S@CD95/Fas has been shown to be somatically hypermutated in human B cells, albeit 100–1,000-fold less frequently than the Ig genes (18).@(((:tag . "NNP") (:stem . "CD95/Fas") (:form . "CD95/Fas") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "RB") (:stem . "somatically") (:form . "somatically") (:end . 41)\n  (:start . 30) (:id . 48))\n ((:tag . "VBN") (:stem . "hypermutate") (:form . "hypermutated") (:end . 54)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "IN") (:stem . "albeit") (:form . "albeit") (:end . 79)\n  (:start . 73) (:id . 55))\n ((:tag . "RB") (:stem . "100–1,000-fold") (:form . "100–1,000-fold")\n  (:end . 94) (:start . 80) (:id . 56))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 99) (:start . 95)\n  (:id . 57))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 110)\n  (:start . 100) (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Ig") (:form . "Ig") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 128)\n  (:start . 123) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 132) (:start . 130)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.207) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500423@unknown@formal@none@1@S@We analyzed the effects of estrogen on CD95/Fas mutations in Ramos HS13.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "analyze") (:form . "analyzed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "CD95/Fas") (:form . "CD95/Fas") (:end . 47)\n  (:start . 39) (:id . 49))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "HS13") (:form . "HS13") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s2.208) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500424@unknown@formal@none@1@S@As with the physiological B cell maturation events of SHM and CSR, estrogen was able to increase the potentially pathogenic mutation frequency in CD95/Fas (Fig. 5 C and Fig. S7 B).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "physiological") (:form . "physiological")\n  (:end . 25) (:start . 12) (:id . 45))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "maturation") (:form . "maturation") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "CSR") (:form . "CSR") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 75)\n  (:start . 67) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "VB") (:stem . "increase") (:form . "increase") (:end . 96)\n  (:start . 88) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "RB") (:stem . "potentially") (:form . "potentially") (:end . 112)\n  (:start . 101) (:id . 61))\n ((:tag . "JJ") (:stem . "pathogenic") (:form . "pathogenic") (:end . 123)\n  (:start . 113) (:id . 62))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 132)\n  (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 142)\n  (:start . 133) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 145) (:start . 143)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "CD95/Fas") (:form . "CD95/Fas") (:end . 154)\n  (:start . 146) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 160) (:start . 156)\n  (:id . 68))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 162) (:start . 161)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "c") (:form . "C") (:end . 164) (:start . 163)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 173) (:start . 169)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 176) (:start . 174)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 178) (:start . 177)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x2.209.1) (:span 101 112)))\n (:hscopes ((:id . :x2.209.1) (:span 101 123)))\n (:identifiers (:sid . :s2.209) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500425@unknown@formal@none@1@S@Because of the direct effect on AID function (mutation), this data provides evidence for a novel way in which estrogen can exert a direct genotoxic effect on oncogenes or tumor suppressors.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 66) (:start . 62)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 75)\n  (:start . 67) (:id . 56))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 84)\n  (:start . 76) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 88) (:start . 85)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 90) (:start . 89)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 96) (:start . 91)\n  (:id . 60))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 100) (:start . 97)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 62))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 109)\n  (:start . 104) (:id . 63))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 118)\n  (:start . 110) (:id . 64))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 122) (:start . 119)\n  (:id . 65))\n ((:tag . "VB") (:stem . "exert") (:form . "exert") (:end . 128)\n  (:start . 123) (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 130) (:start . 129)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 137)\n  (:start . 131) (:id . 68))\n ((:tag . "JJ") (:stem . "genotoxic") (:form . "genotoxic") (:end . 147)\n  (:start . 138) (:id . 69))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 154)\n  (:start . 148) (:id . 70))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 157) (:start . 155)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "oncogene") (:form . "oncogenes") (:end . 167)\n  (:start . 158) (:id . 72))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 170) (:start . 168)\n  (:id . 73))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 176)\n  (:start . 171) (:id . 74))\n ((:tag . "NNS") (:stem . "suppressor") (:form . "suppressors") (:end . 188)\n  (:start . 177) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s2.210) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500426@unknown@formal@none@1@S@Estrogen enhances c-myc IgH translocations@(((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "enhance") (:form . "enhances") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "c-myc") (:form . "c-myc") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "IgH") (:form . "IgH") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 42) (:start . 28) (:id . 46)))@@@1@5@((:identifiers (:sid . :s2.211) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500427@unknown@formal@none@1@S@The off-target effect of AID was also detected in recent work on chromosome translocations of the c-myc oncogene into the IgH locus.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "off-target") (:form . "off-target") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 46)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 56)\n  (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 75)\n  (:start . 65) (:id . 54))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 90) (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 57))\n ((:tag . "NN") (:stem . "c-myc") (:form . "c-myc") (:end . 103) (:start . 98)\n  (:id . 58))\n ((:tag . "NN") (:stem . "oncogene") (:form . "oncogene") (:end . 112)\n  (:start . 104) (:id . 59))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 117) (:start . 113)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "IgH") (:form . "IgH") (:end . 125) (:start . 122)\n  (:id . 62))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 131)\n  (:start . 126) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.212) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500428@unknown@formal@none@1@S@More importantly, the levels of AID protein directly influenced chromosome translocation frequency.@(((:tag . "RBR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "importantly") (:form . "importantly") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 52)\n  (:start . 44) (:id . 50))\n ((:tag . "VBD") (:stem . "influence") (:form . "influenced") (:end . 63)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 74)\n  (:start . 64) (:id . 52))\n ((:tag . "NN") (:stem . "translocation") (:form . "translocation")\n  (:end . 88) (:start . 75) (:id . 53))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 98)\n  (:start . 89) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.213) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500429@unknown@formal@none@1@S@This was determined from both the analysis of AID haploinsufficiency (44) and microRNA regulation of AID protein expression (45, 46).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "haploinsufficiency") (:form . "haploinsufficiency")\n  (:end . 68) (:start . 50) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 52))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "microrna") (:form . "microRNA") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 97)\n  (:start . 87) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 112)\n  (:start . 105) (:id . 60))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 123)\n  (:start . 113) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 62))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 131) (:start . 129)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.214) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500430@unknown@formal@none@1@S@In both cases, reduced levels of AID had a direct bearing on the number of observed c-myc/IgH translocations.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 22)\n  (:start . 15) (:id . 46))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 29)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 49)\n  (:start . 43) (:id . 52))\n ((:tag . "NN") (:stem . "bearing") (:form . "bearing") (:end . 57)\n  (:start . 50) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 60) (:start . 58)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 55))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 71)\n  (:start . 65) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 83)\n  (:start . 75) (:id . 58))\n ((:tag . "NN") (:stem . "c-myc/igh") (:form . "c-myc/IgH") (:end . 93)\n  (:start . 84) (:id . 59))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 108) (:start . 94) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.215) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500431@unknown@formal@none@1@S@Using a previously described assay (16, 47), we were able to determine that estrogen treatment of isolated splenic B cells enhances c-myc/IgH translocations in p53+/- animals (Fig. 5 C and Fig. S8, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1).@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 47) (:start . 45)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 52) (:start . 48)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 57) (:start . 53)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 56))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 70)\n  (:start . 61) (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 75) (:start . 71)\n  (:id . 58))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 84)\n  (:start . 76) (:id . 59))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 94)\n  (:start . 85) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 106)\n  (:start . 98) (:id . 62))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 114)\n  (:start . 107) (:id . 63))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 116) (:start . 115)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 122)\n  (:start . 117) (:id . 65))\n ((:tag . "VBZ") (:stem . "enhance") (:form . "enhances") (:end . 131)\n  (:start . 123) (:id . 66))\n ((:tag . "NN") (:stem . "c-myc/igh") (:form . "c-myc/IgH") (:end . 141)\n  (:start . 132) (:id . 67))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 156) (:start . 142) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 159) (:start . 157)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "p53+/-") (:form . "p53+/-") (:end . 166)\n  (:start . 160) (:id . 70))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 174)\n  (:start . 167) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 180) (:start . 176)\n  (:id . 73))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 182) (:start . 181)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 184) (:start . 183)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 188) (:start . 185)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 193) (:start . 189)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "S8") (:form . "S8") (:end . 196) (:start . 194)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 207)\n  (:start . 198) (:id . 80))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 210) (:start . 208)\n  (:id . 81))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 263) (:start . 211) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 264) (:start . 263)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s2.216) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500432@unknown@formal@none@1@S@Although, the overall frequency of translocations was low, we have not been able to observe any translocations in LPS/DMSO-treated spleen cells, yet we observed five (two in one experiment and three in another) translocations in the LPS/estrogen treatment.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 49) (:start . 35) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 75) (:start . 71)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . "VB") (:stem . "observe") (:form . "observe") (:end . 91)\n  (:start . 84) (:id . 58))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 110) (:start . 96) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "lps/dmso-treated") (:form . "LPS/DMSO-treated")\n  (:end . 130) (:start . 114) (:id . 62))\n ((:tag . "NN") (:stem . "spleen") (:form . "spleen") (:end . 137)\n  (:start . 131) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 143)\n  (:start . 138) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 65))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 148) (:start . 145)\n  (:id . 66))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 151) (:start . 149)\n  (:id . 67))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 160)\n  (:start . 152) (:id . 68))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 165) (:start . 161)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 70))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 170) (:start . 167)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 173) (:start . 171)\n  (:id . 72))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 177) (:start . 174)\n  (:id . 73))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 188)\n  (:start . 178) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 192) (:start . 189)\n  (:id . 75))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 198)\n  (:start . 193) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 201) (:start . 199)\n  (:id . 77))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 209)\n  (:start . 202) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 225) (:start . 211) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 228) (:start . 226)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 232) (:start . 229)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "LPS/estrogen") (:form . "LPS/estrogen")\n  (:end . 245) (:start . 233) (:id . 83))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 255)\n  (:start . 246) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 256) (:start . 255)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s2.217) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500433@unknown@formal@none@1@S@This highlights the importance of regulating AID protein amounts within a cell, and the potential pathogenic consequences of unregulated AID expression.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "highlight") (:form . "highlights") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "regulate") (:form . "regulating") (:end . 44)\n  (:start . 34) (:id . 47))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 56)\n  (:start . 49) (:id . 49))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 64)\n  (:start . 57) (:id . 50))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 71)\n  (:start . 65) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 78) (:start . 74)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 97)\n  (:start . 88) (:id . 57))\n ((:tag . "JJ") (:stem . "pathogenic") (:form . "pathogenic") (:end . 108)\n  (:start . 98) (:id . 58))\n ((:tag . "NNS") (:stem . "consequence") (:form . "consequences") (:end . 121)\n  (:start . 109) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "unregulated") (:form . "unregulated") (:end . 136)\n  (:start . 125) (:id . 61))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 140) (:start . 137)\n  (:id . 62))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 151)\n  (:start . 141) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x2.218.1) (:span 88 97)))\n (:hscopes ((:id . :x2.218.1) (:span 88 151)))\n (:identifiers (:sid . :s2.218) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500434@unknown@formal@none@1@S@AID induction is not limited to B cells@(((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "induction") (:form . "induction") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 39) (:start . 34)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s2.219) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500435@unknown@formal@none@1@S@In the past, we demonstrated that AID mRNA expression is not limited to activated B cells, but can also be detected in oocytes (22).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "past") (:form . "past") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 28)\n  (:start . 16) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 53)\n  (:start . 43) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 68)\n  (:start . 61) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 81)\n  (:start . 72) (:id . 56))\n ((:tag . "NN") (:stem . "b") (:form . "B") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 89) (:start . 84)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 59))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 94) (:start . 91)\n  (:id . 60))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 98) (:start . 95)\n  (:id . 61))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 103) (:start . 99)\n  (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 106) (:start . 104)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 115)\n  (:start . 107) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 118) (:start . 116)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "oocyte") (:form . "oocytes") (:end . 126)\n  (:start . 119) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 67))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 130) (:start . 128)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x2.220.1) (:span 95 98)))\n (:hscopes ((:id . :x2.220.1) (:span 95 126)))\n (:identifiers (:sid . :s2.220) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500436@unknown@formal@none@1@S@We therefore set out to determine if the increase in AID mRNA production by estrogen was also detectable in dissected tissues and various tumor cell lines.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "set") (:form . "set") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 72)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 84)\n  (:start . 76) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 104)\n  (:start . 94) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "dissect") (:form . "dissected") (:end . 117)\n  (:start . 108) (:id . 61))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 125)\n  (:start . 118) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 137)\n  (:start . 130) (:id . 64))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 143)\n  (:start . 138) (:id . 65))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 148) (:start . 144)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 154)\n  (:start . 149) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x2.221.1) (:span 34 36)))\n (:hscopes ((:id . :x2.221.1) (:span 34 154)))\n (:identifiers (:sid . :s2.221) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500437@unknown@formal@none@1@S@Analysis of dissected organs and tissue from mice showed AID responsiveness to hormones outside the immune system in breast and ovarian tissue (Fig. 6).@(((:tag . "NNP") (:stem . "Analysis") (:form . "Analysis") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "dissect") (:form . "dissected") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "organ") (:form . "organs") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 56) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "responsiveness") (:form . "responsiveness")\n  (:end . 75) (:start . 61) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "hormone") (:form . "hormones") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "IN") (:stem . "outside") (:form . "outside") (:end . 95)\n  (:start . 88) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 106)\n  (:start . 100) (:id . 57))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 113)\n  (:start . 107) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 116) (:start . 114)\n  (:id . 59))\n ((:tag . "NN") (:stem . "breast") (:form . "breast") (:end . 123)\n  (:start . 117) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "ovarian") (:form . "ovarian") (:end . 135)\n  (:start . 128) (:id . 62))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 142)\n  (:start . 136) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 144) (:start . 143)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 148) (:start . 144)\n  (:id . 65))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s2.222) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500438@unknown@formal@none@1@S@As we were primarily interested in the hormone sensitivity of the transcripts, we determined the relative fold stimulation compared with DMSO, which did not reflect the absolute AID mRNA in each tissue.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "RB") (:stem . "primarily") (:form . "primarily") (:end . 20)\n  (:start . 11) (:id . 45))\n ((:tag . "JJ") (:stem . "interested") (:form . "interested") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 58)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "transcript") (:form . "transcripts") (:end . 77)\n  (:start . 66) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "determine") (:form . "determined") (:end . 92)\n  (:start . 82) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 105)\n  (:start . 97) (:id . 58))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 110) (:start . 106)\n  (:id . 59))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 122)\n  (:start . 111) (:id . 60))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 131)\n  (:start . 123) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 136) (:start . 132)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "DMSO") (:form . "DMSO") (:end . 141) (:start . 137)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 148)\n  (:start . 143) (:id . 65))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 152) (:start . 149)\n  (:id . 66))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 156) (:start . 153)\n  (:id . 67))\n ((:tag . "VB") (:stem . "reflect") (:form . "reflect") (:end . 164)\n  (:start . 157) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "absolute") (:form . "absolute") (:end . 177)\n  (:start . 169) (:id . 70))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 181) (:start . 178)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 186) (:start . 182)\n  (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 189) (:start . 187)\n  (:id . 73))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 194) (:start . 190)\n  (:id . 74))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 201)\n  (:start . 195) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s2.223) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500439@unknown@formal@none@1@S@Interestingly, in ovaries, AID mRNA was induced almost 25-fold, which is higher than in any other organ or tissue.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "ovary") (:form . "ovaries") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 54)\n  (:start . 48) (:id . 51))\n ((:tag . "RB") (:stem . "25-fold") (:form . "25-fold") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 79) (:start . 73)\n  (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 97) (:start . 92)\n  (:id . 60))\n ((:tag . "NN") (:stem . "organ") (:form . "organ") (:end . 103) (:start . 98)\n  (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 113)\n  (:start . 107) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.224) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500440@unknown@formal@none@1@S@Because isolated oocytes produce AID mRNA (22), we suggest that the increase was predominantly caused by oocytes or other ovarian-derived tissue, rather than infiltrating lymphocytes.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "oocyte") (:form . "oocytes") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "produce") (:form . "produce") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 58)\n  (:start . 51) (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 63) (:start . 59)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 76)\n  (:start . 68) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 94) (:start . 81) (:id . 58))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 101)\n  (:start . 95) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "oocyte") (:form . "oocytes") (:end . 112)\n  (:start . 105) (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 121)\n  (:start . 116) (:id . 63))\n ((:tag . "JJ") (:stem . "ovarian-derived") (:form . "ovarian-derived")\n  (:end . 137) (:start . 122) (:id . 64))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 144)\n  (:start . 138) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 152)\n  (:start . 146) (:id . 67))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 157) (:start . 153)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "infiltrate") (:form . "infiltrating") (:end . 170)\n  (:start . 158) (:id . 69))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 182)\n  (:start . 171) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x2.225.1) (:span 51 58)))\n (:hscopes ((:id . :x2.225.1) (:span 51 182)))\n (:identifiers (:sid . :s2.225) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500441@unknown@formal@none@1@S@Estrogen induces AID and Apobec3 transcription in mouse tissue.@(((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "apobec3") (:form . "Apobec3") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 46) (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 62)\n  (:start . 56) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.226) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500442@unknown@formal@none@1@S@The red and blue colors indicate the results for mApobec3 and mAID, respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "color") (:form . "colors") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "mapobec3") (:form . "mApobec3") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "maid") (:form . "mAID") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 80)\n  (:start . 68) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.227) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500443@unknown@formal@none@1@S@Tissues were treated with DMSO, 1 nM estrogen (E1), or 10 nM estrogen (E10).@(((:tag . "NNPS") (:stem . "Tissue") (:form . "Tissues") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "DMSO") (:form . "DMSO") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 45)\n  (:start . 37) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 47) (:start . 46)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "E1") (:form . "E1") (:end . 49) (:start . 47)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 54) (:start . 52)\n  (:id . 55))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 57) (:start . 55)\n  (:id . 56))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 60) (:start . 58)\n  (:id . 57))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 69)\n  (:start . 61) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "E10") (:form . "E10") (:end . 74) (:start . 71)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.228) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500444@unknown@formal@none@1@S@Gene expression is normalized to the control treatments with DMSO.@(((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "normalize") (:form . "normalized") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 55)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "DMSO") (:form . "DMSO") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.229) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500445@unknown@formal@none@1@S@The tissue expression profiles represent pooled data for the respective tissues from two experiments.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 40)\n  (:start . 31) (:id . 46))\n ((:tag . "VBN") (:stem . "pool") (:form . "pooled") (:end . 47) (:start . 41)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 52) (:start . 48)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 79)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 84) (:start . 80)\n  (:id . 53))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 88) (:start . 85)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 100)\n  (:start . 89) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.230) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500446@unknown@formal@none@1@S@Timelines of cell treatments are indicated below the graphs.@(((:tag . "NNS") (:stem . "timeline") (:form . "Timelines") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "graph") (:form . "graphs") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.231) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500447@unknown@formal@none@1@S@Absolute values as compared with GAPDH mRNA are shown in Fig. S10, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1.@(((:tag . "JJ") (:stem . "absolute") (:form . "Absolute") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "S10") (:form . "S10") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 76)\n  (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 132) (:start . 80) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.232) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500448@unknown@formal@none@1@S@Gross tissue dissection can provide a good indication of possible cell types that can induce AID mRNA upon estrogen treatment, but tissue complexity could also obscure potential targets.@(((:tag . "NNP") (:stem . "Gross") (:form . "Gross") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dissection") (:form . "dissection") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "good") (:form . "good") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "indication") (:form . "indication") (:end . 53)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 65)\n  (:start . 57) (:id . 51))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 70) (:start . 66)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 76) (:start . 71)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 81) (:start . 77)\n  (:id . 54))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 92)\n  (:start . 86) (:id . 56))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 96) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 115)\n  (:start . 107) (:id . 60))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 125)\n  (:start . 116) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 62))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 137)\n  (:start . 131) (:id . 64))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 148)\n  (:start . 138) (:id . 65))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 154)\n  (:start . 149) (:id . 66))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 159) (:start . 155)\n  (:id . 67))\n ((:tag . "VB") (:stem . "obscure") (:form . "obscure") (:end . 167)\n  (:start . 160) (:id . 68))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 177)\n  (:start . 168) (:id . 69))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 185)\n  (:start . 178) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x2.233.1) (:span 168 177)) ((:id . :x2.233.2) (:span 57 65))\n  ((:id . :x2.233.3) (:span 36 56)))\n (:hscopes ((:id . :x2.233.1) (:span 168 185))\n  ((:id . :x2.233.2) (:span 57 76)) ((:id . :x2.233.3) (:span 36 125)))\n (:identifiers (:sid . :s2.233) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500449@unknown@formal@none@1@S@Although we did not detect a substantial mRNA increase in hepatocyte or cervix cell lines (Fig. S9, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1), we were able to show a significant increase (ranging from 2.5- to 22-fold) of AID in cell lines, including T cells, placenta, ovary, breast, and prostate.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "substantial") (:form . 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5500450@unknown@formal@none@1@S@The induction observed in breast cells mimics that of the tissues isolated in Fig. 6 A, and confirms a previous report that AID has been detected in the breast cell line MCF-7 (48).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "induction") (:form . "induction") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "breast") (:form . "breast") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "mimic") (:form . "mimics") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "confirm") (:form . "confirms") (:end . 100)\n  (:start . 92) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 111)\n  (:start . 103) (:id . 62))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 118)\n  (:start . 112) (:id . 63))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 123) (:start . 119)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 127) (:start . 124)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 131) (:start . 128)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 136) (:start . 132)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 145)\n  (:start . 137) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 70))\n ((:tag . "NN") (:stem . "breast") (:form . "breast") (:end . 159)\n  (:start . 153) (:id . 71))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 164) (:start . 160)\n  (:id . 72))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 169) (:start . 165)\n  (:id . 73))\n ((:tag . "NN") (:stem . "mcf-7") (:form . "MCF-7") (:end . 175)\n  (:start . 170) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 75))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 179) (:start . 177)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s2.235) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500451@unknown@formal@none@1@S@Importantly, AID mRNA was not only present at basal levels but was also significantly up-regulated.@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "basal") (:form . "basal") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 58)\n  (:start . 52) (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 71) (:start . 67)\n  (:id . 55))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 85) (:start . 72) (:id . 56))\n ((:tag . "VBN") (:stem . "up-regulate") (:form . "up-regulated") (:end . 98)\n  (:start . 86) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.236) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500452@unknown@formal@none@1@S@Estrogen activates APOBEC3B, 3F, and 3G mRNA transcription@(((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "NNP") (:stem . "APOBEC3B") (:form . "APOBEC3B") (:end . 27)\n  (:start . 19) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 45))\n ((:tag . "NN") (:stem . "3f") (:form . "3F") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "3g") (:form . "3G") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 58) (:start . 45) (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.237) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500453@unknown@formal@none@1@S@AID is the ancestral member of the DNA deaminase family, and the APOBEC3 members are considered to have arisen from AID by gene duplication events (34).@(((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "ancestral") (:form . "ancestral") (:end . 20)\n  (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "member") (:form . "member") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "deaminase") (:form . "deaminase") (:end . 48)\n  (:start . 39) (:id . 50))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "apobec3") (:form . "APOBEC3") (:end . 72)\n  (:start . 65) (:id . 55))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 80)\n  (:start . 73) (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 95)\n  (:start . 85) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 103) (:start . 99)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "arise") (:form . "arisen") (:end . 110)\n  (:start . 104) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 115) (:start . 111)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 119) (:start . 116)\n  (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 122) (:start . 120)\n  (:id . 64))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 127) (:start . 123)\n  (:id . 65))\n ((:tag . "NN") (:stem . "duplication") (:form . "duplication") (:end . 139)\n  (:start . 128) (:id . 66))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 146)\n  (:start . 140) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 68))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 150) (:start . 148)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s2.238) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500454@unknown@formal@none@1@S@Within the DNA deaminase family, APOBEC3 members function predominantly in the cytoplasm and inactivate foreign DNA such as retroviruses and retrotransposable elements (49).@(((:tag . "IN") (:stem . "within") (:form . "Within") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "deaminase") (:form . "deaminase") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "apobec3") (:form . "APOBEC3") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "VBP") (:stem . "function") (:form . "function") (:end . 57)\n  (:start . 49) (:id . 50))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 71) (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cytoplasm") (:form . "cytoplasm") (:end . 88)\n  (:start . 79) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "VB") (:stem . "inactivate") (:form . "inactivate") (:end . 103)\n  (:start . 93) (:id . 56))\n ((:tag . "JJ") (:stem . "foreign") (:form . "foreign") (:end . 111)\n  (:start . 104) (:id . 57))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 115) (:start . 112)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 120) (:start . 116)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 123) (:start . 121)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "retrovirus") (:form . "retroviruses") (:end . 136)\n  (:start . 124) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "retrotransposable") (:form . "retrotransposable")\n  (:end . 158) (:start . 141) (:id . 63))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 167)\n  (:start . 159) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n  (:id . 65))\n ((:tag . "CD") (:stem . "49") (:form . "49") (:end . 171) (:start . 169)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s2.239) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500455@unknown@formal@none@1@S@We hypothesized that hormonal responsiveness may have been conserved among members of the APOBEC3 family.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "hypothesize") (:form . "hypothesized") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "hormonal") (:form . "hormonal") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "responsiveness") (:form . "responsiveness")\n  (:end . 44) (:start . 30) (:id . 46))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 48) (:start . 45)\n  (:id . 47))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 53) (:start . 49)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 58) (:start . 54)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 68)\n  (:start . 59) (:id . 50))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 74) (:start . 69)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 82)\n  (:start . 75) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 54))\n ((:tag . "NN") (:stem . "apobec3") (:form . "APOBEC3") (:end . 97)\n  (:start . 90) (:id . 55))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 104)\n  (:start . 98) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x2.240.1) (:span 45 48)) ((:id . :x2.240.2) (:span 3 15)))\n (:hscopes ((:id . :x2.240.1) (:span 21 104))\n  ((:id . :x2.240.2) (:span 3 104)))\n (:identifiers (:sid . :s2.240) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500456@unknown@formal@none@1@S@To this end, we designed qRT-PCR primers to detect APOBEC family member mRNAs in mouse and human cells.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "design") (:form . "designed") (:end . 24)\n  (:start . 16) (:id . 47))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 32)\n  (:start . 25) (:id . 48))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 40)\n  (:start . 33) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n  (:id . 50))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 50)\n  (:start . 44) (:id . 51))\n ((:tag . "NNP") (:stem . "APOBEC") (:form . "APOBEC") (:end . 57)\n  (:start . 51) (:id . 52))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 64)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "member") (:form . "member") (:end . 71)\n  (:start . 65) (:id . 54))\n ((:tag . "NNS") (:stem . "mrna") (:form . "mRNAs") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 86) (:start . 81)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 96) (:start . 91)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 102) (:start . 97)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.241) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500457@unknown@formal@none@1@S@APOBEC2, a related member of the DNA deaminases without any apparent catalytic activity (34), was not affected by estrogen treatment; however, we were able to show that estrogen enhanced transcription of mouse Apobec3 from ovaries, spleen, and splenic B cells (Fig. 6).@(((:tag . "NNP") (:stem . "APOBEC2") (:form . "APOBEC2") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "related") (:form . "related") (:end . 18)\n  (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "member") (:form . "member") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "dna") (:form . 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5500458@unknown@formal@none@1@S@Expression of human APOBEC3B, 3F, and 3G family members was also enhanced upon estrogen treatment from several different cell lines (including those of T cell, ovarian, placental, and cervical origin; Fig. S9).@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "APOBEC3B") (:form . "APOBEC3B") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "3f") (:form . "3F") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "3g") (:form . "3G") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 47)\n  (:start . 41) (:id . 51))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 55)\n  (:start . 48) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 64) (:start . 60)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 73)\n  (:start . 65) (:id . 55))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 78) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 87)\n  (:start . 79) (:id . 57))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 97)\n  (:start . 88) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 110)\n  (:start . 103) (:id . 60))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 120)\n  (:start . 111) (:id . 61))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 125) (:start . 121)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 131)\n  (:start . 126) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 142)\n  (:start . 133) (:id . 65))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 148)\n  (:start . 143) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 67))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 158) (:start . 154)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "ovarian") (:form . "ovarian") (:end . 167)\n  (:start . 160) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "placental") (:form . "placental") (:end . 178)\n  (:start . 169) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 179) (:start . 178)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 183) (:start . 180)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "cervical") (:form . "cervical") (:end . 192)\n  (:start . 184) (:id . 76))\n ((:tag . "NN") (:stem . "origin") (:form . "origin") (:end . 199)\n  (:start . 193) (:id . 77))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 200) (:start . 199)\n  (:id . 78))\n ((:tag . "FW") (:stem . "fig.") (:form . "Fig.") (:end . 205) (:start . 201)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "S9") (:form . "S9") (:end . 208) (:start . 206)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 209) (:start . 208)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s2.243) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500459@unknown@formal@none@1@S@DISCUSSION@(((:tag . "NN") (:stem . "discussion") (:form . "DISCUSSION") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s2.244) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500460@unknown@formal@none@1@S@The physiological panpleiotropic effects of hormones are well documented in many aspects of development, although their effector mechanisms at the molecular level, as well as their pathogenic effects upon cancer and immunity are not well understood (i.e., the gender bias for autoimmunity [29, 31, 50] is as striking as the gender bias for some cancers [51, 52]).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "physiological") (:form . "physiological")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "panpleiotropic") (:form . "panpleiotropic")\n  (:end . 32) (:start . 18) (:id . 44))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 40)\n  (:start . 33) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "hormone") (:form . 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5500461@unknown@formal@none@1@S@The correlation between the expression of hormones or their cognitive receptors and development of pathologies, has led to several different hypotheses; most of which involve hyperactivation of cell proliferation, unregulated differentiation, alteration in DNA repair, or repression of apoptosis (51).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "hormone") (:form . 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5500462@unknown@formal@none@1@S@Here, we propose another means by which estrogen can be a genotoxin, by directly inducing DNA deaminases such as AID.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "propose") (:form . "propose") (:end . 16)\n  (:start . 9) (:id . 45))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "means") (:form . "means") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 39) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "NN") (:stem . "genotoxin") (:form . "genotoxin") (:end . 67)\n  (:start . 58) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 71) (:start . 69)\n  (:id . 56))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 80)\n  (:start . 72) (:id . 57))\n ((:tag . "VBG") (:stem . "induce") (:form . "inducing") (:end . 89)\n  (:start . 81) (:id . 58))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "deaminas") (:form . "deaminases") (:end . 104)\n  (:start . 94) (:id . 60))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 109) (:start . 105)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 116) (:start . 113)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x2.247.1) (:span 49 52)) ((:id . :x2.247.2) (:span 9 16)))\n (:hscopes ((:id . :x2.247.1) (:span 49 67)) ((:id . :x2.247.2) (:span 9 116)))\n (:identifiers (:sid . :s2.247) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500463@unknown@formal@none@1@S@Our initial experiment using progesterone and estrogen identified AID as being part of a hormonally regulated system.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "progesterone") (:form . "progesterone") (:end . 41)\n  (:start . 29) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 54)\n  (:start . 46) (:id . 48))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 65)\n  (:start . 55) (:id . 49))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 69) (:start . 66)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 78) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 83) (:start . 79)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "RB") (:stem . "hormonally") (:form . "hormonally") (:end . 99)\n  (:start . 89) (:id . 56))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 109)\n  (:start . 100) (:id . 57))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 116)\n  (:start . 110) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.248) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5500466@unknown@formal@none@1@S@Interestingly, AID activation (mRNA) by estrogen was more pronounced than the effect on SHM.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "pronounced") (:form . "pronounced") (:end . 68)\n  (:start . 58) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 84)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.251) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500467@unknown@formal@none@1@S@This could indicate that although AID production is necessary for SHM, other factors (e.g., lesion processing, AID targeting, etc) can play a significant role in overall SHM efficiency (53).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VB") (:stem . "indicate") (:form . "indicate") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 48)\n  (:start . 38) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 61)\n  (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 76) (:start . 71)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 56))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 90) (:start . 86)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "lesion") (:form . "lesion") (:end . 98)\n  (:start . 92) (:id . 59))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 109)\n  (:start . 99) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 114) (:start . 111)\n  (:id . 62))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 124)\n  (:start . 115) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . "FW") (:stem . "etc") (:form . "etc") (:end . 129) (:start . 126)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 66))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 134) (:start . 131)\n  (:id . 67))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 139) (:start . 135)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 141) (:start . 140)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 153)\n  (:start . 142) (:id . 70))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 158) (:start . 154)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 161) (:start . 159)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 169)\n  (:start . 162) (:id . 73))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 173) (:start . 170)\n  (:id . 74))\n ((:tag . "NN") (:stem . "efficiency") (:form . "efficiency") (:end . 184)\n  (:start . 174) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 186) (:start . 185)\n  (:id . 76))\n ((:tag . "CD") (:stem . "53") (:form . "53") (:end . 188) (:start . 186)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x2.252.1) (:span 131 134)) ((:id . :x2.252.2) (:span 11 24))\n  ((:id . :x2.252.3) (:span 5 10)))\n (:hscopes ((:id . :x2.252.1) (:span 131 184))\n  ((:id . :x2.252.2) (:span 11 184)) ((:id . :x2.252.3) (:span 5 184)))\n (:identifiers (:sid . :s2.252) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500468@unknown@formal@none@1@S@Similar to SHM, CSR was enhanced upon estrogen treatment, but was lagging behind AID mRNA production.@(((:tag . "JJ") (:stem . "similar") (:form . "Similar") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "SHM") (:form . "SHM") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "CSR") (:form . "CSR") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 32)\n  (:start . 24) (:id . 48))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 56)\n  (:start . 47) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "lag") (:form . "lagging") (:end . 73) (:start . 66)\n  (:id . 55))\n ((:tag . "IN") (:stem . "behind") (:form . "behind") (:end . 80)\n  (:start . 74) (:id . 56))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 89) (:start . 85)\n  (:id . 58))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 100)\n  (:start . 90) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.253) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500469@unknown@formal@none@1@S@The most dramatic effect from estrogen-induced overexpression of AID was seen at the level of c-myc/IgH translocations.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "dramatic") (:form . "dramatic") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "estrogen-induced") (:form . "estrogen-induced")\n  (:end . 46) (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 61) (:start . 47) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 68) (:start . 65)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 77) (:start . 73)\n  (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 80) (:start . 78)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 54))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 90) (:start . 85)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . "c-myc/igh") (:form . "c-myc/IgH") (:end . 103)\n  (:start . 94) (:id . 57))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 118) (:start . 104) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.254) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500470@unknown@formal@none@1@S@This is analogous to the recent observations that the effect of AID mRNA down-regulation (either by microRNA targeting or haploinsufficiency) was most pronounced at the level of translocations (44–46).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "analogous") (:form . "analogous") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 44)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "down-regulation") (:form . "down-regulation")\n  (:end . 88) (:start . 73) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 56))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 96)\n  (:start . 90) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "microRNA") (:form . "microRNA") (:end . 108)\n  (:start . 100) (:id . 59))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 118)\n  (:start . 109) (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 121) (:start . 119)\n  (:id . 61))\n ((:tag . "NN") (:stem . "haploinsufficiency") (:form . "haploinsufficiency")\n  (:end . 140) (:start . 122) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 145) (:start . 142)\n  (:id . 64))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 150) (:start . 146)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "pronounced") (:form . "pronounced") (:end . 161)\n  (:start . 151) (:id . 66))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 164) (:start . 162)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 68))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 174)\n  (:start . 169) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 192) (:start . 178) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 194) (:start . 193)\n  (:id . 72))\n ((:tag . "CD") (:stem . "44–46") (:form . "44–46") (:end . 199)\n  (:start . 194) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 200) (:start . 199)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s2.255) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500471@unknown@formal@none@1@S@Autoimmunity encompasses a broadly defined area of clinical pathologies that stem from abnormalities in numerous systemic, cellular, and molecular mechanisms, a subset of which are B cell–related pathologies (50).@(((:tag . "NNP") (:stem . "Autoimmunity") (:form . "Autoimmunity") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "encompass") (:form . "encompasses") (:end . 24)\n  (:start . 13) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 44))\n ((:tag . "RB") (:stem . "broadly") (:form . "broadly") (:end . 34)\n  (:start . 27) (:id . 45))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 42)\n  (:start . 35) (:id . 46))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 47) (:start . 43)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 59)\n  (:start . 51) (:id . 49))\n ((:tag . "NNS") (:stem . "pathology") (:form . "pathologies") (:end . 71)\n  (:start . 60) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 76) (:start . 72)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "stem") (:form . "stem") (:end . 81) (:start . 77)\n  (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 86) (:start . 82)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "abnormality") (:form . "abnormalities")\n  (:end . 100) (:start . 87) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "numerous") (:form . "numerous") (:end . 112)\n  (:start . 104) (:id . 56))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 121)\n  (:start . 113) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 131)\n  (:start . 123) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 146)\n  (:start . 137) (:id . 62))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 157)\n  (:start . 147) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 160) (:start . 159)\n  (:id . 65))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 167)\n  (:start . 161) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 170) (:start . 168)\n  (:id . 67))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 176)\n  (:start . 171) (:id . 68))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 180) (:start . 177)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 182) (:start . 181)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "cell–related") (:form . "cell–related") (:end . 195)\n  (:start . 183) (:id . 71))\n ((:tag . "NNS") (:stem . "pathology") (:form . "pathologies") (:end . 207)\n  (:start . 196) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 209) (:start . 208)\n  (:id . 73))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 211) (:start . 209)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 212) (:start . 211)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s2.256) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500472@unknown@formal@none@1@S@In systemic lupus erythematosus, abnormalities in B cell development and the production of autoreactive antibodies play an important pathological role.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "lupus") (:form . "lupus") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "erythematosus") (:form . "erythematosus")\n  (:end . 31) (:start . 18) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "abnormality") (:form . "abnormalities") (:end . 46)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 68)\n  (:start . 57) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 87)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "autoreactive") (:form . "autoreactive") (:end . 103)\n  (:start . 91) (:id . 56))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 114)\n  (:start . 104) (:id . 57))\n ((:tag . "VBP") (:stem . "play") (:form . "play") (:end . 119) (:start . 115)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 122) (:start . 120)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 132)\n  (:start . 123) (:id . 60))\n ((:tag . "JJ") (:stem . "pathological") (:form . "pathological") (:end . 145)\n  (:start . 133) (:id . 61))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 150) (:start . 146)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s2.257) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500473@unknown@formal@none@1@S@Overexpression of AID in autoimmune-prone mice induced a more severe systemic lupus erythematosus–like phenotype (10), whereas breeding AID-deficient mice with autoimmune-prone MRL/lpr mice significantly reduced the onset and extent of disease (11), indicating that alterations in AID can change the severity of B cell autoimmunity.@(((:tag . "NNP") (:stem . "Overexpression") (:form . "Overexpression")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "autoimmune-prone") (:form . "autoimmune-prone")\n  (:end . 41) (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 46) (:start . 42)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "induce") (:form . 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5500474@unknown@formal@none@1@S@Correlating our data with the known effects of estrogen on autoimmunity (28, 30, 50, 54), we propose that the effect of sex-hormones on autoimmunity could partially be through AID transcription and subsequent increase in genome instability.@(((:tag . "VBG") (:stem . "correlate") (:form . "Correlating") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 15) (:start . 12)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 71)\n  (:start . 59) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 83) (:start . 81)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 59))\n ((:tag . "CD") (:stem . "54") (:form . "54") (:end . 87) (:start . 85)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 62))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 92) (:start . 90)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "propose") (:form . "propose") (:end . 100)\n  (:start . 93) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 105) (:start . 101)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 66))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 116)\n  (:start . 110) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "sex-hormone") (:form . "sex-hormones") (:end . 132)\n  (:start . 120) (:id . 69))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 135) (:start . 133)\n  (:id . 70))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 148)\n  (:start . 136) (:id . 71))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 154)\n  (:start . 149) (:id . 72))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 164)\n  (:start . 155) (:id . 73))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 167) (:start . 165)\n  (:id . 74))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 175)\n  (:start . 168) (:id . 75))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 179) (:start . 176)\n  (:id . 76))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 193) (:start . 180) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 197) (:start . 194)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 208)\n  (:start . 198) (:id . 79))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 217)\n  (:start . 209) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 220) (:start . 218)\n  (:id . 81))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 227)\n  (:start . 221) (:id . 82))\n ((:tag . "NN") (:stem . "instability") (:form . "instability") (:end . 239)\n  (:start . 228) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 240) (:start . 239)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x2.259.1) (:span 149 154))\n  ((:id . :x2.259.2) (:span 93 100)))\n (:hscopes ((:id . :x2.259.1) (:span 149 239))\n  ((:id . :x2.259.2) (:span 93 239)))\n (:identifiers (:sid . :s2.259) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500475@unknown@formal@none@1@S@In addition to the direct binding of the estrogen–ER complex to the AID promoter, estrogen may also hyperstimulate AID production through the NF-κB pathway, as we were able to demonstrate that cotreatment of TNF-α and estrogen enhanced NF-κB binding to the AID promoter (Fig. 3 D).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . 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5500476@unknown@formal@none@1@S@Whether this effect is caused by protein–protein interaction or estrogen-induced chromatin modification has yet to be determined, but the synergistic or even cooperative interaction of two important autoimmune modulator pathways on AID expression may have substantially pathogenic effects.@(((:tag . "IN") (:stem . "whether") (:form . "Whether") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "protein–protein") (:form . "protein–protein")\n  (:end . 48) (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 60)\n  (:start . 49) (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "estrogen-induced") (:form . "estrogen-induced")\n  (:end . 80) (:start . 64) (:id . 51))\n ((:tag . "NN") (:stem . "chromatin") (:form . "chromatin") (:end . 90)\n  (:start . 81) (:id . 52))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 103)\n  (:start . 91) (:id . 53))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 107) (:start . 104)\n  (:id . 54))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 111) (:start . 108)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 114) (:start . 112)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 117) (:start . 115)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 128)\n  (:start . 118) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 59))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 133) (:start . 130)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "synergistic") (:form . "synergistic") (:end . 149)\n  (:start . 138) (:id . 62))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 152) (:start . 150)\n  (:id . 63))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 157) (:start . 153)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "cooperative") (:form . "cooperative") (:end . 169)\n  (:start . 158) (:id . 65))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 181)\n  (:start . 170) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n  (:id . 67))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 188) (:start . 185)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 198)\n  (:start . 189) (:id . 69))\n ((:tag . "JJ") (:stem . "autoimmune") (:form . "autoimmune") (:end . 209)\n  (:start . 199) (:id . 70))\n ((:tag . "NN") (:stem . "modulator") (:form . "modulator") (:end . 219)\n  (:start . 210) (:id . 71))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 228)\n  (:start . 220) (:id . 72))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 231) (:start . 229)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 235) (:start . 232)\n  (:id . 74))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 246)\n  (:start . 236) (:id . 75))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 250) (:start . 247)\n  (:id . 76))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 255) (:start . 251)\n  (:id . 77))\n ((:tag . "RB") (:stem . "substantially") (:form . "substantially")\n  (:end . 269) (:start . 256) (:id . 78))\n ((:tag . "JJ") (:stem . "pathogenic") (:form . "pathogenic") (:end . 280)\n  (:start . 270) (:id . 79))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 288)\n  (:start . 281) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 289) (:start . 288)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x2.261.1) (:span 247 250)) ((:id . :x2.261.2) (:span 61 63))\n  ((:id . :x2.261.3) (:span 0 7)))\n (:hscopes ((:id . :x2.261.1) (:span 247 288))\n  ((:id . :x2.261.2) (:span 33 103)) ((:id . :x2.261.3) (:span 0 103)))\n (:identifiers (:sid . :s2.261) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500477@unknown@formal@none@1@S@There are several hypotheses on how unregulated AID can affect autoimmunity in addition to overstimulation of SHM and CSR, e.g., debilitating mutations in the signaling pathways, of tumor suppressors, or of proapoptotic genes, or alterations that activate oncogenes or antiapoptotic genes (for review see reference [55]).@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "hypothesis") (:form . "hypotheses") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "unregulated") (:form . 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5500478@unknown@formal@none@1@S@Mutation and subsequent loss of growth control is usually associated with oncogenesis, and this similarity with autoimmunity has previously been noted (55) (e.g., mutations in CD95/Fas have been associated with autoimmunity, as well as B cell lymphomas).@(((:tag . "NN") (:stem . "mutation") (:form . "Mutation") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 68)\n  (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "oncogenesis") (:form . "oncogenesis") (:end . 85)\n  (:start . 74) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 95) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 106)\n  (:start . 96) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 111) (:start . 107)\n  (:id . 58))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 124)\n  (:start . 112) (:id . 59))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 128) (:start . 125)\n  (:id . 60))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 139)\n  (:start . 129) (:id . 61))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 144) (:start . 140)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 150)\n  (:start . 145) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 152) (:start . 151)\n  (:id . 64))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 154) (:start . 152)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 161) (:start . 157)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 172)\n  (:start . 163) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "NN") (:stem . "cd95/fas") (:form . "CD95/Fas") (:end . 184)\n  (:start . 176) (:id . 72))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 189) (:start . 185)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 194) (:start . 190)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 205)\n  (:start . 195) (:id . 75))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 210) (:start . 206)\n  (:id . 76))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 223)\n  (:start . 211) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 224) (:start . 223)\n  (:id . 78))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 227) (:start . 225)\n  (:id . 79))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 232) (:start . 228)\n  (:id . 80))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 235) (:start . 233)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 237) (:start . 236)\n  (:id . 82))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 242) (:start . 238)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "lymphoma") (:form . "lymphomas") (:end . 252)\n  (:start . 243) (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 253) (:start . 252)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 254) (:start . 253)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s2.263) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500479@unknown@formal@none@1@S@Therefore, our data on estrogen-induced mutations in CD95/Fas (Fig. 5 and Fig. S7), derived from increased AID production, may provide a novel molecular mechanism that is important for both pathologies.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "estrogen-induced") (:form . "estrogen-induced")\n  (:end . 39) (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 49)\n  (:start . 40) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "CD95/Fas") (:form . "CD95/Fas") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 78) (:start . 74)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 91)\n  (:start . 84) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 96) (:start . 92)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 106)\n  (:start . 97) (:id . 61))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 110) (:start . 107)\n  (:id . 62))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 121)\n  (:start . 111) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 64))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 126) (:start . 123)\n  (:id . 65))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 134)\n  (:start . 127) (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 136) (:start . 135)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 142)\n  (:start . 137) (:id . 68))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 152)\n  (:start . 143) (:id . 69))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 162)\n  (:start . 153) (:id . 70))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 167) (:start . 163)\n  (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 170) (:start . 168)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 180)\n  (:start . 171) (:id . 73))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 184) (:start . 181)\n  (:id . 74))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 189) (:start . 185)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "pathology") (:form . "pathologies") (:end . 201)\n  (:start . 190) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x2.264.1) (:span 123 126)))\n (:hscopes ((:id . :x2.264.1) (:span 123 201)))\n (:identifiers (:sid . :s2.264) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500480@unknown@formal@none@1@S@AID's targeting outside the Ig locus, its apparently crucial involvement with germinal center–derived B cell malignancies (43, 56), and its ability to cause various malignancies when overexpressed in transgenic mice (20, 21, 57) are strong indicators for AID's oncogenic potential.@(((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 15)\n  (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "outside") (:form . "outside") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Ig") (:form . "Ig") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . 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5500481@unknown@formal@none@1@S@Estrogen is one of the most important and thoroughly studied mitogenic agents in cancer, but it does not possess any direct DNA mutability, and induces transformation by proliferation.@(((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "RB") (:stem . "thoroughly") (:form . "thoroughly") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . "VBN") (:stem . "study") (:form . "studied") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "JJ") (:stem . "mitogenic") (:form . "mitogenic") (:end . 70)\n  (:start . 61) (:id . 52))\n ((:tag . "NNS") (:stem . "agent") (:form . "agents") (:end . 77)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 92) (:start . 89)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "VB") (:stem . "possess") (:form . "possess") (:end . 112)\n  (:start . 105) (:id . 61))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 123)\n  (:start . 117) (:id . 63))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "NN") (:stem . "mutability") (:form . "mutability") (:end . 138)\n  (:start . 128) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 151)\n  (:start . 144) (:id . 68))\n ((:tag . "NN") (:stem . "transformation") (:form . "transformation")\n  (:end . 166) (:start . 152) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 169) (:start . 167)\n  (:id . 70))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 183) (:start . 170) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s2.266) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500482@unknown@formal@none@1@S@In vitro, high concentrations of estrogen derivatives (usually metabolites) can form DNA adducts or produce reactive oxygen-damaging DNA (for review see reference [58–60]), but their role as physiological genotoxins is limited.@(((:tag . "FW") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 14) (:start . 10)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 29) (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "derivative") (:form . "derivatives") (:end . 53)\n  (:start . 42) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 62)\n  (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "metabolite") (:form . "metabolites") (:end . 74)\n  (:start . 63) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "adduct") (:form . "adducts") (:end . 96)\n  (:start . 89) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 107)\n  (:start . 100) (:id . 59))\n ((:tag . "JJ") (:stem . "reactive") (:form . "reactive") (:end . 116)\n  (:start . 108) (:id . 60))\n ((:tag . "JJ") (:stem . "oxygen-damaging") (:form . "oxygen-damaging")\n  (:end . 132) (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 136) (:start . 133)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 141) (:start . 138)\n  (:id . 64))\n ((:tag . "NN") (:stem . "review") (:form . "review") (:end . 148)\n  (:start . 142) (:id . 65))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 152) (:start . 149)\n  (:id . 66))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 162)\n  (:start . 153) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 164) (:start . 163)\n  (:id . 68))\n ((:tag . "CD") (:stem . "58–60") (:form . "58–60") (:end . 169)\n  (:start . 164) (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 170) (:start . 169)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 171) (:start . 170)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 72))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 176) (:start . 173)\n  (:id . 73))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 182)\n  (:start . 177) (:id . 74))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 187) (:start . 183)\n  (:id . 75))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 190) (:start . 188)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "physiological") (:form . "physiological")\n  (:end . 204) (:start . 191) (:id . 77))\n ((:tag . "NNS") (:stem . "genotoxin") (:form . "genotoxins") (:end . 215)\n  (:start . 205) (:id . 78))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 218) (:start . 216)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 226)\n  (:start . 219) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s2.267) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500483@unknown@formal@none@1@S@Furthermore, because the estrogen derivative Tam (61) can inhibit estrogen's oncogenesis in breast cancer, it is unlikely that estrogen (or its derivatives) form DNA adducts under those conditions.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "derivative") (:form . "derivative") (:end . 44)\n  (:start . 34) (:id . 47))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "CD") (:stem . "61") (:form . "61") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 65)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 74)\n  (:start . 66) (:id . 54))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "oncogenesis") (:form . "oncogenesis") (:end . 88)\n  (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "breast") (:form . "breast") (:end . 98)\n  (:start . 92) (:id . 58))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 105)\n  (:start . 99) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 109) (:start . 107)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 121)\n  (:start . 113) (:id . 63))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 126) (:start . 122)\n  (:id . 64))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 135)\n  (:start . 127) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 139) (:start . 137)\n  (:id . 67))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 143) (:start . 140)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "derivative") (:form . "derivatives") (:end . 155)\n  (:start . 144) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 70))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 161) (:start . 157)\n  (:id . 71))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 165) (:start . 162)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "adduct") (:form . "adducts") (:end . 173)\n  (:start . 166) (:id . 73))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 179)\n  (:start . 174) (:id . 74))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 185)\n  (:start . 180) (:id . 75))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 196)\n  (:start . 186) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x2.268.1) (:span 113 121)))\n (:hscopes ((:id . :x2.268.1) (:span 113 196)))\n (:identifiers (:sid . :s2.268) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500484@unknown@formal@none@1@S@It is interesting to note that the antagonistic activity of Tam has recently been used to inhibit some of the pathologies of estrogen-induced autoimmunity (54).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "interesting") (:form . "interesting") (:end . 17)\n  (:start . 6) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "VB") (:stem . "note") (:form . "note") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "antagonistic") (:form . "antagonistic") (:end . 47)\n  (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 76)\n  (:start . 68) (:id . 54))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 97)\n  (:start . 90) (:id . 58))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "pathology") (:form . "pathologies") (:end . 121)\n  (:start . 110) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "estrogen-induced") (:form . "estrogen-induced")\n  (:end . 141) (:start . 125) (:id . 64))\n ((:tag . "NN") (:stem . "autoimmunity") (:form . "autoimmunity") (:end . 154)\n  (:start . 142) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 66))\n ((:tag . "CD") (:stem . "54") (:form . "54") (:end . 158) (:start . 156)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.269) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500485@unknown@formal@none@1@S@On the other hand, because of the pharmacological action of Tam (binding and altering the ER DNA binding capacity), under certain circumstances Tam acts as an estrogen agonist (62).@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "hand") (:form . "hand") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 26)\n  (:start . 19) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "pharmacological") (:form . "pharmacological")\n  (:end . 49) (:start . 34) (:id . 50))\n ((:tag . "NN") (:stem . "action") (:form . "action") (:end . 56)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 72)\n  (:start . 65) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "alter") (:form . "altering") (:end . 85)\n  (:start . 77) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "ER") (:form . "ER") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 96) (:start . 93)\n  (:id . 60))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 104)\n  (:start . 97) (:id . 61))\n ((:tag . "NN") (:stem . "capacity") (:form . "capacity") (:end . 113)\n  (:start . 105) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 64))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 121)\n  (:start . 116) (:id . 65))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 129)\n  (:start . 122) (:id . 66))\n ((:tag . "NNS") (:stem . "circumstance") (:form . "circumstances")\n  (:end . 143) (:start . 130) (:id . 67))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 147) (:start . 144)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "act") (:form . "acts") (:end . 152) (:start . 148)\n  (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 155) (:start . 153)\n  (:id . 70))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 158) (:start . 156)\n  (:id . 71))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 167)\n  (:start . 159) (:id . 72))\n ((:tag . "NN") (:stem . "agonist") (:form . "agonist") (:end . 175)\n  (:start . 168) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 74))\n ((:tag . "CD") (:stem . "62") (:form . "62") (:end . 179) (:start . 177)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s2.270) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500486@unknown@formal@none@1@S@This activity leads to an increased risk in secondary (e.g., ovarian) cancer after Tam treatment for breast cancer (63).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "risk") (:form . "risk") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "ovarian") (:form . "ovarian") (:end . 68)\n  (:start . 61) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 76)\n  (:start . 70) (:id . 56))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 82) (:start . 77)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 96)\n  (:start . 87) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "NN") (:stem . "breast") (:form . "breast") (:end . 107)\n  (:start . 101) (:id . 61))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 114)\n  (:start . 108) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 63))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 118) (:start . 116)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.271) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500487@unknown@formal@none@1@S@Thus, our findings that low concentrations of Tam induced AID mRNA (Fig. S1) also suggest that Tam acts as an agonist and indicates that the proposed usage of synthetic estrogen derivatives as a means to inhibit AID has to be carefully evaluated.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 18)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 42) (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "induce") (:form . "induced") (:end . 57)\n  (:start . 50) (:id . 51))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n  (:id . 57))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 81) (:start . 77)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 89)\n  (:start . 82) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 94) (:start . 90)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 98) (:start . 95)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "act") (:form . "acts") (:end . 103) (:start . 99)\n  (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 106) (:start . 104)\n  (:id . 63))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 109) (:start . 107)\n  (:id . 64))\n ((:tag . "NN") (:stem . "agonist") (:form . "agonist") (:end . 117)\n  (:start . 110) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 131)\n  (:start . 122) (:id . 67))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 136) (:start . 132)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 149)\n  (:start . 141) (:id . 70))\n ((:tag . "NN") (:stem . "usage") (:form . "usage") (:end . 155)\n  (:start . 150) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "synthetic") (:form . "synthetic") (:end . 168)\n  (:start . 159) (:id . 73))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 177)\n  (:start . 169) (:id . 74))\n ((:tag . "NNS") (:stem . "derivative") (:form . "derivatives") (:end . 189)\n  (:start . 178) (:id . 75))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 192) (:start . 190)\n  (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 194) (:start . 193)\n  (:id . 77))\n ((:tag . "NN") (:stem . "means") (:form . "means") (:end . 200)\n  (:start . 195) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 203) (:start . 201)\n  (:id . 79))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 211)\n  (:start . 204) (:id . 80))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 215) (:start . 212)\n  (:id . 81))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 219) (:start . 216)\n  (:id . 82))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 222) (:start . 220)\n  (:id . 83))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 225) (:start . 223)\n  (:id . 84))\n ((:tag . "RB") (:stem . "carefully") (:form . "carefully") (:end . 235)\n  (:start . 226) (:id . 85))\n ((:tag . "VBN") (:stem . "evaluate") (:form . "evaluated") (:end . 245)\n  (:start . 236) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 87)))@@@1@46@((:hcues ((:id . :x2.272.1) (:span 122 136)) ((:id . :x2.272.2) (:span 82 89)))\n (:hscopes ((:id . :x2.272.1) (:span 122 245))\n  ((:id . :x2.272.2) (:span 82 245)))\n (:identifiers (:sid . :s2.272) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500488@unknown@formal@none@1@S@Future work on identifying a potential role of AID in mouse models of hormonally induced cancers may provide further evidence on how AID can act as an environmentally stimulated oncogene.@(((:tag . "JJ") (:stem . "future") (:form . "Future") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "RB") (:stem . "hormonally") (:form . "hormonally") (:end . 80)\n  (:start . 70) (:id . 55))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 88)\n  (:start . 81) (:id . 56))\n ((:tag . "NNS") (:stem . "cancer") (:form . "cancers") (:end . 96)\n  (:start . 89) (:id . 57))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 108)\n  (:start . 101) (:id . 59))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 116)\n  (:start . 109) (:id . 60))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 125)\n  (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 132) (:start . 129)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 136) (:start . 133)\n  (:id . 64))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 140) (:start . 137)\n  (:id . 65))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 144) (:start . 141)\n  (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 147) (:start . 145)\n  (:id . 67))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 150) (:start . 148)\n  (:id . 68))\n ((:tag . "RB") (:stem . "environmentally") (:form . "environmentally")\n  (:end . 166) (:start . 151) (:id . 69))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 177)\n  (:start . 167) (:id . 70))\n ((:tag . "NN") (:stem . "oncogene") (:form . "oncogene") (:end . 186)\n  (:start . 178) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x2.273.1) (:span 97 100)) ((:id . :x2.273.2) (:span 29 38)))\n (:hscopes ((:id . :x2.273.1) (:span 97 186))\n  ((:id . :x2.273.2) (:span 29 96)))\n (:identifiers (:sid . :s2.273) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500489@unknown@formal@none@1@S@As our data indicate, AID's response to estrogen seems to have been evolutionarily conserved among the APOBEC3 family members, different tissues, and cell lines (Fig. 6 and Fig. S8); mouse Apobec3 and human APOBEC3B, -3F, and -3G (and -H to a lesser extent) mRNA were induced by estrogen treatment.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . 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"treatment") (:end . 297)\n  (:start . 288) (:id . 101))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 298) (:start . 297)\n  (:id . 102)))@@@1@61@((:hcues ((:id . :x2.274.1) (:span 49 54)) ((:id . :x2.274.2) (:span 12 20)))\n (:hscopes ((:id . :x2.274.1) (:span 22 160))\n  ((:id . :x2.274.2) (:span 12 20)))\n (:identifiers (:sid . :s2.274) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500490@unknown@formal@none@1@S@In the past, we have hypothesized that the predominant function of AID and its evolved DNA deaminase family members was to inactivate foreign DNA in the cell (8, 34, 64, 65).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "past") (:form . "past") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 20) (:start . 16)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "hypothesize") (:form . "hypothesized") (:end . 33)\n  (:start . 21) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "predominant") (:form . "predominant") (:end . 54)\n  (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "evolve") (:form . "evolved") (:end . 86)\n  (:start . 79) (:id . 57))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "deaminase") (:form . "deaminase") (:end . 100)\n  (:start . 91) (:id . 59))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 107)\n  (:start . 101) (:id . 60))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 115)\n  (:start . 108) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 119) (:start . 116)\n  (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "VB") (:stem . "inactivate") (:form . "inactivate") (:end . 133)\n  (:start . 123) (:id . 64))\n ((:tag . "JJ") (:stem . "foreign") (:form . "foreign") (:end . 141)\n  (:start . 134) (:id . 65))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 145) (:start . 142)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 68))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 157) (:start . 153)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 70))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 160) (:start . 159)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 72))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 164) (:start . 162)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 74))\n ((:tag . "CD") (:stem . "64") (:form . "64") (:end . 168) (:start . 166)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 76))\n ((:tag . "CD") (:stem . "65") (:form . "65") (:end . 172) (:start . 170)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 173) (:start . 172)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x2.275.1) (:span 21 33)))\n (:hscopes ((:id . :x2.275.1) (:span 21 157)))\n (:identifiers (:sid . :s2.275) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500491@unknown@formal@none@1@S@It is therefore plausible that the observed estrogen response of AID, as well as its expression in oocytes (22), had served a purpose other than targeting AID to Ig genes in B cells.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 15)\n  (:start . 6) (:id . 44))\n ((:tag . "JJ") (:stem . "plausible") (:form . "plausible") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 95)\n  (:start . 85) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "oocyte") (:form . "oocytes") (:end . 106)\n  (:start . 99) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 116) (:start . 113)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "serve") (:form . "served") (:end . 123)\n  (:start . 117) (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 125) (:start . 124)\n  (:id . 67))\n ((:tag . "NN") (:stem . "purpose") (:form . "purpose") (:end . 133)\n  (:start . 126) (:id . 68))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 139)\n  (:start . 134) (:id . 69))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 144) (:start . 140)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 154)\n  (:start . 145) (:id . 71))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 158) (:start . 155)\n  (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 161) (:start . 159)\n  (:id . 73))\n ((:tag . "NN") (:stem . "ig") (:form . "Ig") (:end . 164) (:start . 162)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 170)\n  (:start . 165) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 173) (:start . 171)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 175) (:start . 174)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 181)\n  (:start . 176) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s2.276) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500492@unknown@formal@none@1@S@Data indicating that AID has retained some ability to inhibit retroviral elements have substantiated this hypothesis (66).@(((:tag . "NNP") (:stem . "Datum") (:form . "Data") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "retain") (:form . "retained") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "JJ") (:stem . "retroviral") (:form . "retroviral") (:end . 72)\n  (:start . 62) (:id . 52))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 81)\n  (:start . 73) (:id . 53))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "substantiate") (:form . "substantiated")\n  (:end . 100) (:start . 87) (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 105) (:start . 101)\n  (:id . 56))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 116)\n  (:start . 106) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n  (:id . 58))\n ((:tag . "CD") (:stem . "66") (:form . "66") (:end . 120) (:start . 118)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 121) (:start . 120)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x2.277.1) (:span 5 20)))\n (:hscopes ((:id . :x2.277.1) (:span 5 81)))\n (:identifiers (:sid . :s2.277) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500493@unknown@formal@none@1@S@Our work has highlighted that there is a novel pathway by which the nonmutagenic hormone estrogen can mediate genome instability via the activation of AID and other DNA deaminases, in turn possibly altering the predispositions, induction, or severity for cancer, autoimmunity, and viral infectivity.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . 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5500494@unknown@formal@none@1@S@MATERIALS AND METHODS@(((:tag . "NNP") (:stem . "MATERIALS") (:form . "MATERIALS") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "AND") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "METHODS") (:form . "METHODS") (:end . 21)\n  (:start . 14) (:id . 44)))@@@1@3@((:identifiers (:sid . :s2.279) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500495@unknown@formal@none@1@S@Unless indicated, mouse tissue samples and splenic B cells were derived from 8–12-wk-old female unplugged BALB/c mice, and prepared by standard protocol (see Supplemental materials and methods, available at available at http://www.jem.org/cgi/content/full/jem.20080521/DC1).@(((:tag . "IN") (:stem . "unless") (:form . "Unless") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 16)\n  (:start . 7) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 58) (:start . 53)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 71)\n  (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "8–12-wk-old") (:form . "8–12-wk-old") (:end . 88)\n  (:start . 77) (:id . 55))\n ((:tag . "JJ") (:stem . "female") (:form . "female") (:end . 95)\n  (:start . 89) (:id . 56))\n ((:tag . "JJ") (:stem . "unplugged") (:form . "unplugged") (:end . 105)\n  (:start . 96) (:id . 57))\n ((:tag . "NN") (:stem . "balb/c") (:form . "BALB/c") (:end . 112)\n  (:start . 106) (:id . 58))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 117)\n  (:start . 113) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 131)\n  (:start . 123) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 134) (:start . 132)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 143)\n  (:start . 135) (:id . 64))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 152)\n  (:start . 144) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 66))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 157) (:start . 154)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 170)\n  (:start . 158) (:id . 68))\n ((:tag . "NNS") (:stem . "material") (:form . "materials") (:end . 180)\n  (:start . 171) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 184) (:start . 181)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 192)\n  (:start . 185) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 193) (:start . 192)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 203)\n  (:start . 194) (:id . 73))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 206) (:start . 204)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 216)\n  (:start . 207) (:id . 75))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 219) (:start . 217)\n  (:id . 76))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 272) (:start . 220) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 273) (:start . 272)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 274) (:start . 273)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s2.280) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500496@unknown@formal@none@1@S@Human cell lines Jurkat, T47D, Ramos HS13 (Ramos), JAR, and mouse B cells were cultivated in RPMI-1640+GlutaMax medium (Invitrogen); the cell lines MCF7, JAMA2, HeLa, and HepG2 were cultivated in E4 medium; and PC3 was cultivated in HAMS F12 medium.@(((:tag . "JJ") (:stem . "human") (:form . "Human") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "T47D") (:form . "T47D") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Ramos") (:form . 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5500497@unknown@formal@none@1@S@Chicken DT40 cells were maintained in RPMI-1640+GlutaMax with 10% FCS, 1% chicken serum, 50 µM ß-mercaptoethanol, 100 U/ml penicillin, and 100 µg/ml streptomycin at 39°C with 10% CO2.@(((:tag . "NNP") (:stem . "Chicken") (:form . "Chicken") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "DT40") (:form . "DT40") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "maintain") (:form . "maintained") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "RPMI-1640+GlutaMax") (:form . "RPMI-1640+GlutaMax")\n  (:end . 56) (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 61) (:start . 57)\n  (:id . 49))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 65) (:start . 64)\n  (:id . 51))\n ((:tag . "NN") (:stem . "fcs") (:form . "FCS") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "chicken") (:form . "chicken") (:end . 81)\n  (:start . 74) (:id . 56))\n ((:tag . "NN") (:stem . "serum") (:form . "serum") (:end . 87) (:start . 82)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 58))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "µM") (:form . "µM") (:end . 94) (:start . 92)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "ß-mercaptoethanol") (:form . "ß-mercaptoethanol")\n  (:end . 112) (:start . 95) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 117) (:start . 114)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "U/ml") (:form . "U/ml") (:end . 122) (:start . 118)\n  (:id . 64))\n ((:tag . "NN") (:stem . "penicillin") (:form . "penicillin") (:end . 133)\n  (:start . 123) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n  (:id . 67))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 142) (:start . 139)\n  (:id . 68))\n ((:tag . "NN") (:stem . "µg/ml") (:form . "µg/ml") (:end . 148)\n  (:start . 143) (:id . 69))\n ((:tag . "NN") (:stem . "streptomycin") (:form . "streptomycin") (:end . 161)\n  (:start . 149) (:id . 70))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 164) (:start . 162)\n  (:id . 71))\n ((:tag . "NN") (:stem . "39°c") (:form . "39°C") (:end . 169) (:start . 165)\n  (:id . 72))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 174) (:start . 170)\n  (:id . 73))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 177) (:start . 175)\n  (:id . 74))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 178) (:start . 177)\n  (:id . 75))\n ((:tag . "NN") (:stem . "co2") (:form . "CO2") (:end . 182) (:start . 179)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s2.282) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500498@unknown@formal@none@1@S@For indicated experiments, cells were treated for 72 h in hormone-depleted serum (Opti-MeM Reduced Serum Medium; Invitrogen) supplemented with Charcoal Stripped Fetal Bovine Serum (Invitrogen); and nonessential amino acids (final concentration; Sigma-Aldrich), as follows: l-Alanine (8.9 µg/ml), l-Asparagine (15.0 µg/ml), l-Aspartic acid (13.3 µg/ml), l-Glutamic acid (14.7 µg/ml), Glycine (7.5 µg/ml), Proline (11.5 µg/ml), and l-Serine (10.5 µg/ml).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . 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5500499@unknown@formal@none@1@S@B cell stimulation was performed using 25 µg/ml LPS (Sigma-Aldrich), 50 ng/ml mouse IL-4 (R&D Systems), 20 ng/ml human TNF-α (R&D Systems), and 2 ng/ml human TGF-ß1 (R&D Systems).@(((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 18)\n  (:start . 7) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "µg/ml") (:form . "µg/ml") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "sigma-aldrich") (:form . "Sigma-Aldrich")\n  (:end . 66) (:start . 53) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "NN") (:stem . "ng/ml") (:form . "ng/ml") (:end . 77) (:start . 72)\n  (:id . 56))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 83) (:start . 78)\n  (:id . 57))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 88) (:start . 84)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "R&D") (:form . "R&D") (:end . 93) (:start . 90)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Systems") (:form . "Systems") (:end . 101)\n  (:start . 94) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 63))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 106) (:start . 104)\n  (:id . 64))\n ((:tag . "NN") (:stem . "ng/ml") (:form . "ng/ml") (:end . 112)\n  (:start . 107) (:id . 65))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 118)\n  (:start . 113) (:id . 66))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 124)\n  (:start . 119) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "R&D") (:form . "R&D") (:end . 129) (:start . 126)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Systems") (:form . "Systems") (:end . 137)\n  (:start . 130) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 73))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 145) (:start . 144)\n  (:id . 74))\n ((:tag . "NN") (:stem . "ng/ml") (:form . "ng/ml") (:end . 151)\n  (:start . 146) (:id . 75))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 157)\n  (:start . 152) (:id . 76))\n ((:tag . "NN") (:stem . "tgf-ß1") (:form . "TGF-ß1") (:end . 164)\n  (:start . 158) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 166) (:start . 165)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "R&D") (:form . "R&D") (:end . 169) (:start . 166)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Systems") (:form . "Systems") (:end . 177)\n  (:start . 170) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 178) (:start . 177)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s2.284) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500500@unknown@formal@none@1@S@Estrogen (17-ß-estradiol; Sigma-Aldrich) and progesterone (Sigma-Aldrich) were dissolved in DMSO at a concentration of 100 mM; this solution was then diluted in DMSO to give 1,000× stock solutions, and final dilutions were made in media (final DMSO concentration was never >0.1%).@(((:tag . "NNP") (:stem . "Estrogen") (:form . "Estrogen") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "17-ß-estradiol") (:form . "17-ß-estradiol")\n  (:end . 24) (:start . 10) (:id . 44))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 25) (:start . 24)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "sigma-aldrich") (:form . "Sigma-Aldrich")\n  (:end . 39) (:start . 26) (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 40) (:start . 39)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . 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5500501@unknown@formal@none@1@S@The final concentrations of estrogen are indicated in the text and figure legends.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 24) (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 36)\n  (:start . 28) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 50)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "figure") (:form . "figure") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "legend") (:form . "legends") (:end . 81)\n  (:start . 74) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.286) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500502@unknown@formal@none@1@S@The concentration of Tam (Sigma-Aldrich) was 50 nM unless otherwise stated.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "sigma-aldrich") (:form . "Sigma-Aldrich")\n  (:end . 39) (:start . 26) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "unless") (:form . "unless") (:end . 57)\n  (:start . 51) (:id . 52))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 67)\n  (:start . 58) (:id . 53))\n ((:tag . "VBN") (:stem . "state") (:form . "stated") (:end . 74)\n  (:start . 68) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.287) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500503@unknown@formal@none@1@S@The final concentration for CHX (Sigma-Aldrich) was 10 µg/ml, 20 nM for ACT (Calbiochem), 4 µg/ml for AMA (Calbiochem), and 10 µM for MG-132 (Sigma-Aldrich).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "CHX") (:form . "CHX") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "sigma-aldrich") (:form . "Sigma-Aldrich")\n  (:end . 46) (:start . 33) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "µg/ml") (:form . "µg/ml") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "nM") (:form . "nM") (:end . 67) (:start . 65)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 71) (:start . 68)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "ACT") (:form . "ACT") (:end . 75) (:start . 72)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Calbiochem") (:form . "Calbiochem") (:end . 87)\n  (:start . 77) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 61))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 91) (:start . 90)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "µg/ml") (:form . "µg/ml") (:end . 97) (:start . 92)\n  (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 101) (:start . 98)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "AMA") (:form . "AMA") (:end . 105) (:start . 102)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Calbiochem") (:form . "Calbiochem") (:end . 117)\n  (:start . 107) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 70))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 126) (:start . 124)\n  (:id . 71))\n ((:tag . "NN") (:stem . "µm") (:form . "µM") (:end . 129) (:start . 127)\n  (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 133) (:start . 130)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "MG-132") (:form . "MG-132") (:end . 140)\n  (:start . 134) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "sigma-aldrich") (:form . "Sigma-Aldrich")\n  (:end . 155) (:start . 142) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s2.288) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500504@unknown@formal@none@1@S@qRT-PCR of mRNAs was based on a previous study (67), with modifications (see Supplemental materials and methods).@(((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "mrna") (:form . "mRNAs") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 40)\n  (:start . 32) (:id . 49))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "CD") (:stem . "67") (:form . "67") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 51) (:start . 50)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 57) (:start . 53)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "modification") (:form . "modifications")\n  (:end . 71) (:start . 58) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 76) (:start . 73)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 89)\n  (:start . 77) (:id . 59))\n ((:tag . "NNS") (:stem . "material") (:form . "materials") (:end . 99)\n  (:start . 90) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 111)\n  (:start . 104) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.289) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500505@unknown@formal@none@1@S@The primers for qRT-PCR (Table S1, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1) were designed using PrimerExpress software.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 44)\n  (:start . 35) (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:end . 100) (:start . 48) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 106) (:start . 102)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 115)\n  (:start . 107) (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 121) (:start . 116)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "PrimerExpress") (:form . "PrimerExpress")\n  (:end . 135) (:start . 122) (:id . 57))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 144)\n  (:start . 136) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.290) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500506@unknown@formal@none@1@S@qRT-PCR analysis was performed using the QuantiTect SYBR Green PCR kit (QIAGEN) according to the manufacturer's instructions, Abi 7000 Sequence Detection System (Applied Biosystems), and Abi software.@(((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 36) (:start . 31)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "QuantiTect") (:form . "QuantiTect") (:end . 51)\n  (:start . 41) (:id . 48))\n ((:tag . "NNP") (:stem . "SYBR") (:form . "SYBR") (:end . 56) (:start . 52)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "green") (:form . "Green") (:end . 62) (:start . 57)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "QIAGEN") (:form . "QIAGEN") (:end . 78)\n  (:start . 72) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 89)\n  (:start . 80) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 109)\n  (:start . 97) (:id . 59))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 124)\n  (:start . 112) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Abi") (:form . "Abi") (:end . 129) (:start . 126)\n  (:id . 63))\n ((:tag . "CD") (:stem . "7000") (:form . "7000") (:end . 134) (:start . 130)\n  (:id . 64))\n ((:tag . "NN") (:stem . "sequence") (:form . "Sequence") (:end . 143)\n  (:start . 135) (:id . 65))\n ((:tag . "NNP") (:stem . "Detection") (:form . "Detection") (:end . 153)\n  (:start . 144) (:id . 66))\n ((:tag . "NNP") (:stem . "System") (:form . "System") (:end . 160)\n  (:start . 154) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Applied") (:form . "Applied") (:end . 169)\n  (:start . 162) (:id . 69))\n ((:tag . "NNP") (:stem . "Biosystems") (:form . "Biosystems") (:end . 180)\n  (:start . 170) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 181) (:start . 180)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 182) (:start . 181)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 186) (:start . 183)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Abi") (:form . "Abi") (:end . 190) (:start . 187)\n  (:id . 74))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 199)\n  (:start . 191) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s2.291) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500507@unknown@formal@none@1@S@Tissue or cell line hormone responsiveness was determined by qRT-PCR of gene regulated by breast cancer 1, a known estrogen-responsive gene (36).@(((:tag . "NN") (:stem . "tissue") (:form . "Tissue") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "responsiveness") (:form . "responsiveness")\n  (:end . 42) (:start . 28) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 68)\n  (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 86)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "breast") (:form . "breast") (:end . 96)\n  (:start . 90) (:id . 56))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 103)\n  (:start . 97) (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 114)\n  (:start . 109) (:id . 61))\n ((:tag . "JJ") (:stem . "estrogen-responsive")\n  (:form . "estrogen-responsive") (:end . 134) (:start . 115) (:id . 62))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 139) (:start . 135)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 64))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 143) (:start . 141)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.292) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500508@unknown@formal@none@1@S@Human AID promoter fragments were analyzed using pE1BLuc plasmid backbone (provided by G. Akusjärvi, Uppsala University, Uppsala, Sweden) containing a luciferase ORF and a minimal promoter region.@(((:tag . "JJ") (:stem . "human") (:form . "Human") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "pe1bluc") (:form . "pE1BLuc") (:end . 56)\n  (:start . 49) (:id . 49))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 64)\n  (:start . 57) (:id . 50))\n ((:tag . "NN") (:stem . "backbone") (:form . "backbone") (:end . 73)\n  (:start . 65) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 83)\n  (:start . 75) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 86) (:start . 84)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "G.") (:form . "G.") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Akusjärvi") (:form . "Akusjärvi") (:end . 99)\n  (:start . 90) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Uppsala") (:form . "Uppsala") (:end . 108)\n  (:start . 101) (:id . 58))\n ((:tag . "NNP") (:stem . "University") (:form . "University") (:end . 119)\n  (:start . 109) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Uppsala") (:form . "Uppsala") (:end . 128)\n  (:start . 121) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Sweden") (:form . "Sweden") (:end . 136)\n  (:start . 130) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 148)\n  (:start . 138) (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 161)\n  (:start . 151) (:id . 67))\n ((:tag . "NN") (:stem . "orf") (:form . "ORF") (:end . 165) (:start . 162)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 169) (:start . 166)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 171) (:start . 170)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "minimal") (:form . "minimal") (:end . 179)\n  (:start . 172) (:id . 71))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 188)\n  (:start . 180) (:id . 72))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 195)\n  (:start . 189) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s2.293) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500509@unknown@formal@none@1@S@Primers (Tables S2 and S3, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1) approximately every 500 bp from the human AID transcription start site were used for amplifying AID promoter regions.@(((:tag . "NNP") (:stem . "Primer") (:form . "Primers") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "Table") (:form . "Tables") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 36)\n  (:start . 27) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1") (:end . 92)\n  (:start . 40) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 52))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 107) (:start . 94) (:id . 53))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 113)\n  (:start . 108) (:id . 54))\n ((:tag . "CD") (:stem . "500") (:form . "500") (:end . 117) (:start . 114)\n  (:id . 55))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 120) (:start . 118)\n  (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 125) (:start . 121)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 135)\n  (:start . 130) (:id . 59))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 139) (:start . 136)\n  (:id . 60))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 153) (:start . 140) (:id . 61))\n ((:tag . "NN") (:stem . "start") (:form . "start") (:end . 159)\n  (:start . 154) (:id . 62))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 164) (:start . 160)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 169) (:start . 165)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 174) (:start . 170)\n  (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 178) (:start . 175)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "amplify") (:form . "amplifying") (:end . 189)\n  (:start . 179) (:id . 67))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 193) (:start . 190)\n  (:id . 68))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 202)\n  (:start . 194) (:id . 69))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 210)\n  (:start . 203) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s2.294) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500510@unknown@formal@none@1@S@The obtained PCR products were cloned into pE1BLuc vector, and 3 µg DNA were transfected into SiHa cells using Lipofectamine 2000 (Invitrogen) according to the manufacturer's protocols.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "pcr") (:form . "PCR") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "clone") (:form . "cloned") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "pe1bluc") (:form . "pE1BLuc") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 57)\n  (:start . 51) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "µg") (:form . "µg") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 76) (:start . 72)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 88)\n  (:start . 77) (:id . 57))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "SiHa") (:form . "SiHa") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 104) (:start . 99)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 110) (:start . 105)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Lipofectamine") (:form . "Lipofectamine")\n  (:end . 124) (:start . 111) (:id . 62))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 129) (:start . 125)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 141)\n  (:start . 131) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 152)\n  (:start . 143) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 155) (:start . 153)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 69))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 172)\n  (:start . 160) (:id . 70))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 174) (:start . 172)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "protocol") (:form . "protocols") (:end . 184)\n  (:start . 175) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.295) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500511@unknown@formal@none@1@S@24 h after transfection, cells were treated with the indicated concentrations of hormones or TNF-α for 4 h and analyzed thereafter for luciferase signal using Dual Luciferase Reporter Assay System (Promega) and Glomax luminometer (Promega).@(((:tag . "CD") (:stem . "24") (:form . "24") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 10) (:start . 5)\n  (:id . 44))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 23)\n  (:start . 11) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 77) (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "hormone") (:form . "hormones") (:end . 89)\n  (:start . 81) (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 98) (:start . 93)\n  (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 119)\n  (:start . 111) (:id . 62))\n ((:tag . "RB") (:stem . "thereafter") (:form . "thereafter") (:end . 130)\n  (:start . 120) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 134) (:start . 131)\n  (:id . 64))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 145)\n  (:start . 135) (:id . 65))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 152)\n  (:start . 146) (:id . 66))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 158) (:start . 153)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "dual") (:form . "Dual") (:end . 163) (:start . 159)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Luciferase") (:form . "Luciferase") (:end . 174)\n  (:start . 164) (:id . 69))\n ((:tag . "NNP") (:stem . "Reporter") (:form . "Reporter") (:end . 183)\n  (:start . 175) (:id . 70))\n ((:tag . "NNP") (:stem . "Assay") (:form . "Assay") (:end . 189)\n  (:start . 184) (:id . 71))\n ((:tag . "NNP") (:stem . "System") (:form . "System") (:end . 196)\n  (:start . 190) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 198) (:start . 197)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Promega") (:form . "Promega") (:end . 205)\n  (:start . 198) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 210) (:start . 207)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Glomax") (:form . "Glomax") (:end . 217)\n  (:start . 211) (:id . 77))\n ((:tag . "NN") (:stem . "luminometer") (:form . "luminometer") (:end . 229)\n  (:start . 218) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 231) (:start . 230)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Promega") (:form . "Promega") (:end . 238)\n  (:start . 231) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 239) (:start . 238)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 240) (:start . 239)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s2.296) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500512@unknown@formal@none@1@S@The expression vector containing a dominant-negative mutant for IκBα (S32A S36A; a gift from Felix Randow, Medical Research Council-Laboratory of Molecular Biology, Cambridge, England, UK) was cotransfected with pE1BLuc constructs where indicated.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 32)\n  (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "dominant-negative") (:form . "dominant-negative")\n  (:end . 52) (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 59)\n  (:start . 53) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "IκBα") (:form . "IκBα") (:end . 68) (:start . 64)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "S32A") (:form . "S32A") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "S36A") (:form . "S36A") (:end . 79) (:start . 75)\n  (:id . 53))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 80) (:start . 79)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gift") (:form . "gift") (:end . 87) (:start . 83)\n  (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 92) (:start . 88)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Felix") (:form . "Felix") (:end . 98) (:start . 93)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Randow") (:form . "Randow") (:end . 105)\n  (:start . 99) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Medical") (:form . "Medical") (:end . 114)\n  (:start . 107) (:id . 61))\n ((:tag . "NNP") (:stem . "Research") (:form . "Research") (:end . 123)\n  (:start . 115) (:id . 62))\n ((:tag . "NNP") (:stem . "Council-Laboratory") (:form . "Council-Laboratory")\n  (:end . 142) (:start . 124) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Molecular") (:form . "Molecular") (:end . 155)\n  (:start . 146) (:id . 65))\n ((:tag . "NNP") (:stem . "Biology") (:form . "Biology") (:end . 163)\n  (:start . 156) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Cambridge") (:form . "Cambridge") (:end . 174)\n  (:start . 165) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "England") (:form . "England") (:end . 183)\n  (:start . 176) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "UK") (:form . "UK") (:end . 187) (:start . 185)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 73))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 192) (:start . 189)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "cotransfecte") (:form . "cotransfected")\n  (:end . 206) (:start . 193) (:id . 75))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 211) (:start . 207)\n  (:id . 76))\n ((:tag . "NN") (:stem . "pe1bluc") (:form . "pE1BLuc") (:end . 219)\n  (:start . 212) (:id . 77))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 230)\n  (:start . 220) (:id . 78))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 236)\n  (:start . 231) (:id . 79))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 246)\n  (:start . 237) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 247) (:start . 246)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s2.297) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500513@unknown@formal@none@1@S@1 µg CMV promoter-driven Renilla luciferase expression vector (Promega) was included in all transfections and used as an internal control for transfection efficiency.@(((:tag . "CD") (:stem . "1") (:form . "1") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µg") (:form . "µg") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "CMV") (:form . "CMV") (:end . 8) (:start . 5)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "promoter-driven") (:form . "promoter-driven")\n  (:end . 24) (:start . 9) (:id . 45))\n ((:tag . "NNP") (:stem . "Renilla") (:form . "Renilla") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 54)\n  (:start . 44) (:id . 48))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 61)\n  (:start . 55) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Promega") (:form . "Promega") (:end . 70)\n  (:start . 63) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 75) (:start . 72)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 84)\n  (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "transfection") (:form . "transfections")\n  (:end . 105) (:start . 92) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 114) (:start . 110)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 120) (:start . 118)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 129)\n  (:start . 121) (:id . 62))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 137)\n  (:start . 130) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 141) (:start . 138)\n  (:id . 64))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 154)\n  (:start . 142) (:id . 65))\n ((:tag . "NN") (:stem . "efficiency") (:form . "efficiency") (:end . 165)\n  (:start . 155) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.298) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500514@unknown@formal@none@1@S@Ramos cells were treated for 72 h in hormone-depleted serum before the 4-h hormone treatment.@(((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "hormone-depleted") (:form . "hormone-depleted")\n  (:end . 53) (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "serum") (:form . "serum") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "IN") (:stem . "before") (:form . "before") (:end . 66)\n  (:start . 60) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "4-h") (:form . "4-h") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 82)\n  (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 92)\n  (:start . 83) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s2.299) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500515@unknown@formal@none@1@S@EMSA was performed by standard protocol (68) with minor modifications (for more detail see Supplemental materials and methods).@(((:tag . "NNP") (:stem . "EMSA") (:form . "EMSA") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "CD") (:stem . "68") (:form . "68") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 49) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "minor") (:form . "minor") (:end . 55) (:start . 50)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "modification") (:form . "modifications")\n  (:end . 69) (:start . 56) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 79) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "detail") (:form . "detail") (:end . 86)\n  (:start . 80) (:id . 57))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 103)\n  (:start . 91) (:id . 59))\n ((:tag . "NNS") (:stem . "material") (:form . "materials") (:end . 113)\n  (:start . 104) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 125)\n  (:start . 118) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.300) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500516@unknown@formal@none@1@S@0.25 pmol of complementary oligonucleotides containing either NF-κB or putative ER binding elements were annealed, labeled, and added to 7 µg of Ramos (treated or untreated) nuclear extract.@(((:tag . "CD") (:stem . "0.25") (:form . "0.25") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "pmol") (:form . "pmol") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "complementary") (:form . "complementary")\n  (:end . 26) (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "oligonucleotide") (:form . "oligonucleotides")\n  (:end . 43) (:start . 27) (:id . 46))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 54)\n  (:start . 44) (:id . 47))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 61)\n  (:start . 55) (:id . 48))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 67) (:start . 62)\n  (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 70) (:start . 68)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 79)\n  (:start . 71) (:id . 51))\n ((:tag . "NN") (:stem . "er") (:form . "ER") (:end . 82) (:start . 80)\n  (:id . 52))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 90)\n  (:start . 83) (:id . 53))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 99)\n  (:start . 91) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 104) (:start . 100)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "anneal") (:form . "annealed") (:end . 113)\n  (:start . 105) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 122)\n  (:start . 115) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "add") (:form . "added") (:end . 133) (:start . 128)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 136) (:start . 134)\n  (:id . 62))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 138) (:start . 137)\n  (:id . 63))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 141) (:start . 139)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 152) (:start . 151)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 159)\n  (:start . 152) (:id . 68))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 162) (:start . 160)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 172)\n  (:start . 163) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 173) (:start . 172)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 181)\n  (:start . 174) (:id . 72))\n ((:tag . "NN") (:stem . "extract") (:form . "extract") (:end . 189)\n  (:start . 182) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x2.301.1) (:span 71 79)))\n (:hscopes ((:id . :x2.301.1) (:span 71 99)))\n (:identifiers (:sid . :s2.301) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500517@unknown@formal@none@1@S@Reactions were incubated for 20 min at room temperature in the absence or presence of 1-, 3-, and 10-fold mass excess of unlabeled oligonucleotides or antibodies.@(((:tag . "NNS") (:stem . "reaction") (:form . "Reactions") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "room") (:form . "room") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 55)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 82)\n  (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "1-") (:form . "1-") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 58))\n ((:tag . "NN") (:stem . "3-") (:form . "3-") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "10-fold") (:form . "10-fold") (:end . 105)\n  (:start . 98) (:id . 62))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 110) (:start . 106)\n  (:id . 63))\n ((:tag . "NN") (:stem . "excess") (:form . "excess") (:end . 117)\n  (:start . 111) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "unlabeled") (:form . "unlabeled") (:end . 130)\n  (:start . 121) (:id . 66))\n ((:tag . "NNS") (:stem . "oligonucleotide") (:form . "oligonucleotides")\n  (:end . 147) (:start . 131) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 150) (:start . 148)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 161)\n  (:start . 151) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.302) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500518@unknown@formal@none@1@S@Samples were electrophoresed at 4°C on 4.5% polyacrylamide gels for 120 min, followed by autoradiography on imaging plates (FujiFilm) and analysis with a FLA-5000 Scanner (FujiFilm).@(((:tag . "NNS") (:stem . "sample") (:form . "Samples") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "electrophorese") (:form . "electrophoresed")\n  (:end . 28) (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 31) (:start . 29)\n  (:id . 45))\n ((:tag . "NN") (:stem . "4°c") (:form . "4°C") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "CD") (:stem . "4.5") (:form . "4.5") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "polyacrylamide") (:form . "polyacrylamide")\n  (:end . 58) (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "gel") (:form . "gels") (:end . 63) (:start . 59)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "CD") (:stem . "120") (:form . "120") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 85)\n  (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "autoradiography") (:form . "autoradiography")\n  (:end . 104) (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . "NN") (:stem . "imaging") (:form . "imaging") (:end . 115)\n  (:start . 108) (:id . 60))\n ((:tag . "NNS") (:stem . "plate") (:form . "plates") (:end . 122)\n  (:start . 116) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "FujiFilm") (:form . "FujiFilm") (:end . 132)\n  (:start . 124) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 65))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 146)\n  (:start . 138) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 151) (:start . 147)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "FLA-5000") (:form . "FLA-5000") (:end . 162)\n  (:start . 154) (:id . 69))\n ((:tag . "NNP") (:stem . "Scanner") (:form . "Scanner") (:end . 170)\n  (:start . 163) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "FujiFilm") (:form . "FujiFilm") (:end . 180)\n  (:start . 172) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 181) (:start . 180)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s2.303) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500519@unknown@formal@none@1@S@Ramos cells were treated for 72 h in hormone-depleted serum before the 4-h hormone treatment.@(((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "hormone-depleted") (:form . "hormone-depleted")\n  (:end . 53) (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "serum") (:form . "serum") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "IN") (:stem . "before") (:form . "before") (:end . 66)\n  (:start . 60) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "4-h") (:form . "4-h") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 82)\n  (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 92)\n  (:start . 83) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s2.304) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500520@unknown@formal@none@1@S@ChIP procedure was done as previously published, with minor modifications (69) (for further details see Supplemental materials and methods).@(((:tag . "NN") (:stem . "chip") (:form . "ChIP") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "do") (:form . "done") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "VBN") (:stem . "publish") (:form . "published") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "minor") (:form . "minor") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "modification") (:form . "modifications")\n  (:end . 73) (:start . 60) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "CD") (:stem . "69") (:form . "69") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 91)\n  (:start . 84) (:id . 58))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 99)\n  (:start . 92) (:id . 59))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 116)\n  (:start . 104) (:id . 61))\n ((:tag . "NNS") (:stem . "material") (:form . "materials") (:end . 126)\n  (:start . 117) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 138)\n  (:start . 131) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s2.305) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500521@unknown@formal@none@1@S@Approximately 107 cells were fixed with 1% formaldehyde in the culture media for 10 min at 37°C, and then quenched with 0.125 M glycine for 5 min at RT.@(((:tag . "RB") (:stem . "approximately") (:form . "Approximately")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "CD") (:stem . "107") (:form . "107") (:end . 17) (:start . 14)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "formaldehyde") (:form . "formaldehyde") (:end . 55)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "NNS") (:stem . "medium") (:form . "media") (:end . 76)\n  (:start . 71) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 95) (:start . 91)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 61))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 105) (:start . 101)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "quench") (:form . "quenched") (:end . 114)\n  (:start . 106) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 119) (:start . 115)\n  (:id . 64))\n ((:tag . "CD") (:stem . "0.125") (:form . "0.125") (:end . 125)\n  (:start . 120) (:id . 65))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 127) (:start . 126)\n  (:id . 66))\n ((:tag . "NN") (:stem . "glycine") (:form . "glycine") (:end . 135)\n  (:start . 128) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 139) (:start . 136)\n  (:id . 68))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 141) (:start . 140)\n  (:id . 69))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 145) (:start . 142)\n  (:id . 70))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 148) (:start . 146)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "RT") (:form . "RT") (:end . 151) (:start . 149)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.306) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500522@unknown@formal@none@1@S@Cells were pelleted and washed twice with cold PBS.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "pellete") (:form . "pelleted") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "wash") (:form . "washed") (:end . 30) (:start . 24)\n  (:id . 46))\n ((:tag . "RB") (:stem . "twice") (:form . "twice") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "cold") (:form . "cold") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "PBS") (:form . "PBS") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 51) (:start . 50)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.307) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500523@unknown@formal@none@1@S@The cell pellet was resuspended in 300 µl SDS lysis buffer and incubated on ice for 10 min.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "pellet") (:form . "pellet") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "resuspend") (:form . "resuspended") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "CD") (:stem . "300") (:form . "300") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "SDS") (:form . "SDS") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "lysis") (:form . "lysis") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 58)\n  (:start . 52) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 72)\n  (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "ice") (:form . "ice") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 86) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 90) (:start . 87)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.308) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500524@unknown@formal@none@1@S@Cell lysates were sonicated for 6 min with a 30-s on/off sonication cycle in 1.5 ml eppendorf tubes.@(((:tag . "NN") (:stem . "cell") (:form . "Cell") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "lysate") (:form . "lysates") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "sonicate") (:form . "sonicated") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "30-") (:form . "30-s") (:end . 49) (:start . 45)\n  (:id . 51))\n ((:tag . "IN") (:stem . "on/off") (:form . "on/off") (:end . 56)\n  (:start . 50) (:id . 52))\n ((:tag . "NN") (:stem . "sonication") (:form . "sonication") (:end . 67)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "CD") (:stem . "1.5") (:form . "1.5") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "NN") (:stem . "ml") (:form . "ml") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "eppendorf") (:form . "eppendorf") (:end . 93)\n  (:start . 84) (:id . 58))\n ((:tag . "NNS") (:stem . "tube") (:form . "tubes") (:end . 99) (:start . 94)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.309) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500525@unknown@formal@none@1@S@Samples were centrifuged for 5 min at 13,000 rpm at 4°C, and supernatants were diluted to 1.5 ml with ChIP buffer.@(((:tag . "NNS") (:stem . "sample") (:form . "Samples") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "centrifuge") (:form . "centrifuged") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "CD") (:stem . "13,000") (:form . "13,000") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "rpm") (:form . "rpm") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "4°c") (:form . "4°C") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "supernatant") (:form . "supernatants") (:end . 73)\n  (:start . 61) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 78) (:start . 74)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "dilute") (:form . "diluted") (:end . 86)\n  (:start . 79) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1.5") (:form . "1.5") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "NN") (:stem . "ml") (:form . "ml") (:end . 96) (:start . 94)\n  (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 101) (:start . 97)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "ChIP") (:form . "ChIP") (:end . 106) (:start . 102)\n  (:id . 62))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 113)\n  (:start . 107) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.310) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500526@unknown@formal@none@1@S@An aliquot was kept as input measurement.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "aliquot") (:form . "aliquot") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "keep") (:form . "kept") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "measurement") (:form . "measurement") (:end . 40)\n  (:start . 29) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 41) (:start . 40)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s2.311) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500527@unknown@formal@none@1@S@Samples were precleared with 60 µl Protein G beads (ProtG; Roche) and 1 µg salmon sperm DNA (Invitrogen) for 45 min at 4°C.@(((:tag . "NNS") (:stem . "sample") (:form . "Samples") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "precleare") (:form . "precleared") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "bead") (:form . "beads") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "ProtG") (:form . "ProtG") (:end . 57) (:start . 52)\n  (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Roche") (:form . "Roche") (:end . 64) (:start . 59)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 71) (:start . 70)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "µg") (:form . "µg") (:end . 74) (:start . 72)\n  (:id . 58))\n ((:tag . "NN") (:stem . "salmon") (:form . "salmon") (:end . 81)\n  (:start . 75) (:id . 59))\n ((:tag . "NN") (:stem . "sperm") (:form . "sperm") (:end . 87) (:start . 82)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 91) (:start . 88)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 103)\n  (:start . 93) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 108) (:start . 105)\n  (:id . 65))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 111) (:start . 109)\n  (:id . 66))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 115) (:start . 112)\n  (:id . 67))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 118) (:start . 116)\n  (:id . 68))\n ((:tag . "NN") (:stem . "4°c") (:form . "4°C") (:end . 122) (:start . 119)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s2.312) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500528@unknown@formal@none@1@S@Anti–NF-κB p65 antibody, rabbit anti-ERα HC-20 antibody (Santa Cruz Biotechnology, Inc.), or goat anti–mouse λ control antibody (see Supplemental materials and methods) was added to the supernatant at a concentration of 2 µg/assay and incubated for 12 h at 4°C.@(((:tag . "JJ") (:stem . "anti–nf-κb") (:form . "Anti–NF-κB") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "p65") (:form . "p65") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "rabbit") (:form . "rabbit") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "anti-erα") (:form . "anti-ERα") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "NNP") (:stem . "HC-20") (:form . "HC-20") (:end . 46) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Santa") (:form . "Santa") (:end . 62) (:start . 57)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Cruz") (:form . "Cruz") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Biotechnology") (:form . "Biotechnology")\n  (:end . 81) (:start . 68) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Inc.") (:form . "Inc.") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "goat") (:form . "goat") (:end . 97) (:start . 93)\n  (:id . 59))\n ((:tag . "NN") (:stem . "anti–mouse") (:form . "anti–mouse") (:end . 108)\n  (:start . 98) (:id . 60))\n ((:tag . "NN") (:stem . "λ") (:form . "λ") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 118)\n  (:start . 111) (:id . 62))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 127)\n  (:start . 119) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 64))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 132) (:start . 129)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 145)\n  (:start . 133) (:id . 66))\n ((:tag . "NNS") (:stem . "material") (:form . "materials") (:end . 155)\n  (:start . 146) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 167)\n  (:start . 160) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 168) (:start . 167)\n  (:id . 70))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 172) (:start . 169)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 178) (:start . 173)\n  (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 181) (:start . 179)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n  (:id . 74))\n ((:tag . "NN") (:stem . "supernatant") (:form . "supernatant") (:end . 197)\n  (:start . 186) (:id . 75))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 200) (:start . 198)\n  (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 202) (:start . 201)\n  (:id . 77))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 216) (:start . 203) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 219) (:start . 217)\n  (:id . 79))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 221) (:start . 220)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "µg/assay") (:form . "µg/assay") (:end . 230)\n  (:start . 222) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 234) (:start . 231)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 244)\n  (:start . 235) (:id . 83))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 248) (:start . 245)\n  (:id . 84))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 251) (:start . 249)\n  (:id . 85))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 253) (:start . 252)\n  (:id . 86))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 256) (:start . 254)\n  (:id . 87))\n ((:tag . "NN") (:stem . "4°c") (:form . "4°C") (:end . 260) (:start . 257)\n  (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 261) (:start . 260)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s2.313) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500529@unknown@formal@none@1@S@60 µl of salmon sperm DNA (1 µg DNA/20 µl ProtG) was added to the samples and incubated for 1 h while rotating.@(((:tag . "CD") (:stem . "60") (:form . "60") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "salmon") (:form . "salmon") (:end . 15) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sperm") (:form . "sperm") (:end . 21) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 28) (:start . 27)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "µg") (:form . "µg") (:end . 31) (:start . 29)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "DNA/20") (:form . "DNA/20") (:end . 38)\n  (:start . 32) (:id . 51))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 41) (:start . 39)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "ProtG") (:form . "ProtG") (:end . 47) (:start . 42)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 52) (:start . 49)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 58) (:start . 53)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 73)\n  (:start . 66) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 87)\n  (:start . 78) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 91) (:start . 88)\n  (:id . 62))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 93) (:start . 92)\n  (:id . 63))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 95) (:start . 94)\n  (:id . 64))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 101) (:start . 96)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "rotate") (:form . "rotating") (:end . 110)\n  (:start . 102) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.314) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500530@unknown@formal@none@1@S@The ProtG–antibody–protein complex was pelleted and washed with the following buffers: low-salt wash buffer, high-salt wash buffer, LiCl wash buffer, and standard TE buffer (twice).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "ProtG–antibody–protein")\n  (:form . "ProtG–antibody–protein") (:end . 26) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 34)\n  (:start . 27) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 38) (:start . 35)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "pellete") (:form . "pelleted") (:end . 47)\n  (:start . 39) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "wash") (:form . "washed") (:end . 58) (:start . 52)\n  (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 63) (:start . 59)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 77)\n  (:start . 68) (:id . 51))\n ((:tag . "NNS") (:stem . "buffer") (:form . "buffers") (:end . 85)\n  (:start . 78) (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 86) (:start . 85)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "low-salt") (:form . "low-salt") (:end . 95)\n  (:start . 87) (:id . 54))\n ((:tag . "NN") (:stem . "wash") (:form . "wash") (:end . 100) (:start . 96)\n  (:id . 55))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 107)\n  (:start . 101) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "high-salt") (:form . "high-salt") (:end . 118)\n  (:start . 109) (:id . 58))\n ((:tag . "NN") (:stem . "wash") (:form . "wash") (:end . 123) (:start . 119)\n  (:id . 59))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 130)\n  (:start . 124) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "LiCl") (:form . "LiCl") (:end . 136) (:start . 132)\n  (:id . 62))\n ((:tag . "NN") (:stem . "wash") (:form . "wash") (:end . 141) (:start . 137)\n  (:id . 63))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 148)\n  (:start . 142) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 153) (:start . 150)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 162)\n  (:start . 154) (:id . 67))\n ((:tag . "NN") (:stem . "te") (:form . "TE") (:end . 165) (:start . 163)\n  (:id . 68))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 172)\n  (:start . 166) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 70))\n ((:tag . "RB") (:stem . "twice") (:form . "twice") (:end . 179)\n  (:start . 174) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.315) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500531@unknown@formal@none@1@S@The sample was eluted with 250 µl of elution buffer and incubated for 15 min at room temperature with agitation.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "elute") (:form . "eluted") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "CD") (:stem . "250") (:form . "250") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "µl") (:form . "µl") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "elution") (:form . "elution") (:end . 44)\n  (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 51)\n  (:start . 45) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 65)\n  (:start . 56) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . "NN") (:stem . "room") (:form . "room") (:end . 84) (:start . 80)\n  (:id . 58))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 96)\n  (:start . 85) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 101) (:start . 97)\n  (:id . 60))\n ((:tag . "NN") (:stem . "agitation") (:form . "agitation") (:end . 111)\n  (:start . 102) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.316) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500532@unknown@formal@none@1@S@The beads were centrifuged and the elution was repeated once.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "bead") (:form . "beads") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "centrifuge") (:form . "centrifuged") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "elution") (:form . "elution") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "repeat") (:form . "repeated") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "RB") (:stem . "once") (:form . "once") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.317) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500533@unknown@formal@none@1@S@Bound immunocomplexes were then reverse cross-linked with 200 mM NaCl by incubating it at 65°C for 12 h.@(((:tag . "NN") (:stem . "bound") (:form . "Bound") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "immunocomplex") (:form . "immunocomplexes")\n  (:end . 21) (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 26) (:start . 22)\n  (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 31) (:start . 27)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 39)\n  (:start . 32) (:id . 46))\n ((:tag . "VBN") (:stem . "cross-linke") (:form . "cross-linked") (:end . 52)\n  (:start . 40) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 57) (:start . 53)\n  (:id . 48))\n ((:tag . "CD") (:stem . "200") (:form . "200") (:end . 61) (:start . 58)\n  (:id . 49))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "NaCl") (:form . "NaCl") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "incubate") (:form . "incubating") (:end . 83)\n  (:start . 73) (:id . 53))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 86) (:start . 84)\n  (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "65°c") (:form . "65°C") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 101) (:start . 99)\n  (:id . 58))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s2.318) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500534@unknown@formal@none@1@S@Proteinase K was added to the sample and incubated for 1 h at 45°C.@(((:tag . "NNP") (:stem . "Proteinase") (:form . "Proteinase") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "K") (:form . "K") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 50)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 61) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "45°c") (:form . "45°C") (:end . 66) (:start . 62)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.319) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500535@unknown@formal@none@1@S@DNA was then extracted with phenol/chloroform and precipitated, resuspended in 50 µl of water and subjected to qRT-PCR, using CHIP1 and CHIP2 primers for amplifying the -1,189 to -1,039 region of the AID promoter.@(((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "phenol/chloroform") (:form . "phenol/chloroform")\n  (:end . 45) (:start . 28) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "precipitate") (:form . "precipitated") (:end . 62)\n  (:start . 50) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "resuspend") (:form . "resuspended") (:end . 75)\n  (:start . 64) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 52))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "NN") (:stem . "µl") (:form . "µl") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "water") (:form . "water") (:end . 93) (:start . 88)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "subject") (:form . "subjected") (:end . 107)\n  (:start . 98) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 118)\n  (:start . 111) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 125) (:start . 120)\n  (:id . 62))\n ((:tag . "NN") (:stem . "chip1") (:form . "CHIP1") (:end . 131)\n  (:start . 126) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 64))\n ((:tag . "NN") (:stem . "chip2") (:form . "CHIP2") (:end . 141)\n  (:start . 136) (:id . 65))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 149)\n  (:start . 142) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 153) (:start . 150)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "amplify") (:form . "amplifying") (:end . 164)\n  (:start . 154) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 69))\n ((:tag . "CD") (:stem . "-1,189") (:form . "-1,189") (:end . 175)\n  (:start . 169) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 178) (:start . 176)\n  (:id . 71))\n ((:tag . "CD") (:stem . "-1,039") (:form . "-1,039") (:end . 185)\n  (:start . 179) (:id . 72))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 192)\n  (:start . 186) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 195) (:start . 193)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 199) (:start . 196)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 203) (:start . 200)\n  (:id . 76))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 212)\n  (:start . 204) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s2.320) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500536@unknown@formal@none@1@S@The surface IgM (sIgM) expression was investigated in Ramos HS13 cells (41), which contain a stop codon in the λ locus, with reversion mutations resulting in sIgM production.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "IgM") (:form . "IgM") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "sIgM") (:form . "sIgM") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 33)\n  (:start . 23) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 50)\n  (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "HS13") (:form . "HS13") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 70) (:start . 65)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 82) (:start . 77)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 90)\n  (:start . 83) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 92) (:start . 91)\n  (:id . 61))\n ((:tag . "NN") (:stem . "stop") (:form . "stop") (:end . 97) (:start . 93)\n  (:id . 62))\n ((:tag . "NN") (:stem . "codon") (:form . "codon") (:end . 103) (:start . 98)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 65))\n ((:tag . "NN") (:stem . "λ") (:form . "λ") (:end . 112) (:start . 111)\n  (:id . 66))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 118)\n  (:start . 113) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 124) (:start . 120)\n  (:id . 69))\n ((:tag . "NN") (:stem . "reversion") (:form . "reversion") (:end . 134)\n  (:start . 125) (:id . 70))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 144)\n  (:start . 135) (:id . 71))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 154)\n  (:start . 145) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 157) (:start . 155)\n  (:id . 73))\n ((:tag . "NN") (:stem . "sigm") (:form . "sIgM") (:end . 162) (:start . 158)\n  (:id . 74))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 173)\n  (:start . 163) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s2.321) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500537@unknown@formal@none@1@S@IgM stained (anti–human IgM-FITC [Sigma, UK]) and sorted single sIgM-negative cells were grown for ~20 doublings, with fresh hormone containing media added every 48 h.@(((:tag . "NNP") (:stem . "IgM") (:form . "IgM") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "stain") (:form . "stained") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "anti–human") (:form . "anti–human") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "NNP") (:stem . "IgM-FITC") (:form . "IgM-FITC") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sigma") (:form . "Sigma") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "UK") (:form . "UK") (:end . 43) (:start . 41)\n  (:id . 50))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "sort") (:form . "sorted") (:end . 56) (:start . 50)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 63)\n  (:start . 57) (:id . 55))\n ((:tag . "JJ") (:stem . "sigm-negative") (:form . "sIgM-negative")\n  (:end . 77) (:start . 64) (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 83) (:start . 78)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 88) (:start . 84)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "grow") (:form . "grown") (:end . 94) (:start . 89)\n  (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 98) (:start . 95)\n  (:id . 60))\n ((:tag . "CD") (:stem . "~20") (:form . "~20") (:end . 102) (:start . 99)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "doubling") (:form . "doublings") (:end . 112)\n  (:start . 103) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 118) (:start . 114)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "fresh") (:form . "fresh") (:end . 124)\n  (:start . 119) (:id . 65))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 132)\n  (:start . 125) (:id . 66))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 143)\n  (:start . 133) (:id . 67))\n ((:tag . "NNS") (:stem . "medium") (:form . "media") (:end . 149)\n  (:start . 144) (:id . 68))\n ((:tag . "VBD") (:stem . "add") (:form . "added") (:end . 155) (:start . 150)\n  (:id . 69))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 161)\n  (:start . 156) (:id . 70))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 164) (:start . 162)\n  (:id . 71))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 166) (:start . 165)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s2.322) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500538@unknown@formal@none@1@S@The cells were then stained (anti–human IgM-FITC) for surface expression of IgM and analyzed by flow cytometry.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "anti–human") (:form . "anti–human") (:end . 39)\n  (:start . 29) (:id . 48))\n ((:tag . "NNP") (:stem . "IgM-FITC") (:form . "IgM-FITC") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 72)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "IgM") (:form . "IgM") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 92)\n  (:start . 84) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cytometry") (:form . "cytometry") (:end . 110)\n  (:start . 101) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.323) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500539@unknown@formal@none@1@S@VH and C regions were cloned and sequenced from hormonally treated (20 doublings) Ramos HS13 cells, as previously described (41).@(((:tag . "NNP") (:stem . "VH") (:form . "VH") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 8) (:start . 7)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 16)\n  (:start . 9) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "clone") (:form . "cloned") (:end . 28)\n  (:start . 22) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 42)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "RB") (:stem . "hormonally") (:form . "hormonally") (:end . 58)\n  (:start . 48) (:id . 51))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 66)\n  (:start . 59) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "doubling") (:form . "doublings") (:end . 80)\n  (:start . 71) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 87) (:start . 82)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "HS13") (:form . "HS13") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 98) (:start . 93)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 60))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 102) (:start . 100)\n  (:id . 61))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 113)\n  (:start . 103) (:id . 62))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 123)\n  (:start . 114) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 127) (:start . 125)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.324) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500540@unknown@formal@none@1@S@The human CD95/Fas locus was PCR amplified and sequenced from isolated genomic DNA, as previously described (18).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "CD95/Fas") (:form . "CD95/Fas") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pcr") (:form . "PCR") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "amplify") (:form . "amplified") (:end . 42)\n  (:start . 33) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 56)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 78)\n  (:start . 71) (:id . 53))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 97)\n  (:start . 87) (:id . 57))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 107)\n  (:start . 98) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s2.325) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500541@unknown@formal@none@1@S@Mouse Sγ3 switch regions were analyzed from 2 AID+/- spleens and treated with either DMSO alone or 10 nM estrogen for 6 d.@(((:tag . "NNP") (:stem . "Mouse") (:form . "Mouse") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Sγ3") (:form . "Sγ3") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "aid+/-") (:form . "AID+/-") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "spleen") (:form . "spleens") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 84)\n  (:start . 78) (:id . 55))\n ((:tag . "NN") (:stem . "dmso") (:form . "DMSO") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 95) (:start . 90)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 98) (:start . 96)\n  (:id . 58))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 113)\n  (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 119) (:start . 118)\n  (:id . 63))\n ((:tag . "NN") (:stem . "d") (:form . "d") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.326) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500542@unknown@formal@none@1@S@AID+/- were derived from breeding AID-/- (gift from T. Honjo, Kyoto University, Kyoto, Japan) with BALB/c mice.@(((:tag . "NNP") (:stem . "AID+/-") (:form . "AID+/-") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "breed") (:form . "breeding") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "aid-/-") (:form . "AID-/-") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "gift") (:form . "gift") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "T.") (:form . "T.") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Honjo") (:form . "Honjo") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Kyoto") (:form . "Kyoto") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "University") (:form . "University") (:end . 78)\n  (:start . 68) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Kyoto") (:form . "Kyoto") (:end . 85) (:start . 80)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Japan") (:form . "Japan") (:end . 92) (:start . 87)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 98) (:start . 94)\n  (:id . 61))\n ((:tag . "NN") (:stem . "balb/c") (:form . "BALB/c") (:end . 105)\n  (:start . 99) (:id . 62))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 110)\n  (:start . 106) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s2.327) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500543@unknown@formal@none@1@S@Cloning and sequencing were as previously described (42).@(((:tag . "NN") (:stem . "cloning") (:form . "Cloning") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 51)\n  (:start . 42) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n  (:id . 49))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.328) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500544@unknown@formal@none@1@S@Sequencing was performed at the LRI sequencing facility.@(((:tag . "NNP") (:stem . "Sequencing") (:form . "Sequencing") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "LRI") (:form . "LRI") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 46)\n  (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "facility") (:form . "facility") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s2.329) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500545@unknown@formal@none@1@S@Further details are described in the Supplemental materials and methods.@(((:tag . "JJ") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 29)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 49)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "material") (:form . "materials") (:end . 59)\n  (:start . 50) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 71)\n  (:start . 64) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.330) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500546@unknown@formal@none@1@S@c-myc/IgH translocations were detected by PCR as previously described (47, 70).@(((:tag . "NN") (:stem . "c-myc/igh") (:form . "c-myc/IgH") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 24) (:start . 10) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 38)\n  (:start . 30) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 45) (:start . 42)\n  (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 59)\n  (:start . 49) (:id . 49))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 69)\n  (:start . 60) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 51))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 53))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.331) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500547@unknown@formal@none@1@S@In brief, DNA was isolated from p53+/- B cells after 72 h of LPS stimulation in the presence or absence of 50 nM estrogen.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "brief") (:form . "brief") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 17) (:start . 14)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 26)\n  (:start . 18) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "p53+/-") (:form . "p53+/-") (:end . 38)\n  (:start . 32) (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 46) (:start . 41)\n  (:id . 51))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 52) (:start . 47)\n  (:id . 52))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 55) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 57) (:start . 56)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 64) (:start . 61)\n  (:id . 56))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 76)\n  (:start . 65) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 59))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 92)\n  (:start . 84) (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 95) (:start . 93)\n  (:id . 61))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 103)\n  (:start . 96) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 63))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 109) (:start . 107)\n  (:id . 64))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 112) (:start . 110)\n  (:id . 65))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 121)\n  (:start . 113) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s2.332) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500548@unknown@formal@none@1@S@Two rounds of PCR (for primers see Supplemental materials and methods) were performed using Expand Long Template PCR system (Roche) with primers MycIg1A and primers MycIg1B in the first round, and MycIg2A and MycIg2B in the second round.@(((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "round") (:form . "rounds") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 30)\n  (:start . 23) (:id . 48))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 34) (:start . 31)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 47)\n  (:start . 35) (:id . 50))\n ((:tag . "NNS") (:stem . "material") (:form . "materials") (:end . 57)\n  (:start . 48) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 69)\n  (:start . 62) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 75) (:start . 71)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 85)\n  (:start . 76) (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 91) (:start . 86)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Expand") (:form . "Expand") (:end . 98)\n  (:start . 92) (:id . 58))\n ((:tag . "NNP") (:stem . "Long") (:form . "Long") (:end . 103) (:start . 99)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Template") (:form . "Template") (:end . 112)\n  (:start . 104) (:id . 60))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 123)\n  (:start . 117) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Roche") (:form . "Roche") (:end . 130)\n  (:start . 125) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 136) (:start . 132)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 144)\n  (:start . 137) (:id . 67))\n ((:tag . "NNP") (:stem . "MycIg1A") (:form . "MycIg1A") (:end . 152)\n  (:start . 145) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 164)\n  (:start . 157) (:id . 70))\n ((:tag . "NN") (:stem . "mycig1b") (:form . "MycIg1B") (:end . 172)\n  (:start . 165) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 175) (:start . 173)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 185)\n  (:start . 180) (:id . 74))\n ((:tag . "NN") (:stem . "round") (:form . "round") (:end . 191)\n  (:start . 186) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 192) (:start . 191)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 196) (:start . 193)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "MycIg2A") (:form . "MycIg2A") (:end . 204)\n  (:start . 197) (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 208) (:start . 205)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "MycIg2B") (:form . "MycIg2B") (:end . 216)\n  (:start . 209) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 219) (:start . 217)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 223) (:start . 220)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 230)\n  (:start . 224) (:id . 83))\n ((:tag . "NN") (:stem . "round") (:form . "round") (:end . 236)\n  (:start . 231) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 237) (:start . 236)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s2.333) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500549@unknown@formal@none@1@S@PCR products were separated on agarose gels, transferred to nylon membranes, and probed with γ-[P32]-ATP–labeled oligonucleotides IgH probe and c-myc probe.@(((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "agarose") (:form . "agarose") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "NNS") (:stem . "gel") (:form . "gels") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "transfer") (:form . "transferred") (:end . 56)\n  (:start . 45) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "nylon") (:form . "nylon") (:end . 65) (:start . 60)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 75)\n  (:start . 66) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "probe") (:form . "probed") (:end . 87)\n  (:start . 81) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 92) (:start . 88)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "γ-[P32]-ATP–labeled")\n  (:form . "γ-[P32]-ATP–labeled") (:end . 112) (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "oligonucleotide") (:form . "oligonucleotides")\n  (:end . 129) (:start . 113) (:id . 59))\n ((:tag . "NN") (:stem . "igh") (:form . "IgH") (:end . 133) (:start . 130)\n  (:id . 60))\n ((:tag . "NN") (:stem . "probe") (:form . "probe") (:end . 139)\n  (:start . 134) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 62))\n ((:tag . "NN") (:stem . "c-myc") (:form . "c-myc") (:end . 149)\n  (:start . 144) (:id . 63))\n ((:tag . "NN") (:stem . "probe") (:form . "probe") (:end . 155)\n  (:start . 150) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.334) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500550@unknown@formal@none@1@S@P values were calculated using two-tailed unpaired Student's t test.@(((:tag . "NN") (:stem . "p") (:form . "P") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "two-tailed") (:form . "two-tailed") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "JJ") (:stem . "unpaired") (:form . "unpaired") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 58)\n  (:start . 51) (:id . 49))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "NN") (:stem . "t") (:form . "t") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.335) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500551@unknown@formal@none@1@S@Ig class switching was investigated by detecting switch-circle transcripts in stimulated mouse spleen B cells (40) by qRT-PCR (71).@(((:tag . "NNP") (:stem . "Ig") (:form . "Ig") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "switching") (:form . "switching") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 35)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "detect") (:form . "detecting") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "switch-circle") (:form . "switch-circle")\n  (:end . 62) (:start . 49) (:id . 49))\n ((:tag . "NNS") (:stem . "transcript") (:form . "transcripts") (:end . 74)\n  (:start . 63) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 88)\n  (:start . 78) (:id . 52))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 94) (:start . 89)\n  (:id . 53))\n ((:tag . "NN") (:stem . "spleen") (:form . "spleen") (:end . 101)\n  (:start . 95) (:id . 54))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 103) (:start . 102)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 109)\n  (:start . 104) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 57))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 113) (:start . 111)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 125)\n  (:start . 118) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 62))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s2.336) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500552@unknown@formal@none@1@S@Isolated splenic B-cells were stimulated for up to 72 h with LPS + IL-4 for inducing switching to IgG1 and IgE, LPS + TGF-ß for switching to IgA, and LPS + IFN-γ for switching to IgG3.@(((:tag . "VBN") (:stem . "isolate") (:form . "Isolated") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "splenic") (:form . "splenic") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "b-cell") (:form . "B-cells") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "RB") (:stem . "up") (:form . "up") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "CC") (:stem . "+") (:form . "+") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "NN") (:stem . "il-4") (:form . "IL-4") (:end . 71) (:start . 67)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "induce") (:form . "inducing") (:end . 84)\n  (:start . 76) (:id . 57))\n ((:tag . "NN") (:stem . "switching") (:form . "switching") (:end . 94)\n  (:start . 85) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "IgG1") (:form . "IgG1") (:end . 102) (:start . 98)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "IgE") (:form . "IgE") (:end . 110) (:start . 107)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 115) (:start . 112)\n  (:id . 64))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 117) (:start . 116)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "TGF-ß") (:form . "TGF-ß") (:end . 123)\n  (:start . 118) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 127) (:start . 124)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "switch") (:form . "switching") (:end . 137)\n  (:start . 128) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 140) (:start . 138)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "IgA") (:form . "IgA") (:end . 144) (:start . 141)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 149) (:start . 146)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "LPS") (:form . "LPS") (:end . 153) (:start . 150)\n  (:id . 73))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 155) (:start . 154)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 161)\n  (:start . 156) (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 165) (:start . 162)\n  (:id . 76))\n ((:tag . "VBG") (:stem . "switch") (:form . "switching") (:end . 175)\n  (:start . 166) (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 178) (:start . 176)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "IgG3") (:form . "IgG3") (:end . 183) (:start . 179)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s2.337) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500553@unknown@formal@none@1@S@Hormones were added to the cells together with LPS and cytokines in fresh media.@(((:tag . "NNS") (:stem . "hormone") (:form . "Hormones") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "lps") (:form . "LPS") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 64)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "fresh") (:form . "fresh") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "medium") (:form . "media") (:end . 79)\n  (:start . 74) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.338) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500554@unknown@formal@none@1@S@Primers (Tables S4 and S5, available at http://www.jem.org/cgi/content/full/jem.20080521/DC1) that were used for detecting IgG1 (71), IgG3, IgA (40), and IgE (72), have been previously described.@(((:tag . "NNP") (:stem . "Primer") (:form . "Primers") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "Table") (:form . "Tables") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 36)\n  (:start . 27) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1") (:end . 92)\n  (:start . 40) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 98) (:start . 94)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 103) (:start . 99)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 108) (:start . 104)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 112) (:start . 109)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "detect") (:form . "detecting") (:end . 122)\n  (:start . 113) (:id . 57))\n ((:tag . "NN") (:stem . "igg1") (:form . "IgG1") (:end . 127) (:start . 123)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 59))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 131) (:start . 129)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "IgG3") (:form . "IgG3") (:end . 138) (:start . 134)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "IgA") (:form . "IgA") (:end . 143) (:start . 140)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 147) (:start . 145)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 153) (:start . 150)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "IgE") (:form . "IgE") (:end . 157) (:start . 154)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 72))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 161) (:start . 159)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 75))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 168) (:start . 164)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 173) (:start . 169)\n  (:id . 77))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 184)\n  (:start . 174) (:id . 78))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 194)\n  (:start . 185) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s2.339) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500555@unknown@formal@none@1@S@Mouse tissue was dissected (from two animals) and passed through cell strainers.@(((:tag . "NNP") (:stem . "Mouse") (:form . "Mouse") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "dissect") (:form . "dissected") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "pass") (:form . "passed") (:end . 56) (:start . 50)\n  (:id . 52))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 64)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 69) (:start . 65)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "strainer") (:form . "strainers") (:end . 79)\n  (:start . 70) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.340) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500556@unknown@formal@none@1@S@Cells were incubated for 6 h in hormone-depleted media before estrogen treatment for 4 h.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "hormone-depleted") (:form . "hormone-depleted")\n  (:end . 48) (:start . 32) (:id . 49))\n ((:tag . "NNS") (:stem . "medium") (:form . "media") (:end . 54)\n  (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "before") (:form . "before") (:end . 61)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 80)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 84) (:start . 81)\n  (:id . 54))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s2.341) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500557@unknown@formal@none@1@S@Total RNA was extracted, cDNA was synthesized, and gene expression was analyzed by qRT-PCR.@(((:tag . "JJ") (:stem . "total") (:form . "Total") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "cDNA") (:form . "cDNA") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "synthesize") (:form . "synthesized") (:end . 45)\n  (:start . 34) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 66)\n  (:start . 56) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 79)\n  (:start . 71) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 90)\n  (:start . 83) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.342) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500558@unknown@formal@none@1@S@All experiments were approved by the Cancer Research UK Animal Ethics Committee and the UK Home Office.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "approve") (:form . "approved") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Cancer") (:form . "Cancer") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "NNP") (:stem . "Research") (:form . "Research") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "NNP") (:stem . "UK") (:form . "UK") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Animal") (:form . "Animal") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "NNP") (:stem . "Ethics") (:form . "Ethics") (:end . 69)\n  (:start . 63) (:id . 52))\n ((:tag . "NNP") (:stem . "Committee") (:form . "Committee") (:end . 79)\n  (:start . 70) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "UK") (:form . "UK") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Home") (:form . "Home") (:end . 95) (:start . 91)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Office") (:form . "Office") (:end . 102)\n  (:start . 96) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s2.343) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500559@unknown@formal@none@1@S@The Supplemental materials and methods includes details for cells and reagents, qRT-PCR, promoter analysis, EMSA, ChIP, mutation analysis, and c-myc/IgH translocations.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "material") (:form . "materials") (:end . 26)\n  (:start . 17) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 47)\n  (:start . 39) (:id . 47))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 55)\n  (:start . 48) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 65) (:start . 60)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "reagent") (:form . "reagents") (:end . 78)\n  (:start . 70) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 87)\n  (:start . 80) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 97)\n  (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 106)\n  (:start . 98) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "EMSA") (:form . "EMSA") (:end . 112) (:start . 108)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "ChIP") (:form . "ChIP") (:end . 118) (:start . 114)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 62))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 128)\n  (:start . 120) (:id . 63))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 137)\n  (:start . 129) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 66))\n ((:tag . "NN") (:stem . "c-myc/igh") (:form . "c-myc/IgH") (:end . 152)\n  (:start . 143) (:id . 67))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 167) (:start . 153) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s2.344) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500560@unknown@formal@none@1@S@It also describes in detail the generation of endogenously tagged AID.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "describe") (:form . "describes") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "detail") (:form . "detail") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "RB") (:stem . "endogenously") (:form . "endogenously") (:end . 58)\n  (:start . 46) (:id . 50))\n ((:tag . "VBN") (:stem . "tag") (:form . "tagged") (:end . 65) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.345) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500561@unknown@formal@none@1@S@Fig. S1 describes the effect of Tam treatment and translation inhibitors on AID expression.@(((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "describe") (:form . "describes") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Tam") (:form . "Tam") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 45)\n  (:start . 36) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 61)\n  (:start . 50) (:id . 51))\n ((:tag . "NNS") (:stem . "inhibitor") (:form . "inhibitors") (:end . 72)\n  (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 90)\n  (:start . 80) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s2.346) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500562@unknown@formal@none@1@S@Fig. S2 shows the effect of estrogen on AID splicing.@(((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "AID") (:form . "AID") (:end . 43) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "splicing") (:form . "splicing") (:end . 52)\n  (:start . 44) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s2.347) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500563@unknown@formal@none@1@S@Fig. S3 demonstrates the effect of estrogen on NF-kB promoter binding.@(((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "demonstrate") (:form . "demonstrates") (:end . 20)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "NF-kB") (:form . "NF-kB") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 61)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 69)\n  (:start . 62) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.348) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500564@unknown@formal@none@1@S@Fig. S4 provides details on how we generated the DT40 AID knockin allele.@(((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 44)\n  (:start . 35) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dt40") (:form . "DT40") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "aid") (:form . "AID") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "knockin") (:form . "knockin") (:end . 65)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 72)\n  (:start . 66) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s2.349) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500565@unknown@formal@none@1@S@Fig. S5 is a schematic of class switching and switch circle formation.@(((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "schematic") (:form . "schematic") (:end . 22)\n  (:start . 13) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 31) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "switching") (:form . "switching") (:end . 41)\n  (:start . 32) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "switch") (:form . "switch") (:end . 52)\n  (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "circle") (:form . "circle") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 69)\n  (:start . 60) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s2.350) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500566@unknown@formal@none@1@S@Fig. S6 shows the effect of estrogen on Ramos Ig diversification.@(((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S6") (:form . "S6") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Ramos") (:form . "Ramos") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Ig") (:form . "Ig") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "diversification") (:form . "diversification")\n  (:end . 64) (:start . 49) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.351) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500567@unknown@formal@none@1@S@Fig. S7 provides details on the mutation analysis of IgH and CD95/Fas after estrogen treatment.@(((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "IgH") (:form . "IgH") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "CD95/Fas") (:form . "CD95/Fas") (:end . 69)\n  (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 75) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 84)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s2.352) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500568@unknown@formal@none@1@S@Fig. S8 provides details on the c-myc/IgH translocation analysis.@(((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S8") (:form . "S8") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "c-myc/igh") (:form . "c-myc/IgH") (:end . 41)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "translocation") (:form . "translocation")\n  (:end . 55) (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s2.353) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500569@unknown@formal@none@1@S@Fig. S9 shows the effect of estrogen on the expression of DNA deaminase family members in various cell lines.@(((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S9") (:form . "S9") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "estrogen") (:form . "estrogen") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 54)\n  (:start . 44) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "deaminase") (:form . "deaminase") (:end . 71)\n  (:start . 62) (:id . 54))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 78)\n  (:start . 72) (:id . 55))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 86)\n  (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 97)\n  (:start . 90) (:id . 58))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 108)\n  (:start . 103) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s2.354) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500570@unknown@formal@none@1@S@Fig. S10 provides absolute values of qRT-PCR analysis from selected experiments.@(((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S10") (:form . "S10") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "JJ") (:stem . "absolute") (:form . "absolute") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 53)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 67)\n  (:start . 59) (:id . 51))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 79)\n  (:start . 68) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s2.355) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500571@unknown@formal@none@1@S@We also included primer sequences used in this study in five tables (Tables S1-S5).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "include") (:form . "included") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "table") (:form . "tables") (:end . 67)\n  (:start . 61) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Table") (:form . "Tables") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . "NNP") (:stem . "S1-S5") (:form . "S1-S5") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s2.356) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500572@unknown@formal@none@1@S@Online supplemental material is available at http://www.jem.org/cgi/content/full/jem.20080521/DC1.@(((:tag . "NNP") (:stem . "Online") (:form . "Online") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "supplemental") (:end . 19)\n  (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 28)\n  (:start . 20) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 41)\n  (:start . 32) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "CD")\n  (:stem . "http://www.jem.org/cgi/content/full/jem.20080521/DC1")\n  (:form . "http://www.jem.org/cgi/content/full/jem.20080521/DC1") (:end . 97)\n  (:start . 45) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s2.357) (:did . :pmc2626679) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500573@unknown@formal@none@1@S@A Drosophila Model for EGFR-Ras and PI3K-Dependent Human Glioma@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 12)\n  (:start . 2) (:id . 43))\n ((:tag . "NNP") (:stem . "Model") (:form . "Model") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "pi3k-dependent") (:form . "PI3K-Dependent")\n  (:end . 50) (:start . 36) (:id . 48))\n ((:tag . "JJ") (:stem . "human") (:form . "Human") (:end . 56) (:start . 51)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Glioma") (:form . "Glioma") (:end . 63)\n  (:start . 57) (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.1) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5500574@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.2) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500575@unknown@formal@none@1@S@Gliomas, the most common malignant tumors of the nervous system, frequently harbor mutations that activate the epidermal growth factor receptor (EGFR) and phosphatidylinositol-3 kinase (PI3K) signaling pathways.@(((:tag . "NNP") (:stem . "Glioma") (:form . "Gliomas") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "JJ") (:stem . "malignant") (:form . "malignant") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 75)\n  (:start . 65) (:id . 54))\n ((:tag . "VBP") (:stem . "harbor") (:form . "harbor") (:end . 82)\n  (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 92)\n  (:start . 83) (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 97) (:start . 93)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "activate") (:form . "activate") (:end . 106)\n  (:start . 98) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "epidermal") (:form . "epidermal") (:end . 120)\n  (:start . 111) (:id . 60))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 127)\n  (:start . 121) (:id . 61))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 134)\n  (:start . 128) (:id . 62))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 143)\n  (:start . 135) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 149) (:start . 145)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "phosphatidylinositol-3")\n  (:form . "phosphatidylinositol-3") (:end . 177) (:start . 155) (:id . 68))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 184)\n  (:start . 178) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 186) (:start . 185)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 190) (:start . 186)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 191) (:start . 190)\n  (:id . 72))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 201)\n  (:start . 192) (:id . 73))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 210)\n  (:start . 202) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.3) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500576@unknown@formal@none@1@S@To investigate the genetic basis of this disease, we developed a glioma model in Drosophila.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "develop") (:form . "developed") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 71)\n  (:start . 65) (:id . 54))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 91)\n  (:start . 81) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.4) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500577@unknown@formal@none@1@S@We found that constitutive coactivation of EGFR-Ras and PI3K pathways in Drosophila glia and glial precursors gives rise to neoplastic, invasive glial cells that create transplantable tumor-like growths, mimicking human glioma.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 26)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "coactivation") (:form . "coactivation") (:end . 39)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 69)\n  (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 83)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 88) (:start . 84)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 109)\n  (:start . 99) (:id . 57))\n ((:tag . "VBZ") (:stem . "give") (:form . "gives") (:end . 115)\n  (:start . 110) (:id . 58))\n ((:tag . "NN") (:stem . "rise") (:form . "rise") (:end . 120) (:start . 116)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 123) (:start . 121)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 134)\n  (:start . 124) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 144)\n  (:start . 136) (:id . 63))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 150)\n  (:start . 145) (:id . 64))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 156)\n  (:start . 151) (:id . 65))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 161) (:start . 157)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "create") (:form . "create") (:end . 168)\n  (:start . 162) (:id . 67))\n ((:tag . "JJ") (:stem . "transplantable") (:form . "transplantable")\n  (:end . 183) (:start . 169) (:id . 68))\n ((:tag . "JJ") (:stem . "tumor-like") (:form . "tumor-like") (:end . 194)\n  (:start . 184) (:id . 69))\n ((:tag . "NNS") (:stem . "growth") (:form . "growths") (:end . 202)\n  (:start . 195) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 203) (:start . 202)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "mimic") (:form . "mimicking") (:end . 213)\n  (:start . 204) (:id . 72))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 219)\n  (:start . 214) (:id . 73))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 226)\n  (:start . 220) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.5) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500578@unknown@formal@none@1@S@Our model represents a robust organotypic and cell-type-specific Drosophila cancer model in which malignant cells are created by mutations in signature genes and pathways thought to be driving forces in a homologous human cancer.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "robust") (:form . "robust") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "JJ") (:stem . "organotypic") (:form . "organotypic") (:end . 41)\n  (:start . 30) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "cell-type-specific") (:form . "cell-type-specific")\n  (:end . 64) (:start . 46) (:id . 49))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 75)\n  (:start . 65) (:id . 50))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 82)\n  (:start . 76) (:id . 51))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 88) (:start . 83)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 97) (:start . 92)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "malignant") (:form . "malignant") (:end . 107)\n  (:start . 98) (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 113)\n  (:start . 108) (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 117) (:start . 114)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "create") (:form . "created") (:end . 125)\n  (:start . 118) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 128) (:start . 126)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 138)\n  (:start . 129) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n  (:id . 61))\n ((:tag . "NN") (:stem . "signature") (:form . "signature") (:end . 151)\n  (:start . 142) (:id . 62))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 157)\n  (:start . 152) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 170)\n  (:start . 162) (:id . 65))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 178)\n  (:start . 171) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 181) (:start . 179)\n  (:id . 67))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 184) (:start . 182)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "drive") (:form . "driving") (:end . 192)\n  (:start . 185) (:id . 69))\n ((:tag . "NNS") (:stem . "force") (:form . "forces") (:end . 199)\n  (:start . 193) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 202) (:start . 200)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 204) (:start . 203)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 215)\n  (:start . 205) (:id . 73))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 221)\n  (:start . 216) (:id . 74))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 228)\n  (:start . 222) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x3.6.1) (:span 171 178)))\n (:hscopes ((:id . :x3.6.1) (:span 171 228)))\n (:identifiers (:sid . :s3.6) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500579@unknown@formal@none@1@S@Genetic analyses demonstrated that EGFR and PI3K initiate malignant neoplastic transformation via a combinatorial genetic network composed primarily of other pathways commonly mutated or activated in human glioma, including the Tor, Myc, G1 Cyclins-Cdks, and Rb-E2F pathways.@(((:tag . "JJ") (:stem . "genetic") (:form . "Genetic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 29)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "initiate") (:form . "initiate") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "JJ") (:stem . "malignant") (:form . "malignant") (:end . 67)\n  (:start . 58) (:id . 50))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 78)\n  (:start . 68) (:id . 51))\n ((:tag . "NN") (:stem . "transformation") (:form . "transformation")\n  (:end . 93) (:start . 79) (:id . 52))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 97) (:start . 94)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "combinatorial") (:form . "combinatorial")\n  (:end . 113) (:start . 100) (:id . 55))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 121)\n  (:start . 114) (:id . 56))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 129)\n  (:start . 122) (:id . 57))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 138)\n  (:start . 130) (:id . 58))\n ((:tag . "RB") (:stem . "primarily") (:form . "primarily") (:end . 148)\n  (:start . 139) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 157)\n  (:start . 152) (:id . 61))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 166)\n  (:start . 158) (:id . 62))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 175)\n  (:start . 167) (:id . 63))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 183)\n  (:start . 176) (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 186) (:start . 184)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 196)\n  (:start . 187) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 199) (:start . 197)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 205)\n  (:start . 200) (:id . 68))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 212)\n  (:start . 206) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 213) (:start . 212)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 223)\n  (:start . 214) (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 227) (:start . 224)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 231) (:start . 228)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 232) (:start . 231)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 236) (:start . 233)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 237) (:start . 236)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "G1") (:form . "G1") (:end . 240) (:start . 238)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Cyclins-Cdk") (:form . "Cyclins-Cdks") (:end . 253)\n  (:start . 241) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 254) (:start . 253)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 258) (:start . 255)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Rb-E2F") (:form . "Rb-E2F") (:end . 265)\n  (:start . 259) (:id . 81))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 274)\n  (:start . 266) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 275) (:start . 274)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s3.7) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500580@unknown@formal@none@1@S@This network acts synergistically to coordinately stimulate cell cycle entry and progression, protein translation, and inappropriate cellular growth and migration.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "act") (:form . "acts") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "synergistically") (:form . "synergistically")\n  (:end . 33) (:start . 18) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "RB") (:stem . "coordinately") (:form . "coordinately") (:end . 49)\n  (:start . 37) (:id . 47))\n ((:tag . "VB") (:stem . "stimulate") (:form . "stimulate") (:end . 59)\n  (:start . 50) (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 64) (:start . 60)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 70) (:start . 65)\n  (:id . 50))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 76) (:start . 71)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 52))\n ((:tag . "NN") (:stem . "progression") (:form . "progression") (:end . 92)\n  (:start . 81) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 54))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 101)\n  (:start . 94) (:id . 55))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 113)\n  (:start . 102) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "inappropriate") (:form . "inappropriate")\n  (:end . 132) (:start . 119) (:id . 59))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 141)\n  (:start . 133) (:id . 60))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 148)\n  (:start . 142) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 62))\n ((:tag . "NN") (:stem . "migration") (:form . "migration") (:end . 162)\n  (:start . 153) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.8) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500581@unknown@formal@none@1@S@In particular, we found that the fly orthologs of CyclinE, Cdc25, and Myc are key rate-limiting genes required for glial neoplasia.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "fly") (:form . "fly") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 46)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "CyclinE") (:form . "CyclinE") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Cdc25") (:form . "Cdc25") (:end . 64) (:start . 59)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 73) (:start . 70)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 77) (:start . 74)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 81) (:start . 78)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "rate-limiting") (:form . "rate-limiting")\n  (:end . 95) (:start . 82) (:id . 60))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 101) (:start . 96)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 110)\n  (:start . 102) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 114) (:start . 111)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 120)\n  (:start . 115) (:id . 64))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 130)\n  (:start . 121) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.9) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500582@unknown@formal@none@1@S@Moreover, orthologs of Sin1, Rictor, and Cdk4 are genes required only for abnormal neoplastic glial proliferation but not for glial development.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sin1") (:form . "Sin1") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Rictor") (:form . "Rictor") (:end . 35)\n  (:start . 29) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Cdk4") (:form . "Cdk4") (:end . 45) (:start . 41)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 49) (:start . 46)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 55) (:start . 50)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 64)\n  (:start . 56) (:id . 54))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 69) (:start . 65)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 73) (:start . 70)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 82)\n  (:start . 74) (:id . 57))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 93)\n  (:start . 83) (:id . 58))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 99) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 113) (:start . 100) (:id . 60))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 131)\n  (:start . 126) (:id . 64))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 143)\n  (:start . 132) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.10) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500583@unknown@formal@none@1@S@These and other genes within this network may represent important therapeutic targets in human glioma.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "VB") (:stem . "represent") (:form . "represent") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 65)\n  (:start . 56) (:id . 51))\n ((:tag . "JJ") (:stem . "therapeutic") (:form . "therapeutic") (:end . 77)\n  (:start . 66) (:id . 52))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 85)\n  (:start . 78) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 94) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 101)\n  (:start . 95) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x3.11.1) (:span 42 45)))\n (:hscopes ((:id . :x3.11.1) (:span 42 101)))\n (:identifiers (:sid . :s3.11) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500584@unknown@formal@none@1@S@Author Summary@(((:tag . "NNP") (:stem . "Author") (:form . "Author") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Summary") (:form . "Summary") (:end . 14)\n  (:start . 7) (:id . 43)))@@@1@2@((:identifiers (:sid . :s3.12) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500585@unknown@formal@none@1@S@Malignant gliomas, tumors composed of glial cells and their precursors, are the most common and deadly human brain tumors.@(((:tag . "JJ") (:stem . "malignant") (:form . "Malignant") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 17)\n  (:start . 10) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 59)\n  (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 70)\n  (:start . 60) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 91)\n  (:start . 85) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "deadly") (:form . "deadly") (:end . 102)\n  (:start . 96) (:id . 59))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 108)\n  (:start . 103) (:id . 60))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 114)\n  (:start . 109) (:id . 61))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 121)\n  (:start . 115) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.13) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500586@unknown@formal@none@1@S@These tumors infiltrate the brain and proliferate rapidly, properties that render them largely incurable even with current therapies.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "infiltrate") (:form . "infiltrate") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "proliferate") (:form . "proliferate") (:end . 49)\n  (:start . 38) (:id . 48))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 69)\n  (:start . 59) (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "render") (:form . "render") (:end . 81)\n  (:start . 75) (:id . 53))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 94)\n  (:start . 87) (:id . 55))\n ((:tag . "JJ") (:stem . "incurable") (:form . "incurable") (:end . 104)\n  (:start . 95) (:id . 56))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 109) (:start . 105)\n  (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 114) (:start . 110)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 122)\n  (:start . 115) (:id . 59))\n ((:tag . "NNS") (:stem . "therapy") (:form . "therapies") (:end . 132)\n  (:start . 123) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.14) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500587@unknown@formal@none@1@S@Mutations in genes within the EGFR-Ras and PI3K signaling pathways are common in malignant gliomas, although how these genes specifically control glial pathogenesis is unclear.@(((:tag . "NNS") (:stem . "mutation") (:form . "Mutations") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NNPS") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 66)\n  (:start . 58) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 77)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "malignant") (:form . "malignant") (:end . 90)\n  (:start . 81) (:id . 55))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 98)\n  (:start . 91) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 108)\n  (:start . 100) (:id . 58))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 118)\n  (:start . 113) (:id . 60))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 124)\n  (:start . 119) (:id . 61))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 137)\n  (:start . 125) (:id . 62))\n ((:tag . "VBP") (:stem . "control") (:form . "control") (:end . 145)\n  (:start . 138) (:id . 63))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 151)\n  (:start . 146) (:id . 64))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 164)\n  (:start . 152) (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 167) (:start . 165)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 175)\n  (:start . 168) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x3.15.1) (:span 168 175)))\n (:hscopes ((:id . :x3.15.1) (:span 109 175)))\n (:identifiers (:sid . :s3.15) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500588@unknown@formal@none@1@S@To investigate the genetic basis of this disease, we developed a glioma model in the fruit fly, Drosophila melanogaster.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "develop") (:form . "developed") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 71)\n  (:start . 65) (:id . 54))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 90) (:start . 85)\n  (:id . 58))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 106)\n  (:start . 96) (:id . 61))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 119) (:start . 107) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.16) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500589@unknown@formal@none@1@S@We found that constitutive coactivation of the EGFR-Ras and PI3K pathways in Drosophila glia gives rise to highly proliferative and invasive neoplastic cells that create transplantable tumor-like growths, mimicking human glioma.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 26)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "coactivation") (:form . "coactivation") (:end . 39)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NNPS") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 73)\n  (:start . 65) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 87)\n  (:start . 77) (:id . 54))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 92) (:start . 88)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "give") (:form . "gives") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "rise") (:form . "rise") (:end . 103) (:start . 99)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 113)\n  (:start . 107) (:id . 59))\n ((:tag . "JJ") (:stem . "proliferative") (:form . "proliferative")\n  (:end . 127) (:start . 114) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 140)\n  (:start . 132) (:id . 62))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 151)\n  (:start . 141) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 157)\n  (:start . 152) (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 162) (:start . 158)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "create") (:form . "create") (:end . 169)\n  (:start . 163) (:id . 66))\n ((:tag . "JJ") (:stem . "transplantable") (:form . "transplantable")\n  (:end . 184) (:start . 170) (:id . 67))\n ((:tag . "JJ") (:stem . "tumor-like") (:form . "tumor-like") (:end . 195)\n  (:start . 185) (:id . 68))\n ((:tag . "NNS") (:stem . "growth") (:form . "growths") (:end . 203)\n  (:start . 196) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 204) (:start . 203)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "mimic") (:form . "mimicking") (:end . 214)\n  (:start . 205) (:id . 71))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 220)\n  (:start . 215) (:id . 72))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 227)\n  (:start . 221) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.17) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500590@unknown@formal@none@1@S@This represents a robust cell-type-specific Drosophila cancer model in which malignant cells are created by mutations in genetic pathways thought to be driving forces in a homologous human cancer.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "robust") (:form . "robust") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "cell-type-specific") (:form . "cell-type-specific")\n  (:end . 43) (:start . 25) (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 54)\n  (:start . 44) (:id . 47))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 61)\n  (:start . 55) (:id . 48))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 67) (:start . 62)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 76) (:start . 71)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "malignant") (:form . "malignant") (:end . 86)\n  (:start . 77) (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 92) (:start . 87)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 96) (:start . 93)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "create") (:form . "created") (:end . 104)\n  (:start . 97) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 107) (:start . 105)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 117)\n  (:start . 108) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 128)\n  (:start . 121) (:id . 59))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 137)\n  (:start . 129) (:id . 60))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 145)\n  (:start . 138) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 151) (:start . 149)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "drive") (:form . "driving") (:end . 159)\n  (:start . 152) (:id . 64))\n ((:tag . "NNS") (:stem . "force") (:form . "forces") (:end . 166)\n  (:start . 160) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 169) (:start . 167)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 171) (:start . 170)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 182)\n  (:start . 172) (:id . 68))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 188)\n  (:start . 183) (:id . 69))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 195)\n  (:start . 189) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x3.18.1) (:span 138 145)))\n (:hscopes ((:id . :x3.18.1) (:span 138 195)))\n (:identifiers (:sid . :s3.18) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500591@unknown@formal@none@1@S@Genetic analyses demonstrated that EGFR-Ras and PI3K induce fly glial neoplasia through activation of a combinatorial genetic network composed, in part, of other genetic pathways also commonly mutated in human glioma.@(((:tag . "JJ") (:stem . "genetic") (:form . "Genetic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 29)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 43)\n  (:start . 35) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 52) (:start . 48)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "induce") (:form . "induce") (:end . 59)\n  (:start . 53) (:id . 49))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 69) (:start . 64)\n  (:id . 51))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 79)\n  (:start . 70) (:id . 52))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 87)\n  (:start . 80) (:id . 53))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 98)\n  (:start . 88) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 103) (:start . 102)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "combinatorial") (:form . "combinatorial")\n  (:end . 117) (:start . 104) (:id . 57))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 125)\n  (:start . 118) (:id . 58))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 133)\n  (:start . 126) (:id . 59))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 142)\n  (:start . 134) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n  (:id . 62))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 151) (:start . 147)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 161)\n  (:start . 156) (:id . 66))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 169)\n  (:start . 162) (:id . 67))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 178)\n  (:start . 170) (:id . 68))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 183) (:start . 179)\n  (:id . 69))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 192)\n  (:start . 184) (:id . 70))\n ((:tag . "JJ") (:stem . "mutated") (:form . "mutated") (:end . 200)\n  (:start . 193) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 203) (:start . 201)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 209)\n  (:start . 204) (:id . 73))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 216)\n  (:start . 210) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.19) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500592@unknown@formal@none@1@S@This network acts synergistically to coordinately stimulate cellular proliferation, protein translation, and inappropriate migration.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "act") (:form . "acts") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "synergistically") (:form . "synergistically")\n  (:end . 33) (:start . 18) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "RB") (:stem . "coordinately") (:form . "coordinately") (:end . 49)\n  (:start . 37) (:id . 47))\n ((:tag . "VB") (:stem . "stimulate") (:form . "stimulate") (:end . 59)\n  (:start . 50) (:id . 48))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 68)\n  (:start . 60) (:id . 49))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 82) (:start . 69) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 91)\n  (:start . 84) (:id . 52))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 103)\n  (:start . 92) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "inappropriate") (:form . "inappropriate")\n  (:end . 122) (:start . 109) (:id . 56))\n ((:tag . "NN") (:stem . "migration") (:form . "migration") (:end . 132)\n  (:start . 123) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.20) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500593@unknown@formal@none@1@S@Rate-limiting genes within this network may represent important therapeutic targets in human glioma.@(((:tag . "JJ") (:stem . "rate-limiting") (:form . "Rate-limiting")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 19) (:start . 14)\n  (:id . 43))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 26)\n  (:start . 20) (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 31) (:start . 27)\n  (:id . 45))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 39)\n  (:start . 32) (:id . 46))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . "VB") (:stem . "represent") (:form . "represent") (:end . 53)\n  (:start . 44) (:id . 48))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 63)\n  (:start . 54) (:id . 49))\n ((:tag . "JJ") (:stem . "therapeutic") (:form . "therapeutic") (:end . 75)\n  (:start . 64) (:id . 50))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 83)\n  (:start . 76) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 92) (:start . 87)\n  (:id . 53))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 99)\n  (:start . 93) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 55)))@@@1@14@((:hcues ((:id . :x3.21.1) (:span 40 43)))\n (:hscopes ((:id . :x3.21.1) (:span 40 99)))\n (:identifiers (:sid . :s3.21) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500594@unknown@formal@none@1@S@Introduction@(((:tag . "NN") (:stem . "introduction") (:form . "Introduction") (:end . 12)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.22) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500595@unknown@formal@none@1@S@Malignant gliomas, neoplasms of glial cells and their precursors, are the most common tumors of the central nervous system (CNS).@(((:tag . "JJ") (:stem . "malignant") (:form . "Malignant") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 17)\n  (:start . 10) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "neoplasm") (:form . "neoplasms") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 53)\n  (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 64)\n  (:start . 54) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 78) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 85)\n  (:start . 79) (:id . 56))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 92)\n  (:start . 86) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 107)\n  (:start . 100) (:id . 60))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 115)\n  (:start . 108) (:id . 61))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 122)\n  (:start . 116) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . "NN") (:stem . "cns") (:form . "CNS") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.23) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500596@unknown@formal@none@1@S@These tumors typically proliferate rapidly, diffusely infiltrate the brain, and resist standard chemotherapies, properties that render them largely incurable.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "VBP") (:stem . "proliferate") (:form . "proliferate") (:end . 34)\n  (:start . 23) (:id . 45))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 42)\n  (:start . 35) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 47))\n ((:tag . "RB") (:stem . "diffusely") (:form . "diffusely") (:end . 53)\n  (:start . 44) (:id . 48))\n ((:tag . "VB") (:stem . "infiltrate") (:form . "infiltrate") (:end . 64)\n  (:start . 54) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 50))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 74) (:start . 69)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n  (:id . 53))\n ((:tag . "VB") (:stem . "resist") (:form . "resist") (:end . 86)\n  (:start . 80) (:id . 54))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 95)\n  (:start . 87) (:id . 55))\n ((:tag . "NNS") (:stem . "chemotherapy") (:form . "chemotherapies")\n  (:end . 110) (:start . 96) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 122)\n  (:start . 112) (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 127) (:start . 123)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "render") (:form . "render") (:end . 134)\n  (:start . 128) (:id . 60))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 139) (:start . 135)\n  (:id . 61))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 147)\n  (:start . 140) (:id . 62))\n ((:tag . "JJ") (:stem . "incurable") (:form . "incurable") (:end . 157)\n  (:start . 148) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.24) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500597@unknown@formal@none@1@S@One key to developing more effective therapies against these tumors is to understand the genetic and molecular logic underlying gliomagenesis.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "key") (:form . "key") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 21)\n  (:start . 11) (:id . 45))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "therapy") (:form . "therapies") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 60) (:start . 55)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 67)\n  (:start . 61) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 70) (:start . 68)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "VB") (:stem . "understand") (:form . "understand") (:end . 84)\n  (:start . 74) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 96)\n  (:start . 89) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 110)\n  (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "logic") (:form . "logic") (:end . 116)\n  (:start . 111) (:id . 59))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 127)\n  (:start . 117) (:id . 60))\n ((:tag . "NN") (:stem . "gliomagenesis") (:form . "gliomagenesis")\n  (:end . 141) (:start . 128) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.25) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500598@unknown@formal@none@1@S@The most frequent genetic lesions in gliomas include mutation or amplification of the Epidermal Growth Factor Receptor (EGFR) tyrosine kinase.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "lesion") (:form . "lesions") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 78) (:start . 65) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "epidermal") (:form . "Epidermal") (:end . 95)\n  (:start . 86) (:id . 55))\n ((:tag . "NN") (:stem . "growth") (:form . "Growth") (:end . 102)\n  (:start . 96) (:id . 56))\n ((:tag . "NN") (:stem . "factor") (:form . "Factor") (:end . 109)\n  (:start . 103) (:id . 57))\n ((:tag . "NNP") (:stem . "Receptor") (:form . "Receptor") (:end . 118)\n  (:start . 110) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 120) (:start . 119)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 124) (:start . 120)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "NN") (:stem . "tyrosine") (:form . "tyrosine") (:end . 134)\n  (:start . 126) (:id . 62))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 141)\n  (:start . 135) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.26) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500599@unknown@formal@none@1@S@Glioma-associated EGFR mutant forms show constitutive kinase activity that chronically stimulates Ras signaling to drive cellular proliferation and migration [1],[2].@(((:tag . "JJ") (:stem . "glioma-associated") (:form . "Glioma-associated")\n  (:end . 17) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 22) (:start . 18)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 29)\n  (:start . 23) (:id . 44))\n ((:tag . "NNS") (:stem . "form") (:form . "forms") (:end . 35) (:start . 30)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 40) (:start . 36)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 53)\n  (:start . 41) (:id . 47))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 60)\n  (:start . 54) (:id . 48))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 69)\n  (:start . 61) (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 74) (:start . 70)\n  (:id . 50))\n ((:tag . "RB") (:stem . "chronically") (:form . "chronically") (:end . 86)\n  (:start . 75) (:id . 51))\n ((:tag . "VBZ") (:stem . "stimulate") (:form . "stimulates") (:end . 97)\n  (:start . 87) (:id . 52))\n ((:tag . "NN") (:stem . "ras") (:form . "Ras") (:end . 101) (:start . 98)\n  (:id . 53))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 111)\n  (:start . 102) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 114) (:start . 112)\n  (:id . 55))\n ((:tag . "VB") (:stem . "drive") (:form . "drive") (:end . 120)\n  (:start . 115) (:id . 56))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 129)\n  (:start . 121) (:id . 57))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 143) (:start . 130) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n  (:id . 59))\n ((:tag . "NN") (:stem . "migration") (:form . "migration") (:end . 157)\n  (:start . 148) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 159) (:start . 158)\n  (:id . 61))\n ((:tag . "CD") (:stem . "1],[2") (:form . "1],[2") (:end . 164)\n  (:start . 159) (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 165) (:start . 164)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.27) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500600@unknown@formal@none@1@S@Other common genetic lesions include loss of the lipid phosphatase PTEN, which antagonizes the phosphatidylinositol-3 kinase (PI3K) signaling pathway, and activating mutations in PIK3CA, which encodes the p110α catalytic subunit of PI3K [1],[2].@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "lesion") (:form . "lesions") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "lipid") (:form . "lipid") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "phosphatase") (:form . "phosphatase") (:end . 66)\n  (:start . 55) (:id . 51))\n ((:tag . "NNP") (:stem . "PTEN") (:form . "PTEN") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 78) (:start . 73)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "antagonize") (:form . "antagonizes") (:end . 90)\n  (:start . 79) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "phosphatidylinositol-3")\n  (:form . "phosphatidylinositol-3") (:end . 117) (:start . 95) (:id . 57))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 124)\n  (:start . 118) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 130) (:start . 126)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 61))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 141)\n  (:start . 132) (:id . 62))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 149)\n  (:start . 142) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "activate") (:form . "activating") (:end . 165)\n  (:start . 155) (:id . 66))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 175)\n  (:start . 166) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 178) (:start . 176)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "PIK3CA") (:form . "PIK3CA") (:end . 185)\n  (:start . 179) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 186) (:start . 185)\n  (:id . 70))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 192)\n  (:start . 187) (:id . 71))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 200)\n  (:start . 193) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 204) (:start . 201)\n  (:id . 73))\n ((:tag . "NN") (:stem . "p110α") (:form . "p110α") (:end . 210)\n  (:start . 205) (:id . 74))\n ((:tag . "JJ") (:stem . "catalytic") (:form . "catalytic") (:end . 220)\n  (:start . 211) (:id . 75))\n ((:tag . "NN") (:stem . "subunit") (:form . "subunit") (:end . 228)\n  (:start . 221) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 231) (:start . 229)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 236) (:start . 232)\n  (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 238) (:start . 237)\n  (:id . 79))\n ((:tag . "CD") (:stem . "1],[2") (:form . "1],[2") (:end . 243)\n  (:start . 238) (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 244) (:start . 243)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 245) (:start . 244)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s3.28) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500601@unknown@formal@none@1@S@Gliomas often show constitutively active Akt, a major PI3K effector [1],[2].@(((:tag . "NNP") (:stem . "Glioma") (:form . "Gliomas") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "RB") (:stem . "constitutively") (:form . "constitutively")\n  (:end . 33) (:start . 19) (:id . 45))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 40)\n  (:start . 34) (:id . 46))\n ((:tag . "NNP") (:stem . "Akt") (:form . "Akt") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "pi3k") (:form . "PI3K") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 67)\n  (:start . 59) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1],[2") (:form . "1],[2") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.29) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500602@unknown@formal@none@1@S@However, EGFR-Ras or PI3K mutations alone are not sufficient to transform glial cells, rather multiple mutations that coactivate EGFR-Ras and PI3K-Akt pathways are sufficient to induce glioma [2]–[4].@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 60)\n  (:start . 50) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "VB") (:stem . "transform") (:form . "transform") (:end . 73)\n  (:start . 64) (:id . 53))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 85) (:start . 80)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 56))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 93)\n  (:start . 87) (:id . 57))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 102)\n  (:start . 94) (:id . 58))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 112)\n  (:start . 103) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 117) (:start . 113)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "coactivate") (:form . "coactivate") (:end . 128)\n  (:start . 118) (:id . 61))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 137)\n  (:start . 129) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "PI3K-Akt") (:form . "PI3K-Akt") (:end . 150)\n  (:start . 142) (:id . 64))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 159)\n  (:start . 151) (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 163) (:start . 160)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 174)\n  (:start . 164) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 177) (:start . 175)\n  (:id . 68))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 184)\n  (:start . 178) (:id . 69))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 191)\n  (:start . 185) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 193) (:start . 192)\n  (:id . 71))\n ((:tag . "CD") (:stem . "2]–[4") (:form . "2]–[4") (:end . 198)\n  (:start . 193) (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 199) (:start . 198)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.30) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500603@unknown@formal@none@1@S@Understanding the interplay of these mutations and the neurodevelopmental origins of these tumors could lead to new insights into the mechanisms of gliomagenesis.@(((:tag . "VBG") (:stem . "understand") (:form . "Understanding") (:end . 13)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 43))\n ((:tag . "NN") (:stem . "interplay") (:form . "interplay") (:end . 27)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 36) (:start . 31)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 46)\n  (:start . 37) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "neurodevelopmental") (:form . "neurodevelopmental")\n  (:end . 73) (:start . 55) (:id . 50))\n ((:tag . "NNS") (:stem . "origin") (:form . "origins") (:end . 81)\n  (:start . 74) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 52))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 90) (:start . 85)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 97)\n  (:start . 91) (:id . 54))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 103) (:start . 98)\n  (:id . 55))\n ((:tag . "VB") (:stem . "lead") (:form . "lead") (:end . 108) (:start . 104)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 115) (:start . 112)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "insight") (:form . "insights") (:end . 124)\n  (:start . 116) (:id . 59))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 129) (:start . 125)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 144)\n  (:start . 134) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n  (:id . 63))\n ((:tag . "NN") (:stem . "gliomagenesis") (:form . "gliomagenesis")\n  (:end . 161) (:start . 148) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x3.31.1) (:span 98 103)))\n (:hscopes ((:id . :x3.31.1) (:span 98 161)))\n (:identifiers (:sid . :s3.31) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500604@unknown@formal@none@1@S@The mammalian brain contains multiple glial cell types that maintain proliferative capacities, including differentiated astrocytes, glial progenitors, and multipotent neural stem cells.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 43) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 54) (:start . 49)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "maintain") (:form . "maintain") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . "JJ") (:stem . "proliferative") (:form . "proliferative")\n  (:end . 82) (:start . 69) (:id . 52))\n ((:tag . "NNS") (:stem . "capacity") (:form . "capacities") (:end . 93)\n  (:start . 83) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 104)\n  (:start . 95) (:id . 55))\n ((:tag . "VBN") (:stem . "differentiate") (:form . "differentiated")\n  (:end . 119) (:start . 105) (:id . 56))\n ((:tag . "NNS") (:stem . "astrocyte") (:form . "astrocytes") (:end . 130)\n  (:start . 120) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 137)\n  (:start . 132) (:id . 59))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 149)\n  (:start . 138) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "multipotent") (:form . "multipotent") (:end . 166)\n  (:start . 155) (:id . 63))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 173)\n  (:start . 167) (:id . 64))\n ((:tag . "NN") (:stem . "stem") (:form . "stem") (:end . 178) (:start . 174)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 184)\n  (:start . 179) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.32) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500605@unknown@formal@none@1@S@EGFR-Ras and PTEN-PI3K signaling regulates many developmental processes in these cell types, particularly proliferation and self-renewal, which are also properties of glioma cells [1].@(((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "PTEN-PI3K") (:form . "PTEN-PI3K") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "regulates") (:end . 42)\n  (:start . 33) (:id . 46))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 47) (:start . 43)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 61) (:start . 48) (:id . 48))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 71)\n  (:start . 62) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 50))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 80) (:start . 75)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 85) (:start . 81)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 91) (:start . 86)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 54))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 105)\n  (:start . 93) (:id . 55))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 119) (:start . 106) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 57))\n ((:tag . "NN") (:stem . "self-renewal") (:form . "self-renewal") (:end . 136)\n  (:start . 124) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 143)\n  (:start . 138) (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 147) (:start . 144)\n  (:id . 61))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 152) (:start . 148)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 163)\n  (:start . 153) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 166) (:start . 164)\n  (:id . 64))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 173)\n  (:start . 167) (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 179)\n  (:start . 174) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 181) (:start . 180)\n  (:id . 67))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 182) (:start . 181)\n  (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 183) (:start . 182)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.33) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500606@unknown@formal@none@1@S@Although recent hypotheses favor that gliomas arise from multipotent stem cells, data from mouse models demonstrate that differentiated glia, glial progenitors, and stem cells can all produce gliomas in response to genetic lesions found in human gliomas [5],[6].@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "hypothesis") (:form . "hypotheses") (:end . 26)\n  (:start . 16) (:id . 44))\n ((:tag . "VBP") (:stem . "favor") (:form . "favor") (:end . 32) (:start . 27)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . "VBP") (:stem . "arise") (:form . "arise") (:end . 51) (:start . 46)\n  (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 56) (:start . 52)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "multipotent") (:form . "multipotent") (:end . 68)\n  (:start . 57) (:id . 50))\n ((:tag . "NN") (:stem . "stem") (:form . "stem") (:end . 73) (:start . 69)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 79) (:start . 74)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 85) (:start . 81)\n  (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 90) (:start . 86)\n  (:id . 55))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 103)\n  (:start . 97) (:id . 57))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 115)\n  (:start . 104) (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 120) (:start . 116)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "differentiate") (:form . "differentiated")\n  (:end . 135) (:start . 121) (:id . 60))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 140) (:start . 136)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 147)\n  (:start . 142) (:id . 63))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 159)\n  (:start . 148) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n  (:id . 66))\n ((:tag . "NN") (:stem . "stem") (:form . "stem") (:end . 169) (:start . 165)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 175)\n  (:start . 170) (:id . 68))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 179) (:start . 176)\n  (:id . 69))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 183) (:start . 180)\n  (:id . 70))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 191)\n  (:start . 184) (:id . 71))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 199)\n  (:start . 192) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 202) (:start . 200)\n  (:id . 73))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 211)\n  (:start . 203) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 214) (:start . 212)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 222)\n  (:start . 215) (:id . 76))\n ((:tag . "NNS") (:stem . "lesion") (:form . "lesions") (:end . 230)\n  (:start . 223) (:id . 77))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 236)\n  (:start . 231) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 239) (:start . 237)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 245)\n  (:start . 240) (:id . 80))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 253)\n  (:start . 246) (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 255) (:start . 254)\n  (:id . 82))\n ((:tag . "CD") (:stem . "5],[6") (:form . "5],[6") (:end . 260)\n  (:start . 255) (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 261) (:start . 260)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 262) (:start . 261)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s3.34) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500607@unknown@formal@none@1@S@Thus, misregulation of these genetic pathways may confer unrestricted proliferative capacities to a range of glial cell types, but how this occurs remains unclear.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "misregulation") (:form . "misregulation")\n  (:end . 19) (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "VB") (:stem . "confer") (:form . "confer") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "JJ") (:stem . "unrestricted") (:form . "unrestricted") (:end . 69)\n  (:start . 57) (:id . 51))\n ((:tag . "JJ") (:stem . "proliferative") (:form . "proliferative")\n  (:end . 83) (:start . 70) (:id . 52))\n ((:tag . "NNS") (:stem . "capacity") (:form . "capacities") (:end . 94)\n  (:start . 84) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n  (:id . 55))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 105)\n  (:start . 100) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 114)\n  (:start . 109) (:id . 58))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 119) (:start . 115)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 125)\n  (:start . 120) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 61))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 130) (:start . 127)\n  (:id . 62))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 139) (:start . 135)\n  (:id . 64))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 146)\n  (:start . 140) (:id . 65))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 154)\n  (:start . 147) (:id . 66))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 162)\n  (:start . 155) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x3.35.1) (:span 155 162)) ((:id . :x3.35.2) (:span 46 49)))\n (:hscopes ((:id . :x3.35.1) (:span 131 162))\n  ((:id . :x3.35.2) (:span 46 125)))\n (:identifiers (:sid . :s3.35) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500608@unknown@formal@none@1@S@While many of the same effectors are utilized by EGFR-Ras and PI3K in both glial development and cancer, constitutive activation of these pathways may deploy distinct outputs, not utilized in development, that allow particular cells to escape normal physiological cues that restrain proliferation and self-renewal.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 32)\n  (:start . 23) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . 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"and") (:end . 300) (:start . 297)\n  (:id . 88))\n ((:tag . "NN") (:stem . "self-renewal") (:form . "self-renewal") (:end . 313)\n  (:start . 301) (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 314) (:start . 313)\n  (:id . 90)))@@@1@49@((:hcues ((:id . :x3.36.1) (:span 147 150)))\n (:hscopes ((:id . :x3.36.1) (:span 147 174)))\n (:identifiers (:sid . :s3.36) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500609@unknown@formal@none@1@S@The identity of such outputs remains unclear.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "output") (:form . "outputs") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 49)))@@@1@8@((:hcues ((:id . :x3.37.1) (:span 37 44)))\n (:hscopes ((:id . :x3.37.1) (:span 0 44)))\n (:identifiers (:sid . :s3.37) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500610@unknown@formal@none@1@S@With these issues in mind, we developed a Drosophila glioma model to facilitate genetic analysis of glial pathogenesis.@(((:tag . "IN") (:stem . "with") (:form . "With") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "issue") (:form . "issues") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mind") (:form . "mind") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "develop") (:form . "developed") (:end . 39)\n  (:start . 30) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 52)\n  (:start . 42) (:id . 51))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "VB") (:stem . "facilitate") (:form . "facilitate") (:end . 79)\n  (:start . 69) (:id . 55))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 87)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 96)\n  (:start . 88) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 105)\n  (:start . 100) (:id . 59))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 118)\n  (:start . 106) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.38) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500611@unknown@formal@none@1@S@Drosophila offers many tools for precise manipulation of cell-type-specific gene expression and dissection of multigene interactions.@(((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "offer") (:form . "offers") (:end . 17)\n  (:start . 11) (:id . 43))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "precise") (:form . "precise") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "manipulation") (:form . "manipulation") (:end . 53)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "cell-type-specific") (:form . "cell-type-specific")\n  (:end . 75) (:start . 57) (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 80) (:start . 76)\n  (:id . 51))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 91)\n  (:start . 81) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 53))\n ((:tag . "NN") (:stem . "dissection") (:form . "dissection") (:end . 106)\n  (:start . 96) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "multigene") (:form . "multigene") (:end . 119)\n  (:start . 110) (:id . 56))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 132)\n  (:start . 120) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.39) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500612@unknown@formal@none@1@S@Most human genes, including 70% of known disease genes, have functional Drosophila orthologs [7].@(((:tag . "JJS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 40) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 48)\n  (:start . 41) (:id . 51))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 54) (:start . 49)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 60) (:start . 56)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 71)\n  (:start . 61) (:id . 55))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 82)\n  (:start . 72) (:id . 56))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 92)\n  (:start . 83) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.40) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500613@unknown@formal@none@1@S@Among the most conserved genes are components of major signal transduction pathways, including many gliomagenic genes.@(((:tag . "IN") (:stem . "among") (:form . "Among") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 45)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 61)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 74)\n  (:start . 62) (:id . 52))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 83)\n  (:start . 75) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 94)\n  (:start . 85) (:id . 55))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "gliomagenic") (:form . "gliomagenic") (:end . 111)\n  (:start . 100) (:id . 57))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 117)\n  (:start . 112) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.41) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500614@unknown@formal@none@1@S@Recently, Drosophila has emerged as a model system for human neurological diseases because the CNS shows remarkable evolutionary conservation in cellular composition and neurodevelopmental mechanisms [8].@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "emerge") (:form . "emerged") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "neurological") (:form . "neurological") (:end . 73)\n  (:start . 61) (:id . 53))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 90)\n  (:start . 83) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "CNS") (:form . "CNS") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 104) (:start . 99)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "remarkable") (:form . "remarkable") (:end . 115)\n  (:start . 105) (:id . 59))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 128)\n  (:start . 116) (:id . 60))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 141)\n  (:start . 129) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 153)\n  (:start . 145) (:id . 63))\n ((:tag . "NN") (:stem . "composition") (:form . "composition") (:end . 165)\n  (:start . 154) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 169) (:start . 166)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "neurodevelopmental") (:form . "neurodevelopmental")\n  (:end . 188) (:start . 170) (:id . 66))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 199)\n  (:start . 189) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 201) (:start . 200)\n  (:id . 68))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 202) (:start . 201)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 203) (:start . 202)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.42) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500615@unknown@formal@none@1@S@Similarly, Drosophila have multiple glial cell types that require the EGFR pathway for their normal development, and these cells appear homologous to mammalian glia in terms of function, development, and gene expression [9].@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 65)\n  (:start . 58) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "egfr") (:form . "EGFR") (:end . 74) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 82)\n  (:start . 75) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 92)\n  (:start . 87) (:id . 56))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 99)\n  (:start . 93) (:id . 57))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 111)\n  (:start . 100) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 122)\n  (:start . 117) (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 128)\n  (:start . 123) (:id . 62))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 135)\n  (:start . 129) (:id . 63))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 146)\n  (:start . 136) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 159)\n  (:start . 150) (:id . 66))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 164) (:start . 160)\n  (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 167) (:start . 165)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 173)\n  (:start . 168) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n  (:id . 70))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 185)\n  (:start . 177) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 186) (:start . 185)\n  (:id . 72))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 198)\n  (:start . 187) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 199) (:start . 198)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 203) (:start . 200)\n  (:id . 75))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 208) (:start . 204)\n  (:id . 76))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 219)\n  (:start . 209) (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 221) (:start . 220)\n  (:id . 78))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 222) (:start . 221)\n  (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 223) (:start . 222)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s3.43) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500616@unknown@formal@none@1@S@These similarities between flies and humans make Drosophila an attractive system for modeling gliomas.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "similarity") (:form . "similarities") (:end . 18)\n  (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 26)\n  (:start . 19) (:id . 44))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 32) (:start . 27)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "human") (:form . "humans") (:end . 43)\n  (:start . 37) (:id . 47))\n ((:tag . "VBP") (:stem . "make") (:form . "make") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 59)\n  (:start . 49) (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "attractive") (:form . "attractive") (:end . 73)\n  (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 80)\n  (:start . 74) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 84) (:start . 81)\n  (:id . 53))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 93)\n  (:start . 85) (:id . 54))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 101)\n  (:start . 94) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.44) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500617@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.45) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500618@unknown@formal@none@1@S@Coactivation of EGFR-Ras and PI3K in Drosophila Glia Causes Neoplasia@(((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "NNP") (:stem . "Glia") (:form . "Glia") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Causes") (:form . "Causes") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "NNP") (:stem . "Neoplasia") (:form . "Neoplasia") (:end . 69)\n  (:start . 60) (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.46) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500619@unknown@formal@none@1@S@Since concurrent activation of EGFR-Ras and PI3K signaling in glial precursors induces glioma in the mouse [4], we sought to create mutant phenotypes by hyperactivation of these pathways in fly glia and glial precursors.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "concurrent") (:form . "concurrent") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 27)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 39)\n  (:start . 31) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 58)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 67) (:start . 62)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 78)\n  (:start . 68) (:id . 52))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 86)\n  (:start . 79) (:id . 53))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 93)\n  (:start . 87) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 56))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 106)\n  (:start . 101) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 110) (:start . 109)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 61))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "seek") (:form . "sought") (:end . 121)\n  (:start . 115) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 124) (:start . 122)\n  (:id . 64))\n ((:tag . "VB") (:stem . "create") (:form . "create") (:end . 131)\n  (:start . 125) (:id . 65))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 138)\n  (:start . 132) (:id . 66))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 149)\n  (:start . 139) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 152) (:start . 150)\n  (:id . 68))\n ((:tag . "NN") (:stem . "hyperactivation") (:form . "hyperactivation")\n  (:end . 168) (:start . 153) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 70))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 177)\n  (:start . 172) (:id . 71))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 186)\n  (:start . 178) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 189) (:start . 187)\n  (:id . 73))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 193) (:start . 190)\n  (:id . 74))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 198) (:start . 194)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 202) (:start . 199)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 208)\n  (:start . 203) (:id . 77))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 219)\n  (:start . 209) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s3.47) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500620@unknown@formal@none@1@S@Drosophila has a single functional ortholog each for EGFR(dEGFR), Raf (dRaf), PIK3CA(dp110), PTEN(dPTEN), and Akt(dAkt), and two functional orthologs for Ras(dRas85D, dRas64B) (www.flybase.org).@(((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "EGFR(dEGFR)") (:form . "EGFR(dEGFR)") (:end . 64)\n  (:start . 53) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Raf") (:form . "Raf") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "draf") (:form . "dRaf") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "PIK3CA(dp110)") (:form . "PIK3CA(dp110)")\n  (:end . 91) (:start . 78) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . "CD") (:stem . "PTEN(dPTEN)") (:form . "PTEN(dPTEN)") (:end . 104)\n  (:start . 93) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 61))\n ((:tag . "CD") (:stem . "Akt(dAkt)") (:form . "Akt(dAkt)") (:end . 119)\n  (:start . 110) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 64))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 128) (:start . 125)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 139)\n  (:start . 129) (:id . 66))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 149)\n  (:start . 140) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 153) (:start . 150)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Ras(dRas85D") (:form . "Ras(dRas85D") (:end . 165)\n  (:start . 154) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "dRas64B") (:form . "dRas64B") (:end . 174)\n  (:start . 167) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 175) (:start . 174)\n  (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 73))\n ((:tag . "NN") (:stem . "www.flybase.org") (:form . "www.flybase.org")\n  (:end . 192) (:start . 177) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 193) (:start . 192)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s3.48) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500621@unknown@formal@none@1@S@A diagram of the specific mutant forms of dEGFR used in our assays can be found in Figure S1.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 32)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "form") (:form . "forms") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "dEGFR") (:form . "dEGFR") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 66)\n  (:start . 60) (:id . 54))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 79) (:start . 74)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 89)\n  (:start . 83) (:id . 59))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 92) (:start . 90)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.49) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500622@unknown@formal@none@1@S@We performed glial overexpression assays with the Gal4-UAS system [10], using the repo-Gal4 driver, which gives sustained UAS-transgene expression in almost all glia, from embryogenesis through adulthood.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "perform") (:form . "performed") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 33) (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 40)\n  (:start . 34) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Gal4-UAS") (:form . "Gal4-UAS") (:end . 58)\n  (:start . 50) (:id . 49))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 65)\n  (:start . 59) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 67) (:start . 66)\n  (:id . 51))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 91)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 98)\n  (:start . 92) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 105)\n  (:start . 100) (:id . 60))\n ((:tag . "VBZ") (:stem . "give") (:form . "gives") (:end . 111)\n  (:start . 106) (:id . 61))\n ((:tag . "JJ") (:stem . "sustained") (:form . "sustained") (:end . 121)\n  (:start . 112) (:id . 62))\n ((:tag . "NNP") (:stem . "UAS-transgene") (:form . "UAS-transgene")\n  (:end . 135) (:start . 122) (:id . 63))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 146)\n  (:start . 136) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 65))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 156)\n  (:start . 150) (:id . 66))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 160) (:start . 157)\n  (:id . 67))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 165) (:start . 161)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 171) (:start . 167)\n  (:id . 70))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 185) (:start . 172) (:id . 71))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 193)\n  (:start . 186) (:id . 72))\n ((:tag . "NN") (:stem . "adulthood") (:form . "adulthood") (:end . 203)\n  (:start . 194) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.50) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500623@unknown@formal@none@1@S@For glial-specific RNAi, we employed UAS-dsRNA constructs [11], which we verified with phenotypic tests and/or antibody staining (see Materials and Methods).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "glial-specific") (:form . "glial-specific")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "employ") (:form . "employed") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "NNP") (:stem . "UAS-dsRNA") (:form . "UAS-dsRNA") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 59) (:start . 58)\n  (:id . 50))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "verify") (:form . "verified") (:end . 81)\n  (:start . 73) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "phenotypic") (:form . "phenotypic") (:end . 97)\n  (:start . 87) (:id . 58))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 103) (:start . 98)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 110)\n  (:start . 104) (:id . 60))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 119)\n  (:start . 111) (:id . 61))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 128)\n  (:start . 120) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 133) (:start . 130)\n  (:id . 64))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 143)\n  (:start . 134) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n  (:id . 66))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 155)\n  (:start . 148) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.51) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500624@unknown@formal@none@1@S@Glial morphology was visualized with membrane-localized GFP (CD8GFP) [12].@(((:tag . "JJ") (:stem . "glial") (:form . "Glial") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "visualize") (:form . "visualized") (:end . 31)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "membrane-localized") (:form . "membrane-localized")\n  (:end . 55) (:start . 37) (:id . 47))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 59) (:start . 56)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 67)\n  (:start . 61) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 51))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 70) (:start . 69)\n  (:id . 52))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.52) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500625@unknown@formal@none@1@S@Cell number was determined with staining for Repo, a homeobox transcription factor expressed by repo-Gal4 positive glia [13].@(((:tag . "NN") (:stem . "cell") (:form . "Cell") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "homeobox") (:form . "homeobox") (:end . 61)\n  (:start . 53) (:id . 52))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 75) (:start . 62) (:id . 53))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 82)\n  (:start . 76) (:id . 54))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 92)\n  (:start . 83) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 95) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 105)\n  (:start . 96) (:id . 57))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 114)\n  (:start . 106) (:id . 58))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 119) (:start . 115)\n  (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 121) (:start . 120)\n  (:id . 60))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 123) (:start . 121)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 124) (:start . 123)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.53) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500626@unknown@formal@none@1@S@Glial-specific coactivation of EGFR-Ras and PI3K stimulated glial neoplasia, giving rise to CNS enlargement and malformation, neurologic defects, and late larval lethality.@(((:tag . "JJ") (:stem . "glial-specific") (:form . "Glial-specific")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "coactivation") (:form . "coactivation") (:end . 27)\n  (:start . 15) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 39)\n  (:start . 31) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 48) (:start . 44)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "stimulate") (:form . "stimulated") (:end . 59)\n  (:start . 49) (:id . 48))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 65) (:start . 60)\n  (:id . 49))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 75)\n  (:start . 66) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "give") (:form . "giving") (:end . 83) (:start . 77)\n  (:id . 52))\n ((:tag . "NN") (:stem . "rise") (:form . "rise") (:end . 88) (:start . 84)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "CNS") (:form . "CNS") (:end . 95) (:start . 92)\n  (:id . 55))\n ((:tag . "NN") (:stem . "enlargement") (:form . "enlargement") (:end . 107)\n  (:start . 96) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 57))\n ((:tag . "NN") (:stem . "malformation") (:form . "malformation") (:end . 124)\n  (:start . 112) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "neurologic") (:form . "neurologic") (:end . 136)\n  (:start . 126) (:id . 60))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 144)\n  (:start . 137) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 149) (:start . 146)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 154) (:start . 150)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 161)\n  (:start . 155) (:id . 65))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 171)\n  (:start . 162) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.54) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500627@unknown@formal@none@1@S@repo-Gal4-driven co-overexpression of activated dEGFR (dEGFRλ) and dp110 (dp110CAAX) induced progressive accumulation of ~50-fold excess glia (Figure 1A and 1B) [14],[15].@(((:tag . "JJ") (:stem . "repo-gal4-driven") (:form . "repo-Gal4-driven")\n  (:end . 16) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "co-overexpression") (:form . "co-overexpression")\n  (:end . 34) (:start . 17) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 47)\n  (:start . 38) (:id . 45))\n ((:tag . "NNP") (:stem . "dEGFR") (:form . "dEGFR") (:end . 53) (:start . 48)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 61)\n  (:start . 55) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dp110") (:form . "dp110") (:end . 72) (:start . 67)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 83)\n  (:start . 74) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "induce") (:form . "induced") (:end . 92)\n  (:start . 85) (:id . 55))\n ((:tag . "JJ") (:stem . "progressive") (:form . "progressive") (:end . 104)\n  (:start . 93) (:id . 56))\n ((:tag . "NN") (:stem . "accumulation") (:form . "accumulation") (:end . 117)\n  (:start . 105) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "~50-fold") (:form . "~50-fold") (:end . 129)\n  (:start . 121) (:id . 59))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 136)\n  (:start . 130) (:id . 60))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 141) (:start . 137)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 149)\n  (:start . 143) (:id . 63))\n ((:tag . "NN") (:stem . "1a") (:form . "1A") (:end . 152) (:start . 150)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 65))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 159) (:start . 157)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 162) (:start . 161)\n  (:id . 68))\n ((:tag . "CD") (:stem . "14],[15") (:form . "14],[15") (:end . 169)\n  (:start . 162) (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 170) (:start . 169)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.55) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500628@unknown@formal@none@1@S@dEGFR (dEGFRλ) and dp110 (dp110CAAX) induced progressive accumulation of ~50-fold excess glia (Figure 1A and 1B) [14],[15]. dEGFRλ is a constitutively active dEGFR variant in which a lambda dimerization domain replaces the extracellular domain [14] (Figure S1).@(((:tag . "NNP") (:stem . "dEGFR") (:form . "dEGFR") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 13)\n  (:start . 7) (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dp110") (:form . "dp110") (:end . 24) (:start . 19)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . 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"Figure") (:end . 101)\n  (:start . 95) (:id . 59))\n ((:tag . "NN") (:stem . "1a") (:form . "1A") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 111) (:start . 109)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 114) (:start . 113)\n  (:id . 64))\n ((:tag . "FW") (:stem . "14],[15].") (:form . "14],[15].") (:end . 123)\n  (:start . 114) (:id . 65))\n ((:tag . "NN") (:stem . "degfrλ") (:form . "dEGFRλ") (:end . 130)\n  (:start . 124) (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 133) (:start . 131)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 135) (:start . 134)\n  (:id . 68))\n ((:tag . "RB") (:stem . "constitutively") (:form . 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5500629@unknown@formal@none@1@S@Co-overexpression of combinations of dEGFRλ and core components of the PI3K pathway, such as dAkt, induced phenotypes similar to repo>dEGFRλ;dp110CAAX, although phenotypes varied somewhat depending on strength of pathway activation and transgene expression (Figure S2 and Table S1).@(((:tag . "NN") (:stem . "co-overexpression") (:form . "Co-overexpression")\n  (:end . 17) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 33)\n  (:start . 21) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 45))\n ((:tag . "NN") (:stem . "degfrλ") (:form . "dEGFRλ") (:end . 43)\n  (:start . 37) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 47))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 52) (:start . 48)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 63)\n  (:start . 53) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 75) (:start . 71)\n  (:id . 52))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 83)\n  (:start . 76) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 89) (:start . 85)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dakt") (:form . "dAkt") (:end . 97) (:start . 93)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 106)\n  (:start . 99) (:id . 59))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 117)\n  (:start . 107) (:id . 60))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 125)\n  (:start . 118) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 150) (:start . 129) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n  (:id . 64))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 160)\n  (:start . 152) (:id . 65))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 171)\n  (:start . 161) (:id . 66))\n ((:tag . "VBD") (:stem . "vary") (:form . "varied") (:end . 178)\n  (:start . 172) (:id . 67))\n ((:tag . "RB") (:stem . "somewhat") (:form . "somewhat") (:end . 187)\n  (:start . 179) (:id . 68))\n ((:tag . "VBG") (:stem . "depend") (:form . "depending") (:end . 197)\n  (:start . 188) (:id . 69))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 200) (:start . 198)\n  (:id . 70))\n ((:tag . "NN") (:stem . "strength") (:form . "strength") (:end . 209)\n  (:start . 201) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 212) (:start . 210)\n  (:id . 72))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 220)\n  (:start . 213) (:id . 73))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 231)\n  (:start . 221) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 235) (:start . 232)\n  (:id . 75))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 245)\n  (:start . 236) (:id . 76))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 256)\n  (:start . 246) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 258) (:start . 257)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 264)\n  (:start . 258) (:id . 79))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 267) (:start . 265)\n  (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 271) (:start . 268)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 277)\n  (:start . 272) (:id . 82))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 280) (:start . 278)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 281) (:start . 280)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 282) (:start . 281)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s3.57) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500630@unknown@formal@none@1@S@Dramatic glial overgrowth also occurred upon co-overexpression of constitutively active dRas (dRas85DV12) or its effector dRaf (dRafgof) with dp110CAAX, dAkt, or a dPTENdsRNA, which partially knocked-down dPTEN (Figure S2 and Table S1).@(((:tag . "JJ") (:stem . "dramatic") (:form . "Dramatic") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "occur") (:form . "occurred") (:end . 39)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 44) (:start . 40)\n  (:id . 47))\n ((:tag . "NN") (:stem . "co-overexpression") (:form . "co-overexpression")\n  (:end . 62) (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 49))\n ((:tag . "RB") (:stem . "constitutively") (:form . "constitutively")\n  (:end . 80) (:start . 66) (:id . 50))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 87)\n  (:start . 81) (:id . 51))\n ((:tag . "NN") (:stem . "dras") (:form . "dRas") (:end . 92) (:start . 88)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 53))\n ((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 104)\n  (:start . 94) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 108) (:start . 106)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 112) (:start . 109)\n  (:id . 57))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 121)\n  (:start . 113) (:id . 58))\n ((:tag . "NN") (:stem . "draf") (:form . "dRaf") (:end . 126) (:start . 122)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 60))\n ((:tag . "NN") (:stem . "drafgof") (:form . "dRafgof") (:end . 135)\n  (:start . 128) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 141) (:start . 137)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 151)\n  (:start . 142) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . "NN") (:stem . "dakt") (:form . "dAkt") (:end . 157) (:start . 153)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 161) (:start . 159)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 163) (:start . 162)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "dPTENdsRNA") (:form . "dPTENdsRNA") (:end . 174)\n  (:start . 164) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 71))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 181)\n  (:start . 176) (:id . 72))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 191)\n  (:start . 182) (:id . 73))\n ((:tag . "JJ") (:stem . "knocked-down") (:form . "knocked-down") (:end . 204)\n  (:start . 192) (:id . 74))\n ((:tag . "NNP") (:stem . "dPTEN") (:form . "dPTEN") (:end . 210)\n  (:start . 205) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 212) (:start . 211)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 218)\n  (:start . 212) (:id . 77))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 221) (:start . 219)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 225) (:start . 222)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 231)\n  (:start . 226) (:id . 80))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 234) (:start . 232)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 235) (:start . 234)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 236) (:start . 235)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s3.58) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500631@unknown@formal@none@1@S@Finally, glial overgrowth in repo>dEGFRλ;dp110CAAX larvae was strongly suppressed by co-overexpression of dPTEN or more moderately by dominant negative dRas85D (dRas85DN17) (Figure 1D and 1E), indicating that Ras activity and excess phospho-inositols are essential for neoplasia.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 50) (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 57)\n  (:start . 51) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 61) (:start . 58)\n  (:id . 49))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 70)\n  (:start . 62) (:id . 50))\n ((:tag . "VBN") (:stem . "suppress") (:form . "suppressed") (:end . 81)\n  (:start . 71) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 84) (:start . 82)\n  (:id . 52))\n ((:tag . "NN") (:stem . "co-overexpression") (:form . "co-overexpression")\n  (:end . 102) (:start . 85) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "dPTEN") (:form . "dPTEN") (:end . 111)\n  (:start . 106) (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 114) (:start . 112)\n  (:id . 56))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 119) (:start . 115)\n  (:id . 57))\n ((:tag . "RB") (:stem . "moderately") (:form . "moderately") (:end . 130)\n  (:start . 120) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 133) (:start . 131)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 142)\n  (:start . 134) (:id . 60))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 151)\n  (:start . 143) (:id . 61))\n ((:tag . "NN") (:stem . "dras85d") (:form . "dRas85D") (:end . 159)\n  (:start . 152) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 161) (:start . 160)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dras85dn17") (:form . "dRas85DN17") (:end . 171)\n  (:start . 161) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 180)\n  (:start . 174) (:id . 67))\n ((:tag . "NN") (:stem . "1d") (:form . "1D") (:end . 183) (:start . 181)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 187) (:start . 184)\n  (:id . 69))\n ((:tag . "NN") (:stem . "1e") (:form . "1E") (:end . 190) (:start . 188)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 191) (:start . 190)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 192) (:start . 191)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 203)\n  (:start . 193) (:id . 73))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 208) (:start . 204)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Ras") (:form . "Ras") (:end . 212) (:start . 209)\n  (:id . 75))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 221)\n  (:start . 213) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 225) (:start . 222)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 232)\n  (:start . 226) (:id . 78))\n ((:tag . "NNS") (:stem . "phospho-inositol") (:form . "phospho-inositols")\n  (:end . 250) (:start . 233) (:id . 79))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 254) (:start . 251)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 264)\n  (:start . 255) (:id . 81))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 268) (:start . 265)\n  (:id . 82))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 278)\n  (:start . 269) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 279) (:start . 278)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x3.59.1) (:span 193 208)))\n (:hscopes ((:id . :x3.59.1) (:span 193 278)))\n (:identifiers (:sid . :s3.59) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500632@unknown@formal@none@1@S@Coactivation of EGFR-Ras and PI3K in Drosophila glia causes neoplasia.@(((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 69)\n  (:start . 60) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.60) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500633@unknown@formal@none@1@S@In contrast, glial-specific activation of the EGFR-Ras pathway alone, through overexpression of dEGFRλ or Rafgof, induced 5–10 fold excess glia in the larval brain and later pupal lethality (Figure 1F and Table S1).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "glial-specific") (:form . "glial-specific")\n  (:end . 27) (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 62)\n  (:start . 55) (:id . 50))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 68) (:start . 63)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 92) (:start . 78) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 102)\n  (:start . 96) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 105) (:start . 103)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Rafgof") (:form . "Rafgof") (:end . 112)\n  (:start . 106) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "induce") (:form . "induced") (:end . 121)\n  (:start . 114) (:id . 60))\n ((:tag . "CD") (:stem . "5–10") (:form . "5–10") (:end . 126) (:start . 122)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 131) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 138)\n  (:start . 132) (:id . 63))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 143) (:start . 139)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 157)\n  (:start . 151) (:id . 67))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 163)\n  (:start . 158) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "later") (:form . "later") (:end . 173)\n  (:start . 168) (:id . 70))\n ((:tag . "JJ") (:stem . "pupal") (:form . "pupal") (:end . 179)\n  (:start . 174) (:id . 71))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 189)\n  (:start . 180) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 191) (:start . 190)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 197)\n  (:start . 191) (:id . 74))\n ((:tag . "NN") (:stem . "1f") (:form . "1F") (:end . 200) (:start . 198)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 204) (:start . 201)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 210)\n  (:start . 205) (:id . 77))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 213) (:start . 211)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s3.61) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500634@unknown@formal@none@1@S@dRas85DV12 overexpression induced approximately 5–10-fold excess glia, and these glia were smaller than wild-type or dEGFRλ;dp110CAAX glia.@(((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 25) (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "induce") (:form . "induced") (:end . 33)\n  (:start . 26) (:id . 44))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 47) (:start . 34) (:id . 45))\n ((:tag . "RB") (:stem . "5–10-fold") (:form . "5–10-fold") (:end . 57)\n  (:start . 48) (:id . 46))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 64)\n  (:start . 58) (:id . 47))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 69) (:start . 65)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 50))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 80) (:start . 75)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 85) (:start . 81)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 90) (:start . 86)\n  (:id . 53))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 98)\n  (:start . 91) (:id . 54))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 103) (:start . 99)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 113)\n  (:start . 104) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 116) (:start . 114)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 133) (:start . 117) (:id . 58))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 138) (:start . 134)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.62) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500635@unknown@formal@none@1@S@(Figure 1G).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 7) (:start . 1)\n  (:id . 43))\n ((:tag . "NN") (:stem . "1g") (:form . "1G") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 12) (:start . 11)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.63) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500636@unknown@formal@none@1@S@dRas85DV12 may be more potent than dEGFRλ because dRas85DV12 can activate endogenous PI3K signaling [16].@(((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "potent") (:form . "potent") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "degfrλ") (:form . "dEGFRλ") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "VB") (:stem . "activate") (:form . "activate") (:end . 73)\n  (:start . 65) (:id . 52))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 84)\n  (:start . 74) (:id . 53))\n ((:tag . "NN") (:stem . "pi3k") (:form . "PI3K") (:end . 89) (:start . 85)\n  (:id . 54))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 99)\n  (:start . 90) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 101) (:start . 100)\n  (:id . 56))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 104) (:start . 103)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x3.64.1) (:span 11 14)))\n (:hscopes ((:id . :x3.64.1) (:span 11 41)))\n (:identifiers (:sid . :s3.64) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500637@unknown@formal@none@1@S@Overexpression of dEGFRElp, a classical hypermorphic mutant form of dEGFR [17], induced excess glial proliferation and neural morphogenesis defects (Figure S2), but also caused early lethality which precluded examination of dEGFRElp-dp110 interactions.@(((:tag . "NN") (:stem . "overexpression") (:form . "Overexpression")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NN") (:stem . "degfrelp") (:form . "dEGFRElp") (:end . 26)\n  (:start . 18) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "classical") (:form . "classical") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "JJ") (:stem . "hypermorphic") (:form . "hypermorphic") (:end . 52)\n  (:start . 40) (:id . 48))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 59)\n  (:start . 53) (:id . 49))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 64) (:start . 60)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "dEGFR") (:form . "dEGFR") (:end . 73) (:start . 68)\n  (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "induce") (:form . "induced") (:end . 87)\n  (:start . 80) (:id . 57))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 94)\n  (:start . 88) (:id . 58))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 100) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 114) (:start . 101) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 125)\n  (:start . 119) (:id . 62))\n ((:tag . "NN") (:stem . "morphogenesis") (:form . "morphogenesis")\n  (:end . 139) (:start . 126) (:id . 63))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 147)\n  (:start . 140) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 149) (:start . 148)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 155)\n  (:start . 149) (:id . 66))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 158) (:start . 156)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 69))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 164) (:start . 161)\n  (:id . 70))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 169) (:start . 165)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "cause") (:form . "caused") (:end . 176)\n  (:start . 170) (:id . 72))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 182)\n  (:start . 177) (:id . 73))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 192)\n  (:start . 183) (:id . 74))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 198)\n  (:start . 193) (:id . 75))\n ((:tag . "VBD") (:stem . "preclude") (:form . "precluded") (:end . 208)\n  (:start . 199) (:id . 76))\n ((:tag . "NN") (:stem . "examination") (:form . "examination") (:end . 220)\n  (:start . 209) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 223) (:start . 221)\n  (:id . 78))\n ((:tag . "NN") (:stem . "degfrelp-dp110") (:form . "dEGFRElp-dp110")\n  (:end . 238) (:start . 224) (:id . 79))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 251)\n  (:start . 239) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s3.65) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500638@unknown@formal@none@1@S@As in mouse models, overexpression of wild-type dEGFR failed to induce excess glia [6],[17], and instead retarded CNS growth (Figure S2).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 34) (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "NNP") (:stem . "dEGFR") (:form . "dEGFR") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 60) (:start . 54)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 70)\n  (:start . 64) (:id . 53))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "CD") (:stem . "6],[17") (:form . "6],[17") (:end . 90)\n  (:start . 84) (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 91) (:start . 90)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 60))\n ((:tag . "RB") (:stem . "instead") (:form . "instead") (:end . 104)\n  (:start . 97) (:id . 61))\n ((:tag . "VBN") (:stem . "retard") (:form . "retarded") (:end . 113)\n  (:start . 105) (:id . 62))\n ((:tag . "NN") (:stem . "cns") (:form . "CNS") (:end . 117) (:start . 114)\n  (:id . 63))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 124)\n  (:start . 118) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 132)\n  (:start . 126) (:id . 66))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 135) (:start . 133)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.66) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500639@unknown@formal@none@1@S@Unlike dEGFRλ, dEGFRWT and dEGFRElp have functional ligand-binding domains (Figure S1), and may cause additional defects by sequestering ligand otherwise required for normal development [17].@(((:tag . "IN") (:stem . "unlike") (:form . "Unlike") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 13)\n  (:start . 7) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "degfrwt") (:form . "dEGFRWT") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "degfrelp") (:form . "dEGFRElp") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 51)\n  (:start . 41) (:id . 49))\n ((:tag . "JJ") (:stem . "ligand-binding") (:form . "ligand-binding")\n  (:end . 66) (:start . 52) (:id . 50))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 74)\n  (:start . 67) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 82)\n  (:start . 76) (:id . 53))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 85) (:start . 83)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 57))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "VB") (:stem . "cause") (:form . "cause") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 112)\n  (:start . 102) (:id . 60))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 120)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "sequester") (:form . "sequestering") (:end . 136)\n  (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "ligand") (:form . "ligand") (:end . 143)\n  (:start . 137) (:id . 64))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 153)\n  (:start . 144) (:id . 65))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 162)\n  (:start . 154) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 166) (:start . 163)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 173)\n  (:start . 167) (:id . 68))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 185)\n  (:start . 174) (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 187) (:start . 186)\n  (:id . 70))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 189) (:start . 187)\n  (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 190) (:start . 189)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x3.67.1) (:span 92 95)))\n (:hscopes ((:id . :x3.67.1) (:span 92 185)))\n (:identifiers (:sid . :s3.67) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500640@unknown@formal@none@1@S@Glial-specific activation of the PI3K pathway alone, either by overexpression of dp110CAAX, dp110wild-type, dAkt, or dPTENdsRNA gave viable animals with relatively normal brains (Figure 1H, Figure S2, and Table S1).@(((:tag . "JJ") (:stem . "glial-specific") (:form . "Glial-specific")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 25)\n  (:start . 15) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 51) (:start . 46)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 77) (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 90)\n  (:start . 81) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "dp110wild-type") (:form . "dp110wild-type")\n  (:end . 106) (:start . 92) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dakt") (:form . "dAkt") (:end . 112) (:start . 108)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "dPTENdsRNA") (:form . "dPTENdsRNA") (:end . 127)\n  (:start . 117) (:id . 61))\n ((:tag . "VBD") (:stem . "give") (:form . "gave") (:end . 132) (:start . 128)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 139)\n  (:start . 133) (:id . 63))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 147)\n  (:start . 140) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 152) (:start . 148)\n  (:id . 65))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 163)\n  (:start . 153) (:id . 66))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 170)\n  (:start . 164) (:id . 67))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 177)\n  (:start . 171) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 179) (:start . 178)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 185)\n  (:start . 179) (:id . 70))\n ((:tag . "NN") (:stem . "1h") (:form . "1H") (:end . 188) (:start . 186)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 196)\n  (:start . 190) (:id . 73))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 199) (:start . 197)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 204) (:start . 201)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 210)\n  (:start . 205) (:id . 77))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 213) (:start . 211)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s3.68) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500641@unknown@formal@none@1@S@Therefore, coactivation of the EGFR and PI3K pathways synergize to produce much more severe phenotypes than would be expected if the effects of these pathways were additive.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "coactivation") (:form . "coactivation") (:end . 23)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "VBP") (:stem . "synergize") (:form . "synergize") (:end . 63)\n  (:start . 54) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 74)\n  (:start . 67) (:id . 53))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 91)\n  (:start . 85) (:id . 56))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 102)\n  (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 107) (:start . 103)\n  (:id . 58))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 113)\n  (:start . 108) (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 125)\n  (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 140)\n  (:start . 133) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 65))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 149)\n  (:start . 144) (:id . 66))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 158)\n  (:start . 150) (:id . 67))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 163) (:start . 159)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "additive") (:form . "additive") (:end . 172)\n  (:start . 164) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.69) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500642@unknown@formal@none@1@S@In repo>dEGFRλ;dp110CAAX brains, excess glia emerged in early larval stages and accumulated over 5–7 days. dEGFRλ;dp110CAAX glia severely disrupt the normal cellular architecture of the larval brain (Figure 1A and 1B and Figure 2A–C), lose normal stellate glial morphologies (Figure 2A–C), and generate multilayered aggregations of abnormal glia throughout the brain (Figure 2A–C); in these ways dEGFRλ;dp110CAAX glia are neoplastic [18].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 24) (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 31)\n  (:start . 25) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 39)\n  (:start . 33) (:id . 46))\n ((:tag . "NN") (:stem . 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5500643@unknown@formal@none@1@S@Like neoplastic epithelial cells, dEGFRλ;dp110CAAX glia ectopically expressed an active form of the matrix metalloprotease dMMP1 (Figure S3), which can confer an invasive potential [19],[20], implying that abnormal dEGFRλ;dp110CAAX glia may be invasive within the brain.@(((:tag . "IN") (:stem . "like") (:form . "Like") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "epithelial") (:form . "epithelial") (:end . 26)\n  (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 32) (:start . 27)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 50) (:start . 34) (:id . 47))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 55) (:start . 51)\n  (:id . 48))\n ((:tag . "RB") (:stem . "ectopically") (:form . "ectopically") (:end . 67)\n  (:start . 56) (:id . 49))\n ((:tag . "VBD") (:stem . "express") (:form . "expressed") (:end . 77)\n  (:start . 68) (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 80) (:start . 78)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 87)\n  (:start . 81) (:id . 52))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 92) (:start . 88)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 55))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 106)\n  (:start . 100) (:id . 56))\n ((:tag . "NN") (:stem . "metalloprotease") (:form . "metalloprotease")\n  (:end . 122) (:start . 107) (:id . 57))\n ((:tag . "NN") (:stem . "dmmp1") (:form . "dMMP1") (:end . 128)\n  (:start . 123) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 136)\n  (:start . 130) (:id . 60))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 139) (:start . 137)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 63))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 147)\n  (:start . 142) (:id . 64))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 151) (:start . 148)\n  (:id . 65))\n ((:tag . "VB") (:stem . "confer") (:form . "confer") (:end . 158)\n  (:start . 152) (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 161) (:start . 159)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 170)\n  (:start . 162) (:id . 68))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 180)\n  (:start . 171) (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 182) (:start . 181)\n  (:id . 70))\n ((:tag . "CD") (:stem . "19],[20") (:form . "19],[20") (:end . 189)\n  (:start . 182) (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 190) (:start . 189)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "imply") (:form . "implying") (:end . 200)\n  (:start . 192) (:id . 74))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 205) (:start . 201)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 214)\n  (:start . 206) (:id . 76))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 231) (:start . 215) (:id . 77))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 236) (:start . 232)\n  (:id . 78))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 240) (:start . 237)\n  (:id . 79))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 243) (:start . 241)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 252)\n  (:start . 244) (:id . 81))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 259)\n  (:start . 253) (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 263) (:start . 260)\n  (:id . 83))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 269)\n  (:start . 264) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x3.71.1) (:span 237 240)) ((:id . :x3.71.2) (:span 192 200))\n  ((:id . :x3.71.3) (:span 148 151)))\n (:hscopes ((:id . :x3.71.1) (:span 237 269))\n  ((:id . :x3.71.2) (:span 192 269)) ((:id . :x3.71.3) (:span 148 180)))\n (:identifiers (:sid . :s3.71) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500644@unknown@formal@none@1@S@Unlike neoplastic epithelia, neoplastic neural cells, such as dEGFRλ;dp110CAAX glia, typically retain expression of genes that regulate neural cell fate, such as Repo [21],[22].@(((:tag . "IN") (:stem . "unlike") (:form . "Unlike") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 17)\n  (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "epithelia") (:form . "epithelia") (:end . 27)\n  (:start . 18) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 39)\n  (:start . 29) (:id . 46))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 46)\n  (:start . 40) (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 52) (:start . 47)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 78) (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 83) (:start . 79)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 94)\n  (:start . 85) (:id . 55))\n ((:tag . "VBP") (:stem . "retain") (:form . "retain") (:end . 101)\n  (:start . 95) (:id . 56))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 112)\n  (:start . 102) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 121)\n  (:start . 116) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 126) (:start . 122)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "regulate") (:form . "regulate") (:end . 135)\n  (:start . 127) (:id . 61))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 142)\n  (:start . 136) (:id . 62))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 147) (:start . 143)\n  (:id . 63))\n ((:tag . "NN") (:stem . "fate") (:form . "fate") (:end . 152) (:start . 148)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 158) (:start . 154)\n  (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 161) (:start . 159)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 166) (:start . 162)\n  (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 168) (:start . 167)\n  (:id . 69))\n ((:tag . "CD") (:stem . "21],[22") (:form . "21],[22") (:end . 175)\n  (:start . 168) (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 176) (:start . 175)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.72) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500645@unknown@formal@none@1@S@Coactivation of EGFR and PI3K cell-autonomously promotes cell cycle entry.@(((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "RB") (:stem . "cell-autonomously") (:form . "cell-autonomously")\n  (:end . 47) (:start . 30) (:id . 47))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 56)\n  (:start . 48) (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 61) (:start . 57)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 67) (:start . 62)\n  (:id . 50))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 73) (:start . 68)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.73) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500646@unknown@formal@none@1@S@Relative to controls, many dEGFRλ;dp110CAAX glia showed BrdU incorporation, which marks S-phase cells (Figure 2D and 2E), indicating that neoplastic glia arise from overproliferation.@(((:tag . "JJ") (:stem . "relative") (:form . "Relative") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 43) (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 55) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "BrdU") (:form . "BrdU") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "incorporation") (:form . "incorporation")\n  (:end . 74) (:start . 61) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 81) (:start . 76)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "mark") (:form . "marks") (:end . 87) (:start . 82)\n  (:id . 54))\n ((:tag . "NN") (:stem . "s-phase") (:form . "S-phase") (:end . 95)\n  (:start . 88) (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 101) (:start . 96)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 109)\n  (:start . 103) (:id . 58))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 112) (:start . 110)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "NN") (:stem . "2e") (:form . "2E") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 132)\n  (:start . 122) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 137) (:start . 133)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 148)\n  (:start . 138) (:id . 66))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 153) (:start . 149)\n  (:id . 67))\n ((:tag . "VBP") (:stem . "arise") (:form . "arise") (:end . 159)\n  (:start . 154) (:id . 68))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 164) (:start . 160)\n  (:id . 69))\n ((:tag . "NN") (:stem . "overproliferation") (:form . "overproliferation")\n  (:end . 182) (:start . 165) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x3.74.1) (:span 122 137)))\n (:hscopes ((:id . :x3.74.1) (:span 122 182)))\n (:identifiers (:sid . :s3.74) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500647@unknown@formal@none@1@S@repo>dEGFRλ;dp110CAAX animals also showed reduced BrdU in neuronal precursors (Figure 2E, data not shown), demonstrating that neoplastic glia disrupt neuronal development.@(((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 21) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 29)\n  (:start . 22) (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 34) (:start . 30)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 41) (:start . 35)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 49)\n  (:start . 42) (:id . 46))\n ((:tag . "NNP") (:stem . "BrdU") (:form . "BrdU") (:end . 54) (:start . 50)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 66)\n  (:start . 58) (:id . 49))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 77)\n  (:start . 67) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 85)\n  (:start . 79) (:id . 52))\n ((:tag . "NN") (:stem . "2e") (:form . "2E") (:end . 88) (:start . 86)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 98) (:start . 95)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 104) (:start . 99)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating")\n  (:end . 120) (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 125) (:start . 121)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 136)\n  (:start . 126) (:id . 62))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 141) (:start . 137)\n  (:id . 63))\n ((:tag . "NN") (:stem . "disrupt") (:form . "disrupt") (:end . 149)\n  (:start . 142) (:id . 64))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 158)\n  (:start . 150) (:id . 65))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 170)\n  (:start . 159) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.75) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500648@unknown@formal@none@1@S@The cell cycle is governed by CyclinD-Cdk4 and CyclinE-Cdk2 complexes, which phosphorylate and inactivate Rb proteins, to release E2F activators to stimulate G1-S-phase entry [23].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "govern") (:form . "governed") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cyclind-cdk4") (:form . "CyclinD-Cdk4") (:end . 42)\n  (:start . 30) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cycline-cdk2") (:form . "CyclinE-Cdk2") (:end . 59)\n  (:start . 47) (:id . 50))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 69)\n  (:start . 60) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 76) (:start . 71)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "phosphorylate") (:form . "phosphorylate")\n  (:end . 90) (:start . 77) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "inactivate") (:form . "inactivate") (:end . 105)\n  (:start . 95) (:id . 56))\n ((:tag . "NNP") (:stem . "Rb") (:form . "Rb") (:end . 108) (:start . 106)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 117)\n  (:start . 109) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 121) (:start . 119)\n  (:id . 60))\n ((:tag . "VB") (:stem . "release") (:form . "release") (:end . 129)\n  (:start . 122) (:id . 61))\n ((:tag . "NNP") (:stem . "E2F") (:form . "E2F") (:end . 133) (:start . 130)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "activator") (:form . "activators") (:end . 144)\n  (:start . 134) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 147) (:start . 145)\n  (:id . 64))\n ((:tag . "VB") (:stem . "stimulate") (:form . "stimulate") (:end . 157)\n  (:start . 148) (:id . 65))\n ((:tag . "NNP") (:stem . "G1-S-phase") (:form . "G1-S-phase") (:end . 168)\n  (:start . 158) (:id . 66))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 174)\n  (:start . 169) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 176) (:start . 175)\n  (:id . 68))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 178) (:start . 176)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 179) (:start . 178)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.76) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500649@unknown@formal@none@1@S@Kip-type (p21/p27/p57) and Ink-type cyclin-dependent kinase inhibitors antagonize proliferation by inhibiting CyclinE-Cdk2 and CyclinD-Cdk4, respectively.@(((:tag . "NN") (:stem . "kip-type") (:form . "Kip-type") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "p21/p27/p57") (:form . "p21/p27/p57") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "ink-type") (:form . "Ink-type") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "JJ") (:stem . "cyclin-dependent") (:form . "cyclin-dependent")\n  (:end . 52) (:start . 36) (:id . 48))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 59)\n  (:start . 53) (:id . 49))\n ((:tag . "NNS") (:stem . "inhibitor") (:form . "inhibitors") (:end . 70)\n  (:start . 60) (:id . 50))\n ((:tag . "VBP") (:stem . "antagonize") (:form . "antagonize") (:end . 81)\n  (:start . 71) (:id . 51))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 95) (:start . 82) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 98) (:start . 96)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "inhibit") (:form . "inhibiting") (:end . 109)\n  (:start . 99) (:id . 54))\n ((:tag . "NN") (:stem . "cycline-cdk2") (:form . "CyclinE-Cdk2") (:end . 122)\n  (:start . 110) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cyclind-cdk4") (:form . "CyclinD-Cdk4") (:end . 139)\n  (:start . 127) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 58))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 153)\n  (:start . 141) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.77) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500650@unknown@formal@none@1@S@Cdc25 phosphatases and mitotic cyclins, including CyclinB, promote G2-M progression.@(((:tag . "NNP") (:stem . "Cdc25") (:form . "Cdc25") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "phosphatas") (:form . "phosphatases") (:end . 18)\n  (:start . 6) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "NNS") (:stem . "cyclin") (:form . "cyclins") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 49)\n  (:start . 40) (:id . 48))\n ((:tag . "NNP") (:stem . "CyclinB") (:form . "CyclinB") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "promote") (:form . "promote") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "g2-m") (:form . "G2-M") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "progression") (:form . "progression") (:end . 83)\n  (:start . 72) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.78) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500651@unknown@formal@none@1@S@Flies have single orthologs each for CyclinE, Cdk2, CyclinD, Cdk4, CyclinB, and p21/p27/p57 (Dap), E2F activators (E2F1) and two orthologs for Rb (Rbf1 and Rbf2) and Cdc25 (Stg and Twe) but no Ink ortholog [23].@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "CyclinE") (:form . "CyclinE") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . 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5500652@unknown@formal@none@1@S@dEGFRλ;dp110CAAX glia showed ectopic expression of dCyclinE and dCyclinB (Figure 2F–I), demonstrating that EGFR and PI3K activity upregulated proteins that promote cell cycle entry and progression.@(((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 16) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 21) (:start . 17)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 28) (:start . 22)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 36)\n  (:start . 29) (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 47)\n  (:start . 37) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "dCyclinE") (:form . "dCyclinE") (:end . 59)\n  (:start . 51) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "dCyclinB") (:form . "dCyclinB") (:end . 72)\n  (:start . 64) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 80)\n  (:start . 74) (:id . 52))\n ((:tag . "NNP") (:stem . "2F–I") (:form . "2F–I") (:end . 85) (:start . 81)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating")\n  (:end . 101) (:start . 88) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 106) (:start . 102)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 111) (:start . 107)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 120) (:start . 116)\n  (:id . 60))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 129)\n  (:start . 121) (:id . 61))\n ((:tag . "VBN") (:stem . "upregulate") (:form . "upregulated") (:end . 141)\n  (:start . 130) (:id . 62))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 150)\n  (:start . 142) (:id . 63))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 155) (:start . 151)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "promote") (:form . "promote") (:end . 163)\n  (:start . 156) (:id . 65))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 168) (:start . 164)\n  (:id . 66))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 174)\n  (:start . 169) (:id . 67))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 180)\n  (:start . 175) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 184) (:start . 181)\n  (:id . 69))\n ((:tag . "NN") (:stem . "progression") (:form . "progression") (:end . 196)\n  (:start . 185) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.80) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500653@unknown@formal@none@1@S@High-grade human gliomas contain highly proliferative anaplastic glia and enlarged pleiomorphic polyploid glia [24].@(((:tag . "JJ") (:stem . "high-grade") (:form . "High-grade") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 16) (:start . 11)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 39)\n  (:start . 33) (:id . 46))\n ((:tag . "JJ") (:stem . "proliferative") (:form . "proliferative")\n  (:end . 53) (:start . 40) (:id . 47))\n ((:tag . "JJ") (:stem . "anaplastic") (:form . "anaplastic") (:end . 64)\n  (:start . 54) (:id . 48))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 69) (:start . 65)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "enlarge") (:form . "enlarged") (:end . 82)\n  (:start . 74) (:id . 51))\n ((:tag . "JJ") (:stem . "pleiomorphic") (:form . "pleiomorphic") (:end . 95)\n  (:start . 83) (:id . 52))\n ((:tag . "JJ") (:stem . "polyploid") (:form . "polyploid") (:end . 105)\n  (:start . 96) (:id . 53))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 110) (:start . 106)\n  (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 112) (:start . 111)\n  (:id . 55))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 114) (:start . 112)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 115) (:start . 114)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.81) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500654@unknown@formal@none@1@S@Similarly, repo>dEGFRλ;dp110CAAX larvae showed accumulation of small, highly proliferative glia that strongly expressed cyclins and labeled with BrdU.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 32) (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "larvae") (:form . "larvae") (:end . 39)\n  (:start . 33) (:id . 45))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 46) (:start . 40)\n  (:id . 46))\n ((:tag . "NN") (:stem . "accumulation") (:form . "accumulation") (:end . 59)\n  (:start . 47) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 68) (:start . 63)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 50))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 76)\n  (:start . 70) (:id . 51))\n ((:tag . "JJ") (:stem . "proliferative") (:form . "proliferative")\n  (:end . 90) (:start . 77) (:id . 52))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 95) (:start . 91)\n  (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 100) (:start . 96)\n  (:id . 54))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 109)\n  (:start . 101) (:id . 55))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 119)\n  (:start . 110) (:id . 56))\n ((:tag . "NNS") (:stem . "cyclin") (:form . "cyclins") (:end . 127)\n  (:start . 120) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 139)\n  (:start . 132) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 144) (:start . 140)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "BrdU") (:form . "BrdU") (:end . 149) (:start . 145)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.82) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500655@unknown@formal@none@1@S@repo>dEGFRλ;dp110CAAX larvae showed accumulation of small, highly proliferative glia that strongly expressed cyclins and labeled with BrdU. repo>dEGFRλ;dp110CAAX larval brains also displayed abnormal polyploid glia, as assessed by DAPI staining (data not shown), and these cells typically expressed only dCyclinE but not dCyclinB, and thereby likely underwent ectopic DNA replication without mitosis (Figure 2G and 2I, data not shown).@(((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 21) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "larvae") (:form . "larvae") (:end . 28)\n  (:start . 22) (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 35) (:start . 29)\n  (:id . 44))\n ((:tag . "NN") (:stem . "accumulation") (:form . "accumulation") (:end . 48)\n  (:start . 36) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 46))\n ((:tag . 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5500656@unknown@formal@none@1@S@However, overexpression of dCyclinE-dCdk2, dCyclinD-dCdk4, or dE2F1-dDp complexes and/or Rbf1 knock-down did not cause neoplasia, and instead either doubled glial cell numbers or resulted in embryonic lethality (Figure S4, data not shown).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 23) (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dcycline-dcdk2") (:form . "dCyclinE-dCdk2")\n  (:end . 41) (:start . 27) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dcyclind-dcdk4") (:form . "dCyclinD-dCdk4")\n  (:end . 57) (:start . 43) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "de2f1-ddp") (:form . "dE2F1-dDp") (:end . 71)\n  (:start . 62) (:id . 51))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 81)\n  (:start . 72) (:id . 52))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 88)\n  (:start . 82) (:id . 53))\n ((:tag . "NN") (:stem . "rbf1") (:form . "Rbf1") (:end . 93) (:start . 89)\n  (:id . 54))\n ((:tag . "NN") (:stem . "knock-down") (:form . "knock-down") (:end . 104)\n  (:start . 94) (:id . 55))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 108) (:start . 105)\n  (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 112) (:start . 109)\n  (:id . 57))\n ((:tag . "VB") (:stem . "cause") (:form . "cause") (:end . 118)\n  (:start . 113) (:id . 58))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 128)\n  (:start . 119) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 61))\n ((:tag . "RB") (:stem . "instead") (:form . "instead") (:end . 141)\n  (:start . 134) (:id . 62))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 148)\n  (:start . 142) (:id . 63))\n ((:tag . "VBD") (:stem . "double") (:form . "doubled") (:end . 156)\n  (:start . 149) (:id . 64))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 162)\n  (:start . 157) (:id . 65))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 167) (:start . 163)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 175)\n  (:start . 168) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 178) (:start . 176)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 187)\n  (:start . 179) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 190) (:start . 188)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 200)\n  (:start . 191) (:id . 71))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 210)\n  (:start . 201) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 212) (:start . 211)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 218)\n  (:start . 212) (:id . 74))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 221) (:start . 219)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 222) (:start . 221)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 227)\n  (:start . 223) (:id . 77))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 231) (:start . 228)\n  (:id . 78))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 237)\n  (:start . 232) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 238) (:start . 237)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s3.84) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500657@unknown@formal@none@1@S@We next examined negative regulators of the cell cycle.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "next") (:form . "next") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "regulator") (:form . "regulators") (:end . 36)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.85) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500658@unknown@formal@none@1@S@dEGFRλ;dp110CAAX glia expressed Rbf1, but showed little Dap, a result we also observed in wild-type glia (Figure S5).@(((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 16) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 21) (:start . 17)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "express") (:form . "expressed") (:end . 31)\n  (:start . 22) (:id . 44))\n ((:tag . "NN") (:stem . "rbf1") (:form . "Rbf1") (:end . 36) (:start . 32)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 46))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 48) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "little") (:form . "little") (:end . 55)\n  (:start . 49) (:id . 49))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 99)\n  (:start . 90) (:id . 58))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 104) (:start . 100)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 112)\n  (:start . 106) (:id . 61))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.86) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500659@unknown@formal@none@1@S@Dap inhibits dCyclinE-cdk2 complexes [25], and is transiently expressed in neural progenitors to promote cell cycle exit as they begin differentiation [26].@(((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "dcycline-cdk2") (:form . "dCyclinE-cdk2")\n  (:end . 26) (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 36)\n  (:start . 27) (:id . 45))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 38) (:start . 37)\n  (:id . 46))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "RB") (:stem . "transiently") (:form . "transiently") (:end . 61)\n  (:start . 50) (:id . 52))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 71)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 81)\n  (:start . 75) (:id . 55))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 93)\n  (:start . 82) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 104)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 109) (:start . 105)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 115)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "exit") (:form . "exit") (:end . 120) (:start . 116)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 128) (:start . 124)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "begin") (:form . "begin") (:end . 134)\n  (:start . 129) (:id . 64))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 150) (:start . 135) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 152) (:start . 151)\n  (:id . 66))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 155) (:start . 154)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.87) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500660@unknown@formal@none@1@S@Dap overexpression completely suppressed repo>dEGFRλ;dp110CAAX glial overgrowth (Figure 2L), demonstrating that glial neoplasia is cell-autonomous and requires dCyclinE-dCdk2.@(((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 29)\n  (:start . 19) (:id . 44))\n ((:tag . "VBD") (:stem . "suppress") (:form . "suppressed") (:end . 40)\n  (:start . 30) (:id . 45))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 62) (:start . 41) (:id . 46))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 68) (:start . 63)\n  (:id . 47))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 79)\n  (:start . 69) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 87)\n  (:start . 81) (:id . 50))\n ((:tag . "NN") (:stem . "2l") (:form . "2L") (:end . 90) (:start . 88)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating")\n  (:end . 106) (:start . 93) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 111) (:start . 107)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 117)\n  (:start . 112) (:id . 56))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 127)\n  (:start . 118) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 130) (:start . 128)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "cell-autonomous") (:form . "cell-autonomous")\n  (:end . 146) (:start . 131) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 159)\n  (:start . 151) (:id . 61))\n ((:tag . "NN") (:stem . "dcycline-dcdk2") (:form . "dCyclinE-dCdk2")\n  (:end . 174) (:start . 160) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.88) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500661@unknown@formal@none@1@S@Similarly, overexpressed Rbf1 and dCyclinE mutations also reduced repo>dEGFRλ;dp110CAAX glial overproliferation (Figure 2M, data not shown).@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 24) (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "rbf1") (:form . "Rbf1") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dcycline") (:form . "dCyclinE") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 52)\n  (:start . 43) (:id . 48))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "reduce") (:form . "reduced") (:end . 65)\n  (:start . 58) (:id . 50))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 87) (:start . 66) (:id . 51))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 93) (:start . 88)\n  (:id . 52))\n ((:tag . "NN") (:stem . "overproliferation") (:form . "overproliferation")\n  (:end . 111) (:start . 94) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 119)\n  (:start . 113) (:id . 55))\n ((:tag . "NN") (:stem . "2m") (:form . "2M") (:end . 122) (:start . 120)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 128)\n  (:start . 124) (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 132) (:start . 129)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 138)\n  (:start . 133) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.89) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500662@unknown@formal@none@1@S@The gross neural morphogenesis defects observed in repo>dEGFRλ;dp110CAAX brains may be secondary to glial overproliferation since these defects were largely prevented by Dap or Rbf1 co-overexpression (Figure 2J–M).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "gross") (:form . "gross") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "morphogenesis") (:form . "morphogenesis")\n  (:end . 30) (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 47)\n  (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 72) (:start . 51) (:id . 49))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 79)\n  (:start . 73) (:id . 50))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 83) (:start . 80)\n  (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 86) (:start . 84)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 96)\n  (:start . 87) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 99) (:start . 97)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 105)\n  (:start . 100) (:id . 55))\n ((:tag . "NN") (:stem . "overproliferation") (:form . "overproliferation")\n  (:end . 123) (:start . 106) (:id . 56))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 129)\n  (:start . 124) (:id . 57))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 135)\n  (:start . 130) (:id . 58))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 143)\n  (:start . 136) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 148) (:start . 144)\n  (:id . 60))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 156)\n  (:start . 149) (:id . 61))\n ((:tag . "VBN") (:stem . "prevent") (:form . "prevented") (:end . 166)\n  (:start . 157) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 169) (:start . 167)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 173) (:start . 170)\n  (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 176) (:start . 174)\n  (:id . 65))\n ((:tag . "NN") (:stem . "rbf1") (:form . "Rbf1") (:end . 181) (:start . 177)\n  (:id . 66))\n ((:tag . "NN") (:stem . "co-overexpression") (:form . "co-overexpression")\n  (:end . 199) (:start . 182) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 201) (:start . 200)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 207)\n  (:start . 201) (:id . 69))\n ((:tag . "NNP") (:stem . "2J–M") (:form . "2J–M") (:end . 212) (:start . 208)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x3.90.1) (:span 80 83)))\n (:hscopes ((:id . :x3.90.1) (:span 80 199)))\n (:identifiers (:sid . :s3.90) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500663@unknown@formal@none@1@S@In repo>dEGFRλ;dp110CAAX animals, other mutant glia outside of the brain, such as peripheral glia, also became highly proliferative and invasive, and these defects, too, were corrected by Rbf1 or Dap overexpression (data not shown).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 24) (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 32)\n  (:start . 25) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 39) (:start . 34)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 46)\n  (:start . 40) (:id . 47))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "IN") (:stem . "outside") (:form . "outside") (:end . 59)\n  (:start . 52) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "peripheral") (:form . "peripheral") (:end . 92)\n  (:start . 82) (:id . 56))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 97) (:start . 93)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 103) (:start . 99)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "become") (:form . "became") (:end . 110)\n  (:start . 104) (:id . 60))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 117)\n  (:start . 111) (:id . 61))\n ((:tag . "JJ") (:stem . "proliferative") (:form . "proliferative")\n  (:end . 131) (:start . 118) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 144)\n  (:start . 136) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 149) (:start . 146)\n  (:id . 66))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 155)\n  (:start . 150) (:id . 67))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 163)\n  (:start . 156) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 69))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 168) (:start . 165)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 174) (:start . 170)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "correct") (:form . "corrected") (:end . 184)\n  (:start . 175) (:id . 73))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 187) (:start . 185)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Rbf1") (:form . "Rbf1") (:end . 192) (:start . 188)\n  (:id . 75))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 195) (:start . 193)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 199) (:start . 196)\n  (:id . 77))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 214) (:start . 200) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 216) (:start . 215)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 220)\n  (:start . 216) (:id . 80))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 224) (:start . 221)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 230)\n  (:start . 225) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 231) (:start . 230)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s3.91) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500664@unknown@formal@none@1@S@In controls, Rbf1 or Dap overexpression in wild-type glia inhibited proliferation (Figure S4), reducing numbers of glia by approximately half.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Rbf1") (:form . "Rbf1") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 39) (:start . 25) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 67)\n  (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 81) (:start . 68) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 89)\n  (:start . 83) (:id . 55))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "reduce") (:form . "reducing") (:end . 103)\n  (:start . 95) (:id . 59))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 111)\n  (:start . 104) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 119) (:start . 115)\n  (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 136) (:start . 123) (:id . 64))\n ((:tag . "NN") (:stem . "half") (:form . "half") (:end . 141) (:start . 137)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.92) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5500666@unknown@formal@none@1@S@Coactivation of EGFR and PI3K Does Not Elicit Neoplasia in All Neural Cell Types@(((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Does") (:form . "Does") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "Not") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Elicit") (:form . "Elicit") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "NNP") (:stem . "Neoplasia") (:form . "Neoplasia") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "All") (:form . "All") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Neural") (:form . "Neural") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "NNP") (:stem . "Cell") (:form . "Cell") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Types") (:form . "Types") (:end . 80) (:start . 75)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.94) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500667@unknown@formal@none@1@S@The phenotype triggered by coactivation of EGFR and PI3K in glia is distinct from other Drosophila brain-overgrowth mutant phenotypes, which involve accretion of excess neurons or neuroblasts [21],[29].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "trigger") (:form . "triggered") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "coactivation") (:form . "coactivation") (:end . 39)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 76)\n  (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 87) (:start . 82)\n  (:id . 56))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 98)\n  (:start . 88) (:id . 57))\n ((:tag . "NN") (:stem . "brain-overgrowth") (:form . "brain-overgrowth")\n  (:end . 115) (:start . 99) (:id . 58))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 122)\n  (:start . 116) (:id . 59))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 133)\n  (:start . 123) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 140)\n  (:start . 135) (:id . 62))\n ((:tag . "VBP") (:stem . "involve") (:form . "involve") (:end . 148)\n  (:start . 141) (:id . 63))\n ((:tag . "NN") (:stem . "accretion") (:form . "accretion") (:end . 158)\n  (:start . 149) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 161) (:start . 159)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 168)\n  (:start . 162) (:id . 66))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 176)\n  (:start . 169) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 179) (:start . 177)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 191)\n  (:start . 180) (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 193) (:start . 192)\n  (:id . 70))\n ((:tag . "CD") (:stem . "21],[29") (:form . "21],[29") (:end . 200)\n  (:start . 193) (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 201) (:start . 200)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s3.95) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500668@unknown@formal@none@1@S@repo>dEGFRλ;dp110CAAX cells were not transformed into neurons or neuroblasts as they lacked expression of the Elav and Miranda markers (Figure S6).@(((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 21) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 27) (:start . 22)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 32) (:start . 28)\n  (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 36) (:start . 33)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "transform") (:form . "transformed") (:end . 48)\n  (:start . 37) (:id . 46))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 53) (:start . 49)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 61)\n  (:start . 54) (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 64) (:start . 62)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 76)\n  (:start . 65) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 79) (:start . 77)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 84) (:start . 80)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "lack") (:form . "lacked") (:end . 91) (:start . 85)\n  (:id . 53))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 102)\n  (:start . 92) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Elav") (:form . "Elav") (:end . 114) (:start . 110)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Miranda") (:form . "Miranda") (:end . 126)\n  (:start . 119) (:id . 59))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 134)\n  (:start . 127) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 136) (:start . 135)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 142)\n  (:start . 136) (:id . 62))\n ((:tag . "NNP") (:stem . "S6") (:form . "S6") (:end . 145) (:start . 143)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.96) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500669@unknown@formal@none@1@S@Lineage-tracing with a Su(H)-lacZ neuroblast reporter showed that excess dEGFRλ;dp110CAAX glia did not express LacZ, and thus are not directly derived from larval neuroblasts (data not shown).@(((:tag . "JJ") (:stem . "lineage-tracing") (:form . "Lineage-tracing")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 20) (:start . 16)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Su(H)-lacZ") (:form . "Su(H)-lacZ") (:end . 33)\n  (:start . 23) (:id . 45))\n ((:tag . "NN") (:stem . "neuroblast") (:form . "neuroblast") (:end . 44)\n  (:start . 34) (:id . 46))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 53)\n  (:start . 45) (:id . 47))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 60) (:start . 54)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 65) (:start . 61)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 72)\n  (:start . 66) (:id . 50))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 89) (:start . 73) (:id . 51))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 94) (:start . 90)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 98) (:start . 95)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 102) (:start . 99)\n  (:id . 54))\n ((:tag . "VB") (:stem . "express") (:form . "express") (:end . 110)\n  (:start . 103) (:id . 55))\n ((:tag . "NNP") (:stem . "LacZ") (:form . "LacZ") (:end . 115) (:start . 111)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 58))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 125) (:start . 121)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 129) (:start . 126)\n  (:id . 60))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 133) (:start . 130)\n  (:id . 61))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 142)\n  (:start . 134) (:id . 62))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 150)\n  (:start . 143) (:id . 63))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 155) (:start . 151)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 162)\n  (:start . 156) (:id . 65))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 174)\n  (:start . 163) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 180)\n  (:start . 176) (:id . 68))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 184) (:start . 181)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 190)\n  (:start . 185) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 191) (:start . 190)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.97) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500670@unknown@formal@none@1@S@Moreover, constitutive EGFR-Ras and PI3K signaling does not elicit overgrowth in all neural cell types, as assessed with defined cell-type specific Gal4-drivers (Table S2).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 22)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "egfr-ras") (:form . "EGFR-Ras") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 50)\n  (:start . 41) (:id . 48))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 55) (:start . 51)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "VB") (:stem . "elicit") (:form . "elicit") (:end . 66)\n  (:start . 60) (:id . 51))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 77)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 53))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 84) (:start . 81)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 91)\n  (:start . 85) (:id . 55))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 96) (:start . 92)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 102) (:start . 97)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 115)\n  (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 120) (:start . 116)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 128)\n  (:start . 121) (:id . 62))\n ((:tag . "JJ") (:stem . "cell-type") (:form . "cell-type") (:end . 138)\n  (:start . 129) (:id . 63))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 147)\n  (:start . 139) (:id . 64))\n ((:tag . "NNS") (:stem . "gal4-driver") (:form . "Gal4-drivers") (:end . 160)\n  (:start . 148) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 167)\n  (:start . 162) (:id . 67))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 170) (:start . 168)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 171) (:start . 170)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.98) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500671@unknown@formal@none@1@S@For example, dRas85DV12 overexpression in fly neurons causes defects in fate specification, patterning, and apoptosis [30],[31].@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 38) (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 60)\n  (:start . 54) (:id . 50))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 68)\n  (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "fate") (:form . "fate") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "specification") (:form . "specification")\n  (:end . 90) (:start . 77) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "patterning") (:form . "patterning") (:end . 102)\n  (:start . 92) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "apoptosis") (:form . "apoptosis") (:end . 117)\n  (:start . 108) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . "CD") (:stem . "30],[31") (:form . "30],[31") (:end . 126)\n  (:start . 119) (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 127) (:start . 126)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.99) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500672@unknown@formal@none@1@S@Co-overexpression of dEGFRλ or dRas85DV12 with dp110CAAX in neurons (elav-Gal4, scratch-Gal4, OK107-Gal4, and Appl-Gal4) and neuroblasts/neuronal precursors (pros-Gal4, wor-Gal4, and 1407-Gal4) did not induce overgrowth (Figure S7, data not shown), even with increased transgene expression from Gal4 amplification [32].@(((:tag . "NNP") (:stem . "Co-overexpression") (:form . "Co-overexpression")\n  (:end . 17) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 43))\n ((:tag . "NN") (:stem . "degfrλ") (:form . "dEGFRλ") (:end . 27)\n  (:start . 21) (:id . 44))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 41)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . 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5500673@unknown@formal@none@1@S@In fact, broad co-overexpression of dEGFRλ and dp110CAAX in neuroblasts and neuronal precursors (pros-Gal4) reduced brain size, perhaps because signaling through these pathways stimulates precocious cell cycle exit of neuronal precursors, as in the developing eye [33].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "JJ") (:stem . "broad") (:form . "broad") (:end . 14) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "co-overexpression") (:form . "co-overexpression")\n  (:end . 32) (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 56)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 71)\n  (:start . 60) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 84)\n  (:start . 76) (:id . 54))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 95)\n  (:start . 85) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 56))\n ((:tag . "NN") (:stem . "pros-gal4") (:form . "pros-Gal4") (:end . 106)\n  (:start . 97) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "reduce") (:form . "reduced") (:end . 115)\n  (:start . 108) (:id . 59))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 121)\n  (:start . 116) (:id . 60))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 126) (:start . 122)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 62))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 135)\n  (:start . 128) (:id . 63))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 143)\n  (:start . 136) (:id . 64))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 153)\n  (:start . 144) (:id . 65))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 161)\n  (:start . 154) (:id . 66))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 167)\n  (:start . 162) (:id . 67))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 176)\n  (:start . 168) (:id . 68))\n ((:tag . "VBZ") (:stem . "stimulate") (:form . "stimulates") (:end . 187)\n  (:start . 177) (:id . 69))\n ((:tag . "JJ") (:stem . "precocious") (:form . "precocious") (:end . 198)\n  (:start . 188) (:id . 70))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 203) (:start . 199)\n  (:id . 71))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 209)\n  (:start . 204) (:id . 72))\n ((:tag . "NN") (:stem . "exit") (:form . "exit") (:end . 214) (:start . 210)\n  (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 217) (:start . 215)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 226)\n  (:start . 218) (:id . 75))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 237)\n  (:start . 227) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 238) (:start . 237)\n  (:id . 77))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 241) (:start . 239)\n  (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 244) (:start . 242)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 248) (:start . 245)\n  (:id . 80))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 259)\n  (:start . 249) (:id . 81))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 263) (:start . 260)\n  (:id . 82))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 265) (:start . 264)\n  (:id . 83))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 267) (:start . 265)\n  (:id . 84))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 268) (:start . 267)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 269) (:start . 268)\n  (:id . 86)))@@@1@45@((:hcues ((:id . :x3.101.1) (:span 128 135)))\n (:hscopes ((:id . :x3.101.1) (:span 128 263)))\n (:identifiers (:sid . :s3.101) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500674@unknown@formal@none@1@S@Furthermore, transient expression of dRas85DV12 or dEGFRλ and dp110CAAX in embryonic glia (gcm-Gal4) also failed to promote glial overgrowth (Figure S7) [27], demonstrating that sustained activation of these pathways is required for glial overproliferation.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "transient") (:form . "transient") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 33)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 47)\n  (:start . 37) (:id . 47))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 57)\n  (:start . 51) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 71)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 84)\n  (:start . 75) (:id . 53))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 89) (:start . 85)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gcm-gal4") (:form . "gcm-Gal4") (:end . 99)\n  (:start . 91) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 105) (:start . 101)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 112)\n  (:start . 106) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 123)\n  (:start . 116) (:id . 61))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 129)\n  (:start . 124) (:id . 62))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 140)\n  (:start . 130) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 148)\n  (:start . 142) (:id . 65))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 151) (:start . 149)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 154) (:start . 153)\n  (:id . 68))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 156) (:start . 154)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 157) (:start . 156)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating")\n  (:end . 172) (:start . 159) (:id . 72))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 177) (:start . 173)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "sustained") (:form . "sustained") (:end . 187)\n  (:start . 178) (:id . 74))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 198)\n  (:start . 188) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 201) (:start . 199)\n  (:id . 76))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 207)\n  (:start . 202) (:id . 77))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 216)\n  (:start . 208) (:id . 78))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 219) (:start . 217)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 228)\n  (:start . 220) (:id . 80))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 232) (:start . 229)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 238)\n  (:start . 233) (:id . 82))\n ((:tag . "NN") (:stem . "overproliferation") (:form . "overproliferation")\n  (:end . 256) (:start . 239) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s3.102) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5500676@unknown@formal@none@1@S@Therefore, neoplastic proliferation is not a uniform cellular response to EGFR and PI3K.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 35) (:start . 22) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 38) (:start . 36)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "uniform") (:form . "uniform") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 70)\n  (:start . 62) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 78) (:start . 74)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.104) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500677@unknown@formal@none@1@S@Coactivation of EGFR and PI3K Inhibits Cell Cycle Exit in Glia@(((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "Inhibits") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "NNP") (:stem . "Cell") (:form . "Cell") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Cycle") (:form . "Cycle") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Exit") (:form . "Exit") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Glia") (:form . "Glia") (:end . 62) (:start . 58)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.105) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500678@unknown@formal@none@1@S@Since repo>dEGFRλ;dp110CAAX animals die in 5–7 days, we assessed the proliferative potential of mutant glia using an abdominal transplant assay, a classic test of tumorigencity in flies [37].@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 27) (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 35)\n  (:start . 28) (:id . 44))\n ((:tag . "VBP") (:stem . "die") (:form . "die") (:end . 39) (:start . 36)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 46))\n ((:tag . "CD") (:stem . "5–7") (:form . "5–7") (:end . 46) (:start . 43)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "assess") (:form . "assessed") (:end . 64)\n  (:start . 56) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "proliferative") (:form . "proliferative")\n  (:end . 82) (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 92)\n  (:start . 83) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 102)\n  (:start . 96) (:id . 56))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 107) (:start . 103)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 113) (:start . 108)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 116) (:start . 114)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "abdominal") (:form . "abdominal") (:end . 126)\n  (:start . 117) (:id . 60))\n ((:tag . "NN") (:stem . "transplant") (:form . "transplant") (:end . 137)\n  (:start . 127) (:id . 61))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 143)\n  (:start . 138) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 146) (:start . 145)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "classic") (:form . "classic") (:end . 154)\n  (:start . 147) (:id . 65))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 159) (:start . 155)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 162) (:start . 160)\n  (:id . 67))\n ((:tag . "NN") (:stem . "tumorigencity") (:form . "tumorigencity")\n  (:end . 176) (:start . 163) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 179) (:start . 177)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 185) (:start . 180)\n  (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 187) (:start . 186)\n  (:id . 71))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 189) (:start . 187)\n  (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 190) (:start . 189)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.106) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500679@unknown@formal@none@1@S@Brain fragments from repo>dEGFRλ;dp110CAAX and wild-type larvae were transplanted into young adults.@(((:tag . "NN") (:stem . "brain") (:form . "Brain") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 42) (:start . 21) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 56)\n  (:start . 47) (:id . 47))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 63)\n  (:start . 57) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 68) (:start . 64)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 81)\n  (:start . 69) (:id . 50))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 86) (:start . 82)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "young") (:form . "young") (:end . 92) (:start . 87)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 99)\n  (:start . 93) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.107) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500680@unknown@formal@none@1@S@Wild-type transplants grew and survived over 1–6 weeks, but produced few glia (Figure 3A and 3C).@(((:tag . "JJ") (:stem . "wild-type") (:form . "Wild-type") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "transplant") (:form . "transplants") (:end . 21)\n  (:start . 10) (:id . 43))\n ((:tag . "VBD") (:stem . "grow") (:form . "grew") (:end . 26) (:start . 22)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "survive") (:form . "survived") (:end . 39)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 44) (:start . 40)\n  (:id . 47))\n ((:tag . "CD") (:stem . "1–6") (:form . "1–6") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "week") (:form . "weeks") (:end . 54) (:start . 49)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 68)\n  (:start . 60) (:id . 52))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 85)\n  (:start . 79) (:id . 56))\n ((:tag . "NN") (:stem . "3a") (:form . "3A") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "3c") (:form . "3C") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.108) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500681@unknown@formal@none@1@S@dEGFRλ;dp110CAAX mutant glia survived and proliferated into massive tumors that filled the hosts' abdomens, often causing premature death (Figure 3B).@(((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 16) (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 23)\n  (:start . 17) (:id . 43))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 28) (:start . 24)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "survive") (:form . "survived") (:end . 37)\n  (:start . 29) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "proliferate") (:form . "proliferated") (:end . 54)\n  (:start . 42) (:id . 47))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 59) (:start . 55)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "massive") (:form . "massive") (:end . 67)\n  (:start . 60) (:id . 49))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 74)\n  (:start . 68) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 79) (:start . 75)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "fill") (:form . "filled") (:end . 86) (:start . 80)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "host") (:form . "hosts") (:end . 96) (:start . 91)\n  (:id . 54))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 97) (:start . 96)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "abdomen") (:form . "abdomens") (:end . 106)\n  (:start . 98) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 57))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 113)\n  (:start . 108) (:id . 58))\n ((:tag . "VBG") (:stem . "cause") (:form . "causing") (:end . 121)\n  (:start . 114) (:id . 59))\n ((:tag . "JJ") (:stem . "premature") (:form . "premature") (:end . 131)\n  (:start . 122) (:id . 60))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 137)\n  (:start . 132) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 145)\n  (:start . 139) (:id . 63))\n ((:tag . "NN") (:stem . "3b") (:form . "3B") (:end . 148) (:start . 146)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.109) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500682@unknown@formal@none@1@S@Tumors were composed of small glial cells with little cytoplasm (Figure 3D–F).@(((:tag . "NNS") (:stem . "tumor") (:form . "Tumors") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "little") (:form . "little") (:end . 53)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "cytoplasm") (:form . "cytoplasm") (:end . 63)\n  (:start . 54) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 71)\n  (:start . 65) (:id . 53))\n ((:tag . "NNP") (:stem . "3D–F") (:form . "3D–F") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.110) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500683@unknown@formal@none@1@S@Tumors also contained trachea embedded throughout their mass (Figure 3D and 3E and Video S1), suggesting that tumors stimulated growth of new trachea or enveloped existing trachea, perhaps in a process akin to tumor angiogenesis.@(((:tag . "NNS") (:stem . "tumor") (:form . "Tumors") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "trachea") (:form . "trachea") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "VBN") (:stem . "embed") (:form . "embedded") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 49)\n  (:start . 39) (:id . 47))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 55)\n  (:start . 50) (:id . 48))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 60) (:start . 56)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 68)\n  (:start . 62) (:id . 51))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "3e") (:form . "3E") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Video") (:form . "Video") (:end . 88) (:start . 83)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 104)\n  (:start . 94) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 109) (:start . 105)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 116)\n  (:start . 110) (:id . 62))\n ((:tag . "VBD") (:stem . "stimulate") (:form . "stimulated") (:end . 127)\n  (:start . 117) (:id . 63))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 134)\n  (:start . 128) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 141) (:start . 138)\n  (:id . 66))\n ((:tag . "NN") (:stem . "trachea") (:form . "trachea") (:end . 149)\n  (:start . 142) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 152) (:start . 150)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "envelop") (:form . "enveloped") (:end . 162)\n  (:start . 153) (:id . 69))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 171)\n  (:start . 163) (:id . 70))\n ((:tag . "NN") (:stem . "trachea") (:form . "trachea") (:end . 179)\n  (:start . 172) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n  (:id . 72))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 188)\n  (:start . 181) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 191) (:start . 189)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 193) (:start . 192)\n  (:id . 75))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 201)\n  (:start . 194) (:id . 76))\n ((:tag . "NN") (:stem . "akin") (:form . "akin") (:end . 206) (:start . 202)\n  (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 209) (:start . 207)\n  (:id . 78))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 215)\n  (:start . 210) (:id . 79))\n ((:tag . "NN") (:stem . "angiogenesis") (:form . "angiogenesis") (:end . 228)\n  (:start . 216) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x3.111.1) (:span 181 188))\n  ((:id . :x3.111.2) (:span 150 152)) ((:id . :x3.111.3) (:span 94 104)))\n (:hscopes ((:id . :x3.111.1) (:span 181 228))\n  ((:id . :x3.111.2) (:span 117 179)) ((:id . :x3.111.3) (:span 94 228)))\n (:identifiers (:sid . :s3.111) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500684@unknown@formal@none@1@S@The leading edges of the tumors harbored individual cells invading nearby tissues, such as the ovary (Figure 3F and Video S2), which is consistent with the ectopic expression of active dMMP1 observed in dEGFRλ;dp110CAAX glia in the larval brain (Figure S3).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 11) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "edge") (:form . "edges") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . "VBD") (:stem . "harbor") (:form . "harbored") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 51)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "invade") (:form . "invading") (:end . 66)\n  (:start . 58) (:id . 51))\n ((:tag . "JJ") (:stem . "nearby") (:form . "nearby") (:end . 73)\n  (:start . 67) (:id . 52))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 81)\n  (:start . 74) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 57))\n ((:tag . "NN") (:stem . "ovary") (:form . "ovary") (:end . 100) (:start . 95)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 108)\n  (:start . 102) (:id . 60))\n ((:tag . "NN") (:stem . "3f") (:form . "3F") (:end . 111) (:start . 109)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Video") (:form . "Video") (:end . 121)\n  (:start . 116) (:id . 63))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 124) (:start . 122)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 66))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 132)\n  (:start . 127) (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 135) (:start . 133)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 146)\n  (:start . 136) (:id . 69))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 151) (:start . 147)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 163)\n  (:start . 156) (:id . 72))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 174)\n  (:start . 164) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 184)\n  (:start . 178) (:id . 75))\n ((:tag . "NN") (:stem . "dmmp1") (:form . "dMMP1") (:end . 190)\n  (:start . 185) (:id . 76))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 199)\n  (:start . 191) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 202) (:start . 200)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 219) (:start . 203) (:id . 79))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 224) (:start . 220)\n  (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 227) (:start . 225)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 231) (:start . 228)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 238)\n  (:start . 232) (:id . 83))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 244)\n  (:start . 239) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 246) (:start . 245)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 252)\n  (:start . 246) (:id . 86))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 255) (:start . 253)\n  (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 256) (:start . 255)\n  (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s3.112) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500685@unknown@formal@none@1@S@However, some tissues, such as the gut, did not contain metastases, implying some degree of selective invasion.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 49))\n ((:tag . "NN") (:stem . "gut") (:form . "gut") (:end . 38) (:start . 35)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 43) (:start . 40)\n  (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 47) (:start . 44)\n  (:id . 53))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 55)\n  (:start . 48) (:id . 54))\n ((:tag . "NNS") (:stem . "metastasis") (:form . "metastases") (:end . 66)\n  (:start . 56) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "imply") (:form . "implying") (:end . 76)\n  (:start . 68) (:id . 57))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 81) (:start . 77)\n  (:id . 58))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 88)\n  (:start . 82) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "selective") (:form . "selective") (:end . 101)\n  (:start . 92) (:id . 61))\n ((:tag . "NN") (:stem . "invasion") (:form . "invasion") (:end . 110)\n  (:start . 102) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.113) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500686@unknown@formal@none@1@S@Thus, once unconstrained by the larval life cycle, dEGFRλ;dp110CAAX glia fail to exit the cell cycle, continue to proliferate, and form highly invasive tumors, all properties of human cancer cells.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "once") (:form . "once") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "unconstrained") (:form . "unconstrained")\n  (:end . 24) (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 67) (:start . 51) (:id . 52))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "fail") (:form . "fail") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "VB") (:stem . "exit") (:form . "exit") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 94) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 100) (:start . 95)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "continue") (:form . "continue") (:end . 110)\n  (:start . 102) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n  (:id . 62))\n ((:tag . "VB") (:stem . "proliferate") (:form . "proliferate") (:end . 125)\n  (:start . 114) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 65))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 135) (:start . 131)\n  (:id . 66))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 142)\n  (:start . 136) (:id . 67))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 151)\n  (:start . 143) (:id . 68))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 158)\n  (:start . 152) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n  (:id . 70))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 163) (:start . 160)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 174)\n  (:start . 164) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 183)\n  (:start . 178) (:id . 74))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 190)\n  (:start . 184) (:id . 75))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 196)\n  (:start . 191) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s3.114) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500687@unknown@formal@none@1@S@Coactivation of EGFR and PI3K inhibits cell cycle exit in glia.@(((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "exit") (:form . "exit") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s3.115) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500688@unknown@formal@none@1@S@Coactivation of EGFR-Ras and PI3K Creates Invasive Neoplastic Glia@(((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "create") (:form . "Creates") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "NNP") (:stem . "Invasive") (:form . "Invasive") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "NNP") (:stem . "Neoplastic") (:form . "Neoplastic") (:end . 61)\n  (:start . 51) (:id . 49))\n ((:tag . "NNP") (:stem . "Glia") (:form . "Glia") (:end . 66) (:start . 62)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.116) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500689@unknown@formal@none@1@S@To explore the invasive potential of mutant glia, we used FLP-FRT clonal analysis, a technique in which discrete clones of mutant cells are induced in otherwise normal tissues, a situation analogous to somatic tumorigenesis.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "explore") (:form . "explore") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "FLP-FRT") (:form . "FLP-FRT") (:end . 65)\n  (:start . 58) (:id . 53))\n ((:tag . "JJ") (:stem . "clonal") (:form . "clonal") (:end . 72)\n  (:start . 66) (:id . 54))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "NN") (:stem . "technique") (:form . "technique") (:end . 94)\n  (:start . 85) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 103)\n  (:start . 98) (:id . 60))\n ((:tag . "JJ") (:stem . "discrete") (:form . "discrete") (:end . 112)\n  (:start . 104) (:id . 61))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 119)\n  (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 129)\n  (:start . 123) (:id . 64))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 135)\n  (:start . 130) (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 139) (:start . 136)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 147)\n  (:start . 140) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n  (:id . 68))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 160)\n  (:start . 151) (:id . 69))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 167)\n  (:start . 161) (:id . 70))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 175)\n  (:start . 168) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 176) (:start . 175)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 178) (:start . 177)\n  (:id . 73))\n ((:tag . "NN") (:stem . "situation") (:form . "situation") (:end . 188)\n  (:start . 179) (:id . 74))\n ((:tag . "JJ") (:stem . "analogous") (:form . "analogous") (:end . 198)\n  (:start . 189) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 201) (:start . 199)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "somatic") (:form . "somatic") (:end . 209)\n  (:start . 202) (:id . 77))\n ((:tag . "NN") (:stem . "tumorigenesis") (:form . "tumorigenesis")\n  (:end . 223) (:start . 210) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s3.117) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500690@unknown@formal@none@1@S@We used a heat-shock-driven FLP-recombinase to catalyze mitotic recombination between FRT-bearing chromosomes such that a daughter cell (and all of its clonal progeny) initiated expression of GFP and UAS-containing transgenes only in repo-Gal4-expressing cells [12].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 9) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "heat-shock-driven") (:form . "heat-shock-driven")\n  (:end . 27) (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "flp-recombinase") (:form . "FLP-recombinase")\n  (:end . 43) (:start . 28) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 46) (:start . 44)\n  (:id . 47))\n ((:tag . "VB") (:stem . "catalyze") (:form . "catalyze") (:end . 55)\n  (:start . 47) (:id . 48))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 63)\n  (:start . 56) (:id . 49))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n  (:end . 77) (:start . 64) (:id . 50))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 85)\n  (:start . 78) (:id . 51))\n ((:tag . "JJ") (:stem . "frt-bearing") (:form . "FRT-bearing") (:end . 97)\n  (:start . 86) (:id . 52))\n ((:tag . "NNS") (:stem . "chromosome") (:form . "chromosomes") (:end . 109)\n  (:start . 98) (:id . 53))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 114) (:start . 110)\n  (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 119) (:start . 115)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 121) (:start . 120)\n  (:id . 56))\n ((:tag . "NN") (:stem . "daughter") (:form . "daughter") (:end . 130)\n  (:start . 122) (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 135) (:start . 131)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 60))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 144) (:start . 141)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 151) (:start . 148)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "clonal") (:form . "clonal") (:end . 158)\n  (:start . 152) (:id . 64))\n ((:tag . "NN") (:stem . "progeny") (:form . "progeny") (:end . 166)\n  (:start . 159) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 66))\n ((:tag . "VBD") (:stem . "initiate") (:form . "initiated") (:end . 177)\n  (:start . 168) (:id . 67))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 188)\n  (:start . 178) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 191) (:start . 189)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 195) (:start . 192)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 199) (:start . 196)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "uas-containing") (:form . "UAS-containing")\n  (:end . 214) (:start . 200) (:id . 72))\n ((:tag . "NNS") (:stem . "transgene") (:form . "transgenes") (:end . 225)\n  (:start . 215) (:id . 73))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 230) (:start . 226)\n  (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 233) (:start . 231)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "repo-gal4-expressing")\n  (:form . "repo-Gal4-expressing") (:end . 254) (:start . 234) (:id . 76))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 260)\n  (:start . 255) (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 262) (:start . 261)\n  (:id . 78))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 264) (:start . 262)\n  (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 265) (:start . 264)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 266) (:start . 265)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s3.118) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500691@unknown@formal@none@1@S@Clones were induced late in development, from mitotic founder cells, and were examined in adults.@(((:tag . "NNS") (:stem . "clone") (:form . "Clones") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "RB") (:stem . "late") (:form . "late") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 39)\n  (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "founder") (:form . "founder") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 96)\n  (:start . 90) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.119) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500692@unknown@formal@none@1@S@We could not definitively determine if clones were derived from single cell events since our study of these clones was retrospective, but given the frequency of control clone induction, many mutant clones likely originated from single cells.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "definitively") (:form . "definitively") (:end . 25)\n  (:start . 13) (:id . 45))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 58)\n  (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 63) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 70)\n  (:start . 64) (:id . 52))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 82)\n  (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 88) (:start . 83)\n  (:id . 55))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 98) (:start . 93)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n  (:id . 58))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 107)\n  (:start . 102) (:id . 59))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 114)\n  (:start . 108) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 118) (:start . 115)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "retrospective") (:form . "retrospective")\n  (:end . 132) (:start . 119) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 63))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 137) (:start . 134)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 143)\n  (:start . 138) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n  (:id . 66))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 157)\n  (:start . 148) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n  (:id . 68))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 168)\n  (:start . 161) (:id . 69))\n ((:tag . "NN") (:stem . "clone") (:form . "clone") (:end . 174)\n  (:start . 169) (:id . 70))\n ((:tag . "NN") (:stem . "induction") (:form . "induction") (:end . 184)\n  (:start . 175) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 190) (:start . 186)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 197)\n  (:start . 191) (:id . 74))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 204)\n  (:start . 198) (:id . 75))\n ((:tag . "RB") (:stem . "likely") (:form . "likely") (:end . 211)\n  (:start . 205) (:id . 76))\n ((:tag . "VBN") (:stem . "originate") (:form . "originated") (:end . 222)\n  (:start . 212) (:id . 77))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 227) (:start . 223)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 234)\n  (:start . 228) (:id . 79))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 240)\n  (:start . 235) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 241) (:start . 240)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x3.120.1) (:span 205 211)) ((:id . :x3.120.2) (:span 36 38)))\n (:hscopes ((:id . :x3.120.1) (:span 205 240))\n  ((:id . :x3.120.2) (:span 36 82)))\n (:identifiers (:sid . :s3.120) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500693@unknown@formal@none@1@S@In wild-type controls, we observed clones in 68% of brains examined (N=149).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "CD") (:stem . "68") (:form . "68") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 58)\n  (:start . 52) (:id . 53))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 67)\n  (:start . 59) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "N=149") (:form . "N=149") (:end . 74) (:start . 69)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.121) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500694@unknown@formal@none@1@S@Of the brains with clones, 75% had 1–3 clones, and 83% of these clones consisted of 1–3 cells of the same glial subtype (Figure 4A and 4B).@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "CD") (:stem . "75") (:form . "75") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 30) (:start . 29)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 34) (:start . 31)\n  (:id . 50))\n ((:tag . "CD") (:stem . "1–3") (:form . "1–3") (:end . 38) (:start . 35)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 45)\n  (:start . 39) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 54))\n ((:tag . "CD") (:stem . "83") (:form . "83") (:end . 53) (:start . 51)\n  (:id . 55))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 54) (:start . 53)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 57))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 63) (:start . 58)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 70)\n  (:start . 64) (:id . 59))\n ((:tag . "VBD") (:stem . "consist") (:form . "consisted") (:end . 80)\n  (:start . 71) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 61))\n ((:tag . "CD") (:stem . "1–3") (:form . "1–3") (:end . 87) (:start . 84)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 93) (:start . 88)\n  (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 105) (:start . 101)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 111)\n  (:start . 106) (:id . 67))\n ((:tag . "NN") (:stem . "subtype") (:form . "subtype") (:end . 119)\n  (:start . 112) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 127)\n  (:start . 121) (:id . 70))\n ((:tag . "NN") (:stem . "4a") (:form . "4A") (:end . 130) (:start . 128)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 72))\n ((:tag . "NN") (:stem . "4b") (:form . "4B") (:end . 137) (:start . 135)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.122) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500695@unknown@formal@none@1@S@Glial clones overexpressing dRas85DV12, dEGFRλ, or dEGFRElp alone typically contained 2-fold more cells than wild-type (dRas85DV12 shown in Figure 4C).@(((:tag . "JJ") (:stem . "glial") (:form . "Glial") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "overexpresse") (:form . "overexpressing")\n  (:end . 27) (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 38)\n  (:start . 28) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 46))\n ((:tag . "NN") (:stem . "degfrλ") (:form . "dEGFRλ") (:end . 46)\n  (:start . 40) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "degfrelp") (:form . "dEGFRElp") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 75)\n  (:start . 66) (:id . 52))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 85)\n  (:start . 76) (:id . 53))\n ((:tag . "RB") (:stem . "2-fold") (:form . "2-fold") (:end . 92)\n  (:start . 86) (:id . 54))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 97) (:start . 93)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 103) (:start . 98)\n  (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 108) (:start . 104)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 118)\n  (:start . 109) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 120) (:start . 119)\n  (:id . 59))\n ((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 130)\n  (:start . 120) (:id . 60))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 136)\n  (:start . 131) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 139) (:start . 137)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 146)\n  (:start . 140) (:id . 63))\n ((:tag . "NN") (:stem . "4c") (:form . "4C") (:end . 149) (:start . 147)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 150) (:start . 149)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.123) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500696@unknown@formal@none@1@S@To examine PI3K signaling, we used a dPTEN null allele, which became homozygous in FLP-FRT clones.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "dPTEN") (:form . "dPTEN") (:end . 42) (:start . 37)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 61) (:start . 56)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "become") (:form . "became") (:end . 68)\n  (:start . 62) (:id . 55))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 79)\n  (:start . 69) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "FLP-FRT") (:form . "FLP-FRT") (:end . 90)\n  (:start . 83) (:id . 58))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 97)\n  (:start . 91) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.124) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500697@unknown@formal@none@1@S@dPTEN-/- glia did not overgrow, but did show aberrant cytoplasmic projections (Figure 4D), perhaps reflecting dPTEN function in the cytoskeleton [38].@(((:tag . "JJ") (:stem . "dpten-/-") (:form . "dPTEN-/-") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VB") (:stem . "overgrow") (:form . "overgrow") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "VB") (:stem . "show") (:form . "show") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 53)\n  (:start . 45) (:id . 51))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 65)\n  (:start . 54) (:id . 52))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 77)\n  (:start . 66) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 85)\n  (:start . 79) (:id . 55))\n ((:tag . "NN") (:stem . "4d") (:form . "4D") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 98)\n  (:start . 91) (:id . 59))\n ((:tag . "VBG") (:stem . "reflect") (:form . "reflecting") (:end . 109)\n  (:start . 99) (:id . 60))\n ((:tag . "NN") (:stem . "dpten") (:form . "dPTEN") (:end . 115)\n  (:start . 110) (:id . 61))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 64))\n ((:tag . "NN") (:stem . "cytoskeleton") (:form . "cytoskeleton") (:end . 144)\n  (:start . 132) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 146) (:start . 145)\n  (:id . 66))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 148) (:start . 146)\n  (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 149) (:start . 148)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x3.125.1) (:span 91 98)))\n (:hscopes ((:id . :x3.125.1) (:span 91 144)))\n (:identifiers (:sid . :s3.125) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500698@unknown@formal@none@1@S@Coactivation of EGFR-Ras and PI3K creates invasive neoplastic glia.@(((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "create") (:form . "creates") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 61)\n  (:start . 51) (:id . 49))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 66) (:start . 62)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.126) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500699@unknown@formal@none@1@S@To coactivate EGFR-Ras and PI3K in glial clones, dRas85DV12, dEGFRElp, or dEGFRλ was overexpressed within dPTEN-/- glia, using repo-Gal4.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "coactivate") (:form . "coactivate") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 59)\n  (:start . 49) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "degfrelp") (:form . "dEGFRElp") (:end . 69)\n  (:start . 61) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 80)\n  (:start . 74) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 98) (:start . 85) (:id . 58))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 105)\n  (:start . 99) (:id . 59))\n ((:tag . "JJ") (:stem . "dpten-/-") (:form . "dPTEN-/-") (:end . 114)\n  (:start . 106) (:id . 60))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 119) (:start . 115)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 126) (:start . 121)\n  (:id . 63))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 136)\n  (:start . 127) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.127) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500700@unknown@formal@none@1@S@We observed overgrown and invasive dRas85DV12;dPTEN-/- and dEGFRElp;dPTEN-/- clones (Figure 4E–G). dEGFR;dPTEN-/- clones were less affected (Figure 4F and 4G), consistent with the larval overexpression of dRas85DV12 giving more severe growth phenotypes.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "overgrown") (:form . "overgrown") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "JJ") (:stem . "dRas85DV12;dPTEN-/-")\n  (:form . "dRas85DV12;dPTEN-/-") (:end . 54) (:start . 35) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dEGFRElp;dPTEN-/-") (:form . "dEGFRElp;dPTEN-/-")\n  (:end . 76) (:start . 59) (:id . 49))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 83)\n  (:start . 77) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 91)\n  (:start . 85) (:id . 52))\n ((:tag . "NNP") (:stem . "4E–G).") (:form . "4E–G).") (:end . 98)\n  (:start . 92) (:id . 53))\n ((:tag . "JJ") (:stem . "dEGFR;dPTEN-/-") (:form . "dEGFR;dPTEN-/-")\n  (:end . 113) (:start . 99) (:id . 54))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 120)\n  (:start . 114) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 125) (:start . 121)\n  (:id . 56))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 130) (:start . 126)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "affected") (:form . "affected") (:end . 139)\n  (:start . 131) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 147)\n  (:start . 141) (:id . 60))\n ((:tag . "NN") (:stem . "4f") (:form . "4F") (:end . 150) (:start . 148)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 62))\n ((:tag . "NN") (:stem . "4g") (:form . "4G") (:end . 157) (:start . 155)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 170)\n  (:start . 160) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 175) (:start . 171)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 186)\n  (:start . 180) (:id . 69))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 201) (:start . 187) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 204) (:start . 202)\n  (:id . 71))\n ((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 215)\n  (:start . 205) (:id . 72))\n ((:tag . "VBG") (:stem . "give") (:form . "giving") (:end . 222)\n  (:start . 216) (:id . 73))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 227) (:start . 223)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 234)\n  (:start . 228) (:id . 75))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 241)\n  (:start . 235) (:id . 76))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 252)\n  (:start . 242) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 253) (:start . 252)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s3.128) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500701@unknown@formal@none@1@S@Tumor-like overgrowth was only observed in dEGFR-dRas85D;dPTEN-/- cells, illustrating that chronic EGFR-Ras activation and PTEN loss can cause cell-autonomous over-proliferation.@(((:tag . "JJ") (:stem . "tumor-like") (:form . "Tumor-like") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 44))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 39)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dEGFR-dRas85D;dPTEN-/-")\n  (:form . "dEGFR-dRas85D;dPTEN-/-") (:end . 65) (:start . 43) (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 71) (:start . 66)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "illustrate") (:form . "illustrating") (:end . 85)\n  (:start . 73) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 90) (:start . 86)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "chronic") (:form . "chronic") (:end . 98)\n  (:start . 91) (:id . 53))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 107)\n  (:start . 99) (:id . 54))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 118)\n  (:start . 108) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 56))\n ((:tag . "NN") (:stem . "pten") (:form . "PTEN") (:end . 127) (:start . 123)\n  (:id . 57))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 132) (:start . 128)\n  (:id . 58))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 136) (:start . 133)\n  (:id . 59))\n ((:tag . "VB") (:stem . "cause") (:form . "cause") (:end . 142)\n  (:start . 137) (:id . 60))\n ((:tag . "JJ") (:stem . "cell-autonomous") (:form . "cell-autonomous")\n  (:end . 158) (:start . 143) (:id . 61))\n ((:tag . "NN") (:stem . "over-proliferation") (:form . "over-proliferation")\n  (:end . 177) (:start . 159) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.129) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500702@unknown@formal@none@1@S@Cells from these double mutant clones appeared to invade the brain, typically following fiber tracts, and sometimes induced the formation of trachea (Figure 4E).@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "VB") (:stem . "invade") (:form . "invade") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 77)\n  (:start . 68) (:id . 54))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 87)\n  (:start . 78) (:id . 55))\n ((:tag . "NN") (:stem . "fiber") (:form . "fiber") (:end . 93) (:start . 88)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 100)\n  (:start . 94) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 59))\n ((:tag . "RB") (:stem . "sometimes") (:form . "sometimes") (:end . 115)\n  (:start . 106) (:id . 60))\n ((:tag . "VBD") (:stem . "induce") (:form . "induced") (:end . 123)\n  (:start . 116) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 62))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 137)\n  (:start . 128) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n  (:id . 64))\n ((:tag . "NN") (:stem . "trachea") (:form . "trachea") (:end . 148)\n  (:start . 141) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 156)\n  (:start . 150) (:id . 67))\n ((:tag . "NN") (:stem . "4e") (:form . "4E") (:end . 159) (:start . 157)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x3.130.1) (:span 38 46)))\n (:hscopes ((:id . :x3.130.1) (:span 0 100)))\n (:identifiers (:sid . :s3.130) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500703@unknown@formal@none@1@S@Tumor-like growths of dEGFR-dRas85D;dPTEN-/- cells often penetrated deep into the brain, as exemplified by Videos S3 and S4 which show an animated 88 µm thick confocal z-stack of the dRas85DV12;dPTEN-/- clone in Figure 4E compared to a 16 µm thick z-stack of a wild-type control clone in Figure 4A.@(((:tag . "JJ") (:stem . "tumor-like") (:form . "Tumor-like") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "growth") (:form . "growths") (:end . 18)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "dEGFR-dRas85D;dPTEN-/-")\n  (:form . "dEGFR-dRas85D;dPTEN-/-") (:end . 44) (:start . 22) (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 50) (:start . 45)\n  (:id . 46))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 56) (:start . 51)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "penetrate") (:form . 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5500704@unknown@formal@none@1@S@These phenotypes were reminiscent of invasion and angiogenesis in human gliomas [24].@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "reminiscent") (:form . "reminiscent") (:end . 33)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "NN") (:stem . "invasion") (:form . "invasion") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "NN") (:stem . "angiogenesis") (:form . "angiogenesis") (:end . 62)\n  (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 71) (:start . 66)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 79)\n  (:start . 72) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 81) (:start . 80)\n  (:id . 53))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 83) (:start . 81)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.132) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500705@unknown@formal@none@1@S@We more commonly observed smaller dEGFR-dRas85D;dPTEN-/- clones composed of relatively differentiated, enlarged glia with diffusely invasive projections (Figure 4G); these clones likely derive from glia that differentiated prior to achieving sufficient EGFR-Ras transgene expression, and are consistent with findings that not all glial subtypes become neoplastic.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "JJ") (:stem . "dEGFR-dRas85D;dPTEN-/-")\n  (:form . 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"not") (:end . 325) (:start . 322)\n  (:id . 87))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 329) (:start . 326)\n  (:id . 88))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 335)\n  (:start . 330) (:id . 89))\n ((:tag . "NNS") (:stem . "subtype") (:form . "subtypes") (:end . 344)\n  (:start . 336) (:id . 90))\n ((:tag . "VBP") (:stem . "become") (:form . "become") (:end . 351)\n  (:start . 345) (:id . 91))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 362)\n  (:start . 352) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 363) (:start . 362)\n  (:id . 93)))@@@1@52@((:hcues ((:id . :x3.133.1) (:span 179 185)))\n (:hscopes ((:id . :x3.133.1) (:span 179 282)))\n (:identifiers (:sid . :s3.133) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500706@unknown@formal@none@1@S@Since neoplastic larval glia were concentrated in the outer anterior central brain and developing optic lobe, they may be derived from glial progenitor cells present in these regions [27],[28],[39].@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "larval") (:form . "larval") (:end . 23)\n  (:start . 17) (:id . 44))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "concentrate") (:form . "concentrated") (:end . 46)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "outer") (:form . "outer") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 76)\n  (:start . 69) (:id . 52))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 82) (:start . 77)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 97)\n  (:start . 87) (:id . 55))\n ((:tag . "JJ") (:stem . "optic") (:form . "optic") (:end . 103) (:start . 98)\n  (:id . 56))\n ((:tag . "NN") (:stem . "lobe") (:form . "lobe") (:end . 108) (:start . 104)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 114) (:start . 110)\n  (:id . 59))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 118) (:start . 115)\n  (:id . 60))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 121) (:start . 119)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 129)\n  (:start . 122) (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 134) (:start . 130)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 140)\n  (:start . 135) (:id . 64))\n ((:tag . "NN") (:stem . "progenitor") (:form . "progenitor") (:end . 151)\n  (:start . 141) (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 157)\n  (:start . 152) (:id . 66))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 165)\n  (:start . 158) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 168) (:start . 166)\n  (:id . 68))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 174)\n  (:start . 169) (:id . 69))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 182)\n  (:start . 175) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 184) (:start . 183)\n  (:id . 71))\n ((:tag . "CD") (:stem . "27],[28],[39") (:form . "27],[28],[39") (:end . 196)\n  (:start . 184) (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 197) (:start . 196)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x3.134.1) (:span 115 118)))\n (:hscopes ((:id . :x3.134.1) (:span 110 182)))\n (:identifiers (:sid . :s3.134) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500707@unknown@formal@none@1@S@To create clones from a discrete subpopulation of glial progenitors, we used an eyeless(ey)-promoter driven FLP-recombinase (ey-FLP), which is active in ey-expressing glial progenitors in the optic lobe [27].@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "create") (:form . "create") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "discrete") (:form . "discrete") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "subpopulation") (:form . "subpopulation")\n  (:end . 46) (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 67)\n  (:start . 56) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "eyeless(ey)-promoter")\n  (:form . "eyeless(ey)-promoter") (:end . 100) (:start . 80) (:id . 56))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 107)\n  (:start . 101) (:id . 57))\n ((:tag . "NNP") (:stem . "FLP-recombinase") (:form . "FLP-recombinase")\n  (:end . 123) (:start . 108) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "ey-FLP") (:form . "ey-FLP") (:end . 131)\n  (:start . 125) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 62))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 139)\n  (:start . 134) (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 149)\n  (:start . 143) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 152) (:start . 150)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "ey-expressing") (:form . "ey-expressing")\n  (:end . 166) (:start . 153) (:id . 67))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 172)\n  (:start . 167) (:id . 68))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 184)\n  (:start . 173) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 187) (:start . 185)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "optic") (:form . "optic") (:end . 197)\n  (:start . 192) (:id . 72))\n ((:tag . "NN") (:stem . "lobe") (:form . "lobe") (:end . 202) (:start . 198)\n  (:id . 73))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 204) (:start . 203)\n  (:id . 74))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 206) (:start . 204)\n  (:id . 75))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 207) (:start . 206)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s3.135) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500708@unknown@formal@none@1@S@Single mutant ey-FLP clones of dPTEN-/-, dRas85DV12, or dEGFRElp cells contained a modest number of excess and abnormal glia relative to wild-type controls (Figure 4H–J and Figure S8).@(((:tag . "JJ") (:stem . "single") (:form . "Single") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 13) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "ey-flp") (:form . "ey-FLP") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 27)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dpten-/-") (:form . "dPTEN-/-") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "dras85dv12") (:form . "dRas85DV12") (:end . 51)\n  (:start . 41) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "degfrelp") (:form . "dEGFRElp") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 80)\n  (:start . 71) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "modest") (:form . "modest") (:end . 89)\n  (:start . 83) (:id . 56))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 96)\n  (:start . 90) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 106)\n  (:start . 100) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 119)\n  (:start . 111) (:id . 61))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 124) (:start . 120)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 133)\n  (:start . 125) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 136) (:start . 134)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 146)\n  (:start . 137) (:id . 65))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 155)\n  (:start . 147) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 163)\n  (:start . 157) (:id . 68))\n ((:tag . "NNP") (:stem . "4H–J") (:form . "4H–J") (:end . 168) (:start . 164)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 172) (:start . 169)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 179)\n  (:start . 173) (:id . 71))\n ((:tag . "NNP") (:stem . "S8") (:form . "S8") (:end . 182) (:start . 180)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.136) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500709@unknown@formal@none@1@S@In contrast, the double mutant dRas85DV12;dPTEN-/-, dEGFRElp;dPTEN-/-, or dEGFRλ;dPTEN-/- ey-FLP clones, which emerge as approximately tens of cells in 3rd instar larval brains (Figure 4K), became large invasive tumors composed of hundreds to thousands of cells in adults (Figure 4L and Figure S8).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "dRas85DV12;dPTEN-/-")\n  (:form . "dRas85DV12;dPTEN-/-") (:end . 50) (:start . 31) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dEGFRElp;dPTEN-/-") (:form . "dEGFRElp;dPTEN-/-")\n  (:end . 69) (:start . 52) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dEGFRλ;dPTEN-/-") (:form . "dEGFRλ;dPTEN-/-")\n  (:end . 89) (:start . 74) (:id . 53))\n ((:tag . "NN") (:stem . "ey-flp") (:form . "ey-FLP") (:end . 96)\n  (:start . 90) (:id . 54))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 103)\n  (:start . 97) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 110)\n  (:start . 105) (:id . 57))\n ((:tag . "VBP") (:stem . "emerge") (:form . "emerge") (:end . 117)\n  (:start . 111) (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 120) (:start . 118)\n  (:id . 59))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 134) (:start . 121) (:id . 60))\n ((:tag . "NNS") (:stem . "ten") (:form . "tens") (:end . 139) (:start . 135)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 148)\n  (:start . 143) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 151) (:start . 149)\n  (:id . 64))\n ((:tag . "CD") (:stem . "3rd") (:form . "3rd") (:end . 155) (:start . 152)\n  (:id . 65))\n ((:tag . "IN") (:stem . "instar") (:form . "instar") (:end . 162)\n  (:start . 156) (:id . 66))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 169)\n  (:start . 163) (:id . 67))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 176)\n  (:start . 170) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 178) (:start . 177)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 184)\n  (:start . 178) (:id . 70))\n ((:tag . "NN") (:stem . "4k") (:form . "4K") (:end . 187) (:start . 185)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 73))\n ((:tag . "VBD") (:stem . "become") (:form . "became") (:end . 196)\n  (:start . 190) (:id . 74))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 202)\n  (:start . 197) (:id . 75))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 211)\n  (:start . 203) (:id . 76))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 218)\n  (:start . 212) (:id . 77))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 227)\n  (:start . 219) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 230) (:start . 228)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "hundred") (:form . "hundreds") (:end . 239)\n  (:start . 231) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 242) (:start . 240)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "thousand") (:form . "thousands") (:end . 252)\n  (:start . 243) (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 255) (:start . 253)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 261)\n  (:start . 256) (:id . 84))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 264) (:start . 262)\n  (:id . 85))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 271)\n  (:start . 265) (:id . 86))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 273) (:start . 272)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 279)\n  (:start . 273) (:id . 88))\n ((:tag . "NN") (:stem . "4l") (:form . "4L") (:end . 282) (:start . 280)\n  (:id . 89))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 286) (:start . 283)\n  (:id . 90))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 293)\n  (:start . 287) (:id . 91))\n ((:tag . "NN") (:stem . "s8") (:form . "S8") (:end . 296) (:start . 294)\n  (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 297) (:start . 296)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 298) (:start . 297)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s3.137) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500710@unknown@formal@none@1@S@EGFR;PI3K Induces Glial Neoplasia via Pnt and Stg Expression@(((:tag . "NNP") (:stem . "EGFR;PI3K") (:form . "EGFR;PI3K") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "induce") (:form . "Induces") (:end . 17)\n  (:start . 10) (:id . 43))\n ((:tag . "JJ") (:stem . "glial") (:form . "Glial") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Neoplasia") (:form . "Neoplasia") (:end . 33)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Pnt") (:form . "Pnt") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Stg") (:form . "Stg") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Expression") (:form . "Expression") (:end . 60)\n  (:start . 50) (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.138) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500711@unknown@formal@none@1@S@To address the function of EGFR-Ras and PI3K in glioma, we analyzed the genetic basis of glial pathogenesis in our repo>dEGFRλ;dp110CAAX model, as this model shows robust neoplasia, similarity to human tumor genotypes, and sensitivity to dEGFR and dPTEN gene dosage (data not shown).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "address") (:form . "address") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . 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"NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 107)\n  (:start . 95) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n  (:id . 61))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 114) (:start . 111)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 136) (:start . 115) (:id . 63))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 142)\n  (:start . 137) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 146) (:start . 144)\n  (:id . 66))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 151) (:start . 147)\n  (:id . 67))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 157)\n  (:start . 152) (:id . 68))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 163)\n  (:start . 158) (:id . 69))\n ((:tag . "JJ") (:stem . "robust") (:form . "robust") (:end . 170)\n  (:start . 164) (:id . 70))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 180)\n  (:start . 171) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 181) (:start . 180)\n  (:id . 72))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 192)\n  (:start . 182) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 195) (:start . 193)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 201)\n  (:start . 196) (:id . 75))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 207)\n  (:start . 202) (:id . 76))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 217)\n  (:start . 208) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 218) (:start . 217)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 222) (:start . 219)\n  (:id . 79))\n ((:tag . "NN") (:stem . "sensitivity") (:form . 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"shown") (:end . 281)\n  (:start . 276) (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 282) (:start . 281)\n  (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 283) (:start . 282)\n  (:id . 92)))@@@1@51@((:identifiers (:sid . :s3.139) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500712@unknown@formal@none@1@S@EGFR-Ras signaling can promote proliferation through Erk kinase-mediated induction of nuclear targets.@(((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 44) (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 52)\n  (:start . 45) (:id . 47))\n ((:tag . "NNP") (:stem . "Erk") (:form . "Erk") (:end . 56) (:start . 53)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "kinase-mediated") (:form . "kinase-mediated")\n  (:end . 72) (:start . 57) (:id . 49))\n ((:tag . "NN") (:stem . "induction") (:form . "induction") (:end . 82)\n  (:start . 73) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 93)\n  (:start . 86) (:id . 52))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 101)\n  (:start . 94) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 54)))@@@1@13@((:hcues ((:id . :x3.140.1) (:span 19 22)))\n (:hscopes ((:id . :x3.140.1) (:span 19 101)))\n (:identifiers (:sid . :s3.140) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500713@unknown@formal@none@1@S@In repo>dEGFRλ;dp110CAAX brains, mutant glia showed high levels of nuclear, activated di-phospho-Erk relative to wild-type glia in control brains (Figure 5A and 5B).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 24) (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 31)\n  (:start . 25) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 39)\n  (:start . 33) (:id . 46))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 44) (:start . 40)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 51) (:start . 45)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 56) (:start . 52)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 63)\n  (:start . 57) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 74)\n  (:start . 67) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 85)\n  (:start . 76) (:id . 54))\n ((:tag . "NN") (:stem . "di-phospho-erk") (:form . "di-phospho-Erk")\n  (:end . 100) (:start . 86) (:id . 55))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 109)\n  (:start . 101) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 122)\n  (:start . 113) (:id . 58))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 127) (:start . 123)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 130) (:start . 128)\n  (:id . 60))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 138)\n  (:start . 131) (:id . 61))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 145)\n  (:start . 139) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 153)\n  (:start . 147) (:id . 64))\n ((:tag . "NN") (:stem . "5a") (:form . "5A") (:end . 156) (:start . 154)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 66))\n ((:tag . "NN") (:stem . "5b") (:form . "5B") (:end . 163) (:start . 161)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 164) (:start . 163)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.141) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500714@unknown@formal@none@1@S@In flies, Erk activity can induce expression of PntP1, an ETS-family transcription factor encoded by the pointed (pnt) locus [40],[41].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "NNP") (:stem . "Erk") (:form . "Erk") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 22)\n  (:start . 14) (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 44)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PntP1") (:form . "PntP1") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "ETS-family") (:form . "ETS-family") (:end . 68)\n  (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 82) (:start . 69) (:id . 55))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 89)\n  (:start . 83) (:id . 56))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "pointed") (:form . "pointed") (:end . 112)\n  (:start . 105) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . "NN") (:stem . "pnt") (:form . "pnt") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 63))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 124)\n  (:start . 119) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 126) (:start . 125)\n  (:id . 65))\n ((:tag . "CD") (:stem . "40],[41") (:form . "40],[41") (:end . 133)\n  (:start . 126) (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 134) (:start . 133)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.142) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500715@unknown@formal@none@1@S@PntP1, which is expressed in embryonic glia and is required for their normal development [40], was upregulated in dEGFRλ;dp110CAAX glia (Figure 5C and 5D).@(((:tag . "NNP") (:stem . "PntP1") (:form . "PntP1") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 25)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 38)\n  (:start . 29) (:id . 48))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 59)\n  (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 69)\n  (:start . 64) (:id . 54))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 76)\n  (:start . 70) (:id . 55))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 88)\n  (:start . 77) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 93) (:start . 92)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 98) (:start . 95)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "upregulate") (:form . "upregulated") (:end . 110)\n  (:start . 99) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 130) (:start . 114) (:id . 64))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 135) (:start . 131)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 143)\n  (:start . 137) (:id . 67))\n ((:tag . "NN") (:stem . "5c") (:form . "5C") (:end . 146) (:start . 144)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 69))\n ((:tag . "NN") (:stem . "5d") (:form . "5D") (:end . 153) (:start . 151)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.143) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500716@unknown@formal@none@1@S@High levels of PntP1 can be detected normally in neuronal progenitors (data not shown), suggesting that it promotes a proliferative progenitor state.@(((:tag . "JJ") (:stem . "high") (:form . "High") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "PntP1") (:form . "PntP1") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 45)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 69)\n  (:start . 58) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 98)\n  (:start . 88) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 103) (:start . 99)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 115)\n  (:start . 107) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "proliferative") (:form . "proliferative")\n  (:end . 131) (:start . 118) (:id . 64))\n ((:tag . "NN") (:stem . "progenitor") (:form . "progenitor") (:end . 142)\n  (:start . 132) (:id . 65))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 148)\n  (:start . 143) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x3.144.1) (:span 88 98)))\n (:hscopes ((:id . :x3.144.1) (:span 88 148)))\n (:identifiers (:sid . :s3.144) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500717@unknown@formal@none@1@S@In developing eye tissue, EGFR-Ras-Erk signaling induces Pnt proteins to stimulate G2-M cell cycle progression through direct upregulation of Stg (Cdc25 ortholog) expression [41].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "EGFR-Ras-Erk") (:form . "EGFR-Ras-Erk") (:end . 38)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 56)\n  (:start . 49) (:id . 49))\n ((:tag . "NN") (:stem . "pnt") (:form . "Pnt") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 69)\n  (:start . 61) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "VB") (:stem . "stimulate") (:form . "stimulate") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "NNP") (:stem . "G2-M") (:form . "G2-M") (:end . 87) (:start . 83)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 92) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "progression") (:form . "progression") (:end . 110)\n  (:start . 99) (:id . 57))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 118)\n  (:start . 111) (:id . 58))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 125)\n  (:start . 119) (:id . 59))\n ((:tag . "NN") (:stem . "upregulation") (:form . "upregulation") (:end . 138)\n  (:start . 126) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 141) (:start . 139)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Stg") (:form . "Stg") (:end . 145) (:start . 142)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Cdc25") (:form . "Cdc25") (:end . 152)\n  (:start . 147) (:id . 64))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 161)\n  (:start . 153) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 66))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 173)\n  (:start . 163) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 175) (:start . 174)\n  (:id . 68))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 177) (:start . 175)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 178) (:start . 177)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.145) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500718@unknown@formal@none@1@S@Glial-specific RNAi knock down of pnt reduced Stg expression and completely suppressed dEGFRλ;dp110CAAX neoplasia (Figure 5E–H), demonstrating that Pnt proteins are required for both Stg expression and neoplastic overproliferation in dEGFRλ;dp110CAAX glia.@(((:tag . "JJ") (:stem . "glial-specific") (:form . "Glial-specific")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 19) (:start . 15)\n  (:id . 43))\n ((:tag . "VB") (:stem . "knock") (:form . "knock") (:end . 25) (:start . 20)\n  (:id . 44))\n ((:tag . "RP") (:stem . "down") (:form . "down") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pnt") (:form . "pnt") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "reduce") (:form . "reduced") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "stg") (:form . "Stg") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 75)\n  (:start . 65) (:id . 52))\n ((:tag . "VBD") (:stem . "suppress") (:form . "suppressed") (:end . 86)\n  (:start . 76) (:id . 53))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 103) (:start . 87) (:id . 54))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 113)\n  (:start . 104) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 121)\n  (:start . 115) (:id . 57))\n ((:tag . "NNP") (:stem . "5E–H") (:form . "5E–H") (:end . 126) (:start . 122)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 127) (:start . 126)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating")\n  (:end . 142) (:start . 129) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 147) (:start . 143)\n  (:id . 62))\n ((:tag . "NN") (:stem . "pnt") (:form . "Pnt") (:end . 151) (:start . 148)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 160)\n  (:start . 152) (:id . 64))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 164) (:start . 161)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 173)\n  (:start . 165) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 177) (:start . 174)\n  (:id . 67))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 182) (:start . 178)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Stg") (:form . "Stg") (:end . 186) (:start . 183)\n  (:id . 69))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 197)\n  (:start . 187) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 201) (:start . 198)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 212)\n  (:start . 202) (:id . 72))\n ((:tag . "NN") (:stem . "overproliferation") (:form . "overproliferation")\n  (:end . 230) (:start . 213) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 233) (:start . 231)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 250) (:start . 234) (:id . 75))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 255) (:start . 251)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 256) (:start . 255)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s3.146) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500719@unknown@formal@none@1@S@Notably, in repo>pntdsRNA;dEGFRλ;dp110CAAX brains, glia maintained their fate, as evidenced by repo-Gal4 and Repo expression.@(((:tag . "RB") (:stem . "notably") (:form . "Notably") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "repo>pntdsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>pntdsRNA;dEGFRλ;dp110CAAX") (:end . 42) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 49)\n  (:start . 43) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 47))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 55) (:start . 51)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "maintain") (:form . "maintained") (:end . 66)\n  (:start . 56) (:id . 49))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 72)\n  (:start . 67) (:id . 50))\n ((:tag . "NN") (:stem . "fate") (:form . "fate") (:end . 77) (:start . 73)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "evidence") (:form . "evidenced") (:end . 91)\n  (:start . 82) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 94) (:start . 92)\n  (:id . 55))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 104)\n  (:start . 95) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 113) (:start . 109)\n  (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 124)\n  (:start . 114) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.147) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500720@unknown@formal@none@1@S@EGFR;PI3K induces glial neoplasia via Pnt and Stg expression.@(((:tag . "NNP") (:stem . "EGFR;PI3K") (:form . "EGFR;PI3K") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 17)\n  (:start . 10) (:id . 43))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 33)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Pnt") (:form . "Pnt") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Stg") (:form . "Stg") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.148) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500721@unknown@formal@none@1@S@Stg itself was rate limiting for glial neoplasia.@(((:tag . "NN") (:stem . "stg") (:form . "Stg") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 10)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "limit") (:form . "limiting") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 48)\n  (:start . 39) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.149) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500722@unknown@formal@none@1@S@Reduction of stg with a mutation or a stgdsRNA partially suppressed the repo>dEGFRλ;dp110CAAX phenotype, whereas overexpressed Stg synergistically enhanced neoplasia (Figure 5E and Figure S9, data not shown).@(((:tag . "NNP") (:stem . "Reduction") (:form . "Reduction") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "stg") (:form . "stg") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "stgdsRNA") (:form . "stgdsRNA") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 56)\n  (:start . 47) (:id . 51))\n ((:tag . "VBD") (:stem . "suppress") (:form . "suppressed") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 93) (:start . 72) (:id . 54))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 103)\n  (:start . 94) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 56))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 112)\n  (:start . 105) (:id . 57))\n ((:tag . "VBN") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 126) (:start . 113) (:id . 58))\n ((:tag . "NN") (:stem . "stg") (:form . "Stg") (:end . 130) (:start . 127)\n  (:id . 59))\n ((:tag . "RB") (:stem . "synergistically") (:form . "synergistically")\n  (:end . 146) (:start . 131) (:id . 60))\n ((:tag . "VBD") (:stem . "enhance") (:form . "enhanced") (:end . 155)\n  (:start . 147) (:id . 61))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 165)\n  (:start . 156) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 173)\n  (:start . 167) (:id . 64))\n ((:tag . "NN") (:stem . "5e") (:form . "5E") (:end . 176) (:start . 174)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 180) (:start . 177)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 187)\n  (:start . 181) (:id . 67))\n ((:tag . "NNP") (:stem . "S9") (:form . "S9") (:end . 190) (:start . 188)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 196)\n  (:start . 192) (:id . 70))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 200) (:start . 197)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 206)\n  (:start . 201) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 207) (:start . 206)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.150) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500723@unknown@formal@none@1@S@In contrast, Stg overexpression alone increased glial cell numbers approximately 2-fold, and could not induce neoplasia when combined with PI3K effectors (data not shown).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "stg") (:form . "Stg") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 31) (:start . 17) (:id . 46))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 80) (:start . 67) (:id . 52))\n ((:tag . "RB") (:stem . "2-fold") (:form . "2-fold") (:end . 87)\n  (:start . 81) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 109)\n  (:start . 103) (:id . 58))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 119)\n  (:start . 110) (:id . 59))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 124) (:start . 120)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 133)\n  (:start . 125) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 138) (:start . 134)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 143) (:start . 139)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 153)\n  (:start . 144) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 159)\n  (:start . 155) (:id . 66))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 163) (:start . 160)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 169)\n  (:start . 164) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.151) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500724@unknown@formal@none@1@S@Thus, dEGFRλ;dp110CAAX induces neoplasia via coordinated stimulation of G1-S entry through dCyclinE, and G2-M progression through Stg, both of which are EGFR-Ras dependent outputs [41],[42].@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 22) (:start . 6) (:id . 44))\n ((:tag . "VBZ") (:stem . "induce") (:form . "induces") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 40)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "coordinate") (:form . "coordinated") (:end . 56)\n  (:start . 45) (:id . 48))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 68)\n  (:start . 57) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "G1-S") (:form . "G1-S") (:end . 76) (:start . 72)\n  (:id . 51))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 82) (:start . 77)\n  (:id . 52))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 90)\n  (:start . 83) (:id . 53))\n ((:tag . "NN") (:stem . "dcycline") (:form . "dCyclinE") (:end . 99)\n  (:start . 91) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "G2-M") (:form . "G2-M") (:end . 109) (:start . 105)\n  (:id . 57))\n ((:tag . "NN") (:stem . "progression") (:form . "progression") (:end . 121)\n  (:start . 110) (:id . 58))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 129)\n  (:start . 122) (:id . 59))\n ((:tag . "NNP") (:stem . "Stg") (:form . "Stg") (:end . 133) (:start . 130)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 61))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 139) (:start . 135)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 63))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 148)\n  (:start . 143) (:id . 64))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 152) (:start . 149)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "egfr-ras") (:form . "EGFR-Ras") (:end . 161)\n  (:start . 153) (:id . 66))\n ((:tag . "JJ") (:stem . "dependent") (:form . "dependent") (:end . 171)\n  (:start . 162) (:id . 67))\n ((:tag . "NNS") (:stem . "output") (:form . "outputs") (:end . 179)\n  (:start . 172) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 181) (:start . 180)\n  (:id . 69))\n ((:tag . "CD") (:stem . "41],[42") (:form . "41],[42") (:end . 188)\n  (:start . 181) (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 189) (:start . 188)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.152) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500725@unknown@formal@none@1@S@EGFR;PI3K Glial Neoplasia Requires Akt and Tor Activation and FoxO Inactivation@(((:tag . "NNP") (:stem . "EGFR;PI3K") (:form . "EGFR;PI3K") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "glial") (:form . "Glial") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Neoplasia") (:form . "Neoplasia") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "NNPS") (:stem . "Requires") (:form . "Requires") (:end . 34)\n  (:start . 26) (:id . 45))\n ((:tag . "NNP") (:stem . "Akt") (:form . "Akt") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Activation") (:form . "Activation") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "FoxO") (:form . "FoxO") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Inactivation") (:form . "Inactivation") (:end . 79)\n  (:start . 67) (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.153) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500726@unknown@formal@none@1@S@We sought to determine which PI3K effectors contribute to the repo>dEGFRλ;dp110CAAX phenotype.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "seek") (:form . "sought") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pi3k") (:form . "PI3K") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "VBP") (:stem . "contribute") (:form . "contribute") (:end . 54)\n  (:start . 44) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 83) (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 93)\n  (:start . 84) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.154) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500727@unknown@formal@none@1@S@Genetic reduction of dAkt, a major target of PI3K signaling, with a dAktdsRNA or a mutant allele strongly suppressed repo>dEGFRλ;dp110CAAX glial neoplasia (Figure 6A–C, data not shown).@(((:tag . "JJ") (:stem . "genetic") (:form . "Genetic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dakt") (:form . "dAkt") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 34) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 41)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 49) (:start . 45)\n  (:id . 51))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 59)\n  (:start . 50) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "dAktdsRNA") (:form . "dAktdsRNA") (:end . 77)\n  (:start . 68) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 82) (:start . 81)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 89)\n  (:start . 83) (:id . 59))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 96)\n  (:start . 90) (:id . 60))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 105)\n  (:start . 97) (:id . 61))\n ((:tag . "VBD") (:stem . "suppress") (:form . "suppressed") (:end . 116)\n  (:start . 106) (:id . 62))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 138) (:start . 117) (:id . 63))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 144)\n  (:start . 139) (:id . 64))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 154)\n  (:start . 145) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 162)\n  (:start . 156) (:id . 67))\n ((:tag . "NNP") (:stem . "6A–C") (:form . "6A–C") (:end . 167) (:start . 163)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 173)\n  (:start . 169) (:id . 70))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 177) (:start . 174)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 183)\n  (:start . 178) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.155) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500728@unknown@formal@none@1@S@Therefore, Akt is necessary for the outcome of EGFR-PI3K coactivation.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Akt") (:form . "Akt") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "outcome") (:form . "outcome") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "EGFR-PI3K") (:form . "EGFR-PI3K") (:end . 56)\n  (:start . 47) (:id . 51))\n ((:tag . "NN") (:stem . "coactivation") (:form . "coactivation") (:end . 69)\n  (:start . 57) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s3.156) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500729@unknown@formal@none@1@S@Many Akt effectors are implicated in glioma, and we tested orthologs of these loci in our model (Table S3).@(((:tag . "JJ") (:stem . "many") (:form . "Many") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Akt") (:form . "Akt") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 33)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 58) (:start . 52)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 68)\n  (:start . 59) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "locus") (:form . "loci") (:end . 82) (:start . 78)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 95) (:start . 90)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 102) (:start . 97)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 105) (:start . 103)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.157) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500730@unknown@formal@none@1@S@EGFR;PI3K glial neoplasia requires Akt and Tor activation and FoxO inactivation.@(((:tag . "NNP") (:stem . "EGFR;PI3K") (:form . "EGFR;PI3K") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 34)\n  (:start . 26) (:id . 45))\n ((:tag . "NNP") (:stem . "Akt") (:form . "Akt") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "NN") (:stem . "foxo") (:form . "FoxO") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "inactivation") (:form . "inactivation") (:end . 79)\n  (:start . 67) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s3.158) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500731@unknown@formal@none@1@S@Tor, a kinase that promotes cell growth and proliferation, is a key Akt target.@(((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 6) (:start . 5)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 13)\n  (:start . 7) (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 27)\n  (:start . 19) (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 39)\n  (:start . 33) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 57) (:start . 44) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Akt") (:form . "Akt") (:end . 71) (:start . 68)\n  (:id . 56))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 78)\n  (:start . 72) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.159) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500732@unknown@formal@none@1@S@In glioma models, coactivation of EGFR-Ras and PI3K stimulates Tor, and in humans, Tor activity is correlated with poor patient prognosis [43],[44].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "coactivation") (:form . "coactivation") (:end . 30)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "stimulate") (:form . "stimulates") (:end . 62)\n  (:start . 52) (:id . 51))\n ((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "human") (:form . "humans") (:end . 81)\n  (:start . 75) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 95)\n  (:start . 87) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 98) (:start . 96)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "correlate") (:form . "correlated") (:end . 109)\n  (:start . 99) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 114) (:start . 110)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "poor") (:form . "poor") (:end . 119) (:start . 115)\n  (:id . 63))\n ((:tag . "NN") (:stem . "patient") (:form . "patient") (:end . 127)\n  (:start . 120) (:id . 64))\n ((:tag . "NN") (:stem . "prognosis") (:form . "prognosis") (:end . 137)\n  (:start . 128) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 139) (:start . 138)\n  (:id . 66))\n ((:tag . "CD") (:stem . "43],[44") (:form . "43],[44") (:end . 146)\n  (:start . 139) (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 147) (:start . 146)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.160) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500733@unknown@formal@none@1@S@We tested the single Drosophila Tor ortholog, dTor, by genetically reducing dTor activity in repo>dEGFRλ;dp110CAAX larvae with a viable combination of hypomorphic dTor alleles or by co-overexpression of dominant negative dTor 45,46.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dtor") (:form . "dTor") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "RB") (:stem . "genetically") (:form . "genetically") (:end . 66)\n  (:start . 55) (:id . 53))\n ((:tag . "VBG") (:stem . "reduce") (:form . "reducing") (:end . 75)\n  (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "dtor") (:form . "dTor") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 114) (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 121)\n  (:start . 115) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 126) (:start . 122)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 128) (:start . 127)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 135)\n  (:start . 129) (:id . 62))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 147)\n  (:start . 136) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "hypomorphic") (:form . "hypomorphic") (:end . 162)\n  (:start . 151) (:id . 65))\n ((:tag . "NN") (:stem . "dtor") (:form . "dTor") (:end . 167) (:start . 163)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "allele") (:form . "alleles") (:end . 175)\n  (:start . 168) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 178) (:start . 176)\n  (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 181) (:start . 179)\n  (:id . 69))\n ((:tag . "NN") (:stem . "co-overexpression") (:form . "co-overexpression")\n  (:end . 199) (:start . 182) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 202) (:start . 200)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 211)\n  (:start . 203) (:id . 72))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 220)\n  (:start . 212) (:id . 73))\n ((:tag . "NN") (:stem . "dtor") (:form . "dTor") (:end . 225) (:start . 221)\n  (:id . 74))\n ((:tag . "CD") (:stem . "45,46") (:form . "45,46") (:end . 231)\n  (:start . 226) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s3.161) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500734@unknown@formal@none@1@S@Both of these manipulations reduced glial overgrowth (Figure 6D, data not shown).@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "manipulation") (:form . "manipulations")\n  (:end . 27) (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "reduce") (:form . "reduced") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 52)\n  (:start . 42) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 60)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "6d") (:form . "6D") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 79) (:start . 74)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.162) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500735@unknown@formal@none@1@S@In flies and mammals, Tor exists in two different signaling complexes, TORC1 and TORC2.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "mammal") (:form . "mammals") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "exist") (:form . "exists") (:end . 32)\n  (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 49)\n  (:start . 40) (:id . 51))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 59)\n  (:start . 50) (:id . 52))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 69)\n  (:start . 60) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "TORC1") (:form . "TORC1") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "TORC2") (:form . "TORC2") (:end . 86) (:start . 81)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.163) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500736@unknown@formal@none@1@S@TORC2, a complex including Tor and the Sin1 and Rictor regulatory proteins, directly phosphorylates Akt, creating a positive feedback loop that fully activates Akt [47].@(((:tag . "NNP") (:stem . "TORC2") (:form . "TORC2") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 8) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 16)\n  (:start . 9) (:id . 45))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "NN") (:stem . "sin1") (:form . "Sin1") (:end . 43) (:start . 39)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "rictor") (:form . "Rictor") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 65)\n  (:start . 55) (:id . 53))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 74)\n  (:start . 66) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 84)\n  (:start . 76) (:id . 56))\n ((:tag . "VBZ") (:stem . "phosphorylate") (:form . "phosphorylates")\n  (:end . 99) (:start . 85) (:id . 57))\n ((:tag . "NNP") (:stem . "Akt") (:form . "Akt") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "create") (:form . "creating") (:end . 113)\n  (:start . 105) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . "NN") (:stem . "feedback") (:form . "feedback") (:end . 133)\n  (:start . 125) (:id . 63))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 138) (:start . 134)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 143) (:start . 139)\n  (:id . 65))\n ((:tag . "RB") (:stem . "fully") (:form . "fully") (:end . 149)\n  (:start . 144) (:id . 66))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 159)\n  (:start . 150) (:id . 67))\n ((:tag . "NNP") (:stem . "Akt") (:form . "Akt") (:end . 163) (:start . 160)\n  (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 165) (:start . 164)\n  (:id . 69))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 167) (:start . 165)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 168) (:start . 167)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.164) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500737@unknown@formal@none@1@S@In mouse, Sin1 and Rictor mutants die early due to extraembryonic defects, but dSin1 and dRictor mutant flies are viable as homozygous nulls, allowing us to remove TORC2 function genetically [47],[48].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "NNP") (:stem . "Sin1") (:form . "Sin1") (:end . 14) (:start . 10)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "rictor") (:form . "Rictor") (:end . 25)\n  (:start . 19) (:id . 47))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "VBP") (:stem . "die") (:form . "die") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "RB") (:stem . "early") (:form . "early") (:end . 43) (:start . 38)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "extraembryonic") (:form . "extraembryonic")\n  (:end . 65) (:start . 51) (:id . 53))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 73)\n  (:start . 66) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dsin1") (:form . "dSin1") (:end . 84) (:start . 79)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 58))\n ((:tag . "NN") (:stem . "drictor") (:form . "dRictor") (:end . 96)\n  (:start . 89) (:id . 59))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 103)\n  (:start . 97) (:id . 60))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 109) (:start . 104)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 113) (:start . 110)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 120)\n  (:start . 114) (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 134)\n  (:start . 124) (:id . 65))\n ((:tag . "NNS") (:stem . "null") (:form . "nulls") (:end . 140)\n  (:start . 135) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "allow") (:form . "allowing") (:end . 150)\n  (:start . 142) (:id . 68))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 153) (:start . 151)\n  (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 156) (:start . 154)\n  (:id . 70))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 163)\n  (:start . 157) (:id . 71))\n ((:tag . "NN") (:stem . "torc2") (:form . "TORC2") (:end . 169)\n  (:start . 164) (:id . 72))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 178)\n  (:start . 170) (:id . 73))\n ((:tag . "RB") (:stem . "genetically") (:form . "genetically") (:end . 190)\n  (:start . 179) (:id . 74))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 192) (:start . 191)\n  (:id . 75))\n ((:tag . "CD") (:stem . "47],[48") (:form . "47],[48") (:end . 199)\n  (:start . 192) (:id . 76))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 200) (:start . 199)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s3.165) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500738@unknown@formal@none@1@S@dSin1-/-; repo>dEGFRλ;dp110CAAX larval brains showed a near-wild type phenotype (Figure 6E).@(((:tag . "JJ") (:stem . "dsin1-/-") (:form . "dSin1-/-") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 31) (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "larval") (:form . "larval") (:end . 38)\n  (:start . 32) (:id . 45))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 45)\n  (:start . 39) (:id . 46))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 52) (:start . 46)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "near-wild") (:form . "near-wild") (:end . 64)\n  (:start . 55) (:id . 49))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 69) (:start . 65)\n  (:id . 50))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 79)\n  (:start . 70) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 87)\n  (:start . 81) (:id . 53))\n ((:tag . "NN") (:stem . "6e") (:form . "6E") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.166) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500739@unknown@formal@none@1@S@Results were similar with a dRictor null allele and a dSin1dsRNA (data not shown).@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "drictor") (:form . "dRictor") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "dsin1dsrna") (:form . "dSin1dsRNA") (:end . 64)\n  (:start . 54) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.167) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500740@unknown@formal@none@1@S@dSin1-/- and dRictor-/- mutants display reduced Akt-dependent phosphorylation and inactivation of dFoxO [49], the single Drosophila ortholog of FoxO transcription factors.@(((:tag . "JJ") (:stem . "dsin1-/-") (:form . "dSin1-/-") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "drictor-/-") (:form . "dRictor-/-") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 31)\n  (:start . 24) (:id . 45))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 39)\n  (:start . 32) (:id . 46))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 47)\n  (:start . 40) (:id . 47))\n ((:tag . "JJ") (:stem . "akt-dependent") (:form . "Akt-dependent")\n  (:end . 61) (:start . 48) (:id . 48))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 77) (:start . 62) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 50))\n ((:tag . "NN") (:stem . "inactivation") (:form . "inactivation") (:end . 94)\n  (:start . 82) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 52))\n ((:tag . "NN") (:stem . "dfoxo") (:form . "dFoxO") (:end . 103) (:start . 98)\n  (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 105) (:start . 104)\n  (:id . 54))\n ((:tag . "CD") (:stem . "49") (:form . "49") (:end . 107) (:start . 105)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 108) (:start . 107)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 120)\n  (:start . 114) (:id . 59))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 131)\n  (:start . 121) (:id . 60))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 140)\n  (:start . 132) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "FoxO") (:form . "FoxO") (:end . 148) (:start . 144)\n  (:id . 63))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 162) (:start . 149) (:id . 64))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 170)\n  (:start . 163) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.168) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500741@unknown@formal@none@1@S@This suggests that TORC2 loss might antagonize glial neoplasia through dFoxO upregulation.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "torc2") (:form . "TORC2") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "VB") (:stem . "antagonize") (:form . "antagonize") (:end . 46)\n  (:start . 36) (:id . 48))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 62)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 70)\n  (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "dfoxo") (:form . "dFoxO") (:end . 76) (:start . 71)\n  (:id . 52))\n ((:tag . "NN") (:stem . "upregulation") (:form . "upregulation") (:end . 89)\n  (:start . 77) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 54)))@@@1@13@((:hcues ((:id . :x3.169.1) (:span 30 35)) ((:id . :x3.169.2) (:span 5 13)))\n (:hscopes ((:id . :x3.169.1) (:span 30 89)) ((:id . :x3.169.2) (:span 5 89)))\n (:identifiers (:sid . :s3.169) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500742@unknown@formal@none@1@S@However, excess dFoxOSA, which is resistant to dAkt phosphorylation [45], only partially suppressed repo>dEGFRλ;dp110CAAX glial overproliferation (Figure 6F), arguing that TORC2 has additional roles.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "dFoxOSA") (:form . "dFoxOSA") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "resistant") (:form . "resistant") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dakt") (:form . "dAkt") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 67) (:start . 52) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 78) (:start . 74)\n  (:id . 57))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 88)\n  (:start . 79) (:id . 58))\n ((:tag . "VBD") (:stem . "suppress") (:form . "suppressed") (:end . 99)\n  (:start . 89) (:id . 59))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 121) (:start . 100) (:id . 60))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 127)\n  (:start . 122) (:id . 61))\n ((:tag . "NN") (:stem . "overproliferation") (:form . "overproliferation")\n  (:end . 145) (:start . 128) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 153)\n  (:start . 147) (:id . 64))\n ((:tag . "NN") (:stem . "6f") (:form . "6F") (:end . 156) (:start . 154)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "argue") (:form . "arguing") (:end . 166)\n  (:start . 159) (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 171) (:start . 167)\n  (:id . 69))\n ((:tag . "NN") (:stem . "torc2") (:form . "TORC2") (:end . 177)\n  (:start . 172) (:id . 70))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 181) (:start . 178)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 192)\n  (:start . 182) (:id . 72))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 198)\n  (:start . 193) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.170) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500743@unknown@formal@none@1@S@Notably, on their own, dSin1-/- and dRictor-/- mutant flies did not show any detectable glial defects (Figure 6G, data not shown).@(((:tag . "RB") (:stem . "notably") (:form . "Notably") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 17)\n  (:start . 12) (:id . 45))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dsin1-/-") (:form . "dSin1-/-") (:end . 31)\n  (:start . 23) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "drictor-/-") (:form . "dRictor-/-") (:end . 46)\n  (:start . 36) (:id . 50))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 53)\n  (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "VB") (:stem . "show") (:form . "show") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 87)\n  (:start . 77) (:id . 57))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 93) (:start . 88)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 101)\n  (:start . 94) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 109)\n  (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "6g") (:form . "6G") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 118)\n  (:start . 114) (:id . 64))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 122) (:start . 119)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 128)\n  (:start . 123) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.171) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500744@unknown@formal@none@1@S@Thus, TORC2 is dispensible for normal glial development, but is necessary for dEGFRλ;dp110CAAX glial neoplasia.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "TORC2") (:form . "TORC2") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "dispensible") (:form . "dispensible") (:end . 26)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 55)\n  (:start . 44) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 73)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 94) (:start . 78) (:id . 56))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 100) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 110)\n  (:start . 101) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.172) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500745@unknown@formal@none@1@S@TORC1, a complex including Tor and the Raptor regulatory protein, drives cellular growth by stimulating protein synthesis through its effectors S6 kinase and the eIF-4E translation initiation factor [47].@(((:tag . "NNP") (:stem . "TORC1") (:form . "TORC1") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 8) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 16)\n  (:start . 9) (:id . 45))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Raptor") (:form . "Raptor") (:end . 45)\n  (:start . 39) (:id . 50))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 56)\n  (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "drive") (:form . "drives") (:end . 72)\n  (:start . 66) (:id . 54))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 88)\n  (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "stimulate") (:form . "stimulating") (:end . 103)\n  (:start . 92) (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 111)\n  (:start . 104) (:id . 59))\n ((:tag . "NN") (:stem . "synthesis") (:form . "synthesis") (:end . 121)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 129)\n  (:start . 122) (:id . 61))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 133) (:start . 130)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 143)\n  (:start . 134) (:id . 63))\n ((:tag . "NNP") (:stem . "S6") (:form . "S6") (:end . 146) (:start . 144)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 153)\n  (:start . 147) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 67))\n ((:tag . "NN") (:stem . "eif-4e") (:form . "eIF-4E") (:end . 168)\n  (:start . 162) (:id . 68))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 180)\n  (:start . 169) (:id . 69))\n ((:tag . "NN") (:stem . "initiation") (:form . "initiation") (:end . 191)\n  (:start . 181) (:id . 70))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 198)\n  (:start . 192) (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 200) (:start . 199)\n  (:id . 72))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 202) (:start . 200)\n  (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 203) (:start . 202)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.173) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500746@unknown@formal@none@1@S@Akt and Erk stimulate TORC1 through phosphorylation and inactivation of the TSC1-TSC2 protein complex, which activates Rheb, and stimulates TORC1 kinase activity.@(((:tag . "NNP") (:stem . "Akt") (:form . "Akt") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Erk") (:form . "Erk") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "stimulate") (:form . "stimulate") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "torc1") (:form . "TORC1") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 51) (:start . 36) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "inactivation") (:form . "inactivation") (:end . 68)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "NN") (:stem . "tsc1-tsc2") (:form . "TSC1-TSC2") (:end . 85)\n  (:start . 76) (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 93)\n  (:start . 86) (:id . 54))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 101)\n  (:start . 94) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 108)\n  (:start . 103) (:id . 57))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 118)\n  (:start . 109) (:id . 58))\n ((:tag . "NNP") (:stem . "Rheb") (:form . "Rheb") (:end . 123) (:start . 119)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "stimulate") (:form . "stimulates") (:end . 139)\n  (:start . 129) (:id . 62))\n ((:tag . "NNP") (:stem . "TORC1") (:form . "TORC1") (:end . 145)\n  (:start . 140) (:id . 63))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 152)\n  (:start . 146) (:id . 64))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 161)\n  (:start . 153) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.174) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500747@unknown@formal@none@1@S@We tested TORC1 function by glial-specific overexpression of dsRNAs for the single Drosophila orthologs of Raptor (dRaptor), S6-kinase (dS6K), and eIF4E (deIF4E); these all significantly reduced accumulation of dEGFRλ;dp110CAAX mutant glial cells, but only caused mild glial hypoplasia in controls (Figure 6I–K and Figure S10).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "torc1") (:form . "TORC1") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "glial-specific") (:form . "glial-specific")\n  (:end . 42) (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "overexpression") (:form . 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5500748@unknown@formal@none@1@S@Co-overexpression of d4EBP, a deIF4E antagonist and dFoxO target gene, also blocked glial neoplasia (Figure 6L).@(((:tag . "NNP") (:stem . "Co-overexpression") (:form . "Co-overexpression")\n  (:end . 17) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "d4EBP") (:form . "d4EBP") (:end . 26) (:start . 21)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "deif4e") (:form . "deIF4E") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "antagonist") (:form . "antagonist") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dfoxo") (:form . "dFoxO") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 64)\n  (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 69) (:start . 65)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "block") (:form . "blocked") (:end . 83)\n  (:start . 76) (:id . 55))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 89) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 99)\n  (:start . 90) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 107)\n  (:start . 101) (:id . 59))\n ((:tag . "NN") (:stem . "6l") (:form . "6L") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.176) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500749@unknown@formal@none@1@S@Glial-specific RNAi of dTSC1 enhanced repo>dEGFRλ;dp110CAAX glial overgrowth (Figure 6H).@(((:tag . "JJ") (:stem . "glial-specific") (:form . "Glial-specific")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 19) (:start . 15)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dtsc1") (:form . "dTSC1") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "enhance") (:form . "enhanced") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 59) (:start . 38) (:id . 47))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 65) (:start . 60)\n  (:id . 48))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 76)\n  (:start . 66) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 84)\n  (:start . 78) (:id . 51))\n ((:tag . "NN") (:stem . "6h") (:form . "6H") (:end . 87) (:start . 85)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.177) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500750@unknown@formal@none@1@S@However, overexpression of dTSC1dsRNA, dRheb, activated dS6K (dS6Kact), or deIF4E alone did not produce glial overproliferation, even though these constructs can mimic TORC1 activation (Figure S10, data not shown) [47],[49].@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 23) (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "dTSC1dsRNA") (:form . "dTSC1dsRNA") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "drheb") (:form . "dRheb") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "activate") (:form . "activated") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "ds6k") (:form . "dS6K") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "ds6kact") (:form . "dS6Kact") (:end . 69)\n  (:start . 62) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "deIF4E") (:form . "deIF4E") (:end . 81)\n  (:start . 75) (:id . 57))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 87) (:start . 82)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 95) (:start . 92)\n  (:id . 60))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 103)\n  (:start . 96) (:id . 61))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 109)\n  (:start . 104) (:id . 62))\n ((:tag . "NN") (:stem . "overproliferation") (:form . "overproliferation")\n  (:end . 127) (:start . 110) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 133) (:start . 129)\n  (:id . 65))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 140)\n  (:start . 134) (:id . 66))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 146)\n  (:start . 141) (:id . 67))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 157)\n  (:start . 147) (:id . 68))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 161) (:start . 158)\n  (:id . 69))\n ((:tag . "VB") (:stem . "mimic") (:form . "mimic") (:end . 167)\n  (:start . 162) (:id . 70))\n ((:tag . "NN") (:stem . "torc1") (:form . "TORC1") (:end . 173)\n  (:start . 168) (:id . 71))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 184)\n  (:start . 174) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 186) (:start . 185)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 192)\n  (:start . 186) (:id . 74))\n ((:tag . "NNP") (:stem . "S10") (:form . "S10") (:end . 196) (:start . 193)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 202)\n  (:start . 198) (:id . 77))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 206) (:start . 203)\n  (:id . 78))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 212)\n  (:start . 207) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n  (:id . 80))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 215) (:start . 214)\n  (:id . 81))\n ((:tag . "CD") (:stem . "47],[49") (:form . "47],[49") (:end . 222)\n  (:start . 215) (:id . 82))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 223) (:start . 222)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s3.178) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500751@unknown@formal@none@1@S@Thus, TORC1 activity is necessary for EGFR-PI3K-driven glial neoplasia, but is not sufficient.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "torc1") (:form . "TORC1") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "egfr-pi3k-driven") (:form . "EGFR-PI3K-driven")\n  (:end . 54) (:start . 38) (:id . 49))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 60) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 70)\n  (:start . 61) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 75) (:start . 72)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 93)\n  (:start . 83) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.179) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500752@unknown@formal@none@1@S@Moreover, neither deIF4E nor dS6Kact produced glial neoplasia when co-overexpressed with dEGFRλ (data not shown), illustrating that additional dTor-dependent outputs synergize with dEGFR signaling to drive neoplasia.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "CC") (:stem . "neither") (:form . "neither") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "deif4e") (:form . "deIF4E") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "CC") (:stem . "nor") (:form . "nor") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "ds6kact") (:form . "dS6Kact") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 51) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 61)\n  (:start . 52) (:id . 50))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "co-overexpresse") (:form . "co-overexpressed")\n  (:end . 83) (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 88) (:start . 84)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 95)\n  (:start . 89) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 101) (:start . 97)\n  (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 105) (:start . 102)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 111)\n  (:start . 106) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "illustrate") (:form . "illustrating") (:end . 126)\n  (:start . 114) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 131) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 142)\n  (:start . 132) (:id . 63))\n ((:tag . "JJ") (:stem . "dtor-dependent") (:form . "dTor-dependent")\n  (:end . 157) (:start . 143) (:id . 64))\n ((:tag . "NNS") (:stem . "output") (:form . "outputs") (:end . 165)\n  (:start . 158) (:id . 65))\n ((:tag . "VBP") (:stem . "synergize") (:form . "synergize") (:end . 175)\n  (:start . 166) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 180) (:start . 176)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "dEGFR") (:form . "dEGFR") (:end . 186)\n  (:start . 181) (:id . 68))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 196)\n  (:start . 187) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 199) (:start . 197)\n  (:id . 70))\n ((:tag . "VB") (:stem . "drive") (:form . "drive") (:end . 205)\n  (:start . 200) (:id . 71))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 215)\n  (:start . 206) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s3.180) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500753@unknown@formal@none@1@S@Myc and Max Drive EGFR;PI3K Glial Neoplasia via CyclinD-Cdk4@(((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Max") (:form . "Max") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Drive") (:form . "Drive") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "EGFR;PI3K") (:form . "EGFR;PI3K") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "JJ") (:stem . "glial") (:form . "Glial") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Neoplasia") (:form . "Neoplasia") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "CyclinD-Cdk4") (:form . "CyclinD-Cdk4") (:end . 60)\n  (:start . 48) (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.181) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500754@unknown@formal@none@1@S@dTor coordinates increased translation, mediated by dS6K and deIF4E, with expression of cell cycle regulators and ribosomal components, through dMyc, the single Drosophila ortholog of the Myc bHLH transcription factors [49].@(((:tag . "NN") (:stem . "dtor") (:form . "dTor") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "coordinate") (:form . "coordinates") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 26)\n  (:start . 17) (:id . 44))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 38)\n  (:start . 27) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 48)\n  (:start . 40) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 51) (:start . 49)\n  (:id . 48))\n ((:tag . "NN") (:stem . "ds6k") (:form . "dS6K") (:end . 56) (:start . 52)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "deif4e") (:form . "deIF4E") (:end . 67)\n  (:start . 61) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 84)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 98) (:start . 93)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "regulator") (:form . "regulators") (:end . 109)\n  (:start . 99) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "ribosomal") (:form . "ribosomal") (:end . 123)\n  (:start . 114) (:id . 60))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 134)\n  (:start . 124) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 143)\n  (:start . 136) (:id . 63))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 148) (:start . 144)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 160)\n  (:start . 154) (:id . 67))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 171)\n  (:start . 161) (:id . 68))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 180)\n  (:start . 172) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 183) (:start . 181)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 187) (:start . 184)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 191) (:start . 188)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "bhlh") (:form . "bHLH") (:end . 196) (:start . 192)\n  (:id . 73))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 210) (:start . 197) (:id . 74))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 218)\n  (:start . 211) (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 220) (:start . 219)\n  (:id . 76))\n ((:tag . "CD") (:stem . "49") (:form . "49") (:end . 222) (:start . 220)\n  (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 223) (:start . 222)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s3.182) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500755@unknown@formal@none@1@S@Within developing epithelial tissues, dMyc is required for TORC1-dependent growth and can substitute for dTor activity [49],[50].@(((:tag . "IN") (:stem . "within") (:form . "Within") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 17)\n  (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "epithelial") (:form . "epithelial") (:end . 28)\n  (:start . 18) (:id . 44))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 36)\n  (:start . 29) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 58) (:start . 55)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "torc1-dependent") (:form . "TORC1-dependent")\n  (:end . 74) (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 81)\n  (:start . 75) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 53))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 89) (:start . 86)\n  (:id . 54))\n ((:tag . "VB") (:stem . "substitute") (:form . "substitute") (:end . 100)\n  (:start . 90) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 104) (:start . 101)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dtor") (:form . "dTor") (:end . 109) (:start . 105)\n  (:id . 57))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 118)\n  (:start . 110) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 120) (:start . 119)\n  (:id . 59))\n ((:tag . "CD") (:stem . "49],[50") (:form . "49],[50") (:end . 127)\n  (:start . 120) (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 128) (:start . 127)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.183) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500756@unknown@formal@none@1@S@Myc protein levels can also be posttranslationally upregulated by EGFR-Ras-Raf signaling [16],[51].@(((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "RB") (:stem . "posttranslationally")\n  (:form . "posttranslationally") (:end . 50) (:start . 31) (:id . 48))\n ((:tag . "VBN") (:stem . "upregulate") (:form . "upregulated") (:end . 62)\n  (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "EGFR-Ras-Raf") (:form . "EGFR-Ras-Raf") (:end . 78)\n  (:start . 66) (:id . 51))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 88)\n  (:start . 79) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 90) (:start . 89)\n  (:id . 53))\n ((:tag . "CD") (:stem . "16],[51") (:form . "16],[51") (:end . 97)\n  (:start . 90) (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 98) (:start . 97)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x3.184.1) (:span 19 22)))\n (:hscopes ((:id . :x3.184.1) (:span 0 88)))\n (:identifiers (:sid . :s3.184) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500757@unknown@formal@none@1@S@Thus, we suspected that dMyc might mediate signal integration between EGFR-Ras and PI3K.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "suspect") (:form . "suspected") (:end . 18)\n  (:start . 9) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 34) (:start . 29)\n  (:id . 48))\n ((:tag . "VB") (:stem . "mediate") (:form . "mediate") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 49)\n  (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 61)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 69)\n  (:start . 62) (:id . 52))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 78)\n  (:start . 70) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x3.185.1) (:span 29 34)) ((:id . :x3.185.2) (:span 9 18)))\n (:hscopes ((:id . :x3.185.1) (:span 29 87)) ((:id . :x3.185.2) (:span 9 87)))\n (:identifiers (:sid . :s3.185) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500758@unknown@formal@none@1@S@dEGFRλ;dp110CAAX glia showed high levels of nuclear dMyc compared to wild-type glia (Figure 7A and 7B).@(((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 16) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 21) (:start . 17)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 28) (:start . 22)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 33) (:start . 29)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 40)\n  (:start . 34) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 56) (:start . 52)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 65)\n  (:start . 57) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 78)\n  (:start . 69) (:id . 52))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 83) (:start . 79)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 54))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 91)\n  (:start . 85) (:id . 55))\n ((:tag . "NN") (:stem . "7a") (:form . "7A") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "7b") (:form . "7B") (:end . 101) (:start . 99)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.186) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500759@unknown@formal@none@1@S@dMyc was also highly expressed in wild-type neuroblasts (Figure 7A), suggesting that dMyc promotes a proliferative progenitor state [21].@(((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 55)\n  (:start . 44) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 63)\n  (:start . 57) (:id . 51))\n ((:tag . "NN") (:stem . "7a") (:form . "7A") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 79)\n  (:start . 69) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 89) (:start . 85)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 98)\n  (:start . 90) (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "proliferative") (:form . "proliferative")\n  (:end . 114) (:start . 101) (:id . 60))\n ((:tag . "NN") (:stem . "progenitor") (:form . "progenitor") (:end . 125)\n  (:start . 115) (:id . 61))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 131)\n  (:start . 126) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 133) (:start . 132)\n  (:id . 63))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 135) (:start . 133)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 136) (:start . 135)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x3.187.1) (:span 69 79)))\n (:hscopes ((:id . :x3.187.1) (:span 69 131)))\n (:identifiers (:sid . :s3.187) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500760@unknown@formal@none@1@S@Genetic reduction of dMyc with a dsRNA or a single loss-of-function allele strongly suppressed dEGFRλ;dp110CAAX glial neoplasia (Figure 7D, data not shown).@(((:tag . "JJ") (:stem . "genetic") (:form . "Genetic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 50)\n  (:start . 44) (:id . 51))\n ((:tag . "JJ") (:stem . "loss-of-function") (:form . "loss-of-function")\n  (:end . 67) (:start . 51) (:id . 52))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 74)\n  (:start . 68) (:id . 53))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 83)\n  (:start . 75) (:id . 54))\n ((:tag . "VBD") (:stem . "suppress") (:form . "suppressed") (:end . 94)\n  (:start . 84) (:id . 55))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 111) (:start . 95) (:id . 56))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 117)\n  (:start . 112) (:id . 57))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 127)\n  (:start . 118) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 135)\n  (:start . 129) (:id . 60))\n ((:tag . "NN") (:stem . "7d") (:form . "7D") (:end . 138) (:start . 136)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 144)\n  (:start . 140) (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 148) (:start . 145)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 154)\n  (:start . 149) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.188) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500761@unknown@formal@none@1@S@In fact, some dMyc+/-; repo>dEGFRλ;dp110CAAX animals were rescued to viability, indicating that dMyc is an essential rate-limiting output of EGFR-PI3K coactivation.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 13) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dmyc+/-") (:form . "dMyc+/-") (:end . 21)\n  (:start . 14) (:id . 46))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 44) (:start . 23) (:id . 48))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 65)\n  (:start . 58) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 90)\n  (:start . 80) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 95) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 100) (:start . 96)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 103) (:start . 101)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 116)\n  (:start . 107) (:id . 60))\n ((:tag . "JJ") (:stem . "rate-limiting") (:form . "rate-limiting")\n  (:end . 130) (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 137)\n  (:start . 131) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "EGFR-PI3K") (:form . "EGFR-PI3K") (:end . 150)\n  (:start . 141) (:id . 64))\n ((:tag . "NN") (:stem . "coactivation") (:form . "coactivation") (:end . 163)\n  (:start . 151) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x3.189.1) (:span 80 95)))\n (:hscopes ((:id . :x3.189.1) (:span 80 163)))\n (:identifiers (:sid . :s3.189) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500762@unknown@formal@none@1@S@Myc and Max are required to drive EGFR;PI3K glial neoplasia via CyclinD-Cdk4.@(((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Max") (:form . "Max") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VB") (:stem . "drive") (:form . "drive") (:end . 33) (:start . 28)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "EGFR;PI3K") (:form . "EGFR;PI3K") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 59)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cyclind-cdk4") (:form . "CyclinD-Cdk4") (:end . 76)\n  (:start . 64) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.190) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500763@unknown@formal@none@1@S@Myc proteins activate transcription through heterodimerization with the bHLH Max.@(((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "activate") (:form . "activate") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 35) (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 43)\n  (:start . 36) (:id . 46))\n ((:tag . "NN") (:stem . "heterodimerization") (:form . "heterodimerization")\n  (:end . 62) (:start . 44) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 67) (:start . 63)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "bhlh") (:form . "bHLH") (:end . 76) (:start . 72)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Max") (:form . "Max") (:end . 80) (:start . 77)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.191) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500764@unknown@formal@none@1@S@Max activity was also required for glial neoplasia; a dsRNA for dMax, the single Drosophila Max ortholog, strongly suppressed repo>dEGFRλ;dp110CAAX overgrowth (Figure 7E).@(((:tag . "NNP") (:stem . "Max") (:form . "Max") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "dmax") (:form . "dMax") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 80)\n  (:start . 74) (:id . 57))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 91)\n  (:start . 81) (:id . 58))\n ((:tag . "NNP") (:stem . "Max") (:form . "Max") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 104)\n  (:start . 96) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 61))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 114)\n  (:start . 106) (:id . 62))\n ((:tag . "VBD") (:stem . "suppress") (:form . "suppressed") (:end . 125)\n  (:start . 115) (:id . 63))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 147) (:start . 126) (:id . 64))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 158)\n  (:start . 148) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 166)\n  (:start . 160) (:id . 67))\n ((:tag . "NN") (:stem . "7e") (:form . "7E") (:end . 169) (:start . 167)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.192) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500765@unknown@formal@none@1@S@dMyc-dMax heterodimers promote proliferation by activating expression of multiple cell cycle genes, including dCyclinD and dCdk4 [52].@(((:tag . "NN") (:stem . "dmyc-dmax") (:form . "dMyc-dMax") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "heterodimer") (:form . "heterodimers") (:end . 22)\n  (:start . 10) (:id . 43))\n ((:tag . "VBP") (:stem . "promote") (:form . "promote") (:end . 30)\n  (:start . 23) (:id . 44))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 44) (:start . 31) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 47) (:start . 45)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "activate") (:form . "activating") (:end . 58)\n  (:start . 48) (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 69)\n  (:start . 59) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 81)\n  (:start . 73) (:id . 50))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 86) (:start . 82)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 92) (:start . 87)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 98) (:start . 93)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 109)\n  (:start . 100) (:id . 55))\n ((:tag . "NN") (:stem . "dcyclind") (:form . "dCyclinD") (:end . 118)\n  (:start . 110) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dcdk4") (:form . "dCdk4") (:end . 128)\n  (:start . 123) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 130) (:start . 129)\n  (:id . 59))\n ((:tag . "CD") (:stem . "52") (:form . "52") (:end . 132) (:start . 130)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 133) (:start . 132)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.193) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500766@unknown@formal@none@1@S@dCyclinD expression, which is high in repo>dEGFRλ;dp110CAAX glia, was inhibited by a dMycdsRNA (Figure 7F–H), suggesting that dMyc reduction suppresses glial neoplasia through reduced dCyclinD-dCdk4 activity.@(((:tag . "NN") (:stem . "dcyclind") (:form . "dCyclinD") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 19)\n  (:start . 9) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 44))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 59) (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 64) (:start . 60)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "inhibit") (:form . "inhibited") (:end . 79)\n  (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "dMycdsRNA") (:form . "dMycdsRNA") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 102)\n  (:start . 96) (:id . 58))\n ((:tag . "NNP") (:stem . "7F–H") (:form . "7F–H") (:end . 107) (:start . 103)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 120)\n  (:start . 110) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 125) (:start . 121)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 130) (:start . 126)\n  (:id . 64))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 140)\n  (:start . 131) (:id . 65))\n ((:tag . "VBZ") (:stem . "suppress") (:form . "suppresses") (:end . 151)\n  (:start . 141) (:id . 66))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 157)\n  (:start . 152) (:id . 67))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 167)\n  (:start . 158) (:id . 68))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 175)\n  (:start . 168) (:id . 69))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 183)\n  (:start . 176) (:id . 70))\n ((:tag . "NN") (:stem . "dcyclind-dcdk4") (:form . "dCyclinD-dCdk4")\n  (:end . 198) (:start . 184) (:id . 71))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 207)\n  (:start . 199) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x3.194.1) (:span 110 120)))\n (:hscopes ((:id . :x3.194.1) (:span 110 207)))\n (:identifiers (:sid . :s3.194) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500767@unknown@formal@none@1@S@To test this we used loss-of-function mutations in dCdk4, which are viable [23].@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "loss-of-function") (:form . "loss-of-function")\n  (:end . 37) (:start . 21) (:id . 47))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dcdk4") (:form . "dCdk4") (:end . 56) (:start . 51)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 74)\n  (:start . 68) (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 79) (:start . 78)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.195) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500768@unknown@formal@none@1@S@dCdk4-/-; repo>dEGFRλ;dp110CAAX larvae showed near complete absence of excess glia and rescue of glial morphogenesis defects (Figure 7I).@(((:tag . "JJ") (:stem . "dcdk4-/-") (:form . "dCdk4-/-") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 31) (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 38)\n  (:start . 32) (:id . 45))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 45) (:start . 39)\n  (:id . 46))\n ((:tag . "IN") (:stem . "near") (:form . "near") (:end . 50) (:start . 46)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 59)\n  (:start . 51) (:id . 48))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 67)\n  (:start . 60) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 77)\n  (:start . 71) (:id . 51))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 82) (:start . 78)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 53))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 93)\n  (:start . 87) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 102) (:start . 97)\n  (:id . 56))\n ((:tag . "NN") (:stem . "morphogenesis") (:form . "morphogenesis")\n  (:end . 116) (:start . 103) (:id . 57))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 124)\n  (:start . 117) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 132)\n  (:start . 126) (:id . 60))\n ((:tag . "NNP") (:stem . "7I") (:form . "7I") (:end . 135) (:start . 133)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.196) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500769@unknown@formal@none@1@S@Moreover, a dCdk4dsRNA and dCyclinDdsRNA suppressed repo>dEGFRλ;dp110CAAX (data not shown).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "dCdk4dsRNA") (:form . "dCdk4dsRNA") (:end . 22)\n  (:start . 12) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "dCyclinDdsRNA") (:form . "dCyclinDdsRNA")\n  (:end . 40) (:start . 27) (:id . 47))\n ((:tag . "VBD") (:stem . "suppress") (:form . "suppressed") (:end . 51)\n  (:start . 41) (:id . 48))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 73) (:start . 52) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 79) (:start . 75)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 83) (:start . 80)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 89) (:start . 84)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.197) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500770@unknown@formal@none@1@S@Thus, dCyclinD-dCdk4 is essential for EGFR-PI3K glial neoplasia, although dCdk4 is not required for development (Figure 7J).@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "dcyclind-dcdk4") (:form . "dCyclinD-dCdk4")\n  (:end . 20) (:start . 6) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "EGFR-PI3K") (:form . "EGFR-PI3K") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 63)\n  (:start . 54) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 51))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 73)\n  (:start . 65) (:id . 52))\n ((:tag . "NN") (:stem . "dcdk4") (:form . "dCdk4") (:end . 79) (:start . 74)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 95)\n  (:start . 87) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 99) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 111)\n  (:start . 100) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 119)\n  (:start . 113) (:id . 60))\n ((:tag . "NN") (:stem . "7j") (:form . "7J") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.198) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500771@unknown@formal@none@1@S@Myc Overexpression or Rb Loss Synergizes with EGFR@(((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Overexpression") (:form . "Overexpression")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Rb") (:form . "Rb") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "loss") (:form . "Loss") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "synergize") (:form . "Synergizes") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 50) (:start . 46)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s3.199) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500772@unknown@formal@none@1@S@dMyc is necessary for glial neoplasia, but is not sufficient when overexpressed alone (Figure 8C).@(((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 37)\n  (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 60)\n  (:start . 50) (:id . 52))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 65) (:start . 61)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 79) (:start . 66) (:id . 54))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 85) (:start . 80)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 93)\n  (:start . 87) (:id . 57))\n ((:tag . "NN") (:stem . "8c") (:form . "8C") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.200) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500773@unknown@formal@none@1@S@dMyc-overexpressing glia showed polyploidy (Figure 8C, data not shown), indicating that these cells undergo DNA replication without mitosis, but require additional signals for cell cycle progression.@(((:tag . "JJ") (:stem . "dmyc-overexpressing")\n  (:form . "dMyc-overexpressing") (:end . 19) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 24) (:start . 20)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 31) (:start . 25)\n  (:id . 44))\n ((:tag . "NN") (:stem . "polyploidy") (:form . "polyploidy") (:end . 42)\n  (:start . 32) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 50)\n  (:start . 44) (:id . 47))\n ((:tag . "NN") (:stem . "8c") (:form . "8C") (:end . 53) (:start . 51)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 82)\n  (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 87) (:start . 83)\n  (:id . 56))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 99) (:start . 94)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "undergo") (:form . "undergo") (:end . 107)\n  (:start . 100) (:id . 59))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 111) (:start . 108)\n  (:id . 60))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 123)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 131)\n  (:start . 124) (:id . 62))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 139)\n  (:start . 132) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 64))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 144) (:start . 141)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 152)\n  (:start . 145) (:id . 66))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 163)\n  (:start . 153) (:id . 67))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 171)\n  (:start . 164) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 175) (:start . 172)\n  (:id . 69))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 180) (:start . 176)\n  (:id . 70))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 186)\n  (:start . 181) (:id . 71))\n ((:tag . "NN") (:stem . "progression") (:form . "progression") (:end . 198)\n  (:start . 187) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x3.201.1) (:span 72 87)))\n (:hscopes ((:id . :x3.201.1) (:span 72 198)))\n (:identifiers (:sid . :s3.201) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500774@unknown@formal@none@1@S@In contrast, co-overexpression of dMyc with dEGFRλ produced a phenotype on par with that of repo>dEGFRλ;dp110CAAX (Figure 8D), indicating that dMyc overexpression can substitute for PI3K activation and promote neoplasia when combined with EGFR signaling.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "co-overexpression") (:form . "co-overexpression")\n  (:end . 30) (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 71)\n  (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "par") (:form . "par") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 113) (:start . 92) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 121)\n  (:start . 115) (:id . 60))\n ((:tag . "NN") (:stem . "8d") (:form . "8D") (:end . 124) (:start . 122)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 137)\n  (:start . 127) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 142) (:start . 138)\n  (:id . 65))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 147) (:start . 143)\n  (:id . 66))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 162) (:start . 148) (:id . 67))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 166) (:start . 163)\n  (:id . 68))\n ((:tag . "VB") (:stem . "substitute") (:form . "substitute") (:end . 177)\n  (:start . 167) (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 181) (:start . 178)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 186) (:start . 182)\n  (:id . 71))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 197)\n  (:start . 187) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 201) (:start . 198)\n  (:id . 73))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 209)\n  (:start . 202) (:id . 74))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 219)\n  (:start . 210) (:id . 75))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 224) (:start . 220)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 233)\n  (:start . 225) (:id . 77))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 238) (:start . 234)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 243) (:start . 239)\n  (:id . 79))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 253)\n  (:start . 244) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 254) (:start . 253)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x3.202.1) (:span 127 142)))\n (:hscopes ((:id . :x3.202.1) (:span 127 253)))\n (:identifiers (:sid . :s3.202) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500775@unknown@formal@none@1@S@Myc overexpression or Rb loss synergizes with EGFR.@(((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Rb") (:form . "Rb") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "synergize") (:form . "synergizes") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 51) (:start . 50)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.203) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5500776@unknown@formal@none@1@S@Given that the dMyc targets dCyclinD-dCdk4 are required for dEGFRλ;dp110CAAX neoplasia, we tested whether dCyclinD-dCdk4 overexpression could cooperate with dEGFRλ.@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "dcyclind-dcdk4") (:form . "dCyclinD-dCdk4")\n  (:end . 42) (:start . 28) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 76) (:start . 60) (:id . 51))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 86)\n  (:start . 77) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 97) (:start . 91)\n  (:id . 55))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 105)\n  (:start . 98) (:id . 56))\n ((:tag . "NN") (:stem . "dcyclind-dcdk4") (:form . "dCyclinD-dCdk4")\n  (:end . 120) (:start . 106) (:id . 57))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 135) (:start . 121) (:id . 58))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 141)\n  (:start . 136) (:id . 59))\n ((:tag . "VB") (:stem . "cooperate") (:form . "cooperate") (:end . 151)\n  (:start . 142) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 156) (:start . 152)\n  (:id . 61))\n ((:tag . "NN") (:stem . "degfrλ") (:form . "dEGFRλ") (:end . 163)\n  (:start . 157) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x3.204.1) (:span 136 141))\n  ((:id . :x3.204.2) (:span 98 105)))\n (:hscopes ((:id . :x3.204.1) (:span 136 163))\n  ((:id . :x3.204.2) (:span 98 163)))\n (:identifiers (:sid . :s3.204) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500777@unknown@formal@none@1@S@Additionally, we tested loss of Rbf1, the only known dCdk4 substrate that controls proliferation [23].@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 23) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Rbf1") (:form . "Rbf1") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 46) (:start . 42)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 52) (:start . 47)\n  (:id . 52))\n ((:tag . "NN") (:stem . "dcdk4") (:form . "dCdk4") (:end . 58) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "substrate") (:form . "substrate") (:end . 68)\n  (:start . 59) (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 73) (:start . 69)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "control") (:form . "controls") (:end . 82)\n  (:start . 74) (:id . 56))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 96) (:start . 83) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 101) (:start . 100)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.205) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500778@unknown@formal@none@1@S@repo>dCyclinD;dCdk4;dEGFRλ and repo>Rbf1dsRNA;dEGFRλ animals showed glial overgrowth, but did not accumulate as many cells as repo>dEGFRλ;dp110CAAX animals (Figure 8E and 8F).@(((:tag . "NNP") (:stem . "repo>dCyclinD;dCdk4;dEGFRλ")\n  (:form . "repo>dCyclinD;dCdk4;dEGFRλ") (:end . 26) (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "repo>Rbf1dsRNA;dEGFRλ")\n  (:form . "repo>Rbf1dsRNA;dEGFRλ") (:end . 52) (:start . 31) (:id . 44))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 60)\n  (:start . 53) (:id . 45))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 67) (:start . 61)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 73) (:start . 68)\n  (:id . 47))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 84)\n  (:start . 74) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 49))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 89) (:start . 86)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 93) (:start . 90)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 97) (:start . 94)\n  (:id . 52))\n ((:tag . "VB") (:stem . "accumulate") (:form . "accumulate") (:end . 108)\n  (:start . 98) (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 111) (:start . 109)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 116) (:start . 112)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 122)\n  (:start . 117) (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 125) (:start . 123)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 147) (:start . 126) (:id . 58))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 155)\n  (:start . 148) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 163)\n  (:start . 157) (:id . 61))\n ((:tag . "NN") (:stem . "8e") (:form . "8E") (:end . 166) (:start . 164)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 170) (:start . 167)\n  (:id . 63))\n ((:tag . "NN") (:stem . "8f") (:form . "8F") (:end . 173) (:start . 171)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 174) (:start . 173)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.206) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500779@unknown@formal@none@1@S@Thus, glia likely require additional dp110 or dMyc effectors to undergo full neoplastic proliferation.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "RB") (:stem . "likely") (:form . "likely") (:end . 17)\n  (:start . 11) (:id . 45))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 36)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "dp110") (:form . "dp110") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 60)\n  (:start . 51) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "VB") (:stem . "undergo") (:form . "undergo") (:end . 71)\n  (:start . 64) (:id . 53))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 87)\n  (:start . 77) (:id . 55))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 101) (:start . 88) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x3.207.1) (:span 11 17)))\n (:hscopes ((:id . :x3.207.1) (:span 11 101)))\n (:identifiers (:sid . :s3.207) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500780@unknown@formal@none@1@S@Other known PI3K and dMyc-dMax target genes that promote proliferation include ribosomal proteins and translation regulators [49],[52], such as eIF4E, which is highly expressed in dEGFRλ;dp110CAAX glia and required for neoplasia (Figure 6 and Figure S11).@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "pi3k") (:form . "PI3K") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dmyc-dmax") (:form . "dMyc-dMax") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "promote") (:form . "promote") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 70) (:start . 57) (:id . 51))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 78)\n  (:start . 71) (:id . 52))\n ((:tag . "JJ") (:stem . "ribosomal") (:form . "ribosomal") (:end . 88)\n  (:start . 79) (:id . 53))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 97)\n  (:start . 89) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 55))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 113)\n  (:start . 102) (:id . 56))\n ((:tag . "NNS") (:stem . "regulator") (:form . "regulators") (:end . 124)\n  (:start . 114) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 126) (:start . 125)\n  (:id . 58))\n ((:tag . "CD") (:stem . "49],[52") (:form . "49],[52") (:end . 133)\n  (:start . 126) (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 134) (:start . 133)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 140) (:start . 136)\n  (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 143) (:start . 141)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "eIF4E") (:form . "eIF4E") (:end . 149)\n  (:start . 144) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 156)\n  (:start . 151) (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 159) (:start . 157)\n  (:id . 67))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 166)\n  (:start . 160) (:id . 68))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 176)\n  (:start . 167) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 179) (:start . 177)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 196) (:start . 180) (:id . 71))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 201) (:start . 197)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 205) (:start . 202)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 214)\n  (:start . 206) (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 218) (:start . 215)\n  (:id . 75))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 228)\n  (:start . 219) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 230) (:start . 229)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 236)\n  (:start . 230) (:id . 78))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 238) (:start . 237)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 242) (:start . 239)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 249)\n  (:start . 243) (:id . 81))\n ((:tag . "NNP") (:stem . "S11") (:form . "S11") (:end . 253) (:start . 250)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 254) (:start . 253)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 255) (:start . 254)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s3.208) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500781@unknown@formal@none@1@S@Our data imply that PI3K, dMyc, and dCyclinD-dCdk4 exist in a linear system, in which Rbf1 inactivation by dCyclinD-dCdk4 is one direct output of dp110CAAX or dMyc.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "imply") (:form . "imply") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 30) (:start . 26)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dcyclind-dcdk4") (:form . "dCyclinD-dCdk4")\n  (:end . 50) (:start . 36) (:id . 51))\n ((:tag . "VBP") (:stem . "exist") (:form . "exist") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "linear") (:form . "linear") (:end . 68)\n  (:start . 62) (:id . 55))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 75)\n  (:start . 69) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 85) (:start . 80)\n  (:id . 59))\n ((:tag . "NN") (:stem . "rbf1") (:form . "Rbf1") (:end . 90) (:start . 86)\n  (:id . 60))\n ((:tag . "NN") (:stem . "inactivation") (:form . "inactivation") (:end . 103)\n  (:start . 91) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "NN") (:stem . "dcyclind-dcdk4") (:form . "dCyclinD-dCdk4")\n  (:end . 121) (:start . 107) (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 124) (:start . 122)\n  (:id . 64))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 128) (:start . 125)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 135)\n  (:start . 129) (:id . 66))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 142)\n  (:start . 136) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 155)\n  (:start . 146) (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 158) (:start . 156)\n  (:id . 70))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 163) (:start . 159)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x3.209.1) (:span 9 14)))\n (:hscopes ((:id . :x3.209.1) (:span 9 163)))\n (:identifiers (:sid . :s3.209) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500782@unknown@formal@none@1@S@However, in high-grade glioma, Rb loss co-occurs with EGFR and PTEN mutations [2], implying that these mutations cooperate to promote gliomagenesis.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "high-grade") (:form . "high-grade") (:end . 22)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Rb") (:form . "Rb") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "co-occur") (:form . "co-occurs") (:end . 48)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "PTEN") (:form . "PTEN") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 77)\n  (:start . 68) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 81) (:start . 80)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "imply") (:form . "implying") (:end . 91)\n  (:start . 83) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 96) (:start . 92)\n  (:id . 61))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 102) (:start . 97)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 112)\n  (:start . 103) (:id . 63))\n ((:tag . "VBP") (:stem . "cooperate") (:form . "cooperate") (:end . 122)\n  (:start . 113) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 125) (:start . 123)\n  (:id . 65))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 133)\n  (:start . 126) (:id . 66))\n ((:tag . "NN") (:stem . "gliomagenesis") (:form . "gliomagenesis")\n  (:end . 147) (:start . 134) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x3.210.1) (:span 83 91)))\n (:hscopes ((:id . :x3.210.1) (:span 83 147)))\n (:identifiers (:sid . :s3.210) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500783@unknown@formal@none@1@S@To explore interactions between Rb and EGFR-PI3K, we created the triple mutant repo>Rbf1dsRNA;dEGFRλ;dp110CAAX.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "explore") (:form . "explore") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 23)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 31)\n  (:start . 24) (:id . 45))\n ((:tag . "NNP") (:stem . "Rb") (:form . "Rb") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "EGFR-PI3K") (:form . "EGFR-PI3K") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "create") (:form . "created") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "triple") (:form . "triple") (:end . 71)\n  (:start . 65) (:id . 53))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 78)\n  (:start . 72) (:id . 54))\n ((:tag . "NNP") (:stem . "repo>Rbf1dsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>Rbf1dsRNA;dEGFRλ;dp110CAAX") (:end . 110) (:start . 79)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.211) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500784@unknown@formal@none@1@S@These animals displayed exacerbated glial neoplasia, with a substantial increase in small anaplastic-like glia throughout the CNS (Figure 8G).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "JJ") (:stem . "exacerbated") (:form . "exacerbated") (:end . 35)\n  (:start . 24) (:id . 45))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 41) (:start . 36)\n  (:id . 46))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 51)\n  (:start . 42) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 59) (:start . 58)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "substantial") (:form . "substantial") (:end . 71)\n  (:start . 60) (:id . 51))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 80)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 83) (:start . 81)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 89) (:start . 84)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "anaplastic-like") (:form . "anaplastic-like")\n  (:end . 105) (:start . 90) (:id . 55))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 110) (:start . 106)\n  (:id . 56))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 121)\n  (:start . 111) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "CNS") (:form . "CNS") (:end . 129) (:start . 126)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 137)\n  (:start . 131) (:id . 61))\n ((:tag . "NN") (:stem . "8g") (:form . "8G") (:end . 140) (:start . 138)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.212) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500785@unknown@formal@none@1@S@This synergistic interaction likely derives from derepression of dE2F1 upon Rbf1 loss, and concomitant increased expression of dE2F1 target genes, including Stg and dCyclinE [53].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "synergistic") (:form . "synergistic") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 28)\n  (:start . 17) (:id . 44))\n ((:tag . "RB") (:stem . "likely") (:form . "likely") (:end . 35)\n  (:start . 29) (:id . 45))\n ((:tag . "VBZ") (:stem . "derive") (:form . "derives") (:end . 43)\n  (:start . 36) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 48) (:start . 44)\n  (:id . 47))\n ((:tag . "NN") (:stem . "derepression") (:form . "derepression") (:end . 61)\n  (:start . 49) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 49))\n ((:tag . "NN") (:stem . "de2f1") (:form . "dE2F1") (:end . 70) (:start . 65)\n  (:id . 50))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 75) (:start . 71)\n  (:id . 51))\n ((:tag . "NN") (:stem . "rbf1") (:form . "Rbf1") (:end . 80) (:start . 76)\n  (:id . 52))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 85) (:start . 81)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "concomitant") (:form . "concomitant") (:end . 102)\n  (:start . 91) (:id . 56))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 112)\n  (:start . 103) (:id . 57))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 123)\n  (:start . 113) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 59))\n ((:tag . "NN") (:stem . "de2f1") (:form . "dE2F1") (:end . 132)\n  (:start . 127) (:id . 60))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 139)\n  (:start . 133) (:id . 61))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 145)\n  (:start . 140) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 156)\n  (:start . 147) (:id . 64))\n ((:tag . "NNP") (:stem . "Stg") (:form . "Stg") (:end . 160) (:start . 157)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "dCyclinE") (:form . "dCyclinE") (:end . 173)\n  (:start . 165) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 175) (:start . 174)\n  (:id . 68))\n ((:tag . "CD") (:stem . "53") (:form . "53") (:end . 177) (:start . 175)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 178) (:start . 177)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x3.213.1) (:span 29 35)))\n (:hscopes ((:id . :x3.213.1) (:span 29 173)))\n (:identifiers (:sid . :s3.213) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500786@unknown@formal@none@1@S@Increased dCyclinE and Stg expression may accelerate cell cycle progression, perhaps through increased dCdk2 and dCdk1 activity and/or truncated G1 and G2 gap phases caused by constant dCyclinE and Stg protein levels [23].@(((:tag . "VBN") (:stem . "increase") (:form . "Increased") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "dcycline") (:form . "dCyclinE") (:end . 18)\n  (:start . 10) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "stg") (:form . "Stg") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "VB") (:stem . "accelerate") (:form . "accelerate") (:end . 52)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 63) (:start . 58)\n  (:id . 50))\n ((:tag . "NN") (:stem . "progression") (:form . "progression") (:end . 75)\n  (:start . 64) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 52))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 84)\n  (:start . 77) (:id . 53))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 92)\n  (:start . 85) (:id . 54))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 102)\n  (:start . 93) (:id . 55))\n ((:tag . "NN") (:stem . "dcdk2") (:form . "dCdk2") (:end . 108)\n  (:start . 103) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dcdk1") (:form . "dCdk1") (:end . 118)\n  (:start . 113) (:id . 58))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 127)\n  (:start . 119) (:id . 59))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 134)\n  (:start . 128) (:id . 60))\n ((:tag . "VBN") (:stem . "truncate") (:form . "truncated") (:end . 144)\n  (:start . 135) (:id . 61))\n ((:tag . "NN") (:stem . "g1") (:form . "G1") (:end . 147) (:start . 145)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 151) (:start . 148)\n  (:id . 63))\n ((:tag . "NN") (:stem . "g2") (:form . "G2") (:end . 154) (:start . 152)\n  (:id . 64))\n ((:tag . "NN") (:stem . "gap") (:form . "gap") (:end . 158) (:start . 155)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "phase") (:form . "phases") (:end . 165)\n  (:start . 159) (:id . 66))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 172)\n  (:start . 166) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 175) (:start . 173)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "constant") (:form . "constant") (:end . 184)\n  (:start . 176) (:id . 69))\n ((:tag . "NN") (:stem . "dcycline") (:form . "dCyclinE") (:end . 193)\n  (:start . 185) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 197) (:start . 194)\n  (:id . 71))\n ((:tag . "NN") (:stem . "stg") (:form . "Stg") (:end . 201) (:start . 198)\n  (:id . 72))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 209)\n  (:start . 202) (:id . 73))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 216)\n  (:start . 210) (:id . 74))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 218) (:start . 217)\n  (:id . 75))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 220) (:start . 218)\n  (:id . 76))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 221) (:start . 220)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x3.214.1) (:span 77 84)) ((:id . :x3.214.2) (:span 38 41)))\n (:hscopes ((:id . :x3.214.1) (:span 77 216))\n  ((:id . :x3.214.2) (:span 38 216)))\n (:identifiers (:sid . :s3.214) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500787@unknown@formal@none@1@S@Consistent with this, we observed increased dCyclinE expression in Rbf1dsRNA;dEGFRλ;dp110CAAX glia relative to dEGFRλ;dp110CAAX glia (Figure 8H and 8I), and co-overexpression of Stg or dCyclinE-dCdk2 with dEGFRλ;dp110CAAX synergistically exacerbated glial neoplasia, yielding phenotypes similar to repo>RbfdsRNA;dEGFRλ;dp110CAAX (Figure 5E and Figure S9, data not shown).@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "VBN") (:stem . 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5500788@unknown@formal@none@1@S@To assess dCdk2 activity in repo>Rbf1dsRNA;dEGFRλ;dp110CAAX brains compared to repo>dEGFRλ;dp110CAAX brains, we stained for phospho-MPM2 (Figure S12), which detects nuclear foci in cells with active dCyclinE-dCdk2 complexes [54].@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dcdk2") (:form . "dCdk2") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "repo>Rbf1dsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>Rbf1dsRNA;dEGFRλ;dp110CAAX") (:end . 59) (:start . 28)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 66)\n  (:start . 60) (:id . 48))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 75)\n  (:start . 67) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 100) (:start . 79) (:id . 51))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 107)\n  (:start . 101) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 111) (:start . 109)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "stain") (:form . "stained") (:end . 119)\n  (:start . 112) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 123) (:start . 120)\n  (:id . 56))\n ((:tag . "NN") (:stem . "phospho-mpm2") (:form . "phospho-MPM2") (:end . 136)\n  (:start . 124) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 144)\n  (:start . 138) (:id . 59))\n ((:tag . "NN") (:stem . "s12") (:form . "S12") (:end . 148) (:start . 145)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 62))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 156)\n  (:start . 151) (:id . 63))\n ((:tag . "VBZ") (:stem . "detect") (:form . "detects") (:end . 164)\n  (:start . 157) (:id . 64))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 172)\n  (:start . 165) (:id . 65))\n ((:tag . "NNS") (:stem . "focus") (:form . "foci") (:end . 177)\n  (:start . 173) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 180) (:start . 178)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 186)\n  (:start . 181) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 191) (:start . 187)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 198)\n  (:start . 192) (:id . 70))\n ((:tag . "NN") (:stem . "dcycline-dcdk2") (:form . "dCyclinE-dCdk2")\n  (:end . 213) (:start . 199) (:id . 71))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 223)\n  (:start . 214) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 225) (:start . 224)\n  (:id . 73))\n ((:tag . "CD") (:stem . "54") (:form . "54") (:end . 227) (:start . 225)\n  (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 228) (:start . 227)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s3.216) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500789@unknown@formal@none@1@S@Phospho-MPM2 foci were present in glia of both genotypes, although repo>Rbf1dsRNA;dEGFRλ;dp110CAAX brains appeared to have a higher density of glia with phospho-MPM2 foci (Figure S12), suggesting that expanded expression of dCyclinE results in broader activation of dCdk2.@(((:tag . "NN") (:stem . "phospho-mpm2") (:form . "Phospho-MPM2") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "focus") (:form . "foci") (:end . 17) (:start . 13)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 56)\n  (:start . 47) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 66)\n  (:start . 58) (:id . 52))\n ((:tag . "NNP") (:stem . "repo>Rbf1dsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>Rbf1dsRNA;dEGFRλ;dp110CAAX") (:end . 98) (:start . 67)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 105)\n  (:start . 99) (:id . 54))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 114)\n  (:start . 106) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n  (:id . 56))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 122) (:start . 118)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 124) (:start . 123)\n  (:id . 58))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 131)\n  (:start . 125) (:id . 59))\n ((:tag . "NN") (:stem . "density") (:form . "density") (:end . 139)\n  (:start . 132) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 61))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 147) (:start . 143)\n  (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 152) (:start . 148)\n  (:id . 63))\n ((:tag . "NN") (:stem . "phospho-mpm2") (:form . "phospho-MPM2") (:end . 165)\n  (:start . 153) (:id . 64))\n ((:tag . "NNS") (:stem . "focus") (:form . "foci") (:end . 170)\n  (:start . 166) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 178)\n  (:start . 172) (:id . 67))\n ((:tag . "NNP") (:stem . "S12") (:form . "S12") (:end . 182) (:start . 179)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 195)\n  (:start . 185) (:id . 71))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 200) (:start . 196)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "expand") (:form . "expanded") (:end . 209)\n  (:start . 201) (:id . 73))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 220)\n  (:start . 210) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 223) (:start . 221)\n  (:id . 75))\n ((:tag . "NN") (:stem . "dcycline") (:form . "dCyclinE") (:end . 232)\n  (:start . 224) (:id . 76))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 240)\n  (:start . 233) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 243) (:start . 241)\n  (:id . 78))\n ((:tag . "JJR") (:stem . "broad") (:form . "broader") (:end . 251)\n  (:start . 244) (:id . 79))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 262)\n  (:start . 252) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 265) (:start . 263)\n  (:id . 81))\n ((:tag . "NN") (:stem . "dcdk2") (:form . "dCdk2") (:end . 271)\n  (:start . 266) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 272) (:start . 271)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x3.217.1) (:span 185 195))\n  ((:id . :x3.217.2) (:span 106 114)))\n (:hscopes ((:id . :x3.217.1) (:span 185 271))\n  ((:id . :x3.217.2) (:span 67 170)))\n (:identifiers (:sid . :s3.217) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500790@unknown@formal@none@1@S@Thus, while PI3K and Rbf1 act in a common genetic pathway linked by dCyclinD-dCdk4, Rbf1 loss nevertheless synergizes with mitogenic stimulation from combined EGFR and PI3K signaling, and this synergy emerges from increased expression of dCyclinE and Stg, rate-limiting regulators of the cell cycle.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "rbf1") (:form . "Rbf1") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "act") (:form . "act") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "IN") (:stem . 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"cycle") (:end . 298)\n  (:start . 293) (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 299) (:start . 298)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s3.218) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500791@unknown@formal@none@1@S@Discussion@(((:tag . "NN") (:stem . "discussion") (:form . "Discussion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s3.219) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500792@unknown@formal@none@1@S@We show that constitutive coactivation of EGFR-Ras and PI3K signaling in Drosophila glia and glial precursors gives rise to neoplastic, invasive cells that create transplantable tumor-like growths, mimicking human glioma, and mirroring mouse glioma models.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 25)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "coactivation") (:form . "coactivation") (:end . 38)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 69)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 83)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 88) (:start . 84)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 109)\n  (:start . 99) (:id . 57))\n ((:tag . "VBZ") (:stem . "give") (:form . "gives") (:end . 115)\n  (:start . 110) (:id . 58))\n ((:tag . "NN") (:stem . "rise") (:form . "rise") (:end . 120) (:start . 116)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 123) (:start . 121)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 134)\n  (:start . 124) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 144)\n  (:start . 136) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 150)\n  (:start . 145) (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 155) (:start . 151)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "create") (:form . "create") (:end . 162)\n  (:start . 156) (:id . 66))\n ((:tag . "JJ") (:stem . "transplantable") (:form . "transplantable")\n  (:end . 177) (:start . 163) (:id . 67))\n ((:tag . "JJ") (:stem . "tumor-like") (:form . "tumor-like") (:end . 188)\n  (:start . 178) (:id . 68))\n ((:tag . "NNS") (:stem . "growth") (:form . "growths") (:end . 196)\n  (:start . 189) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "mimic") (:form . "mimicking") (:end . 207)\n  (:start . 198) (:id . 71))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 213)\n  (:start . 208) (:id . 72))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 220)\n  (:start . 214) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 221) (:start . 220)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 225) (:start . 222)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "mirror") (:form . "mirroring") (:end . 235)\n  (:start . 226) (:id . 76))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 241)\n  (:start . 236) (:id . 77))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 248)\n  (:start . 242) (:id . 78))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 255)\n  (:start . 249) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 256) (:start . 255)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s3.220) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500793@unknown@formal@none@1@S@This represents a robust organotypic and cell-type specific Drosophila cancer model in which malignant cells are created by mutations in the signature genes and pathways thought to be driving forces in a homologous human cancer.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "robust") (:form . "robust") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "organotypic") (:form . "organotypic") (:end . 36)\n  (:start . 25) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "cell-type") (:form . "cell-type") (:end . 50)\n  (:start . 41) (:id . 48))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 59)\n  (:start . 51) (:id . 49))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 70)\n  (:start . 60) (:id . 50))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 77)\n  (:start . 71) (:id . 51))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 83) (:start . 78)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 92) (:start . 87)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "malignant") (:form . "malignant") (:end . 102)\n  (:start . 93) (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 108)\n  (:start . 103) (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 112) (:start . 109)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "create") (:form . "created") (:end . 120)\n  (:start . 113) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 123) (:start . 121)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 133)\n  (:start . 124) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 62))\n ((:tag . "NN") (:stem . "signature") (:form . "signature") (:end . 150)\n  (:start . 141) (:id . 63))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 156)\n  (:start . 151) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 169)\n  (:start . 161) (:id . 66))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 177)\n  (:start . 170) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 180) (:start . 178)\n  (:id . 68))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 183) (:start . 181)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "drive") (:form . "driving") (:end . 191)\n  (:start . 184) (:id . 70))\n ((:tag . "NNS") (:stem . "force") (:form . "forces") (:end . 198)\n  (:start . 192) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 201) (:start . 199)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 203) (:start . 202)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 214)\n  (:start . 204) (:id . 74))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 220)\n  (:start . 215) (:id . 75))\n ((:tag . "NN") (:stem . "cancer") (:form . "cancer") (:end . 227)\n  (:start . 221) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x3.221.1) (:span 170 177)))\n (:hscopes ((:id . :x3.221.1) (:span 170 227)))\n (:identifiers (:sid . :s3.221) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500794@unknown@formal@none@1@S@This was not necessarily an expected result since fly and human glia show many biological differences despite displaying important similarities [9],[55],[56].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "necessarily") (:form . "necessarily") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "VBP") (:stem . "result") (:form . "result") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 78) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 89)\n  (:start . 79) (:id . 56))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 101)\n  (:start . 90) (:id . 57))\n ((:tag . "IN") (:stem . "despite") (:form . "despite") (:end . 109)\n  (:start . 102) (:id . 58))\n ((:tag . "VBG") (:stem . "display") (:form . "displaying") (:end . 120)\n  (:start . 110) (:id . 59))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 130)\n  (:start . 121) (:id . 60))\n ((:tag . "NNS") (:stem . "similarity") (:form . "similarities") (:end . 143)\n  (:start . 131) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 145) (:start . 144)\n  (:id . 62))\n ((:tag . "CD") (:stem . "9],[55],[56") (:form . "9],[55],[56") (:end . 156)\n  (:start . 145) (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 157) (:start . 156)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.222) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500795@unknown@formal@none@1@S@Through genetic analysis of our model, we identified crucial downstream effectors of EGFR and PI3K signaling, many of which are mutated and/or activated in human glioma.@(((:tag . "IN") (:stem . "through") (:form . "Through") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "JJ") (:stem . "downstream") (:form . "downstream") (:end . 71)\n  (:start . 61) (:id . 52))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 81)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 89) (:start . 85)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 98) (:start . 94)\n  (:id . 57))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 108)\n  (:start . 99) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 114) (:start . 110)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 123)\n  (:start . 118) (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 135)\n  (:start . 128) (:id . 64))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 142)\n  (:start . 136) (:id . 65))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 152)\n  (:start . 143) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 155) (:start . 153)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 161)\n  (:start . 156) (:id . 68))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 168)\n  (:start . 162) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.223) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500796@unknown@formal@none@1@S@These effectors act in a combinatorial network to coordinately stimulate cell cycle entry and progression, block cell cycle exit, and promote inappropriate cellular growth and migration (Figure 8J).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "act") (:form . "act") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "combinatorial") (:form . "combinatorial")\n  (:end . 38) (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "RB") (:stem . "coordinately") (:form . "coordinately") (:end . 62)\n  (:start . 50) (:id . 50))\n ((:tag . "VB") (:stem . "stimulate") (:form . "stimulate") (:end . 72)\n  (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 77) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 83) (:start . 78)\n  (:id . 53))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 89) (:start . 84)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "progression") (:form . "progression") (:end . 105)\n  (:start . 94) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 57))\n ((:tag . "NN") (:stem . "block") (:form . "block") (:end . 112)\n  (:start . 107) (:id . 58))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 117) (:start . 113)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 123)\n  (:start . 118) (:id . 60))\n ((:tag . "NN") (:stem . "exit") (:form . "exit") (:end . 128) (:start . 124)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 63))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 141)\n  (:start . 134) (:id . 64))\n ((:tag . "JJ") (:stem . "inappropriate") (:form . "inappropriate")\n  (:end . 155) (:start . 142) (:id . 65))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 164)\n  (:start . 156) (:id . 66))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 171)\n  (:start . 165) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n  (:id . 68))\n ((:tag . "NN") (:stem . "migration") (:form . "migration") (:end . 185)\n  (:start . 176) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 187) (:start . 186)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 193)\n  (:start . 187) (:id . 71))\n ((:tag . "NN") (:stem . "8j") (:form . "8J") (:end . 196) (:start . 194)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 197) (:start . 196)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.224) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500797@unknown@formal@none@1@S@Pathways within this network, while interdependent, act synergistically, rather than additively.@(((:tag . "NNS") (:stem . "pathway") (:form . "Pathways") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "interdependent") (:form . "interdependent")\n  (:end . 50) (:start . 36) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "RB") (:stem . "synergistically") (:form . "synergistically")\n  (:end . 71) (:start . 56) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 79)\n  (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 84) (:start . 80)\n  (:id . 54))\n ((:tag . "RB") (:stem . "additively") (:form . "additively") (:end . 95)\n  (:start . 85) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.225) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500798@unknown@formal@none@1@S@Thus, Drosophila shows evolutionary conservation of oncogene cooperation.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 16)\n  (:start . 6) (:id . 44))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 35)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 48)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 48))\n ((:tag . "NN") (:stem . "oncogene") (:form . "oncogene") (:end . 60)\n  (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "cooperation") (:form . "cooperation") (:end . 72)\n  (:start . 61) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.226) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500799@unknown@formal@none@1@S@At least four pathway circuits are necessary for glial neoplasia initiated by EGFR and PI3K signaling, including dRas and dMyc circuits, which induce dCyclinE and dCyclinD to drive cell cycle entry, a Pnt circuit, which induces Stg to promote cell cycle progression, and a Tor-eIF4E-S6K pathway, which provides protein translation necessary for proliferation and growth (Figure 8J).@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "NNS") (:stem . "circuit") (:form . "circuits") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . 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5500800@unknown@formal@none@1@S@When activated individually, these pathways fail to elicit glial neoplasia, implying a requirement for coordinated stimulation of multiple effectors and inactivation of negative regulators.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "RB") (:stem . "individually") (:form . "individually") (:end . 27)\n  (:start . 15) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "VBP") (:stem . "fail") (:form . "fail") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "VB") (:stem . "elicit") (:form . "elicit") (:end . 58)\n  (:start . 52) (:id . 50))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 64) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 74)\n  (:start . 65) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "imply") (:form . "implying") (:end . 84)\n  (:start . 76) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "requirement") (:form . "requirement") (:end . 98)\n  (:start . 87) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "coordinate") (:form . "coordinated") (:end . 114)\n  (:start . 103) (:id . 58))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 126)\n  (:start . 115) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 138)\n  (:start . 130) (:id . 61))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 148)\n  (:start . 139) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 63))\n ((:tag . "NN") (:stem . "inactivation") (:form . "inactivation") (:end . 165)\n  (:start . 153) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 177)\n  (:start . 169) (:id . 66))\n ((:tag . "NNS") (:stem . "regulator") (:form . "regulators") (:end . 188)\n  (:start . 178) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x3.228.1) (:span 76 84)))\n (:hscopes ((:id . :x3.228.1) (:span 76 188)))\n (:identifiers (:sid . :s3.228) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500801@unknown@formal@none@1@S@Orthologs for many of the genes within these pathways, such as dRictor, are implicated in human glioma, although specific roles for some, such as ETS transcription factors, have not been defined despite their expression in glioma [2],[57],[58].@(((:tag . "NNS") (:stem . "ortholog") (:form . "Orthologs") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "drictor") (:form . "dRictor") (:end . 70)\n  (:start . 63) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 86)\n  (:start . 76) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 95) (:start . 90)\n  (:id . 59))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 102)\n  (:start . 96) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 112)\n  (:start . 104) (:id . 62))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 121)\n  (:start . 113) (:id . 63))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 127)\n  (:start . 122) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 131) (:start . 128)\n  (:id . 65))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 136) (:start . 132)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 142) (:start . 138)\n  (:id . 68))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 145) (:start . 143)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "ETS") (:form . "ETS") (:end . 149) (:start . 146)\n  (:id . 70))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 163) (:start . 150) (:id . 71))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 171)\n  (:start . 164) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 73))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 177) (:start . 173)\n  (:id . 74))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 181) (:start . 178)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 186) (:start . 182)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 194)\n  (:start . 187) (:id . 77))\n ((:tag . "IN") (:stem . "despite") (:form . "despite") (:end . 202)\n  (:start . 195) (:id . 78))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 208)\n  (:start . 203) (:id . 79))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 219)\n  (:start . 209) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 222) (:start . 220)\n  (:id . 81))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 229)\n  (:start . 223) (:id . 82))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 231) (:start . 230)\n  (:id . 83))\n ((:tag . "CD") (:stem . "2],[57],[58") (:form . "2],[57],[58") (:end . 242)\n  (:start . 231) (:id . 84))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 243) (:start . 242)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 86)))@@@1@45@((:hcues ((:id . :x3.229.1) (:span 76 86)))\n (:hscopes ((:id . :x3.229.1) (:span 0 102)))\n (:identifiers (:sid . :s3.229) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500802@unknown@formal@none@1@S@While many of these genes are known EGFR and PI3K pathway components, we did not necessarily expect them to be required for EGFR and PI3K dependent glial neoplasia.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 49) (:start . 45)\n  (:id . 51))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 68)\n  (:start . 58) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "RB") (:stem . "necessarily") (:form . "necessarily") (:end . 92)\n  (:start . 81) (:id . 58))\n ((:tag . "VB") (:stem . "expect") (:form . "expect") (:end . 99)\n  (:start . 93) (:id . 59))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 104) (:start . 100)\n  (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 107) (:start . 105)\n  (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 119)\n  (:start . 111) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 123) (:start . 120)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 128) (:start . 124)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 137) (:start . 133)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "dependent") (:form . "dependent") (:end . 147)\n  (:start . 138) (:id . 68))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 153)\n  (:start . 148) (:id . 69))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 163)\n  (:start . 154) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.230) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500803@unknown@formal@none@1@S@Indeed, we have tested many other pathway components and outputs, such as Jun kinase, that did not significantly suppress repo>dEGFRλ;dp110CAAX phenotypes upon reduced function (unpublished data).@(((:tag . "RB") (:stem . "indeed") (:form . "Indeed") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 22) (:start . 16)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 33) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "output") (:form . "outputs") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Jun") (:form . "Jun") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 84)\n  (:start . 78) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 90) (:start . 86)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 94) (:start . 91)\n  (:id . 60))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 98) (:start . 95)\n  (:id . 61))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 112) (:start . 99) (:id . 62))\n ((:tag . "VB") (:stem . "suppress") (:form . "suppress") (:end . 121)\n  (:start . 113) (:id . 63))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 143) (:start . 122) (:id . 64))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 154)\n  (:start . 144) (:id . 65))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 159) (:start . 155)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 167)\n  (:start . 160) (:id . 67))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 176)\n  (:start . 168) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 178) (:start . 177)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "unpublished") (:form . "unpublished") (:end . 189)\n  (:start . 178) (:id . 70))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 194)\n  (:start . 190) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s3.231) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500804@unknown@formal@none@1@S@Coactivation of EGFR and PI3K signaling upregulates dMyc, which is necessary for glial neoplasia.@(((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "VBZ") (:stem . "upregulate") (:form . "upregulates") (:end . 51)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 56) (:start . 52)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 76)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 86) (:start . 81)\n  (:id . 55))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 96)\n  (:start . 87) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.232) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500805@unknown@formal@none@1@S@This is consistent with findings that, in flies and mammals, EGFR-Ras, PI3K, and Tor signaling upregulate Myc protein levels [16],[49],[51],[59],[60].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "mammal") (:form . "mammals") (:end . 59)\n  (:start . 52) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 69)\n  (:start . 61) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 84) (:start . 81)\n  (:id . 59))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 94)\n  (:start . 85) (:id . 60))\n ((:tag . "VBP") (:stem . "upregulate") (:form . "upregulate") (:end . 105)\n  (:start . 95) (:id . 61))\n ((:tag . "NN") (:stem . "myc") (:form . "Myc") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 117)\n  (:start . 110) (:id . 63))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 124)\n  (:start . 118) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 126) (:start . 125)\n  (:id . 65))\n ((:tag . "CD") (:stem . "16],[49],[51],[59],[60")\n  (:form . "16],[49],[51],[59],[60") (:end . 148) (:start . 126) (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 149) (:start . 148)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.233) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500806@unknown@formal@none@1@S@Myc oncogenes are well-known to cooperate with RTK-Ras signaling to drive neoplastic transformation [51], and we demonstrate that this property of Myc is conserved in flies.@(((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "oncogene") (:form . "oncogenes") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "well-known") (:form . "well-known") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "VB") (:stem . "cooperate") (:form . "cooperate") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "rtk-ras") (:form . "RTK-Ras") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 64)\n  (:start . 55) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "VB") (:stem . "drive") (:form . "drive") (:end . 73) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 84)\n  (:start . 74) (:id . 53))\n ((:tag . "NN") (:stem . "transformation") (:form . "transformation")\n  (:end . 99) (:start . 85) (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 101) (:start . 100)\n  (:id . 55))\n ((:tag . "CD") (:stem . "51") (:form . "51") (:end . 103) (:start . 101)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 104) (:start . 103)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 124)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 129) (:start . 125)\n  (:id . 62))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 134) (:start . 130)\n  (:id . 63))\n ((:tag . "NN") (:stem . "property") (:form . "property") (:end . 143)\n  (:start . 135) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 146) (:start . 144)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 150) (:start . 147)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 153) (:start . 151)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 163)\n  (:start . 154) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 166) (:start . 164)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 172) (:start . 167)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.234) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500807@unknown@formal@none@1@S@We also observed sensitivity to reduced Myc gene dosage in our glioma model, which has also been recently documented in a mouse model of PTEN-dependent glioma [61].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 28)\n  (:start . 17) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dosage") (:form . "dosage") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 75) (:start . 70)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 82) (:start . 77)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 86) (:start . 83)\n  (:id . 57))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 91) (:start . 87)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 96) (:start . 92)\n  (:id . 59))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 105)\n  (:start . 97) (:id . 60))\n ((:tag . "VBN") (:stem . "document") (:form . "documented") (:end . 116)\n  (:start . 106) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 121) (:start . 120)\n  (:id . 63))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 127)\n  (:start . 122) (:id . 64))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 133)\n  (:start . 128) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "pten-dependent") (:form . "PTEN-dependent")\n  (:end . 151) (:start . 137) (:id . 67))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 158)\n  (:start . 152) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 160) (:start . 159)\n  (:id . 69))\n ((:tag . "CD") (:stem . "61") (:form . "61") (:end . 162) (:start . 160)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 163) (:start . 162)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.235) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500808@unknown@formal@none@1@S@c-myc is commonly amplified in gliomas [62], implying that Myc is rate limiting, and c-myc amplification may be selected for this reason.@(((:tag . "NN") (:stem . "c-myc") (:form . "c-myc") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "VBN") (:stem . "amplify") (:form . "amplified") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "CD") (:stem . "62") (:form . "62") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "imply") (:form . "implying") (:end . 53)\n  (:start . 45) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 58) (:start . 54)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 70) (:start . 66)\n  (:id . 56))\n ((:tag . "NN") (:stem . "limiting") (:form . "limiting") (:end . 79)\n  (:start . 71) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 59))\n ((:tag . "NN") (:stem . "c-myc") (:form . "c-myc") (:end . 90) (:start . 85)\n  (:id . 60))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 104) (:start . 91) (:id . 61))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 108) (:start . 105)\n  (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 111) (:start . 109)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 120)\n  (:start . 112) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 124) (:start . 121)\n  (:id . 65))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 129) (:start . 125)\n  (:id . 66))\n ((:tag . "NN") (:stem . "reason") (:form . "reason") (:end . 136)\n  (:start . 130) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x3.236.1) (:span 105 108)) ((:id . :x3.236.2) (:span 45 53)))\n (:hscopes ((:id . :x3.236.1) (:span 85 136))\n  ((:id . :x3.236.2) (:span 45 136)))\n (:identifiers (:sid . :s3.236) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500809@unknown@formal@none@1@S@D-cyclins, established Myc target genes, and Cdk4 are also commonly amplified and/or overexpressed in gliomas [1],[51].@(((:tag . "NNP") (:stem . "D-cyclin") (:form . "D-cyclins") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "established") (:form . "established") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Cdk4") (:form . "Cdk4") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 67)\n  (:start . 59) (:id . 53))\n ((:tag . "VBN") (:stem . "amplify") (:form . "amplified") (:end . 77)\n  (:start . 68) (:id . 54))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 84)\n  (:start . 78) (:id . 55))\n ((:tag . "VBN") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 98) (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 101) (:start . 99)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 109)\n  (:start . 102) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 111) (:start . 110)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1],[51") (:form . "1],[51") (:end . 117)\n  (:start . 111) (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.237) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500810@unknown@formal@none@1@S@We observed dMyc-dependent dCyclinD overexpression, and a requirement for dCyclinD-dCdk4 in repo>dEGFRλ;dp110CAAX neoplasia, although dCdk4 itself is not required for normal glial proliferation.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "dmyc-dependent") (:form . "dMyc-dependent")\n  (:end . 26) (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "dcyclind") (:form . "dCyclinD") (:end . 35)\n  (:start . 27) (:id . 45))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 50) (:start . 36) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 49))\n ((:tag . "NN") (:stem . "requirement") (:form . "requirement") (:end . 69)\n  (:start . 58) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 73) (:start . 70)\n  (:id . 51))\n ((:tag . "NN") (:stem . "dcyclind-dcdk4") (:form . "dCyclinD-dCdk4")\n  (:end . 88) (:start . 74) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 113) (:start . 92) (:id . 54))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 123)\n  (:start . 114) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 56))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 133)\n  (:start . 125) (:id . 57))\n ((:tag . "NN") (:stem . "dcdk4") (:form . "dCdk4") (:end . 139)\n  (:start . 134) (:id . 58))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 146)\n  (:start . 140) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 149) (:start . 147)\n  (:id . 60))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 153) (:start . 150)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 162)\n  (:start . 154) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 166) (:start . 163)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 173)\n  (:start . 167) (:id . 64))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 179)\n  (:start . 174) (:id . 65))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 193) (:start . 180) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.238) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500811@unknown@formal@none@1@S@Together with our analysis of TORC2, this illustrates that oncogenic EGFR-PI3K co-opts effectors that do not control normal glial development.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "TORC2") (:form . "TORC2") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "illustrate") (:form . "illustrates") (:end . 53)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "oncogenic") (:form . "oncogenic") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . "NN") (:stem . "egfr-pi3k") (:form . "EGFR-PI3K") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "co-opt") (:form . "co-opts") (:end . 86)\n  (:start . 79) (:id . 54))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 96)\n  (:start . 87) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 101) (:start . 97)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 104) (:start . 102)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 108) (:start . 105)\n  (:id . 58))\n ((:tag . "VB") (:stem . "control") (:form . "control") (:end . 116)\n  (:start . 109) (:id . 59))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 123)\n  (:start . 117) (:id . 60))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 129)\n  (:start . 124) (:id . 61))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 141)\n  (:start . 130) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.239) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500812@unknown@formal@none@1@S@Similarly, cdk4-/- mutant mice show normal proliferation in many tissues, but are resistant to ErbB-2-driven breast cancers [63],[64].@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "cdk4-/-") (:form . "cdk4-/-") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 56) (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 72)\n  (:start . 65) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 77) (:start . 74)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "resistant") (:form . "resistant") (:end . 91)\n  (:start . 82) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "erbb-2-driven") (:form . "ErbB-2-driven")\n  (:end . 108) (:start . 95) (:id . 58))\n ((:tag . "NN") (:stem . "breast") (:form . "breast") (:end . 115)\n  (:start . 109) (:id . 59))\n ((:tag . "NNS") (:stem . "cancer") (:form . "cancers") (:end . 123)\n  (:start . 116) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "CD") (:stem . "63],[64") (:form . "63],[64") (:end . 132)\n  (:start . 125) (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 133) (:start . 132)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.240) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500813@unknown@formal@none@1@S@Our data argue that Cdk4 activity is a key tumor-specific rate-limiting output of EGFR and PI3K signaling in glioma as well.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "argue") (:form . "argue") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cdk4") (:form . "Cdk4") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "tumor-specific") (:form . "tumor-specific")\n  (:end . 57) (:start . 43) (:id . 51))\n ((:tag . "JJ") (:stem . "rate-limiting") (:form . "rate-limiting")\n  (:end . 71) (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 78)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 86) (:start . 82)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 95) (:start . 91)\n  (:id . 57))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 105)\n  (:start . 96) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 115)\n  (:start . 109) (:id . 60))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 118) (:start . 116)\n  (:id . 61))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 123) (:start . 119)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x3.241.1) (:span 9 14)))\n (:hscopes ((:id . :x3.241.1) (:span 9 123)))\n (:identifiers (:sid . :s3.241) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500814@unknown@formal@none@1@S@In contrast to glia, coactivation of EGFR-Ras and PI3K in neuroblasts, which are fly neural stem cells, does not promote unchecked proliferation, despite the fact that neuroblasts express dMyc and are capable of undergoing neoplastic transformation in response to other genetic mutations [21].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "coactivation") (:form . "coactivation") (:end . 33)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "NNP") (:stem . 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"21") (:end . 291) (:start . 289)\n  (:id . 89))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 292) (:start . 291)\n  (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 293) (:start . 292)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s3.242) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500815@unknown@formal@none@1@S@Thus, in Drosophila, neither a neural stem cell fate nor Myc activity confer competence to undergo EGFR-PI3K neoplastic transformation.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 19)\n  (:start . 9) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "CC") (:stem . "neither") (:form . "neither") (:end . 28)\n  (:start . 21) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 37)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "stem") (:form . "stem") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "fate") (:form . "fate") (:end . 52) (:start . 48)\n  (:id . 52))\n ((:tag . "CC") (:stem . "nor") (:form . "nor") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "myc") (:form . "Myc") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 69)\n  (:start . 61) (:id . 55))\n ((:tag . "VBP") (:stem . "confer") (:form . "confer") (:end . 76)\n  (:start . 70) (:id . 56))\n ((:tag . "NN") (:stem . "competence") (:form . "competence") (:end . 87)\n  (:start . 77) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "VB") (:stem . "undergo") (:form . "undergo") (:end . 98)\n  (:start . 91) (:id . 59))\n ((:tag . "NNP") (:stem . "EGFR-PI3K") (:form . "EGFR-PI3K") (:end . 108)\n  (:start . 99) (:id . 60))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 119)\n  (:start . 109) (:id . 61))\n ((:tag . "NN") (:stem . "transformation") (:form . "transformation")\n  (:end . 134) (:start . 120) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.243) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500816@unknown@formal@none@1@S@Rather, our results suggest that neoplastic cells arise from committed glial progenitors: dEGFR-dRas85D;dPTEN-/- clones derived from progenitor cells produce large tumors, and anaplastic cells in repo>dEGFRλ;dp110CAAX brains are concentrated in regions enriched for glial progenitors.@(((:tag . "RB") (:stem . "rather") (:form . "Rather") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "arise") (:form . "arise") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "commit") (:form . "committed") (:end . 70)\n  (:start . 61) (:id . 52))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 76) (:start . 71)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 88)\n  (:start . 77) (:id . 54))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "dEGFR-dRas85D;dPTEN-/-")\n  (:form . "dEGFR-dRas85D;dPTEN-/-") (:end . 112) (:start . 90) (:id . 56))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 119)\n  (:start . 113) (:id . 57))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 127)\n  (:start . 120) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 132) (:start . 128)\n  (:id . 59))\n ((:tag . "NN") (:stem . "progenitor") (:form . "progenitor") (:end . 143)\n  (:start . 133) (:id . 60))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 149)\n  (:start . 144) (:id . 61))\n ((:tag . "VBP") (:stem . "produce") (:form . "produce") (:end . 157)\n  (:start . 150) (:id . 62))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 163)\n  (:start . 158) (:id . 63))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 170)\n  (:start . 164) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "anaplastic") (:form . "anaplastic") (:end . 186)\n  (:start . 176) (:id . 67))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 192)\n  (:start . 187) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 195) (:start . 193)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 217) (:start . 196) (:id . 70))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 224)\n  (:start . 218) (:id . 71))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 228) (:start . 225)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "concentrate") (:form . "concentrated") (:end . 241)\n  (:start . 229) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 244) (:start . 242)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 252)\n  (:start . 245) (:id . 75))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 261)\n  (:start . 253) (:id . 76))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 265) (:start . 262)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 271)\n  (:start . 266) (:id . 78))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 283)\n  (:start . 272) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 284) (:start . 283)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x3.244.1) (:span 20 27)))\n (:hscopes ((:id . :x3.244.1) (:span 20 283)))\n (:identifiers (:sid . :s3.244) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500817@unknown@formal@none@1@S@Notably, regulated developmental signaling through the EGFR pathway promotes proliferation of normal Repo-expressing glial progenitors [27], and our results show that constitutive EGFR and PI3K signaling prolongs this proliferative progenitor state.@(((:tag . "RB") (:stem . "notably") (:form . "Notably") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 32) (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 42)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 50)\n  (:start . 43) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 59) (:start . 55)\n  (:id . 49))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 67)\n  (:start . 60) (:id . 50))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 76)\n  (:start . 68) (:id . 51))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 90) (:start . 77) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 100)\n  (:start . 94) (:id . 54))\n ((:tag . "JJ") (:stem . "repo-expressing") (:form . "Repo-expressing")\n  (:end . 116) (:start . 101) (:id . 55))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 122)\n  (:start . 117) (:id . 56))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 134)\n  (:start . 123) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 136) (:start . 135)\n  (:id . 58))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 138) (:start . 136)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 139) (:start . 138)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 148) (:start . 145)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 156)\n  (:start . 149) (:id . 64))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 161) (:start . 157)\n  (:id . 65))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 166) (:start . 162)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 179)\n  (:start . 167) (:id . 67))\n ((:tag . "NN") (:stem . "egfr") (:form . "EGFR") (:end . 184) (:start . 180)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 188) (:start . 185)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 193) (:start . 189)\n  (:id . 70))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 203)\n  (:start . 194) (:id . 71))\n ((:tag . "VBZ") (:stem . "prolong") (:form . "prolongs") (:end . 212)\n  (:start . 204) (:id . 72))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 217) (:start . 213)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "proliferative") (:form . "proliferative")\n  (:end . 231) (:start . 218) (:id . 74))\n ((:tag . "NN") (:stem . "progenitor") (:form . "progenitor") (:end . 242)\n  (:start . 232) (:id . 75))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 248)\n  (:start . 243) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 249) (:start . 248)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s3.245) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500818@unknown@formal@none@1@S@Further studies of Drosophila glial progenitors and glioma-like cells may illuminate the cellular origins of human gliomas, which are thought to arise from progenitor-like glial cells.@(((:tag . "JJ") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 47)\n  (:start . 36) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "glioma-like") (:form . "glioma-like") (:end . 63)\n  (:start . 52) (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 69) (:start . 64)\n  (:id . 50))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 73) (:start . 70)\n  (:id . 51))\n ((:tag . "VB") (:stem . "illuminate") (:form . "illuminate") (:end . 84)\n  (:start . 74) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 97)\n  (:start . 89) (:id . 54))\n ((:tag . "NNS") (:stem . "origin") (:form . "origins") (:end . 105)\n  (:start . 98) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 114)\n  (:start . 109) (:id . 57))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 122)\n  (:start . 115) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 129)\n  (:start . 124) (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 133) (:start . 130)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 141)\n  (:start . 134) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 144) (:start . 142)\n  (:id . 63))\n ((:tag . "VB") (:stem . "arise") (:form . "arise") (:end . 150)\n  (:start . 145) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 155) (:start . 151)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "progenitor-like") (:form . "progenitor-like")\n  (:end . 171) (:start . 156) (:id . 66))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 177)\n  (:start . 172) (:id . 67))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 183)\n  (:start . 178) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x3.246.1) (:span 134 141)) ((:id . :x3.246.2) (:span 70 73)))\n (:hscopes ((:id . :x3.246.1) (:span 124 183))\n  ((:id . :x3.246.2) (:span 70 183)))\n (:identifiers (:sid . :s3.246) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500819@unknown@formal@none@1@S@Moreover, our results argue that cell-type specific factors govern glial neoplasia.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "VBP") (:stem . "argue") (:form . "argue") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "cell-type") (:form . "cell-type") (:end . 42)\n  (:start . 33) (:id . 48))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . "VBP") (:stem . "govern") (:form . "govern") (:end . 66)\n  (:start . 60) (:id . 51))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 54)))@@@1@13@((:hcues ((:id . :x3.247.1) (:span 22 27)))\n (:hscopes ((:id . :x3.247.1) (:span 22 82)))\n (:identifiers (:sid . :s3.247) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500820@unknown@formal@none@1@S@One such factor may be Dap, the single p21/p27 ortholog, which is normally expressed in only 5% of all glia (Figure S4).@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 38)\n  (:start . 32) (:id . 50))\n ((:tag . "NN") (:stem . "p21/p27") (:form . "p21/p27") (:end . 46)\n  (:start . 39) (:id . 51))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 55)\n  (:start . 47) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 62) (:start . 57)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 74)\n  (:start . 66) (:id . 56))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 84)\n  (:start . 75) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 92) (:start . 88)\n  (:id . 59))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 94) (:start . 93)\n  (:id . 60))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 95) (:start . 94)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 62))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 102) (:start . 99)\n  (:id . 63))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 107) (:start . 103)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 115)\n  (:start . 109) (:id . 66))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 118) (:start . 116)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x3.248.1) (:span 16 19)))\n (:hscopes ((:id . :x3.248.1) (:span 16 55)))\n (:identifiers (:sid . :s3.248) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500821@unknown@formal@none@1@S@Perhaps glial progenitors do not express Dap, whereas neuronal progenitors do [26], and this underlies susceptibility to transformation by EGFR-Ras and PI3K.@(((:tag . "RB") (:stem . "perhaps") (:form . "Perhaps") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "VB") (:stem . "express") (:form . "express") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 74)\n  (:start . 63) (:id . 52))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 92) (:start . 88)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "underlie") (:form . "underlies") (:end . 102)\n  (:start . 93) (:id . 60))\n ((:tag . "NN") (:stem . "susceptibility") (:form . "susceptibility")\n  (:end . 117) (:start . 103) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 120) (:start . 118)\n  (:id . 62))\n ((:tag . "NN") (:stem . "transformation") (:form . "transformation")\n  (:end . 135) (:start . 121) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 138) (:start . 136)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 147)\n  (:start . 139) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 151) (:start . 148)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 156) (:start . 152)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x3.249.1) (:span 0 7)))\n (:hscopes ((:id . :x3.249.1) (:span 0 156)))\n (:identifiers (:sid . :s3.249) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500822@unknown@formal@none@1@S@Dap is highly regulated in a cell-type specific manner [26], and studies of Dap regulation in glia may further illuminate the genetic origins of glioma, especially given that lack of p21 expression may underlie the tumorigenic response of mammalian glial progenitors to constitutively active EGFR [65].@(((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "cell-type") (:form . "cell-type") (:end . 38)\n  (:start . 29) (:id . 48))\n ((:tag . 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5500823@unknown@formal@none@1@S@While EGFR-Ras and PI3K are commonly upregulated in gliomas and experimental models demonstrate that these pathways are required for tumorigenesis, therapies that target EGFR and PI3K signaling have proven disappointing.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "VBN") (:stem . "upregulate") (:form . "upregulated") (:end . 48)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 76)\n  (:start . 64) (:id . 52))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 83)\n  (:start . 77) (:id . 53))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 95)\n  (:start . 84) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 100) (:start . 96)\n  (:id . 55))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 106)\n  (:start . 101) (:id . 56))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 115)\n  (:start . 107) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 119) (:start . 116)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 128)\n  (:start . 120) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 132) (:start . 129)\n  (:id . 60))\n ((:tag . "NN") (:stem . "tumorigenesis") (:form . "tumorigenesis")\n  (:end . 146) (:start . 133) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "therapy") (:form . "therapies") (:end . 157)\n  (:start . 148) (:id . 63))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 162) (:start . 158)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "target") (:form . "target") (:end . 169)\n  (:start . 163) (:id . 65))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 174) (:start . 170)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 178) (:start . 175)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 183) (:start . 179)\n  (:id . 68))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 193)\n  (:start . 184) (:id . 69))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 198) (:start . 194)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "prove") (:form . "proven") (:end . 205)\n  (:start . 199) (:id . 71))\n ((:tag . "JJ") (:stem . "disappointing") (:form . "disappointing")\n  (:end . 219) (:start . 206) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s3.251) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500824@unknown@formal@none@1@S@This discrepancy between clinical and experimental data has many possible explanations.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "discrepancy") (:form . "discrepancy") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 50)\n  (:start . 38) (:id . 47))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 55) (:start . 51)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 59) (:start . 56)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 64) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 73)\n  (:start . 65) (:id . 51))\n ((:tag . "NNS") (:stem . "explanation") (:form . "explanations") (:end . 86)\n  (:start . 74) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s3.252) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500825@unknown@formal@none@1@S@For example, recent studies have demonstrated that EGFR inhibitors are attenuated by particular mutations found in glioma cells, such as PTEN loss or RTK co-amplification [2].@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "demonstrate") (:form . "demonstrated") (:end . 45)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "inhibitor") (:form . "inhibitors") (:end . 66)\n  (:start . 56) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "attenuate") (:form . "attenuated") (:end . 81)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 95)\n  (:start . 85) (:id . 55))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 105)\n  (:start . 96) (:id . 56))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 111)\n  (:start . 106) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 58))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 121)\n  (:start . 115) (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 127)\n  (:start . 122) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 133) (:start . 129)\n  (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 136) (:start . 134)\n  (:id . 63))\n ((:tag . "NN") (:stem . "pten") (:form . "PTEN") (:end . 141) (:start . 137)\n  (:id . 64))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 146) (:start . 142)\n  (:id . 65))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 149) (:start . 147)\n  (:id . 66))\n ((:tag . "NN") (:stem . "rtk") (:form . "RTK") (:end . 153) (:start . 150)\n  (:id . 67))\n ((:tag . "NN") (:stem . "co-amplification") (:form . "co-amplification")\n  (:end . 170) (:start . 154) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 172) (:start . 171)\n  (:id . 69))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 173) (:start . 172)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 174) (:start . 173)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.253) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500826@unknown@formal@none@1@S@Addressing these and other possibilities remains a challenge that dictates a need for new experimental models.@(((:tag . "VBG") (:stem . "address") (:form . "Addressing") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 16) (:start . 11)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "possibility") (:form . "possibilities") (:end . 40)\n  (:start . 27) (:id . 46))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 48)\n  (:start . 41) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n  (:id . 48))\n ((:tag . "NN") (:stem . "challenge") (:form . "challenge") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 65) (:start . 61)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "dictate") (:form . "dictates") (:end . 74)\n  (:start . 66) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 76) (:start . 75)\n  (:id . 52))\n ((:tag . "NN") (:stem . "need") (:form . "need") (:end . 81) (:start . 77)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 89) (:start . 86)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 102)\n  (:start . 90) (:id . 56))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 109)\n  (:start . 103) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.254) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500827@unknown@formal@none@1@S@The results presented here establish Drosophila as a viable model system for the study of glioma, offering a complex organismal system for rapidly identifying and evaluating therapeutic targets using genetic approaches.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "FW") (:stem . "establish") (:form . "establish") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 47)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 72)\n  (:start . 66) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 86) (:start . 81)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "glioma") (:form . "glioma") (:end . 96)\n  (:start . 90) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "offer") (:form . "offering") (:end . 106)\n  (:start . 98) (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 116)\n  (:start . 109) (:id . 61))\n ((:tag . "JJ") (:stem . "organismal") (:form . "organismal") (:end . 127)\n  (:start . 117) (:id . 62))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 134)\n  (:start . 128) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 138) (:start . 135)\n  (:id . 64))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 146)\n  (:start . 139) (:id . 65))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 158)\n  (:start . 147) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "evaluate") (:form . "evaluating") (:end . 173)\n  (:start . 163) (:id . 68))\n ((:tag . "JJ") (:stem . "therapeutic") (:form . "therapeutic") (:end . 185)\n  (:start . 174) (:id . 69))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 193)\n  (:start . 186) (:id . 70))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 199) (:start . 194)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 207)\n  (:start . 200) (:id . 72))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 218)\n  (:start . 208) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.255) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500828@unknown@formal@none@1@S@Such a system may be especially useful for distinguishing those genetic mutations and pathways that drive tumorigenesis from the large number of genes that show mutations and altered expression in glioblastomas uncovered by recent genomic analyses of patient samples [66],[67].@(((:tag . "PDT") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "RB") (:stem . "especially") (:form . "especially") (:end . 31)\n  (:start . 21) (:id . 47))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "distinguish") (:form . "distinguishing")\n  (:end . 57) (:start . 43) (:id . 50))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 81)\n  (:start . 72) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 94)\n  (:start . 86) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "drive") (:form . "drive") (:end . 105)\n  (:start . 100) (:id . 57))\n ((:tag . "NN") (:stem . "tumorigenesis") (:form . "tumorigenesis")\n  (:end . 119) (:start . 106) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 124) (:start . 120)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 134)\n  (:start . 129) (:id . 61))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 141)\n  (:start . 135) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 150)\n  (:start . 145) (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 155) (:start . 151)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 160) (:start . 156)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 170)\n  (:start . 161) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 174) (:start . 171)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "altered") (:form . "altered") (:end . 182)\n  (:start . 175) (:id . 69))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 193)\n  (:start . 183) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 196) (:start . 194)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "glioblastoma") (:form . "glioblastomas")\n  (:end . 210) (:start . 197) (:id . 72))\n ((:tag . "VBN") (:stem . "uncover") (:form . "uncovered") (:end . 220)\n  (:start . 211) (:id . 73))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 223) (:start . 221)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 230)\n  (:start . 224) (:id . 75))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 238)\n  (:start . 231) (:id . 76))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 247)\n  (:start . 239) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 250) (:start . 248)\n  (:id . 78))\n ((:tag . "NN") (:stem . "patient") (:form . "patient") (:end . 258)\n  (:start . 251) (:id . 79))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 266)\n  (:start . 259) (:id . 80))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 268) (:start . 267)\n  (:id . 81))\n ((:tag . "CD") (:stem . "66],[67") (:form . "66],[67") (:end . 275)\n  (:start . 268) (:id . 82))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 276) (:start . 275)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 277) (:start . 276)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x3.256.1) (:span 14 17)))\n (:hscopes ((:id . :x3.256.1) (:span 14 266)))\n (:identifiers (:sid . :s3.256) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500829@unknown@formal@none@1@S@Our studies have already identified key rate-limiting genes, such as dCyclinE, Stg, and dMyc, and genes only required for abnormal neoplastic glial proliferation, such as dSin1, dRictor, and dCdk4, which may represent important therapeutic targets in human gliomas.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "rate-limiting") (:form . "rate-limiting")\n  (:end . 53) (:start . 40) (:id . 48))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 59) (:start . 54)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "dCyclinE") (:form . "dCyclinE") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Stg") (:form . "Stg") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 103) (:start . 98)\n  (:id . 61))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 117)\n  (:start . 109) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 121) (:start . 118)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 130)\n  (:start . 122) (:id . 65))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 141)\n  (:start . 131) (:id . 66))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 147)\n  (:start . 142) (:id . 67))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 161) (:start . 148) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 167) (:start . 163)\n  (:id . 70))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 170) (:start . 168)\n  (:id . 71))\n ((:tag . "NN") (:stem . "dsin1") (:form . "dSin1") (:end . 176)\n  (:start . 171) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 73))\n ((:tag . "NN") (:stem . "drictor") (:form . "dRictor") (:end . 185)\n  (:start . 178) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 186) (:start . 185)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 190) (:start . 187)\n  (:id . 76))\n ((:tag . "NN") (:stem . "dcdk4") (:form . "dCdk4") (:end . 196)\n  (:start . 191) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 78))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 203)\n  (:start . 198) (:id . 79))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 207) (:start . 204)\n  (:id . 80))\n ((:tag . "VB") (:stem . "represent") (:form . "represent") (:end . 217)\n  (:start . 208) (:id . 81))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 227)\n  (:start . 218) (:id . 82))\n ((:tag . "JJ") (:stem . "therapeutic") (:form . "therapeutic") (:end . 239)\n  (:start . 228) (:id . 83))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 247)\n  (:start . 240) (:id . 84))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 250) (:start . 248)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 256)\n  (:start . 251) (:id . 86))\n ((:tag . "NNS") (:stem . "glioma") (:form . "gliomas") (:end . 264)\n  (:start . 257) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 88)))@@@1@47@((:hcues ((:id . :x3.257.1) (:span 204 207)))\n (:hscopes ((:id . :x3.257.1) (:span 204 264)))\n (:identifiers (:sid . :s3.257) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500830@unknown@formal@none@1@S@Materials and Methods@(((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 21)\n  (:start . 14) (:id . 44)))@@@1@3@((:identifiers (:sid . :s3.258) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500831@unknown@formal@none@1@S@Fly Stocks, Genetics, and Culture Conditions@(((:tag . "NNP") (:stem . "Fly") (:form . "Fly") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Stocks") (:form . "Stocks") (:end . 10)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Genetics") (:form . "Genetics") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Culture") (:form . "Culture") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "NNPS") (:stem . "Condition") (:form . "Conditions") (:end . 44)\n  (:start . 34) (:id . 49)))@@@1@8@((:identifiers (:sid . :s3.259) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500832@unknown@formal@none@1@S@Flies were cultured at 25°C.@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "25°c") (:form . "25°C") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 28) (:start . 27)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s3.260) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500833@unknown@formal@none@1@S@All genotypes were established by standard genetics.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "establish") (:form . "established") (:end . 30)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "NNS") (:stem . "genetic") (:form . "genetics") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 52) (:start . 51)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s3.261) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500834@unknown@formal@none@1@S@To assess larval brain overgrowth phenotypes, embryos were collected for 6–24 hrs, grown for 120–140 hrs, and wandering 3rd instar larvae were selected for dissection.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 33)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 44)\n  (:start . 34) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 68)\n  (:start . 59) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "CD") (:stem . "6–24") (:form . "6–24") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "hr") (:form . "hrs") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "grow") (:form . "grown") (:end . 88) (:start . 83)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 92) (:start . 89)\n  (:id . 57))\n ((:tag . "CD") (:stem . "120–140") (:form . "120–140") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "hr") (:form . "hrs") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "wander") (:form . "wandering") (:end . 119)\n  (:start . 110) (:id . 62))\n ((:tag . "CD") (:stem . "3rd") (:form . "3rd") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 130)\n  (:start . 124) (:id . 64))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 137)\n  (:start . 131) (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 142) (:start . 138)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 151)\n  (:start . 143) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 155) (:start . 152)\n  (:id . 68))\n ((:tag . "NN") (:stem . "dissection") (:form . "dissection") (:end . 166)\n  (:start . 156) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.262) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500835@unknown@formal@none@1@S@Stocks were obtained from the Bloomington Stock Center unless otherwise noted.@(((:tag . "NNS") (:stem . "stock") (:form . "Stocks") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Bloomington") (:form . "Bloomington") (:end . 41)\n  (:start . 30) (:id . 47))\n ((:tag . "NNP") (:stem . "Stock") (:form . "Stock") (:end . 47) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Center") (:form . "Center") (:end . 54)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "unless") (:form . "unless") (:end . 61)\n  (:start . 55) (:id . 50))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 71)\n  (:start . 62) (:id . 51))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 77) (:start . 72)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s3.263) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500836@unknown@formal@none@1@S@Other than UAS-PTENdsRNA lines from Bloomington, all UAS-dsRNA lines were obtained from the VDRC stock center [11].@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "UAS-PTENdsRNA") (:form . "UAS-PTENdsRNA")\n  (:end . 24) (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 30) (:start . 25)\n  (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Bloomington") (:form . "Bloomington") (:end . 47)\n  (:start . 36) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "UAS-dsRNA") (:form . "UAS-dsRNA") (:end . 62)\n  (:start . 53) (:id . 50))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 68) (:start . 63)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 82)\n  (:start . 74) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 87) (:start . 83)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "VDRC") (:form . "VDRC") (:end . 96) (:start . 92)\n  (:id . 56))\n ((:tag . "NN") (:stem . "stock") (:form . "stock") (:end . 102) (:start . 97)\n  (:id . 57))\n ((:tag . "NN") (:stem . "center") (:form . "center") (:end . 109)\n  (:start . 103) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 111) (:start . 110)\n  (:id . 59))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.264) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500837@unknown@formal@none@1@S@The following stocks were obtained from other investigators: UAS-dEGFRλ ( T. Schubach), UAS-dEGFRElp, UAS-dEGFRwild-type (N. Baker), UAS-dPTEN, FRT40A dPTEN2L117, UAS-dFoxOSA (S. Oldham), UAS-dap (I. Hariharan), UAS-dp110wild-type, UAS-dCycD, UAS-dCdk4, UAS-dMyc, dMyc4 (B. Edgar), UAS-Rbf1 (N. Dyson), appl-Gal4 (K. Finley), pros-Gal4 (B. Ohlstein), wor-Gal4 (C. Doe), gcm-Gal4 (V. Hartenstein), dTor2L7, dTorl(2)k17004 (R. Bodmer), dRictorΔ2 (S. Cohen), and stgCB03726 (A. Spradling)@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "stock") (:form . "stocks") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "investigator") (:form . "investigators")\n  (:end . 59) (:start . 46) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 60) (:start . 59)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "UAS-dEGFRλ") (:form . "UAS-dEGFRλ") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "T.") (:form . "T.") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Schubach") (:form . "Schubach") (:end . 85)\n  (:start . 77) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "UAS-dEGFRElp") (:form . "UAS-dEGFRElp")\n  (:end . 100) (:start . 88) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "uas-degfrwild-type") (:form . "UAS-dEGFRwild-type")\n  (:end . 120) (:start . 102) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "N.") (:form . "N.") (:end . 124) (:start . 122)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Baker") (:form . "Baker") (:end . 130)\n  (:start . 125) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "UAS-dPTEN") (:form . "UAS-dPTEN") (:end . 142)\n  (:start . 133) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "FRT40A") (:form . "FRT40A") (:end . 150)\n  (:start . 144) (:id . 67))\n ((:tag . "NN") (:stem . "dpten2l117") (:form . "dPTEN2L117") (:end . 161)\n  (:start . 151) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "UAS-dFoxOSA") (:form . "UAS-dFoxOSA") (:end . 174)\n  (:start . 163) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "S.") (:form . "S.") (:end . 178) (:start . 176)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Oldham") (:form . "Oldham") (:end . 185)\n  (:start . 179) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 186) (:start . 185)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 187) (:start . 186)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "UAS-dap") (:form . "UAS-dap") (:end . 195)\n  (:start . 188) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 197) (:start . 196)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 199) (:start . 197)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Hariharan") (:form . "Hariharan") (:end . 209)\n  (:start . 200) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 211) (:start . 210)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "UAS-dp110wild-type") (:form . "UAS-dp110wild-type")\n  (:end . 230) (:start . 212) (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 231) (:start . 230)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "UAS-dCycD") (:form . "UAS-dCycD") (:end . 241)\n  (:start . 232) (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 242) (:start . 241)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "UAS-dCdk4") (:form . "UAS-dCdk4") (:end . 252)\n  (:start . 243) (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 253) (:start . 252)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "UAS-dMyc") (:form . "UAS-dMyc") (:end . 262)\n  (:start . 254) (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 263) (:start . 262)\n  (:id . 89))\n ((:tag . "NN") (:stem . "dmyc4") (:form . "dMyc4") (:end . 269)\n  (:start . 264) (:id . 90))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 271) (:start . 270)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "B.") (:form . "B.") (:end . 273) (:start . 271)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "Edgar") (:form . "Edgar") (:end . 279)\n  (:start . 274) (:id . 93))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 280) (:start . 279)\n  (:id . 94))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 281) (:start . 280)\n  (:id . 95))\n ((:tag . "NNP") (:stem . "UAS-Rbf1") (:form . "UAS-Rbf1") (:end . 290)\n  (:start . 282) (:id . 96))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 292) (:start . 291)\n  (:id . 97))\n ((:tag . "NNP") (:stem . "N.") (:form . "N.") (:end . 294) (:start . 292)\n  (:id . 98))\n ((:tag . "NNP") (:stem . "Dyson") (:form . "Dyson") (:end . 300)\n  (:start . 295) (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 301) (:start . 300)\n  (:id . 100))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 302) (:start . 301)\n  (:id . 101))\n ((:tag . "NN") (:stem . "appl-gal4") (:form . "appl-Gal4") (:end . 312)\n  (:start . 303) (:id . 102))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 314) (:start . 313)\n  (:id . 103))\n ((:tag . "NNP") (:stem . "K.") (:form . "K.") (:end . 316) (:start . 314)\n  (:id . 104))\n ((:tag . "NNP") (:stem . "Finley") (:form . "Finley") (:end . 323)\n  (:start . 317) (:id . 105))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 324) (:start . 323)\n  (:id . 106))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 325) (:start . 324)\n  (:id . 107))\n ((:tag . "NN") (:stem . "pros-gal4") (:form . "pros-Gal4") (:end . 335)\n  (:start . 326) (:id . 108))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 337) (:start . 336)\n  (:id . 109))\n ((:tag . "NNP") (:stem . "B.") (:form . "B.") (:end . 339) (:start . 337)\n  (:id . 110))\n ((:tag . "NNP") (:stem . "Ohlstein") (:form . "Ohlstein") (:end . 348)\n  (:start . 340) (:id . 111))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 349) (:start . 348)\n  (:id . 112))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 350) (:start . 349)\n  (:id . 113))\n ((:tag . "NN") (:stem . "wor-gal4") (:form . "wor-Gal4") (:end . 359)\n  (:start . 351) (:id . 114))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 361) (:start . 360)\n  (:id . 115))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 363) (:start . 361)\n  (:id . 116))\n ((:tag . "NNP") (:stem . "Doe") (:form . "Doe") (:end . 367) (:start . 364)\n  (:id . 117))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 368) (:start . 367)\n  (:id . 118))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 369) (:start . 368)\n  (:id . 119))\n ((:tag . "NN") (:stem . "gcm-gal4") (:form . "gcm-Gal4") (:end . 378)\n  (:start . 370) (:id . 120))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 380) (:start . 379)\n  (:id . 121))\n ((:tag . "NNP") (:stem . "V.") (:form . "V.") (:end . 382) (:start . 380)\n  (:id . 122))\n ((:tag . "NNP") (:stem . "Hartenstein") (:form . "Hartenstein") (:end . 394)\n  (:start . 383) (:id . 123))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 395) (:start . 394)\n  (:id . 124))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 396) (:start . 395)\n  (:id . 125))\n ((:tag . "NN") (:stem . "dtor2l7") (:form . "dTor2L7") (:end . 404)\n  (:start . 397) (:id . 126))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 405) (:start . 404)\n  (:id . 127))\n ((:tag . "CD") (:stem . "dTorl(2)k17004") (:form . "dTorl(2)k17004")\n  (:end . 420) (:start . 406) (:id . 128))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 422) (:start . 421)\n  (:id . 129))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 424) (:start . 422)\n  (:id . 130))\n ((:tag . "NNP") (:stem . "Bodmer") (:form . "Bodmer") (:end . 431)\n  (:start . 425) (:id . 131))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 432) (:start . 431)\n  (:id . 132))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 433) (:start . 432)\n  (:id . 133))\n ((:tag . "NN") (:stem . "drictorδ2") (:form . "dRictorΔ2") (:end . 443)\n  (:start . 434) (:id . 134))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 445) (:start . 444)\n  (:id . 135))\n ((:tag . "NNP") (:stem . "S.") (:form . "S.") (:end . 447) (:start . 445)\n  (:id . 136))\n ((:tag . "NNP") (:stem . "Cohen") (:form . "Cohen") (:end . 453)\n  (:start . 448) (:id . 137))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 454) (:start . 453)\n  (:id . 138))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 455) (:start . 454)\n  (:id . 139))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 459) (:start . 456)\n  (:id . 140))\n ((:tag . "NN") (:stem . "stgcb03726") (:form . "stgCB03726") (:end . 470)\n  (:start . 460) (:id . 141))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 472) (:start . 471)\n  (:id . 142))\n ((:tag . "NNP") (:stem . "A.") (:form . "A.") (:end . 474) (:start . 472)\n  (:id . 143))\n ((:tag . "NNP") (:stem . "Spradling") (:form . "Spradling") (:end . 484)\n  (:start . 475) (:id . 144))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 485) (:start . 484)\n  (:id . 145)))@@@1@104@((:identifiers (:sid . :s3.265) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500838@unknown@formal@none@1@S@UAS-dsRNA Validation@(((:tag . "NNP") (:stem . "UAS-dsRNA") (:form . "UAS-dsRNA") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "validation") (:form . "Validation") (:end . 20)\n  (:start . 10) (:id . 43)))@@@1@2@((:identifiers (:sid . :s3.266) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500839@unknown@formal@none@1@S@UAS-dMycdsRNA, UAS-TSC1dsRNA lines were validated in prior publications [48].@(((:tag . "NNP") (:stem . "UAS-dMycdsRNA") (:form . "UAS-dMycdsRNA")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "UAS-TSC1dsRNA") (:form . "UAS-TSC1dsRNA")\n  (:end . 28) (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 34) (:start . 29)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "validate") (:form . "validated") (:end . 49)\n  (:start . 40) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 58) (:start . 53)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "publication") (:form . "publications") (:end . 71)\n  (:start . 59) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 73) (:start . 72)\n  (:id . 51))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 75) (:start . 73)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.267) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500840@unknown@formal@none@1@S@UAS-dsRNA lines were crossed to actin-Gal4, ey-Gal4, and GMR-Gal4 to assess phenotypes.@(((:tag . "NNP") (:stem . "UAS-dsRNA") (:form . "UAS-dsRNA") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "cross") (:form . "crossed") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "actin-gal4") (:form . "actin-Gal4") (:end . 42)\n  (:start . 32) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "ey-gal4") (:form . "ey-Gal4") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gmr-gal4") (:form . "GMR-Gal4") (:end . 65)\n  (:start . 57) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 75)\n  (:start . 69) (:id . 54))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 86)\n  (:start . 76) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.268) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500841@unknown@formal@none@1@S@Lines that showed phenotypes inconsistent with known phenotypes for their target genes were excluded from analysis.@(((:tag . "NNP") (:stem . "Line") (:form . "Lines") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 17) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "inconsistent") (:form . "inconsistent") (:end . 41)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 52) (:start . 47)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 63)\n  (:start . 53) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 67) (:start . 64)\n  (:id . 50))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 73)\n  (:start . 68) (:id . 51))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 80)\n  (:start . 74) (:id . 52))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 86) (:start . 81)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 91) (:start . 87)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 100)\n  (:start . 92) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 105) (:start . 101)\n  (:id . 56))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 114)\n  (:start . 106) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.269) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500842@unknown@formal@none@1@S@Gene knock-down in repo-Gal4 glia was verified with immunohistochemical stains for the following constructs: UAS-dMycdsRNA, UAS-dAktdsRNA, UAS-dS6KdsRNA, UAS-eIF4EdsRNA, UAS-Rbf1dsRNA, and UAS-pntdsRNA (Figure S11).@(((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "knock-down") (:form . "knock-down") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 51) (:start . 47)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "immunohistochemical")\n  (:form . "immunohistochemical") (:end . 71) (:start . 52) (:id . 50))\n ((:tag . "NNS") (:stem . "stain") (:form . "stains") (:end . 78)\n  (:start . 72) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 82) (:start . 79)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 96)\n  (:start . 87) (:id . 54))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 107)\n  (:start . 97) (:id . 55))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 108) (:start . 107)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "UAS-dMycdsRNA") (:form . "UAS-dMycdsRNA")\n  (:end . 122) (:start . 109) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "UAS-dAktdsRNA") (:form . "UAS-dAktdsRNA")\n  (:end . 137) (:start . 124) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "UAS-dS6KdsRNA") (:form . "UAS-dS6KdsRNA")\n  (:end . 152) (:start . 139) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "UAS-eIF4EdsRNA") (:form . "UAS-eIF4EdsRNA")\n  (:end . 168) (:start . 154) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "UAS-Rbf1dsRNA") (:form . "UAS-Rbf1dsRNA")\n  (:end . 183) (:start . 170) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 188) (:start . 185)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "UAS-pntdsRNA") (:form . "UAS-pntdsRNA")\n  (:end . 201) (:start . 189) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 203) (:start . 202)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 209)\n  (:start . 203) (:id . 70))\n ((:tag . "NNP") (:stem . "S11") (:form . "S11") (:end . 213) (:start . 210)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s3.270) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500843@unknown@formal@none@1@S@Abdominal Transplants@(((:tag . "JJ") (:stem . "abdominal") (:form . "Abdominal") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNPS") (:stem . "Transplant") (:form . "Transplants") (:end . 21)\n  (:start . 10) (:id . 43)))@@@1@2@((:identifiers (:sid . :s3.271) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500844@unknown@formal@none@1@S@Larval brains were dissected into sterile PBS, washed, and cut into fragments.@(((:tag . "JJ") (:stem . "larval") (:form . "Larval") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 13) (:start . 7)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "dissect") (:form . "dissected") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "sterile") (:form . "sterile") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "NNP") (:stem . "PBS") (:form . "PBS") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "wash") (:form . "washed") (:end . 53) (:start . 47)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "cut") (:form . "cut") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 77)\n  (:start . 68) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.272) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500845@unknown@formal@none@1@S@Abdominal incisions were made in virgin female hosts and single brain fragments were inserted.@(((:tag . "JJ") (:stem . "abdominal") (:form . "Abdominal") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "incision") (:form . "incisions") (:end . 19)\n  (:start . 10) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "virgin") (:form . "virgin") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "JJ") (:stem . "female") (:form . "female") (:end . 46)\n  (:start . 40) (:id . 48))\n ((:tag . "NNS") (:stem . "host") (:form . "hosts") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 63)\n  (:start . 57) (:id . 51))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 79)\n  (:start . 70) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 84) (:start . 80)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 93)\n  (:start . 85) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.273) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500846@unknown@formal@none@1@S@Hosts were cultured for 1–6 weeks, dissected and fixed in 4% paraformaldehyde, incubated in 10% sucrose and embedded in O.C.T. Thick 50 µm sections were stained as described below.@(((:tag . "NNS") (:stem . "host") (:form . "Hosts") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "CD") (:stem . "1–6") (:form . "1–6") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "week") (:form . "weeks") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "dissect") (:form . "dissected") (:end . 44)\n  (:start . 35) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "paraformaldehyde") (:form . "paraformaldehyde")\n  (:end . 77) (:start . 61) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 88)\n  (:start . 79) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 94) (:start . 92)\n  (:id . 59))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "NN") (:stem . "sucrose") (:form . "sucrose") (:end . 103)\n  (:start . 96) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "embed") (:form . "embedded") (:end . 116)\n  (:start . 108) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "O.C.T.") (:form . "O.C.T.") (:end . 126)\n  (:start . 120) (:id . 65))\n ((:tag . "NNP") (:stem . "Thick") (:form . "Thick") (:end . 132)\n  (:start . 127) (:id . 66))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 135) (:start . 133)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 138) (:start . 136)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 147)\n  (:start . 139) (:id . 69))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 152) (:start . 148)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 160)\n  (:start . 153) (:id . 71))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 163) (:start . 161)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 173)\n  (:start . 164) (:id . 73))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 179)\n  (:start . 174) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.274) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500847@unknown@formal@none@1@S@Clonal Analysis@(((:tag . "JJ") (:stem . "clonal") (:form . "Clonal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Analysis") (:form . "Analysis") (:end . 15)\n  (:start . 7) (:id . 43)))@@@1@2@((:identifiers (:sid . :s3.275) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500848@unknown@formal@none@1@S@For hs-FLP clones, genotypes are indicated in figure legends.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "hs-flp") (:form . "hs-FLP") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 42)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "figure") (:form . "figure") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "legend") (:form . "legends") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.276) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500849@unknown@formal@none@1@S@Flies were initially grown at 18°C or 20°C to minimize spontaneous clones, which occurred at a low frequency during late larval-pupal stages.@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "initially") (:form . "initially") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "VBN") (:stem . "grow") (:form . "grown") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "18°c") (:form . "18°C") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "20°c") (:form . "20°C") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "VB") (:stem . "minimize") (:form . "minimize") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . "JJ") (:stem . "spontaneous") (:form . "spontaneous") (:end . 66)\n  (:start . 55) (:id . 52))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 80) (:start . 75)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "occur") (:form . "occurred") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 108)\n  (:start . 99) (:id . 60))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 115)\n  (:start . 109) (:id . 61))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 120) (:start . 116)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "larval-pupal") (:form . "larval-pupal") (:end . 133)\n  (:start . 121) (:id . 63))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 140)\n  (:start . 134) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.277) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500850@unknown@formal@none@1@S@3rd instar larvae, 0–48 hr pupae, or 0–2 day old young adults were treated with heat shock to induce clones and subsequently cultured at 25°C for 1–4 weeks.@(((:tag . "LS") (:stem . "3rd") (:form . "3rd") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "CD") (:stem . "0–48") (:form . "0–48") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "hr") (:form . "hr") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "pupa") (:form . "pupae") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 36) (:start . 34)\n  (:id . 50))\n ((:tag . "CD") (:stem . "0–2") (:form . "0–2") (:end . 40) (:start . 37)\n  (:id . 51))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 44) (:start . 41)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "old") (:form . "old") (:end . 48) (:start . 45)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "young") (:form . "young") (:end . 54) (:start . 49)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 61)\n  (:start . 55) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 74)\n  (:start . 67) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 79) (:start . 75)\n  (:id . 58))\n ((:tag . "NN") (:stem . "heat") (:form . "heat") (:end . 84) (:start . 80)\n  (:id . 59))\n ((:tag . "NN") (:stem . "shock") (:form . "shock") (:end . 90) (:start . 85)\n  (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 61))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 100)\n  (:start . 94) (:id . 62))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 107)\n  (:start . 101) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 64))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 124)\n  (:start . 112) (:id . 65))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 133)\n  (:start . 125) (:id . 66))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 136) (:start . 134)\n  (:id . 67))\n ((:tag . "NN") (:stem . "25°c") (:form . "25°C") (:end . 141) (:start . 137)\n  (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 145) (:start . 142)\n  (:id . 69))\n ((:tag . "CD") (:stem . "1–4") (:form . "1–4") (:end . 149) (:start . 146)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "week") (:form . "weeks") (:end . 155)\n  (:start . 150) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.278) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500851@unknown@formal@none@1@S@For ey-FLP clones, flies were cultured at 25°C continuously.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "ey-flp") (:form . "ey-FLP") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 38)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "25°c") (:form . "25°C") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "RB") (:stem . "continuously") (:form . "continuously") (:end . 59)\n  (:start . 47) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.279) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500852@unknown@formal@none@1@S@Immunohistochemistry and Imaging@(((:tag . "NNP") (:stem . "Immunohistochemistry")\n  (:form . "Immunohistochemistry") (:end . 20) (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Imaging") (:form . "Imaging") (:end . 32)\n  (:start . 25) (:id . 44)))@@@1@3@((:identifiers (:sid . :s3.280) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5500853@unknown@formal@none@1@S@Larval tissue was fixed for 30–50 minutes in 1×PBS 4% paraformaldehyde.@(((:tag . "JJ") (:stem . "larval") (:form . "Larval") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 13) (:start . 7)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "CD") (:stem . "30–50") (:form . "30–50") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "minute") (:form . "minutes") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "1×PBS") (:form . "1×PBS") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "paraformaldehyde") (:form . "paraformaldehyde")\n  (:end . 70) (:start . 54) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.281) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500854@unknown@formal@none@1@S@Adult brains were fixed for 1–2 hr in 1×PBS 4% paraformaldehyde or in PLP with 2% paraformaldehyde.@(((:tag . "JJ") (:stem . "adult") (:form . "Adult") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "CD") (:stem . "1–2") (:form . "1–2") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "hr") (:form . "hr") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "1×PBS") (:form . "1×PBS") (:end . 43) (:start . 38)\n  (:id . 50))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 46) (:start . 45)\n  (:id . 52))\n ((:tag . "NN") (:stem . "paraformaldehyde") (:form . "paraformaldehyde")\n  (:end . 63) (:start . 47) (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PLP") (:form . "PLP") (:end . 73) (:start . 70)\n  (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 78) (:start . 74)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 81) (:start . 80)\n  (:id . 59))\n ((:tag . "NN") (:stem . "paraformaldehyde") (:form . "paraformaldehyde")\n  (:end . 98) (:start . 82) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.282) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500855@unknown@formal@none@1@S@For BrdU labeling, larvae were cultured in food with 1 mg/ml BrdU for 4–6 hrs, and fixed larval brains were treated with 2 N HCl for 30 minutes followed by DNase for 1 hr.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "BrdU") (:form . "BrdU") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "labeling") (:form . "labeling") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "food") (:form . "food") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mg/ml") (:form . "mg/ml") (:end . 60) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "brdu") (:form . "BrdU") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "CD") (:stem . "4–6") (:form . "4–6") (:end . 73) (:start . 70)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "hr") (:form . "hrs") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 88) (:start . 83)\n  (:id . 60))\n ((:tag . "NN") (:stem . "larval") (:form . "larval") (:end . 95)\n  (:start . 89) (:id . 61))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 102)\n  (:start . 96) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 107) (:start . 103)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 115)\n  (:start . 108) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 120) (:start . 116)\n  (:id . 65))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 122) (:start . 121)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 124) (:start . 123)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "HCl") (:form . "HCl") (:end . 128) (:start . 125)\n  (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 132) (:start . 129)\n  (:id . 69))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 135) (:start . 133)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "minute") (:form . "minutes") (:end . 143)\n  (:start . 136) (:id . 71))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 152)\n  (:start . 144) (:id . 72))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 155) (:start . 153)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "DNase") (:form . "DNase") (:end . 161)\n  (:start . 156) (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 165) (:start . 162)\n  (:id . 75))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 167) (:start . 166)\n  (:id . 76))\n ((:tag . "NN") (:stem . "hr") (:form . "hr") (:end . 170) (:start . 168)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s3.283) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500856@unknown@formal@none@1@S@Stains were performed in 1×PBS 10% BSA with 0.3% Triton-X100 for larval brains and 0.5% Triton-X100 for adult samples.@(((:tag . "NNS") (:stem . "stain") (:form . "Stains") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "1×PBS") (:form . "1×PBS") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "BSA") (:form . "BSA") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 43) (:start . 39)\n  (:id . 50))\n ((:tag . "CD") (:stem . "0.3") (:form . "0.3") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 48) (:start . 47)\n  (:id . 52))\n ((:tag . "NN") (:stem . "triton-x100") (:form . "Triton-X100") (:end . 60)\n  (:start . 49) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 71)\n  (:start . 65) (:id . 55))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 78)\n  (:start . 72) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "CD") (:stem . "0.5") (:form . "0.5") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 87) (:start . 86)\n  (:id . 59))\n ((:tag . "NN") (:stem . "triton-x100") (:form . "Triton-X100") (:end . 99)\n  (:start . 88) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 103) (:start . 100)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 109)\n  (:start . 104) (:id . 62))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 117)\n  (:start . 110) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.284) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500857@unknown@formal@none@1@S@The following antibodies were obtained from the Developmental Studies Hybridoma Bank and diluted 15–110: 8D12 anti-Repo, anti-dMMP1, anti-dCyclinB, anti-Elav, and 40-1a anti-lacZ.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Developmental") (:form . "Developmental")\n  (:end . 61) (:start . 48) (:id . 49))\n ((:tag . "NNPS") (:stem . "Studies") (:form . "Studies") (:end . 69)\n  (:start . 62) (:id . 50))\n ((:tag . "NNP") (:stem . "Hybridoma") (:form . "Hybridoma") (:end . 79)\n  (:start . 70) (:id . 51))\n ((:tag . "NNP") (:stem . "Bank") (:form . "Bank") (:end . 84) (:start . 80)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "dilute") (:form . "diluted") (:end . 96)\n  (:start . 89) (:id . 54))\n ((:tag . "CD") (:stem . "15–110") (:form . "15–110") (:end . 103)\n  (:start . 97) (:id . 55))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 104) (:start . 103)\n  (:id . 56))\n ((:tag . "CD") (:stem . "8d12") (:form . "8D12") (:end . 109) (:start . 105)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "anti-repo") (:form . "anti-Repo") (:end . 119)\n  (:start . 110) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 59))\n ((:tag . "NN") (:stem . "anti-dmmp1") (:form . "anti-dMMP1") (:end . 131)\n  (:start . 121) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "anti-dCyclinB") (:form . "anti-dCyclinB")\n  (:end . 146) (:start . 133) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "anti-Elav") (:form . "anti-Elav") (:end . 157)\n  (:start . 148) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "40-1a") (:form . "40-1a") (:end . 168)\n  (:start . 163) (:id . 67))\n ((:tag . "NN") (:stem . "anti-lacz") (:form . "anti-lacZ") (:end . 178)\n  (:start . 169) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.285) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500858@unknown@formal@none@1@S@Larval and/or adult brains were also stained with rabbit anti-Repo (G. Technau, 1500), rat anti-dCyclinE (H. Richardson, 1100), anti-BrdU (BD, 1100), rat anti-Miranda (C. Doe, 1100), mouse anti-diphospho-Erk (Sigma, 1200), mouse anti-Rbf1 (N. Dyson, 15), mouse anti-Dap (I. Hariharan, 110), rabbit anti-PntP1 (J. Skeath, 1500), rabbit anti-eIF4E (P. Lasko, 1100), rabbit anti-dMyc (D. Stein, 11000), and anti-phospho-MPM2 (Upstate Biotechnology, 1200).@(((:tag . "JJ") (:stem . "larval") (:form . "Larval") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 13) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . 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5500859@unknown@formal@none@1@S@Anti-HRP-Cy5 and anti-HRP-Cy3 (Jackson Labs) were used at 1250–1500.@(((:tag . "NNP") (:stem . "Anti-HRP-Cy5") (:form . "Anti-HRP-Cy5") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "anti-hrp-cy3") (:form . "anti-HRP-Cy3") (:end . 29)\n  (:start . 17) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Jackson") (:form . "Jackson") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . "NNPS") (:stem . "Labs") (:form . "Labs") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1250–1500") (:form . "1250–1500") (:end . 67)\n  (:start . 58) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s3.287) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500860@unknown@formal@none@1@S@Secondary antibodies were conjugated to Cy3 (Jackson Labs) or Alexa-488 or Alexa-647 (Molecular Probes).@(((:tag . "JJ") (:stem . "secondary") (:form . "Secondary") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 20)\n  (:start . 10) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 25) (:start . 21)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "conjugate") (:form . "conjugated") (:end . 36)\n  (:start . 26) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Cy3") (:form . "Cy3") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Jackson") (:form . "Jackson") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "NNPS") (:stem . "Labs") (:form . "Labs") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Alexa-488") (:form . "Alexa-488") (:end . 71)\n  (:start . 62) (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Alexa-647") (:form . "Alexa-647") (:end . 84)\n  (:start . 75) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "molecular") (:form . "Molecular") (:end . 95)\n  (:start . 86) (:id . 57))\n ((:tag . "NNP") (:stem . "Probe") (:form . "Probes") (:end . 102)\n  (:start . 96) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.288) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500861@unknown@formal@none@1@S@Actin was visualized with Rhodamine-labeled phalloidin (Invitrogen).@(((:tag . "NNP") (:stem . "Actin") (:form . "Actin") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "visualize") (:form . "visualized") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "rhodamine-labeled") (:form . "Rhodamine-labeled")\n  (:end . 43) (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "phalloidin") (:form . "phalloidin") (:end . 54)\n  (:start . 44) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 66)\n  (:start . 56) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.289) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500862@unknown@formal@none@1@S@Brains were imaged as whole mounts on a Zeiss LSM 510 confocal system.@(((:tag . "NNS") (:stem . "brain") (:form . "Brains") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "image") (:form . "imaged") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mount") (:form . "mounts") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Zeiss") (:form . "Zeiss") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "LSM") (:form . "LSM") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "CD") (:stem . "510") (:form . "510") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 62)\n  (:start . 54) (:id . 53))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 69)\n  (:start . 63) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.290) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500863@unknown@formal@none@1@S@Images were analyzed in Zeiss LSM Image Browser and processed in Photoshop CS3.@(((:tag . "NNS") (:stem . "image") (:form . "Images") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Zeiss") (:form . "Zeiss") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "LSM") (:form . "LSM") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Image") (:form . "Image") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Browser") (:form . "Browser") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "process") (:form . "processed") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Photoshop") (:form . "Photoshop") (:end . 74)\n  (:start . 65) (:id . 53))\n ((:tag . "NNP") (:stem . "CS3") (:form . "CS3") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.291) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500864@unknown@formal@none@1@S@For experiments in which protein levels were compared between genotypes, all sample preparation, histochemistry, imaging, and image processing was performed in parallel in the same manner.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 53)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 71)\n  (:start . 62) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 83)\n  (:start . 77) (:id . 54))\n ((:tag . "NN") (:stem . "preparation") (:form . "preparation") (:end . 95)\n  (:start . 84) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "NN") (:stem . "histochemistry") (:form . "histochemistry")\n  (:end . 111) (:start . 97) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 58))\n ((:tag . "NN") (:stem . "imaging") (:form . "imaging") (:end . 120)\n  (:start . 113) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "NN") (:stem . "image") (:form . "image") (:end . 131)\n  (:start . 126) (:id . 62))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 142)\n  (:start . 132) (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 146) (:start . 143)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 156)\n  (:start . 147) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 159) (:start . 157)\n  (:id . 66))\n ((:tag . "NN") (:stem . "parallel") (:form . "parallel") (:end . 168)\n  (:start . 160) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 171) (:start . 169)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 175) (:start . 172)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 180) (:start . 176)\n  (:id . 70))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 187)\n  (:start . 181) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.292) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500865@unknown@formal@none@1@S@Supporting Information@(((:tag . "VBG") (:stem . "support") (:form . "Supporting") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Information") (:form . "Information") (:end . 22)\n  (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s3.293) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5500866@unknown@formal@none@1@S@Figure S1 Diagram of Drosophila EGFR mutant forms.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Diagram") (:form . "Diagram") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "form") (:form . "forms") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 50) (:start . 49)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.294) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500867@unknown@formal@none@1@S@Proteins are shown as horizontal bars along which functional domains are indicated, and the locations of alterations in mutant forms are noted.@(((:tag . "NNPS") (:stem . "Protein") (:form . "Proteins") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "horizontal") (:form . "horizontal") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 68)\n  (:start . 61) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "location") (:form . "locations") (:end . 101)\n  (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "alteration") (:form . "alterations") (:end . 116)\n  (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 126)\n  (:start . 120) (:id . 61))\n ((:tag . "NNS") (:stem . "form") (:form . "forms") (:end . 132)\n  (:start . 127) (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 136) (:start . 133)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 142)\n  (:start . 137) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.295) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500868@unknown@formal@none@1@S@Wild-type human EGFR and Drosophila EGFR (dEGFR) show extensive conservation, with 55% homology in the kinase domain and 41% homology in the ligand-binding portion of the extracellular domain, which includes extensive cysteine repeats.@(((:tag . "JJ") (:stem . "wild-type") (:form . "Wild-type") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "dEGFR") (:form . "dEGFR") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 76)\n  (:start . 64) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "NN") (:stem . "homology") (:form . "homology") (:end . 95)\n  (:start . 87) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 109)\n  (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 116)\n  (:start . 110) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 63))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 124) (:start . 123)\n  (:id . 65))\n ((:tag . "NN") (:stem . "homology") (:form . "homology") (:end . 133)\n  (:start . 125) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "ligand-binding") (:form . "ligand-binding")\n  (:end . 155) (:start . 141) (:id . 69))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 163)\n  (:start . 156) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 166) (:start . 164)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 184) (:start . 171) (:id . 73))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 191)\n  (:start . 185) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 192) (:start . 191)\n  (:id . 75))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 198)\n  (:start . 193) (:id . 76))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 207)\n  (:start . 199) (:id . 77))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 217)\n  (:start . 208) (:id . 78))\n ((:tag . "NN") (:stem . "cysteine") (:form . "cysteine") (:end . 226)\n  (:start . 218) (:id . 79))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 234)\n  (:start . 227) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 235) (:start . 234)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s3.296) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500869@unknown@formal@none@1@S@The signal peptide is labeled in yellow.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "yellow") (:form . "yellow") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 40) (:start . 39)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s3.297) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500870@unknown@formal@none@1@S@Following the signal peptide, the entire cytoplasmic domain is replaced with the lambda dimerization domain in dEGFRλ, which causes constitutive activation.@(((:tag . "VBG") (:stem . "follow") (:form . "Following") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 52)\n  (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "replace") (:form . "replaced") (:end . 71)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "SYM") (:stem . "lambda") (:form . "lambda") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . "NN") (:stem . "dimerization") (:form . "dimerization") (:end . 100)\n  (:start . 88) (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 107)\n  (:start . 101) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 117)\n  (:start . 111) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 124)\n  (:start . 119) (:id . 61))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 131)\n  (:start . 125) (:id . 62))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 144)\n  (:start . 132) (:id . 63))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 155)\n  (:start . 145) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.298) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500871@unknown@formal@none@1@S@Both human EGFR and dEGFR show extensive cysteine repeats in the extracellular domain, indicated in blue.@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "dEGFR") (:form . "dEGFR") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "cysteine") (:form . "cysteine") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 78) (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 85)\n  (:start . 79) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 96)\n  (:start . 87) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 104) (:start . 100)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.299) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500872@unknown@formal@none@1@S@The tyrosine kinase domain is labeled in magenta.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "tyrosine") (:form . "tyrosine") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "magenta") (:form . "magenta") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.300) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500873@unknown@formal@none@1@S@The Elp mutant form of dEGFR contains an A887T substitution in the N-lobe of the kinase domain, which causes constitutive activation. (0.23 MB TIF)@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Elp") (:form . "Elp") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "dEGFR") (:form . "dEGFR") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "a887t") (:form . "A887T") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 59)\n  (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "n-lobe") (:form . "N-lobe") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 87)\n  (:start . 81) (:id . 57))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 94)\n  (:start . 88) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 101)\n  (:start . 96) (:id . 60))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 108)\n  (:start . 102) (:id . 61))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 121)\n  (:start . 109) (:id . 62))\n ((:tag . "FW") (:stem . "activation.") (:form . "activation.") (:end . 133)\n  (:start . 122) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 64))\n ((:tag . "CD") (:stem . "0.23") (:form . "0.23") (:end . 139) (:start . 135)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 142) (:start . 140)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 146) (:start . 143)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.301) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500874@unknown@formal@none@1@S@Figure S2 Coactivation of Ras-Raf and PI3K in Drosophila glia causes neoplasia.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 22)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Ras-Raf") (:form . "Ras-Raf") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.302) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500875@unknown@formal@none@1@S@2 µm optical sections of representative larval brain hemispheres from wandering 3rd instar larvae (A–H) and an early 2nd instar larval brain (I), all displayed at the same scale.@(((:tag . "LS") (:stem . "2") (:form . "2") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . "µm") (:form . "µm") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 39) (:start . 25) (:id . 47))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 46)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "hemisphere") (:form . "hemispheres") (:end . 64)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "wander") (:form . "wandering") (:end . 79)\n  (:start . 70) (:id . 52))\n ((:tag . "JJ") (:stem . "3rd") (:form . "3rd") (:end . 83) (:start . 80)\n  (:id . 53))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 90)\n  (:start . 84) (:id . 54))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 97)\n  (:start . 91) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "A–H") (:form . "A–H") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 116)\n  (:start . 111) (:id . 61))\n ((:tag . "NN") (:stem . "2nd") (:form . "2nd") (:end . 120) (:start . 117)\n  (:id . 62))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 127)\n  (:start . 121) (:id . 63))\n ((:tag . "NN") (:stem . "larval") (:form . "larval") (:end . 134)\n  (:start . 128) (:id . 64))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 140)\n  (:start . 135) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 66))\n ((:tag . "NN") (:stem . "i") (:form . "I") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 69))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 149) (:start . 146)\n  (:id . 70))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 159)\n  (:start . 150) (:id . 71))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 162) (:start . 160)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 171) (:start . 167)\n  (:id . 74))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 177)\n  (:start . 172) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s3.303) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500876@unknown@formal@none@1@S@20 µm scale bars.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.304) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500877@unknown@formal@none@1@S@Frontal sections; midway through brains.@(((:tag . "JJ") (:stem . "frontal") (:form . "Frontal") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "RB") (:stem . "midway") (:form . "midway") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 40) (:start . 39)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.305) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500878@unknown@formal@none@1@S@Anterior up; midline to left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "left") (:form . "left") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.306) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500879@unknown@formal@none@1@S@Glial cell nuclei are labeled with Repo (red).@(((:tag . "JJ") (:stem . "glial") (:form . "Glial") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.307) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500880@unknown@formal@none@1@S@CD8GFP (green), driven by the repo-Gal4 driver, labels glial cell bodies and membranes.@(((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 22)\n  (:start . 16) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 25) (:start . 23)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 49))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 39)\n  (:start . 30) (:id . 50))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 46)\n  (:start . 40) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "label") (:form . "labels") (:end . 54)\n  (:start . 48) (:id . 53))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 60) (:start . 55)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 65) (:start . 61)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 72) (:start . 66)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 86)\n  (:start . 77) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.308) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500881@unknown@formal@none@1@S@An anti-HRP counterstain (blue) reveals neuropil (neuronal fiber tracts) at high intensity and some cell bodies of neurons and neuronal precursors at low intensity, and this varies slightly according to exact plane of section and mutant phenotype.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "anti-hrp") (:form . "anti-HRP") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "counterstain") (:form . "counterstain") (:end . 24)\n  (:start . 12) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "neuropil") (:form . "neuropil") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 58)\n  (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "fiber") (:form . "fiber") (:end . 64) (:start . 59)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 71)\n  (:start . 65) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 90)\n  (:start . 81) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 99) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 104) (:start . 100)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 111)\n  (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 122)\n  (:start . 115) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 135)\n  (:start . 127) (:id . 65))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 146)\n  (:start . 136) (:id . 66))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 149) (:start . 147)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 153) (:start . 150)\n  (:id . 68))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 163)\n  (:start . 154) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 71))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 173) (:start . 169)\n  (:id . 72))\n ((:tag . "VBZ") (:stem . "vary") (:form . "varies") (:end . 180)\n  (:start . 174) (:id . 73))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 189)\n  (:start . 181) (:id . 74))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 199)\n  (:start . 190) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 202) (:start . 200)\n  (:id . 76))\n ((:tag . "VB") (:stem . "exact") (:form . "exact") (:end . 208)\n  (:start . 203) (:id . 77))\n ((:tag . "NN") (:stem . "plane") (:form . "plane") (:end . 214)\n  (:start . 209) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 217) (:start . 215)\n  (:id . 79))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 225)\n  (:start . 218) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 229) (:start . 226)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 236)\n  (:start . 230) (:id . 82))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 246)\n  (:start . 237) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 247) (:start . 246)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s3.309) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500882@unknown@formal@none@1@S@repo>dEGFRλ;dp110CAAX (A), repo>dRas85DV12;dPTENdsRNA (B), and repo>dRafgof;dp110CAAX (C) brains show increased numbers of glia relative to wild-type (D), repo>dRas85DV12 alone (E), or repo>dPTENdsRNA alone (F).@(((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 21) (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 24) (:start . 23)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "repo>dRas85DV12;dPTENdsRNA")\n  (:form . "repo>dRas85DV12;dPTENdsRNA") (:end . 53) (:start . 27) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 56) (:start . 55)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "repo>dRafgof;dp110CAAX")\n  (:form . "repo>dRafgof;dp110CAAX") (:end . 85) (:start . 63) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 96)\n  (:start . 90) (:id . 57))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 111)\n  (:start . 102) (:id . 59))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 119)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 127) (:start . 123)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 136)\n  (:start . 128) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 149)\n  (:start . 140) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 152) (:start . 151)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 69))\n ((:tag . "CD") (:stem . "repo>dRas85DV12") (:form . "repo>dRas85DV12")\n  (:end . 170) (:start . 155) (:id . 70))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 176)\n  (:start . 171) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 178) (:start . 177)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 179) (:start . 178)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 181) (:start . 180)\n  (:id . 75))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 184) (:start . 182)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "repo>dPTENdsRNA") (:form . "repo>dPTENdsRNA")\n  (:end . 200) (:start . 185) (:id . 77))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 206)\n  (:start . 201) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 208) (:start . 207)\n  (:id . 79))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 209) (:start . 208)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s3.310) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500883@unknown@formal@none@1@S@Compared to wild-type (D), repo>dEGFRwild-type (H) brains show reduced neurons (HRP, low intensity blue), which renders glia more densely packed and the entire brain smaller than normal.@(((:tag . "VBN") (:stem . "compare") (:form . "Compared") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "repo>dEGFRwild-type")\n  (:form . "repo>dEGFRwild-type") (:end . 46) (:start . 27) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 57)\n  (:start . 51) (:id . 53))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 62) (:start . 58)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 70)\n  (:start . 63) (:id . 55))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 78)\n  (:start . 71) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 83) (:start . 80)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 88) (:start . 85)\n  (:id . 60))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 98)\n  (:start . 89) (:id . 61))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 103) (:start . 99)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 111)\n  (:start . 106) (:id . 65))\n ((:tag . "VBZ") (:stem . "render") (:form . "renders") (:end . 119)\n  (:start . 112) (:id . 66))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 124) (:start . 120)\n  (:id . 67))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 129) (:start . 125)\n  (:id . 68))\n ((:tag . "RB") (:stem . "densely") (:form . "densely") (:end . 137)\n  (:start . 130) (:id . 69))\n ((:tag . "VBN") (:stem . "pack") (:form . "packed") (:end . 144)\n  (:start . 138) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 159)\n  (:start . 153) (:id . 73))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 165)\n  (:start . 160) (:id . 74))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 173)\n  (:start . 166) (:id . 75))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 178) (:start . 174)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 185)\n  (:start . 179) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s3.311) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500884@unknown@formal@none@1@S@However, repo>dEGFRwild-type brains (H) do not show a substantial increase the number of glia compared to wild-type (D).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "repo>dEGFRwild-type")\n  (:form . "repo>dEGFRwild-type") (:end . 28) (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 35)\n  (:start . 29) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 38) (:start . 37)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "VB") (:stem . "show") (:form . "show") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "substantial") (:form . "substantial") (:end . 65)\n  (:start . 54) (:id . 53))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 74)\n  (:start . 66) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 85)\n  (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 115)\n  (:start . 106) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 118) (:start . 117)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.312) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500885@unknown@formal@none@1@S@Brains of repo>dEGFRElp 2nd instar larvae (I) show substantial neuron loss, brain malformation, and excess glia for that stage of development.@(((:tag . "NNS") (:stem . "brain") (:form . "Brains") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "repo>dEGFRElp") (:form . "repo>dEGFRElp")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "2nd") (:form . "2nd") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 41)\n  (:start . 35) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "i") (:form . "I") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "substantial") (:form . "substantial") (:end . 62)\n  (:start . 51) (:id . 52))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . "NN") (:stem . "malformation") (:form . "malformation") (:end . 94)\n  (:start . 82) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "excess") (:form . "excess") (:end . 106)\n  (:start . 100) (:id . 60))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 111) (:start . 107)\n  (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 115) (:start . 112)\n  (:id . 62))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 120) (:start . 116)\n  (:id . 63))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 126)\n  (:start . 121) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 65))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 141)\n  (:start . 130) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.313) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500886@unknown@formal@none@1@S@Genotypes: (A) UAS-dEGFRλ UAS-dp110CAAX/+; repo-Gal4 UAS-CD8GFP/+ (B) UAS-CD8GFP/+; repo-Gal4/UAS-dRas85DV12 UAS-dPTENdsRNA (C) UAS-dp110CAAX; repo-Gal4 UAS-CD8GFP/UAS-dRafgof (D) repo-Gal4 UAS-CD8GFP/+ (E) repo-Gal4 UAS-CD8GFP/UAS-dRas85DV12 (F) UAS-CD8GFP/+; repo-Gal4/UAS-dPTENdsRNA (G) UAS-dEGFRλ/+; repo-Gal4 UAS-CD8GFP/+ (H) UAS-CD8GFP/+; repo-Gal4/UAS-dEGFRwild-type (I) UAS-CD8GFP/+; repo-Gal4/UAS-dEGFRElp. (10.31 MB TIF)@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotypes") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "UAS-dEGFRλ") (:form . 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"repo-Gal4") (:end . 313)\n  (:start . 304) (:id . 87))\n ((:tag . "NN") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 326)\n  (:start . 314) (:id . 88))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 328) (:start . 327)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 329) (:start . 328)\n  (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 330) (:start . 329)\n  (:id . 91))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 343)\n  (:start . 331) (:id . 92))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 344) (:start . 343)\n  (:id . 93))\n ((:tag . "NN") (:stem . "repo-gal4/uas-degfrwild-type")\n  (:form . "repo-Gal4/UAS-dEGFRwild-type") (:end . 373) (:start . 345)\n  (:id . 94))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 375) (:start . 374)\n  (:id . 95))\n ((:tag . "NN") (:stem . "i") (:form . "I") (:end . 376) (:start . 375)\n  (:id . 96))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 377) (:start . 376)\n  (:id . 97))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 390)\n  (:start . 378) (:id . 98))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 391) (:start . 390)\n  (:id . 99))\n ((:tag . "NN") (:stem . "repo-gal4/uas-degfrelp.")\n  (:form . "repo-Gal4/UAS-dEGFRElp.") (:end . 415) (:start . 392) (:id . 100))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 417) (:start . 416)\n  (:id . 101))\n ((:tag . "CD") (:stem . "10.31") (:form . "10.31") (:end . 422)\n  (:start . 417) (:id . 102))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 425) (:start . 423)\n  (:id . 103))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 429) (:start . 426)\n  (:id . 104))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 430) (:start . 429)\n  (:id . 105)))@@@1@64@((:identifiers (:sid . :s3.314) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500887@unknown@formal@none@1@S@Figure S3 dMMP1 expression in wild-type and dEGFRλ;dp110CAAX glia.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dmmp1") (:form . "dMMP1") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 60) (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 65) (:start . 61)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.315) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500888@unknown@formal@none@1@S@(A,B) 3rd instar larval brains.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A,B") (:form . "A,B") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "CD") (:stem . "3rd") (:form . "3rd") (:end . 9) (:start . 6)\n  (:id . 45))\n ((:tag . "IN") (:stem . "instar") (:form . "instar") (:end . 16)\n  (:start . 10) (:id . 46))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 23)\n  (:start . 17) (:id . 47))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 30)\n  (:start . 24) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 31) (:start . 30)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s3.316) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500889@unknown@formal@none@1@S@Frontal sections, showing medial regions enriched for proliferating glia.@(((:tag . "JJ") (:stem . "frontal") (:form . "Frontal") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 49)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "proliferate") (:form . "proliferating") (:end . 67)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 72) (:start . 68)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.317) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500890@unknown@formal@none@1@S@Anterior up; midline to left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "left") (:form . "left") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.318) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500891@unknown@formal@none@1@S@4.5 µm optical projections, matched in scale.@(((:tag . "CD") (:stem . "4.5") (:form . "4.5") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "µm") (:form . "µm") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "match") (:form . "matched") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.319) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500892@unknown@formal@none@1@S@20 µm scale bars.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.320) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500893@unknown@formal@none@1@S@Expression of the active form of dMMP1 (red) in wild-type (A) and repo>dEGFRλ;dp110CAAX brains (B), shown alone (left panels) and overlaid with an HRP (blue) neuronal label and a CD8GFP (green) glial label (right panels).@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dmmp1") (:form . "dMMP1") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . 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5500894@unknown@formal@none@1@S@In wild-type brains, glia (‘G’) rarely express active dMMP1, although some glia on the surface of the brain show low levels of dMMP1 staining (arrow).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 29) (:start . 28)\n  (:id . 49))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 30) (:start . 29)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 31) (:start . 30)\n  (:id . 51))\n ((:tag . "RB") (:stem . "rarely") (:form . "rarely") (:end . 38)\n  (:start . 32) (:id . 52))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 46)\n  (:start . 39) (:id . 53))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 53)\n  (:start . 47) (:id . 54))\n ((:tag . "NN") (:stem . "dmmp1") (:form . "dMMP1") (:end . 59) (:start . 54)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 69)\n  (:start . 61) (:id . 57))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 74) (:start . 70)\n  (:id . 58))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 79) (:start . 75)\n  (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 82) (:start . 80)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 61))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 94)\n  (:start . 87) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 64))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 107)\n  (:start . 102) (:id . 65))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 112) (:start . 108)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 116) (:start . 113)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 123)\n  (:start . 117) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 69))\n ((:tag . "NN") (:stem . "dmmp1") (:form . "dMMP1") (:end . 132)\n  (:start . 127) (:id . 70))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 141)\n  (:start . 133) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 72))\n ((:tag . "NN") (:stem . "arrow") (:form . "arrow") (:end . 148)\n  (:start . 143) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.322) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500895@unknown@formal@none@1@S@In repo>dEGFRλ;dp110CAAX brains (B), some neoplastic glia (‘G’) express active dMMP1 (red in right panel, yellow in overlay), which is largely membrane-localized in individual cells (arrow).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 24) (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 31)\n  (:start . 25) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 33) (:start . 32)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 34) (:start . 33)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 61) (:start . 60)\n  (:id . 54))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 71)\n  (:start . 64) (:id . 57))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 78)\n  (:start . 72) (:id . 58))\n ((:tag . "NN") (:stem . "dmmp1") (:form . "dMMP1") (:end . 84) (:start . 79)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 89) (:start . 86)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 98) (:start . 93)\n  (:id . 63))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 104) (:start . 99)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 112)\n  (:start . 106) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 67))\n ((:tag . "NN") (:stem . "overlay") (:form . "overlay") (:end . 123)\n  (:start . 116) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 70))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 131)\n  (:start . 126) (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 134) (:start . 132)\n  (:id . 72))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 142)\n  (:start . 135) (:id . 73))\n ((:tag . "JJ") (:stem . "membrane-localized") (:form . "membrane-localized")\n  (:end . 161) (:start . 143) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 164) (:start . 162)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 175)\n  (:start . 165) (:id . 76))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 181)\n  (:start . 176) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 183) (:start . 182)\n  (:id . 78))\n ((:tag . "NN") (:stem . "arrow") (:form . "arrow") (:end . 188)\n  (:start . 183) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s3.323) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500896@unknown@formal@none@1@S@Genotypes: (A) UAS-CD8GFP/+; repo-Gal4/+ (B) UAS-dEGFRλ UAS-dp110CAAX/+; UAS-CD8GFP/+; repo-Gal4/+. (3.93 MB TIF)@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotypes") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 27)\n  (:start . 15) (:id . 47))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "repo-gal4/+") (:form . "repo-Gal4/+") (:end . 40)\n  (:start . 29) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 43) (:start . 42)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "UAS-dEGFRλ") (:form . "UAS-dEGFRλ") (:end . 55)\n  (:start . 45) (:id . 53))\n ((:tag . "JJ") (:stem . "uas-dp110caax/+") (:form . "UAS-dp110CAAX/+")\n  (:end . 71) (:start . 56) (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 85)\n  (:start . 73) (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "repo-Gal4/+.") (:form . "repo-Gal4/+.") (:end . 99)\n  (:start . 87) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . "CD") (:stem . "3.93") (:form . "3.93") (:end . 105) (:start . 101)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 108) (:start . 106)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 112) (:start . 109)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.324) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500897@unknown@formal@none@1@S@Figure S4 Glial-specific Rbf1 knock-down or overexpression of G1 Cyclin-Cdks, Dap, and Rbf1 affects glial proliferation.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "glial-specific") (:form . "Glial-specific")\n  (:end . 24) (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "rbf1") (:form . "Rbf1") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "knock-down") (:form . "knock-down") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 58) (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "G1") (:form . "G1") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Cyclin-Cdk") (:form . "Cyclin-Cdks") (:end . 76)\n  (:start . 65) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 81) (:start . 78)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Rbf1") (:form . "Rbf1") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "affect") (:form . "affects") (:end . 99)\n  (:start . 92) (:id . 57))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 105)\n  (:start . 100) (:id . 58))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 119) (:start . 106) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.325) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500898@unknown@formal@none@1@S@(A–F) 2 µm optical sections of larval brain hemispheres from wandering 3rd instar larvae displayed at the same scale.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–F") (:form . "A–F") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 7) (:start . 6)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 10) (:start . 8)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 18)\n  (:start . 11) (:id . 47))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 27)\n  (:start . 19) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 37)\n  (:start . 31) (:id . 50))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 43) (:start . 38)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "hemisphere") (:form . "hemispheres") (:end . 55)\n  (:start . 44) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 60) (:start . 56)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "wander") (:form . "wandering") (:end . 70)\n  (:start . 61) (:id . 54))\n ((:tag . "JJ") (:stem . "3rd") (:form . "3rd") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 81)\n  (:start . 75) (:id . 56))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 88)\n  (:start . 82) (:id . 57))\n ((:tag . "VBN") (:stem . "display") (:form . "displayed") (:end . 98)\n  (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 110) (:start . 106)\n  (:id . 61))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 116)\n  (:start . 111) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.326) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500899@unknown@formal@none@1@S@20 µm scale bars.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.327) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500900@unknown@formal@none@1@S@Frontal sections; midway through brains.@(((:tag . "JJ") (:stem . "frontal") (:form . "Frontal") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "RB") (:stem . "midway") (:form . "midway") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 40) (:start . 39)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.328) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500901@unknown@formal@none@1@S@Anterior up; midline to left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "left") (:form . "left") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.329) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500902@unknown@formal@none@1@S@Glial cell nuclei are labeled with Repo (red).@(((:tag . "JJ") (:stem . "glial") (:form . "Glial") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.330) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500903@unknown@formal@none@1@S@Glial cell bodies and membranes are labeled with CD8GFP (green) driven by repo-Gal4.@(((:tag . "JJ") (:stem . "glial") (:form . "Glial") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 17) (:start . 11)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 70)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 83)\n  (:start . 74) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.331) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500904@unknown@formal@none@1@S@HRP counter-staining (blue) reveals neuropil at high intensity and some cell bodies of neurons and neuronal precursors at low intensity.@(((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "counter-staining") (:form . "counter-staining")\n  (:end . 20) (:start . 4) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 44))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "neuropil") (:form . "neuropil") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 62)\n  (:start . 53) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 83) (:start . 77)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 94)\n  (:start . 87) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 107)\n  (:start . 99) (:id . 59))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 118)\n  (:start . 108) (:id . 60))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 121) (:start . 119)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 125) (:start . 122)\n  (:id . 62))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 135)\n  (:start . 126) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.332) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500905@unknown@formal@none@1@S@Rbf1 knock-down in repo>Rbf1dsRNA (B) does not significantly alter glial cell numbers (red nuclei) compared to wild-type (A).@(((:tag . "NN") (:stem . "rbf1") (:form . "Rbf1") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "knock-down") (:form . "knock-down") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "repo>Rbf1dsRNA") (:form . "repo>Rbf1dsRNA")\n  (:end . 33) (:start . 19) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 35) (:start . 34)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 60) (:start . 47) (:id . 51))\n ((:tag . "VB") (:stem . "alter") (:form . "alter") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 72) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 85)\n  (:start . 78) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 90) (:start . 87)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 97)\n  (:start . 91) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 107)\n  (:start . 99) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 120)\n  (:start . 111) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 123) (:start . 122)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.333) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500906@unknown@formal@none@1@S@Ectopic expression of dCyclinE-dCdk2 (C) or dCyclinD-dCdk4 in repo-Gal4-glia promotes an approximate doubling of glial cells numbers (red nuclei), even when combined with Rbf1dsRNA (D).@(((:tag . "JJ") (:stem . "ectopic") (:form . "Ectopic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dcycline-dcdk2") (:form . "dCyclinE-dCdk2")\n  (:end . 36) (:start . 22) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 39) (:start . 38)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dcyclind-dcdk4") (:form . "dCyclinD-dCdk4")\n  (:end . 58) (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "repo-gal4-glia") (:form . "repo-Gal4-glia")\n  (:end . 76) (:start . 62) (:id . 52))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 85)\n  (:start . 77) (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "approximate") (:form . "approximate") (:end . 100)\n  (:start . 89) (:id . 55))\n ((:tag . "NN") (:stem . "doubling") (:form . "doubling") (:end . 109)\n  (:start . 101) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 118)\n  (:start . 113) (:id . 58))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 124)\n  (:start . 119) (:id . 59))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 132)\n  (:start . 125) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 137) (:start . 134)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 144)\n  (:start . 138) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 65))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 151) (:start . 147)\n  (:id . 66))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 156) (:start . 152)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 165)\n  (:start . 157) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 170) (:start . 166)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Rbf1dsRNA") (:form . "Rbf1dsRNA") (:end . 180)\n  (:start . 171) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 182) (:start . 181)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 183) (:start . 182)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.334) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5500909@unknown@formal@none@1@S@Figure S5 Dap and Rbf1 expression in wild-type and dEGFRλ;dp110CAAX glia.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "rbf1") (:form . "Rbf1") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 67) (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s3.337) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500910@unknown@formal@none@1@S@3rd instar larval brains.@(((:tag . "LS") (:stem . "3rd") (:form . "3rd") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "instar") (:form . "instar") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 25) (:start . 24)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.338) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500911@unknown@formal@none@1@S@Frontal sections, showing superficial dorsal regions enriched for Dap- and Rbf1-expressing cells.@(((:tag . "JJ") (:stem . "frontal") (:form . "Frontal") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "superficial") (:form . "superficial") (:end . 37)\n  (:start . 26) (:id . 46))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 44)\n  (:start . 38) (:id . 47))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 61)\n  (:start . 53) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 65) (:start . 62)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dap-") (:form . "Dap-") (:end . 70) (:start . 66)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 52))\n ((:tag . "NN") (:stem . "rbf1-expressing") (:form . "Rbf1-expressing")\n  (:end . 90) (:start . 75) (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 96) (:start . 91)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.339) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500912@unknown@formal@none@1@S@Anterior up; midline to left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "left") (:form . "left") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.340) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500913@unknown@formal@none@1@S@7 µm optical projections, all matched in scale.@(((:tag . "CD") (:stem . "7") (:form . "7") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "match") (:form . "matched") (:end . 37)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.341) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500914@unknown@formal@none@1@S@20 µm scale bars.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.342) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500915@unknown@formal@none@1@S@(A,B) Dap expression (red) in wild-type (A) and repo>dEGFRλ;dp110CAAX brains (B), shown alone (left panels) and overlaid with Repo (blue) and repo>CD8GFP (green) glial markers (right panels).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A,B") (:form . "A,B") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 9) (:start . 6)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 20)\n  (:start . 10) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 25) (:start . 22)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 26) (:start . 25)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 39)\n  (:start . 30) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 42) (:start . 41)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 69) (:start . 48) (:id . 56))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 76)\n  (:start . 70) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 79) (:start . 78)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 87) (:start . 82)\n  (:id . 62))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 93) (:start . 88)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "left") (:form . "left") (:end . 99) (:start . 95)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 106)\n  (:start . 100) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "overlay") (:form . "overlaid") (:end . 120)\n  (:start . 112) (:id . 69))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 125) (:start . 121)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 130) (:start . 126)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 132) (:start . 131)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 136) (:start . 132)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "repo>CD8GFP") (:form . "repo>CD8GFP") (:end . 153)\n  (:start . 142) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 77))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 160)\n  (:start . 155) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 167)\n  (:start . 162) (:id . 80))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 175)\n  (:start . 168) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 182)\n  (:start . 177) (:id . 83))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 189)\n  (:start . 183) (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s3.343) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500916@unknown@formal@none@1@S@In both genotypes, Dap is primarily expressed in neuroblasts (‘NB’) and ganglion mother cell neuronal precursors (‘NP’), rarely in glia (‘G’), and almost never in neurons (‘N’).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "RB") (:stem . "primarily") (:form . "primarily") (:end . 35)\n  (:start . 26) (:id . 48))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 45)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 60)\n  (:start . 49) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "NB") (:form . "NB") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 57))\n ((:tag . "NN") (:stem . "ganglion") (:form . "ganglion") (:end . 80)\n  (:start . 72) (:id . 58))\n ((:tag . "NN") (:stem . "mother") (:form . "mother") (:end . 87)\n  (:start . 81) (:id . 59))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 92) (:start . 88)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 101)\n  (:start . 93) (:id . 61))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 112)\n  (:start . 102) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 63))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 115) (:start . 114)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "NP") (:form . "NP") (:end . 117) (:start . 115)\n  (:id . 65))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 118) (:start . 117)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 68))\n ((:tag . "RB") (:stem . "rarely") (:form . "rarely") (:end . 127)\n  (:start . 121) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 130) (:start . 128)\n  (:id . 70))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 135) (:start . 131)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 72))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 138) (:start . 137)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 139) (:start . 138)\n  (:id . 74))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 140) (:start . 139)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 146) (:start . 143)\n  (:id . 78))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 153)\n  (:start . 147) (:id . 79))\n ((:tag . "RB") (:stem . "never") (:form . "never") (:end . 159)\n  (:start . 154) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 162) (:start . 160)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 170)\n  (:start . 163) (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 83))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 173) (:start . 172)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 174) (:start . 173)\n  (:id . 85))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 175) (:start . 174)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s3.344) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500917@unknown@formal@none@1@S@In repo>dEGFRλ;dp110CAAX brains, Dap is rarely expressed in glia as seen by the lack of substantial overlap between Dap expression and glial markers (B, right panel).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 24) (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 31)\n  (:start . 25) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "RB") (:stem . "rarely") (:form . "rarely") (:end . 46)\n  (:start . 40) (:id . 48))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 56)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "substantial") (:form . "substantial") (:end . 99)\n  (:start . 88) (:id . 58))\n ((:tag . "NN") (:stem . "overlap") (:form . "overlap") (:end . 107)\n  (:start . 100) (:id . 59))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 115)\n  (:start . 108) (:id . 60))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 119) (:start . 116)\n  (:id . 61))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 130)\n  (:start . 120) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 140)\n  (:start . 135) (:id . 64))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 148)\n  (:start . 141) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 151) (:start . 150)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 158)\n  (:start . 153) (:id . 69))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 164)\n  (:start . 159) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.345) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500918@unknown@formal@none@1@S@White arrows denote rare Dap-positive glia in both wild-type and repo>dEGFRλ;dp110CAAX brains; these glia show lower levels of Dap protein than neighboring neuroblasts and neuronal precursors.@(((:tag . "NNP") (:stem . "White") (:form . "White") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "arrow") (:form . "arrows") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "VB") (:stem . "denote") (:form . "denote") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "JJ") (:stem . "rare") (:form . "rare") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "dap-positive") (:form . "Dap-positive") (:end . 37)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 86) (:start . 65) (:id . 52))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 93)\n  (:start . 87) (:id . 53))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 94) (:start . 93)\n  (:id . 54))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 100) (:start . 95)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 105) (:start . 101)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 110) (:start . 106)\n  (:id . 57))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 116) (:start . 111)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 123)\n  (:start . 117) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 130) (:start . 127)\n  (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 138)\n  (:start . 131) (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 143) (:start . 139)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "neighbor") (:form . "neighboring") (:end . 155)\n  (:start . 144) (:id . 64))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 167)\n  (:start . 156) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 180)\n  (:start . 172) (:id . 67))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 191)\n  (:start . 181) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.346) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500919@unknown@formal@none@1@S@Dap-positive glia were counted in 3 repo>dEGFRλ;dp110CAAX brains and an average of 5% of all glia expressed Dap (87 glia expressed Dap out of 1738 total glia counted).@(((:tag . "JJ") (:stem . "dap-positive") (:form . "Dap-positive") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 17) (:start . 13)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "count") (:form . "counted") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 57) (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 64)\n  (:start . 58) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 71) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 79)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 53))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 85) (:start . 84)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 92) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 97) (:start . 93)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 107)\n  (:start . 98) (:id . 59))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 111) (:start . 108)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 61))\n ((:tag . "CD") (:stem . "87") (:form . "87") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 120) (:start . 116)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "express") (:form . "expressed") (:end . 130)\n  (:start . 121) (:id . 64))\n ((:tag . "NNP") (:stem . "Dap") (:form . "Dap") (:end . 134) (:start . 131)\n  (:id . 65))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 138) (:start . 135)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 141) (:start . 139)\n  (:id . 67))\n ((:tag . "CD") (:stem . "1738") (:form . "1738") (:end . 146) (:start . 142)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 152)\n  (:start . 147) (:id . 69))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 157) (:start . 153)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "count") (:form . "counted") (:end . 165)\n  (:start . 158) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s3.347) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500920@unknown@formal@none@1@S@(C–D) Rbf1 expression (red) in wild-type (E) and repo>dEGFRλ;dp110CAAX brains (F), shown alone (left) and overlaid (right) with the CD8GFP (green) glial marker and HRP (blue) neuronal marker.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C–D") (:form . "C–D") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NN") (:stem . "rbf1") (:form . "Rbf1") (:end . 10) (:start . 6)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 21)\n  (:start . 11) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 26) (:start . 23)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 40)\n  (:start . 31) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 52))\n ((:tag . "NN") (:stem . "e") (:form . "E") (:end . 43) (:start . 42)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 70) (:start . 49) (:id . 56))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 77)\n  (:start . 71) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 58))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 80) (:start . 79)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 88) (:start . 83)\n  (:id . 62))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 94) (:start . 89)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 64))\n ((:tag . "RB") (:stem . "left") (:form . "left") (:end . 100) (:start . 96)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "overlaid") (:form . "overlaid") (:end . 114)\n  (:start . 106) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 121)\n  (:start . 116) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 71))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 127) (:start . 123)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 138)\n  (:start . 132) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 75))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 145)\n  (:start . 140) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 152)\n  (:start . 147) (:id . 78))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 159)\n  (:start . 153) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 163) (:start . 160)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 167) (:start . 164)\n  (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 173) (:start . 169)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 174) (:start . 173)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 183)\n  (:start . 175) (:id . 85))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 190)\n  (:start . 184) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s3.348) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500921@unknown@formal@none@1@S@In both genotypes, Rbf1 is highly expressed in glia (‘G’) and neuroblasts (‘NB’), which were identified by their characteristic positions and large cell bodies.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Rbf1") (:form . "Rbf1") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 54) (:start . 53)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 55) (:start . 54)\n  (:id . 54))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 56) (:start . 55)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 73)\n  (:start . 62) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 59))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 76) (:start . 75)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "NB") (:form . "NB") (:end . 78) (:start . 76)\n  (:id . 61))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 79) (:start . 78)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 87) (:start . 82)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 92) (:start . 88)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 103)\n  (:start . 93) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 106) (:start . 104)\n  (:id . 68))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 112)\n  (:start . 107) (:id . 69))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 127) (:start . 113) (:id . 70))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 137)\n  (:start . 128) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 147)\n  (:start . 142) (:id . 73))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 152) (:start . 148)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 159)\n  (:start . 153) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s3.349) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500922@unknown@formal@none@1@S@Neurons (‘N’) show lower expression.@(((:tag . "NNP") (:stem . "Neuron") (:form . "Neurons") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 12) (:start . 11)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 13) (:start . 12)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 18) (:start . 14)\n  (:id . 48))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 24) (:start . 19)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 35)\n  (:start . 25) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 36) (:start . 35)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.350) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500923@unknown@formal@none@1@S@Genotypes: (A,C) UAS-CD8GFP/+; repo-Gal4/+ (B,D) UAS-dEGFRλ UAS-dp110CAAX/+; UAS-CD8GFP/+; repo-Gal4/+. (7.96 MB TIF)@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotypes") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "A,C") (:form . "A,C") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 29)\n  (:start . 17) (:id . 47))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "repo-gal4/+") (:form . "repo-Gal4/+") (:end . 42)\n  (:start . 31) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "B,D") (:form . "B,D") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "UAS-dEGFRλ") (:form . "UAS-dEGFRλ") (:end . 59)\n  (:start . 49) (:id . 53))\n ((:tag . "JJ") (:stem . "uas-dp110caax/+") (:form . "UAS-dp110CAAX/+")\n  (:end . 75) (:start . 60) (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 89)\n  (:start . 77) (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "repo-Gal4/+.") (:form . "repo-Gal4/+.")\n  (:end . 103) (:start . 91) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n  (:id . 59))\n ((:tag . "CD") (:stem . "7.96") (:form . "7.96") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 117) (:start . 116)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.351) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500924@unknown@formal@none@1@S@Figure S6 dEGFRλ; dp110CAAX glia do not express neuronal and neuroblast markers.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S6") (:form . "S6") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "VB") (:stem . "express") (:form . "express") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 56)\n  (:start . 48) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "neuroblast") (:form . "neuroblast") (:end . 71)\n  (:start . 61) (:id . 53))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.352) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500925@unknown@formal@none@1@S@Late 3rd instar larval brains.@(((:tag . "RB") (:stem . "late") (:form . "Late") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "3rd") (:form . "3rd") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "instar") (:form . "instar") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 30) (:start . 29)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s3.353) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500926@unknown@formal@none@1@S@Medial anterior regions shown.@(((:tag . "JJ") (:stem . "medial") (:form . "Medial") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 15)\n  (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 29) (:start . 24)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 30) (:start . 29)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.354) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500927@unknown@formal@none@1@S@Anterior up; midline to left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "left") (:form . "left") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.355) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500928@unknown@formal@none@1@S@2 µm optical sections.@(((:tag . "LS") (:stem . "2") (:form . "2") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . "µm") (:form . "µm") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 22) (:start . 21)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.356) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500929@unknown@formal@none@1@S@CD8GFP (green), driven by the repo-Gal4 driver, labels glial cell bodies and membranes.@(((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 22)\n  (:start . 16) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 25) (:start . 23)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 49))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 39)\n  (:start . 30) (:id . 50))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 46)\n  (:start . 40) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "label") (:form . "labels") (:end . 54)\n  (:start . 48) (:id . 53))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 60) (:start . 55)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 65) (:start . 61)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 72) (:start . 66)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 86)\n  (:start . 77) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.357) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500930@unknown@formal@none@1@S@An HRP counter-stain (blue) reveals neuropil at high intensity and cell bodies of neurons and some neuronal precursors at low intensity.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "counter-stain") (:form . "counter-stain")\n  (:end . 20) (:start . 7) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "neuropil") (:form . "neuropil") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 78) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 89)\n  (:start . 82) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 107)\n  (:start . 99) (:id . 60))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 118)\n  (:start . 108) (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 135)\n  (:start . 126) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.358) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500931@unknown@formal@none@1@S@(A,B) Repo expression (red) in glial cell nuclei in wild-type (A) and repo>dEGFRλ;dp110CAAX brains (B).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A,B") (:form . "A,B") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 10) (:start . 6)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 21)\n  (:start . 11) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 26) (:start . 23)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 36) (:start . 31)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 41) (:start . 37)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 48)\n  (:start . 42) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 61)\n  (:start . 52) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 64) (:start . 63)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 65) (:start . 64)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 91) (:start . 70) (:id . 60))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 98)\n  (:start . 92) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 101) (:start . 100)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.359) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500932@unknown@formal@none@1@S@In wild-type brains, neuronal fibers and neurons (blue) are enveloped by glial processes (green) to give the brain a honeycombed appearance.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "fiber") (:form . "fibers") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "envelop") (:form . "enveloped") (:end . 69)\n  (:start . 60) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 78) (:start . 73)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 88)\n  (:start . 79) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 95) (:start . 90)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 99) (:start . 97)\n  (:id . 61))\n ((:tag . "VB") (:stem . "give") (:form . "give") (:end . 104) (:start . 100)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 63))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 114)\n  (:start . 109) (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "honeycombed") (:form . "honeycombed") (:end . 128)\n  (:start . 117) (:id . 66))\n ((:tag . "NN") (:stem . "appearance") (:form . "appearance") (:end . 139)\n  (:start . 129) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.360) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500933@unknown@formal@none@1@S@In repo>dEGFRλ;dp110CAAX brains, neurons (‘N’) lack GFP or Repo expression, in contrast to glia (‘G’).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 24) (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 31)\n  (:start . 25) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 40)\n  (:start . 33) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 47))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "POS") (:stem . "’") (:form . "’") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "lack") (:form . "lack") (:end . 51) (:start . 47)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 55) (:start . 52)\n  (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 58) (:start . 56)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 63) (:start . 59)\n  (:id . 55))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 74)\n  (:start . 64) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 58))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 87)\n  (:start . 79) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 60))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 95) (:start . 91)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 62))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 98) (:start . 97)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 99) (:start . 98)\n  (:id . 64))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 100) (:start . 99)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.361) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500934@unknown@formal@none@1@S@(C–D) Elav expression (red) in wild-type (C) and repo>dEGFRλ;dp110CAAX brains (D), shown alone (left panels) and overlaid (right panels) with the CD8GFP (green) glial marker and HRP (blue) neuronal marker.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C–D") (:form . "C–D") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Elav") (:form . "Elav") (:end . 10) (:start . 6)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 21)\n  (:start . 11) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 26) (:start . 23)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 40)\n  (:start . 31) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 43) (:start . 42)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 70) (:start . 49) (:id . 56))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 77)\n  (:start . 71) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 80) (:start . 79)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 88) (:start . 83)\n  (:id . 62))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 94) (:start . 89)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "left") (:form . "left") (:end . 100) (:start . 96)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 107)\n  (:start . 101) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "overlaid") (:form . "overlaid") (:end . 121)\n  (:start . 113) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 128)\n  (:start . 123) (:id . 71))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 135)\n  (:start . 129) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 73))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 141) (:start . 137)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 152)\n  (:start . 146) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 77))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 159)\n  (:start . 154) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 166)\n  (:start . 161) (:id . 80))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 173)\n  (:start . 167) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 177) (:start . 174)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 181) (:start . 178)\n  (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 183) (:start . 182)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 187) (:start . 183)\n  (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 197)\n  (:start . 189) (:id . 87))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 204)\n  (:start . 198) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s3.362) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500935@unknown@formal@none@1@S@In both genotypes, Elav is highly expressed in neurons (‘N’) but absent from glia (green cell bodies indicated by white arrows).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Elav") (:form . "Elav") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 58) (:start . 57)\n  (:id . 54))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 59) (:start . 58)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 64) (:start . 61)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "absent") (:form . "absent") (:end . 71)\n  (:start . 65) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 76) (:start . 72)\n  (:id . 59))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 81) (:start . 77)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 88) (:start . 83)\n  (:id . 62))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 93) (:start . 89)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 100)\n  (:start . 94) (:id . 64))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 110)\n  (:start . 101) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 113) (:start . 111)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 119)\n  (:start . 114) (:id . 67))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 126)\n  (:start . 120) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 127) (:start . 126)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.363) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500936@unknown@formal@none@1@S@(E–F) Miranda expression (red) in wild-type (E) and repo>dEGFRλ;dp110CAAX (F) brains, shown alone (left panels) and overlaid (right panels) with CD8GFP (green) glial marker and HRP (blue) neuronal marker.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E–F") (:form . "E–F") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Miranda") (:form . "Miranda") (:end . 13)\n  (:start . 6) (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 24)\n  (:start . 14) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 30) (:start . 29)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 43)\n  (:start . 34) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "NN") (:stem . "e") (:form . "E") (:end . 46) (:start . 45)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 73) (:start . 52) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 76) (:start . 75)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 84)\n  (:start . 78) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 91) (:start . 86)\n  (:id . 62))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 97) (:start . 92)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "left") (:form . "left") (:end . 103) (:start . 99)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 110)\n  (:start . 104) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "overlaid") (:form . "overlaid") (:end . 124)\n  (:start . 116) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 131)\n  (:start . 126) (:id . 71))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 138)\n  (:start . 132) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 73))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 144) (:start . 140)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 151)\n  (:start . 145) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 76))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 158)\n  (:start . 153) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 165)\n  (:start . 160) (:id . 79))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 172)\n  (:start . 166) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 180) (:start . 177)\n  (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 182) (:start . 181)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 186) (:start . 182)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 196)\n  (:start . 188) (:id . 86))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 203)\n  (:start . 197) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s3.364) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500937@unknown@formal@none@1@S@In both genotypes, Miranda is highly expressed in neuroblasts (‘NB’), which are identified by their characteristic positions and large cell bodies, but is absent from glia (green cell bodies, indicated by white arrows).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Miranda") (:form . "Miranda") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 61)\n  (:start . 50) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "NB") (:form . "NB") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 75) (:start . 70)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 79) (:start . 76)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 90)\n  (:start . 80) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 93) (:start . 91)\n  (:id . 61))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 99)\n  (:start . 94) (:id . 62))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 114) (:start . 100) (:id . 63))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 124)\n  (:start . 115) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 134)\n  (:start . 129) (:id . 66))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 139) (:start . 135)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 146)\n  (:start . 140) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 151) (:start . 148)\n  (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 154) (:start . 152)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "absent") (:form . "absent") (:end . 161)\n  (:start . 155) (:id . 72))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 166) (:start . 162)\n  (:id . 73))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 171) (:start . 167)\n  (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 173) (:start . 172)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 178)\n  (:start . 173) (:id . 76))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 183) (:start . 179)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 190)\n  (:start . 184) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 201)\n  (:start . 192) (:id . 80))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 204) (:start . 202)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 210)\n  (:start . 205) (:id . 82))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 217)\n  (:start . 211) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 218) (:start . 217)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s3.365) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500938@unknown@formal@none@1@S@Genotypes: (A,C,E) UAS-CD8GFP/+; repo-Gal4/+ (B,D,F) UAS-dEGFRλ UAS-dp110CAAX/+; UAS-CD8GFP/+; repo-Gal4/+. (9.24 MB TIF)@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotypes") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "A,C,E") (:form . "A,C,E") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 31)\n  (:start . 19) (:id . 47))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "repo-gal4/+") (:form . "repo-Gal4/+") (:end . 44)\n  (:start . 33) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "B,D,F") (:form . "B,D,F") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "UAS-dEGFRλ") (:form . "UAS-dEGFRλ") (:end . 63)\n  (:start . 53) (:id . 53))\n ((:tag . "JJ") (:stem . "uas-dp110caax/+") (:form . "UAS-dp110CAAX/+")\n  (:end . 79) (:start . 64) (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 93)\n  (:start . 81) (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "repo-Gal4/+.") (:form . "repo-Gal4/+.")\n  (:end . 107) (:start . 95) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "CD") (:stem . "9.24") (:form . "9.24") (:end . 113) (:start . 109)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 116) (:start . 114)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 120) (:start . 117)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 121) (:start . 120)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.366) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500939@unknown@formal@none@1@S@Figure S7 dEGFRλ and dp110CAAX do not induce neoplasia from neurons, neuroblasts, or certain glia.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 54)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 67)\n  (:start . 60) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 80)\n  (:start . 69) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 97) (:start . 93)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x3.367.1) (:span 82 84)))\n (:hscopes ((:id . :x3.367.1) (:span 60 97)))\n (:identifiers (:sid . :s3.367) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500940@unknown@formal@none@1@S@Late 3rd instar larval brain hemispheres.@(((:tag . "RB") (:stem . "late") (:form . "Late") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "3rd") (:form . "3rd") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "larval") (:form . "larval") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "hemisphere") (:form . "hemispheres") (:end . 40)\n  (:start . 29) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 41) (:start . 40)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.368) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500941@unknown@formal@none@1@S@Medial anterior regions shown.@(((:tag . "JJ") (:stem . "medial") (:form . "Medial") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 15)\n  (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 29) (:start . 24)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 30) (:start . 29)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.369) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500942@unknown@formal@none@1@S@Anterior up; midline to left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "left") (:form . "left") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.370) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500943@unknown@formal@none@1@S@3.5 µm optical projections.@(((:tag . "CD") (:stem . "3.5") (:form . "3.5") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "µm") (:form . "µm") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 27) (:start . 26)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.371) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500944@unknown@formal@none@1@S@Repo expression (red) in glial cell nuclei in all genotypes.@(((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 30) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 35) (:start . 31)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 42)\n  (:start . 36) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 51))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 49) (:start . 46)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 59)\n  (:start . 50) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.372) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500945@unknown@formal@none@1@S@An HRP counter-stain (blue) reveals neuropil at high intensity and cell bodies of neurons and some neuronal precursors at low intensity, and this varies slightly according to variance in exact section plane.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "counter-stain") (:form . "counter-stain")\n  (:end . 20) (:start . 7) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "neuropil") (:form . "neuropil") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 78) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 89)\n  (:start . 82) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 107)\n  (:start . 99) (:id . 60))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 118)\n  (:start . 108) (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 135)\n  (:start . 126) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 66))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 145) (:start . 141)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "vary") (:form . "varies") (:end . 152)\n  (:start . 146) (:id . 68))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 161)\n  (:start . 153) (:id . 69))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 171)\n  (:start . 162) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 174) (:start . 172)\n  (:id . 71))\n ((:tag . "NN") (:stem . "variance") (:form . "variance") (:end . 183)\n  (:start . 175) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 186) (:start . 184)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "exact") (:form . "exact") (:end . 192)\n  (:start . 187) (:id . 74))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 200)\n  (:start . 193) (:id . 75))\n ((:tag . "NN") (:stem . "plane") (:form . "plane") (:end . 206)\n  (:start . 201) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s3.373) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500946@unknown@formal@none@1@S@(A–D) Wild-type (A), dEGFRλ; dp110CAAX overexpressed using the 1407-Gal4 neuroblast driver (B), dEGFRλ; dp110CAAX overexpressed using the pros-Gal4 neural driver (C), and dEGFRλ;dp110CAAX overexpressed using the gcm-Gal4 embryonic glial driver (D).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–D") (:form . "A–D") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "Wild-type") (:end . 15)\n  (:start . 6) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 18) (:start . 17)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 19) (:start . 18)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 27)\n  (:start . 21) (:id . 50))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 28) (:start . 27)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 38)\n  (:start . 29) (:id . 52))\n ((:tag . "VBD") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 52) (:start . 39) (:id . 53))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 58) (:start . 53)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 55))\n ((:tag . "NN") (:stem . "1407-gal4") (:form . "1407-Gal4") (:end . 72)\n  (:start . 63) (:id . 56))\n ((:tag . "NN") (:stem . "neuroblast") (:form . "neuroblast") (:end . 83)\n  (:start . 73) (:id . 57))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 90)\n  (:start . 84) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 94) (:start . 93)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 102)\n  (:start . 96) (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 103) (:start . 102)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 113)\n  (:start . 104) (:id . 65))\n ((:tag . "VBD") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 127) (:start . 114) (:id . 66))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 133) (:start . 128)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 68))\n ((:tag . "NN") (:stem . "pros-gal4") (:form . "pros-Gal4") (:end . 147)\n  (:start . 138) (:id . 69))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 154)\n  (:start . 148) (:id . 70))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 161)\n  (:start . 155) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 163) (:start . 162)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 164) (:start . 163)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 170) (:start . 167)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 187) (:start . 171) (:id . 77))\n ((:tag . "VBD") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 201) (:start . 188) (:id . 78))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 207) (:start . 202)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 211) (:start . 208)\n  (:id . 80))\n ((:tag . "NN") (:stem . "gcm-gal4") (:form . "gcm-Gal4") (:end . 220)\n  (:start . 212) (:id . 81))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 230)\n  (:start . 221) (:id . 82))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 236)\n  (:start . 231) (:id . 83))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 243)\n  (:start . 237) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 245) (:start . 244)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 246) (:start . 245)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 247) (:start . 246)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 248) (:start . 247)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s3.374) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500947@unknown@formal@none@1@S@In all cases, dEGFRλ;dp110CAAX overexpression did not induce neoplastic overgrowth of glial or neuronal cell types, as determined by brain size and cell-type specific stains.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 30) (:start . 14) (:id . 46))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 45) (:start . 31) (:id . 47))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 60)\n  (:start . 54) (:id . 50))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "overgrowth") (:form . "overgrowth") (:end . 82)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 91) (:start . 86)\n  (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 94) (:start . 92)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 103)\n  (:start . 95) (:id . 56))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 108) (:start . 104)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 114)\n  (:start . 109) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 118) (:start . 116)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 129)\n  (:start . 119) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 132) (:start . 130)\n  (:id . 62))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 138)\n  (:start . 133) (:id . 63))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 143) (:start . 139)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "cell-type") (:form . "cell-type") (:end . 157)\n  (:start . 148) (:id . 66))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 166)\n  (:start . 158) (:id . 67))\n ((:tag . "NNS") (:stem . "stain") (:form . "stains") (:end . 173)\n  (:start . 167) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.375) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500948@unknown@formal@none@1@S@(E,F) Cytoplasmic GFP (green), driven by the Nrv2-Gal4 driver, labels cell bodies and cytoplasmic processes, as seen in wild-type (E).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E,F") (:form . "E,F") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "Cytoplasmic") (:end . 17)\n  (:start . 6) (:id . 45))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 28) (:start . 23)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 37)\n  (:start . 31) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 40) (:start . 38)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 53))\n ((:tag . "NN") (:stem . "nrv2-gal4") (:form . "Nrv2-Gal4") (:end . 54)\n  (:start . 45) (:id . 54))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 61)\n  (:start . 55) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "label") (:form . "labels") (:end . 69)\n  (:start . 63) (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 74) (:start . 70)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 81) (:start . 75)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 97)\n  (:start . 86) (:id . 61))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 107)\n  (:start . 98) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 111) (:start . 109)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 116) (:start . 112)\n  (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 129)\n  (:start . 120) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 68))\n ((:tag . "NN") (:stem . "e") (:form . "E") (:end . 132) (:start . 131)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.376) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500949@unknown@formal@none@1@S@dEGFRλ;dp110CAAX overexpressed using the Nrv2-Gal4 glial driver (B).@(((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 16) (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 30) (:start . 17) (:id . 43))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 36) (:start . 31)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 45))\n ((:tag . "NN") (:stem . "nrv2-gal4") (:form . "Nrv2-Gal4") (:end . 50)\n  (:start . 41) (:id . 46))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 56) (:start . 51)\n  (:id . 47))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 63)\n  (:start . 57) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 66) (:start . 65)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.377) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500950@unknown@formal@none@1@S@Nrv2-Gal4 is expressed by post-mitotic cortex glia, which proliferate somewhat in response to dEGFRλ;dp110CAAX to cause slight brain enlargement, but do not become neoplastic like repo>dEGFRλ;dp110CAAX glia.@(((:tag . "NNP") (:stem . "Nrv2-Gal4") (:form . "Nrv2-Gal4") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "post-mitotic") (:form . "post-mitotic") (:end . 38)\n  (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "cortex") (:form . "cortex") (:end . 45)\n  (:start . 39) (:id . 47))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 50) (:start . 46)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "proliferate") (:form . "proliferate") (:end . 69)\n  (:start . 58) (:id . 51))\n ((:tag . "RB") (:stem . "somewhat") (:form . "somewhat") (:end . 78)\n  (:start . 70) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 90)\n  (:start . 82) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 110) (:start . 94) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n  (:id . 57))\n ((:tag . "VB") (:stem . "cause") (:form . "cause") (:end . 119)\n  (:start . 114) (:id . 58))\n ((:tag . "JJ") (:stem . "slight") (:form . "slight") (:end . 126)\n  (:start . 120) (:id . 59))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 132)\n  (:start . 127) (:id . 60))\n ((:tag . "NN") (:stem . "enlargement") (:form . "enlargement") (:end . 144)\n  (:start . 133) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 62))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 149) (:start . 146)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 152) (:start . 150)\n  (:id . 64))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 156) (:start . 153)\n  (:id . 65))\n ((:tag . "VB") (:stem . "become") (:form . "become") (:end . 163)\n  (:start . 157) (:id . 66))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 174)\n  (:start . 164) (:id . 67))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 179) (:start . 175)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 201) (:start . 180) (:id . 69))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 206) (:start . 202)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.378) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500951@unknown@formal@none@1@S@Genotypes: (A) +/CyO (B) UAS-dEGFRλ UAS-dp110CAAX/+; 1407-Gal4/UAS-Gal4 (C) UAS-dEGFRλ UAS-dp110CAAX/+; UAS-Gal4/+; pros-Gal4/+ (D) UAS-dEGFRλ UAS-dp110CAAX/+; gcm-Gal4/+ (E) Nrv2-Gal4 UAS-GFP/+; Nrv2-Gal4 UAS-GFP/+ (F) UAS-dEGFRλ UAS-dp110CAAX/+; Nrv2-Gal4 UAS-GFP/UAS-Gal4; Nrv2-Gal4 UAS-GFP/+. (7.96 MB TIF)@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotypes") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "+/CyO") (:form . "+/CyO") (:end . 20) (:start . 15)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 48))\n ((:tag . "NNP") (:stem . 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5500952@unknown@formal@none@1@S@Figure S8 Coactivation of EGFR and PI3K in glial progenitors creates invasive neoplastic glia.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S8") (:form . "S8") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 22)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 60)\n  (:start . 49) (:id . 51))\n ((:tag . "VBZ") (:stem . "create") (:form . "creates") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 88)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 93) (:start . 89)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.380) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500953@unknown@formal@none@1@S@(A–E) FLP/FRT clones in adult brains derived from a population of ey-FLP and repo-Gal4-expressing cells.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–E") (:form . "A–E") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "FLP/FRT") (:form . "FLP/FRT") (:end . 13)\n  (:start . 6) (:id . 45))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 20)\n  (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 29) (:start . 24)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 36)\n  (:start . 30) (:id . 49))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 44)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 49) (:start . 45)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 62)\n  (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "NN") (:stem . "ey-flp") (:form . "ey-FLP") (:end . 72)\n  (:start . 66) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "NN") (:stem . "repo-gal4-expressing")\n  (:form . "repo-Gal4-expressing") (:end . 97) (:start . 77) (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 103) (:start . 98)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.381) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500954@unknown@formal@none@1@S@CD8GFP (green) marks cell bodies and membranes of glial clones derived by FLP/FRT mitotic recombination (see text).@(((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "mark") (:form . "marks") (:end . 20) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 32) (:start . 26)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 46)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 55) (:start . 50)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 62)\n  (:start . 56) (:id . 53))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 70)\n  (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "FLP/FRT") (:form . "FLP/FRT") (:end . 81)\n  (:start . 74) (:id . 56))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 89)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n  (:end . 103) (:start . 90) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n  (:id . 59))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 108) (:start . 105)\n  (:id . 60))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.382) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500955@unknown@formal@none@1@S@Repo (red) marks all glial cell nuclei, in both clones and surrounding normal tissue.@(((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 10) (:start . 9)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "mark") (:form . "marks") (:end . 16) (:start . 11)\n  (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 20) (:start . 17)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 26) (:start . 21)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 31) (:start . 27)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 38)\n  (:start . 32) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 52))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 47) (:start . 43)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 54)\n  (:start . 48) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "surround") (:form . "surrounding") (:end . 70)\n  (:start . 59) (:id . 56))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 77)\n  (:start . 71) (:id . 57))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 84)\n  (:start . 78) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.383) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500956@unknown@formal@none@1@S@8.5 µm confocal optical sections through brains of similarly aged adults, all matched to scale.@(((:tag . "CD") (:stem . "8.5") (:form . "8.5") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 15)\n  (:start . 7) (:id . 44))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 47)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "RB") (:stem . "similarly") (:form . "similarly") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 72)\n  (:start . 66) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 77) (:start . 74)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "match") (:form . "matched") (:end . 85)\n  (:start . 78) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 94) (:start . 89)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.384) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500957@unknown@formal@none@1@S@20 µm scale bars.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.385) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500958@unknown@formal@none@1@S@Each panel shows half brains, including a whole optic lobe and adjacent central brain.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "half") (:form . "half") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 39)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "optic") (:form . "optic") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "lobe") (:form . "lobe") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 71)\n  (:start . 63) (:id . 54))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 79)\n  (:start . 72) (:id . 55))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.386) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500959@unknown@formal@none@1@S@dEGFRElp (C) and dPTEN-/- (J) clones are composed of 2–5-fold more cells than wild-type controls (H).@(((:tag . "NN") (:stem . "degfrelp") (:form . "dEGFRElp") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "dpten-/-") (:form . "dPTEN-/-") (:end . 25)\n  (:start . 17) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "j") (:form . "J") (:end . 28) (:start . 27)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 36)\n  (:start . 30) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 49)\n  (:start . 41) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "2–5-fold") (:form . "2–5-fold") (:end . 61)\n  (:start . 53) (:id . 55))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 66) (:start . 62)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 72) (:start . 67)\n  (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 77) (:start . 73)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 87)\n  (:start . 78) (:id . 59))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 96)\n  (:start . 88) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 99) (:start . 98)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.387) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500960@unknown@formal@none@1@S@In contrast, dEGFRλ;dPTEN-/- (D) and dEGFRElp;PTEN-/- double mutant clones form large tumors visible in adult brains.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "dEGFRλ;dPTEN-/-") (:form . "dEGFRλ;dPTEN-/-")\n  (:end . 28) (:start . 13) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dEGFRElp;PTEN-/-") (:form . "dEGFRElp;PTEN-/-")\n  (:end . 53) (:start . 37) (:id . 50))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 67)\n  (:start . 61) (:id . 52))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 74)\n  (:start . 68) (:id . 53))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 85) (:start . 80)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "tumor") (:form . "tumors") (:end . 92)\n  (:start . 86) (:id . 56))\n ((:tag . "JJ") (:stem . "visible") (:form . "visible") (:end . 100)\n  (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 109)\n  (:start . 104) (:id . 59))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 116)\n  (:start . 110) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.388) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500961@unknown@formal@none@1@S@As with hs-FLP clones, dEGFRλ;dPTEN-/- and dEGFRElp;dPTEN-/- clones are less cellular and more invasive than dRas85DV12;PTEN-/- clones (see Figure 4).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "hs-flp") (:form . "hs-FLP") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "dEGFRλ;dPTEN-/-") (:form . "dEGFRλ;dPTEN-/-")\n  (:end . 38) (:start . 23) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dEGFRElp;dPTEN-/-") (:form . "dEGFRElp;dPTEN-/-")\n  (:end . 60) (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 67)\n  (:start . 61) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 71) (:start . 68)\n  (:id . 51))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 76) (:start . 72)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 85)\n  (:start . 77) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 54))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "invasive") (:form . "invasive") (:end . 103)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 108) (:start . 104)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "dRas85DV12;PTEN-/-") (:form . "dRas85DV12;PTEN-/-")\n  (:end . 127) (:start . 109) (:id . 58))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 134)\n  (:start . 128) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 136) (:start . 135)\n  (:id . 60))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 139) (:start . 136)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 146)\n  (:start . 140) (:id . 62))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 148) (:start . 147)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.389) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500962@unknown@formal@none@1@S@Genotypes: (A) ey-flp/+; FRT40A tubGal80/FRT,40A; repo-Gal4 UAS-CD8GFP/+ (B) ey-flp/+; FRT40A tubGal80/FRT40A PTEN2L117; repo-Gal4 UAS-CD8GFP/+ (C) ey-flp/+; FRTG13 tubGal80/FRTG13 UAS-CD8GFP; repo-Gal4/UAS-dEGFRElp (D) ey-flp/UAS- dEGFRλ; FRT40A tubGal80/FRT40A PTEN2L117; repo-Gal4 UAS-CD8GFP/UAS- dEGFRλ (E) ey-flp/+; FRT40A tubGal80/FRT40A PTEN2L117; repo-Gal4 UAS-CD8GFP/UAS-dEGFRElp. (7.84 MB TIF)@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotypes") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "ey-flp/+") (:form . "ey-flp/+") (:end . 23)\n  (:start . 15) (:id . 47))\n ((:tag . ":") (:stem . 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5500963@unknown@formal@none@1@S@Figure S9 Stg overexpression exacerbates EGFR-PI3K glial neoplasia.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S9") (:form . "S9") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Stg") (:form . "Stg") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 28) (:start . 14) (:id . 45))\n ((:tag . "VBZ") (:stem . "exacerbate") (:form . "exacerbates") (:end . 40)\n  (:start . 29) (:id . 46))\n ((:tag . "NNP") (:stem . "EGFR-PI3K") (:form . "EGFR-PI3K") (:end . 50)\n  (:start . 41) (:id . 47))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 56) (:start . 51)\n  (:id . 48))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 66)\n  (:start . 57) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.391) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500964@unknown@formal@none@1@S@2 µm optical sections of larval brain hemispheres from late 3rd instar larvae, displayed at the same scale.@(((:tag . "LS") (:stem . "2") (:form . "2") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . "µm") (:form . "µm") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "hemisphere") (:form . "hemispheres") (:end . 49)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "3rd") (:form . "3rd") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 70)\n  (:start . 64) (:id . 53))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "display") (:form . "displayed") (:end . 88)\n  (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.392) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500965@unknown@formal@none@1@S@20 µm scale bars.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.393) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500966@unknown@formal@none@1@S@Frontal sections, midway through brains.@(((:tag . "JJ") (:stem . "frontal") (:form . "Frontal") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "RB") (:stem . "midway") (:form . "midway") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 40) (:start . 39)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.394) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500967@unknown@formal@none@1@S@Anterior up; midline to left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "left") (:form . "left") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.395) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500968@unknown@formal@none@1@S@Glial cell nuclei are labeled with Repo (red); glial cell bodies and membranes are labeled with CD8GFP (green) driven by repo-Gal4.@(((:tag . "JJ") (:stem . "glial") (:form . "Glial") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 46) (:start . 45)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 52) (:start . 47)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 57) (:start . 53)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 64) (:start . 58)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 78)\n  (:start . 69) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 90)\n  (:start . 83) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 95) (:start . 91)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 102)\n  (:start . 96) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 109)\n  (:start . 104) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 117)\n  (:start . 111) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 120) (:start . 118)\n  (:id . 66))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 130)\n  (:start . 121) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.396) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500969@unknown@formal@none@1@S@An HRP counter-stain (blue) reveals neuropil at high intensity and neuronal cell bodies at low intensity.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "counter-stain") (:form . "counter-stain")\n  (:end . 20) (:start . 7) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "neuropil") (:form . "neuropil") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 75)\n  (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 87) (:start . 81)\n  (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 104)\n  (:start . 95) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s3.397) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500970@unknown@formal@none@1@S@HRP stains varied between the two samples according to effects of mutant glia and slight variance in section plane.@(((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "stain") (:form . "stains") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "vary") (:form . "varied") (:end . 17) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 62)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 72)\n  (:start . 66) (:id . 53))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "slight") (:form . "slight") (:end . 88)\n  (:start . 82) (:id . 56))\n ((:tag . "NN") (:stem . "variance") (:form . "variance") (:end . 97)\n  (:start . 89) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 108)\n  (:start . 101) (:id . 59))\n ((:tag . "NN") (:stem . "plane") (:form . "plane") (:end . 114)\n  (:start . 109) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.398) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500971@unknown@formal@none@1@S@Stg co-overexpression with dEGFRλ;dp110CAAX (B) enhances neoplasia compared to dEGFRλ;dp110CAAX (A), leading to a dramatic increase in aberrant glia and yielding a phenotype similar to that of repo>Rbf1dsRNA;dEGFRλ;dp110CAAX (see Figure 8G).@(((:tag . "NN") (:stem . "stg") (:form . "Stg") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "co-overexpression") (:form . "co-overexpression")\n  (:end . 21) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 43) (:start . 27) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 46) (:start . 45)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "enhance") (:form . "enhances") (:end . 56)\n  (:start . 48) (:id . 49))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 66)\n  (:start . 57) (:id . 50))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 75)\n  (:start . 67) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 95) (:start . 79) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 98) (:start . 97)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 108)\n  (:start . 101) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "dramatic") (:form . "dramatic") (:end . 122)\n  (:start . 114) (:id . 61))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 131)\n  (:start . 123) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 143)\n  (:start . 135) (:id . 64))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 148) (:start . 144)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "yield") (:form . "yielding") (:end . 161)\n  (:start . 153) (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 163) (:start . 162)\n  (:id . 68))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 173)\n  (:start . 164) (:id . 69))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 181)\n  (:start . 174) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 184) (:start . 182)\n  (:id . 71))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 189) (:start . 185)\n  (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 192) (:start . 190)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "repo>Rbf1dsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>Rbf1dsRNA;dEGFRλ;dp110CAAX") (:end . 224) (:start . 193)\n  (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 226) (:start . 225)\n  (:id . 75))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 229) (:start . 226)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 236)\n  (:start . 230) (:id . 77))\n ((:tag . "NN") (:stem . "8g") (:form . "8G") (:end . 239) (:start . 237)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 240) (:start . 239)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 241) (:start . 240)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s3.399) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500972@unknown@formal@none@1@S@Genotypes: (A) UAS-dEGFRλ UAS-dp110CAAX/+; repo-Gal4 UAS-CD8GFP/+ (B) UAS-dEGFRλ UAS-dp110CAAX/+; UAS-stg/+; repo-Gal4 UAS-CD8GFP/+. (6.27 MB TIF)@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotypes") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "UAS-dEGFRλ") (:form . "UAS-dEGFRλ") (:end . 25)\n  (:start . 15) (:id . 47))\n ((:tag . "JJ") (:stem . "uas-dp110caax/+") (:form . "UAS-dp110CAAX/+")\n  (:end . 41) (:start . 26) (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 65)\n  (:start . 53) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "UAS-dEGFRλ") (:form . "UAS-dEGFRλ") (:end . 80)\n  (:start . 70) (:id . 55))\n ((:tag . "JJ") (:stem . "uas-dp110caax/+") (:form . "UAS-dp110CAAX/+")\n  (:end . 96) (:start . 81) (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 97) (:start . 96)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "uas-stg/+") (:form . "UAS-stg/+") (:end . 107)\n  (:start . 98) (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 108) (:start . 107)\n  (:id . 59))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 118)\n  (:start . 109) (:id . 60))\n ((:tag . "NNP") (:stem . "UAS-CD8GFP/+.") (:form . "UAS-CD8GFP/+.")\n  (:end . 132) (:start . 119) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 62))\n ((:tag . "CD") (:stem . "6.27") (:form . "6.27") (:end . 138) (:start . 134)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 141) (:start . 139)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 145) (:start . 142)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.400) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500973@unknown@formal@none@1@S@Figure S10 Knock-down and/or overexpression of dTor and dTor effectors.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S10") (:form . "S10") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Knock-down") (:form . "Knock-down") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 43) (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dtor") (:form . "dTor") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dtor") (:form . "dTor") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "effector") (:form . "effectors") (:end . 70)\n  (:start . 61) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s3.401) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500974@unknown@formal@none@1@S@2 µm optical sections of larval brain hemispheres from wandering 3rd instar larvae, approximately 130hr AED, all displayed at the same scale.@(((:tag . "LS") (:stem . "2") (:form . "2") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . "µm") (:form . "µm") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "hemisphere") (:form . "hemispheres") (:end . 49)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "wander") (:form . "wandering") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "JJ") (:stem . "3rd") (:form . "3rd") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 75)\n  (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 82)\n  (:start . 76) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 97) (:start . 84) (:id . 56))\n ((:tag . "CD") (:stem . "130hr") (:form . "130hr") (:end . 103) (:start . 98)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "AED") (:form . "AED") (:end . 107) (:start . 104)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 59))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 112) (:start . 109)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 122)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 125) (:start . 123)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 134) (:start . 130)\n  (:id . 64))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 140)\n  (:start . 135) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.402) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500975@unknown@formal@none@1@S@20 µm scale bars.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.403) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500976@unknown@formal@none@1@S@Anterior up; midline to the left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "left") (:form . "left") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 33) (:start . 32)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s3.404) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500977@unknown@formal@none@1@S@Frontal sections; midway through brains.@(((:tag . "JJ") (:stem . "frontal") (:form . "Frontal") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "RB") (:stem . "midway") (:form . "midway") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 40) (:start . 39)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.405) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500978@unknown@formal@none@1@S@Repo (red) marks glial cell nuclei; CD8GFP (green), driven by repo-Gal4, labels glial cell bodies and membranes.@(((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 10) (:start . 9)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "mark") (:form . "marks") (:end . 16) (:start . 11)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 22) (:start . 17)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 27) (:start . 23)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 34)\n  (:start . 28) (:id . 49))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 35) (:start . 34)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 42)\n  (:start . 36) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 49) (:start . 44)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 58)\n  (:start . 52) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 61) (:start . 59)\n  (:id . 57))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 71)\n  (:start . 62) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "label") (:form . "labels") (:end . 79)\n  (:start . 73) (:id . 60))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 85) (:start . 80)\n  (:id . 61))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 90) (:start . 86)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 97) (:start . 91)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 111)\n  (:start . 102) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.406) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500979@unknown@formal@none@1@S@An HRP-counter stain (blue) reveals neuropil (neuronal fiber tracts) at high intensity and some cell bodies of neurons and neuronal precursors at low intensity, and this varies slightly according to exact plane of section, brain orientation, and mutant phenotype.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "hrp-counter") (:form . "HRP-counter") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "stain") (:form . "stain") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "neuropil") (:form . "neuropil") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "fiber") (:form . "fiber") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 67)\n  (:start . 61) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 76) (:start . 72)\n  (:id . 56))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 86)\n  (:start . 77) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 95) (:start . 91)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 107)\n  (:start . 101) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 118)\n  (:start . 111) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 131)\n  (:start . 123) (:id . 65))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 142)\n  (:start . 132) (:id . 66))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 145) (:start . 143)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 149) (:start . 146)\n  (:id . 68))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 159)\n  (:start . 150) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n  (:id . 71))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 169) (:start . 165)\n  (:id . 72))\n ((:tag . "VBZ") (:stem . "vary") (:form . "varies") (:end . 176)\n  (:start . 170) (:id . 73))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 185)\n  (:start . 177) (:id . 74))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 195)\n  (:start . 186) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 198) (:start . 196)\n  (:id . 76))\n ((:tag . "VB") (:stem . "exact") (:form . "exact") (:end . 204)\n  (:start . 199) (:id . 77))\n ((:tag . "NN") (:stem . "plane") (:form . "plane") (:end . 210)\n  (:start . 205) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 213) (:start . 211)\n  (:id . 79))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 221)\n  (:start . 214) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 222) (:start . 221)\n  (:id . 81))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 228)\n  (:start . 223) (:id . 82))\n ((:tag . "NN") (:stem . "orientation") (:form . "orientation") (:end . 240)\n  (:start . 229) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 241) (:start . 240)\n  (:id . 84))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 245) (:start . 242)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 252)\n  (:start . 246) (:id . 86))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 262)\n  (:start . 253) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 263) (:start . 262)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s3.407) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500980@unknown@formal@none@1@S@repo>dAktdsRNA brains (B) are smaller and have fewer glia than wild-type controls (A).@(((:tag . "JJ") (:stem . "repo>dAktdsRNA") (:form . "repo>dAktdsRNA")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 21)\n  (:start . 15) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 37)\n  (:start . 30) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 52) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 72)\n  (:start . 63) (:id . 54))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.408) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500981@unknown@formal@none@1@S@All other genotypes have relatively normal sized brains.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 42)\n  (:start . 36) (:id . 47))\n ((:tag . "JJ") (:stem . "sized") (:form . "sized") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 55)\n  (:start . 49) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s3.409) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500982@unknown@formal@none@1@S@By gross examination, repo>TorTED (C), repo>dRaptordsRNA (E), repo>deIF4EdsRNA (F) and repo>dS6KdsRNA (G) display an estimated 10–20% reduction in glial cell numbers.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "gross") (:form . "gross") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "examination") (:form . "examination") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "repo>TorTED") (:form . "repo>TorTED") (:end . 33)\n  (:start . 22) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "repo>dRaptordsRNA") (:form . "repo>dRaptordsRNA")\n  (:end . 56) (:start . 39) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "repo>deIF4EdsRNA") (:form . "repo>deIF4EdsRNA")\n  (:end . 78) (:start . 62) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 81) (:start . 80)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "repo>dS6KdsRNA") (:form . "repo>dS6KdsRNA")\n  (:end . 101) (:start . 87) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 104) (:start . 103)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 113)\n  (:start . 106) (:id . 65))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 116) (:start . 114)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "estimated") (:form . "estimated") (:end . 126)\n  (:start . 117) (:id . 67))\n ((:tag . "CD") (:stem . "10–20") (:form . "10–20") (:end . 132)\n  (:start . 127) (:id . 68))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 133) (:start . 132)\n  (:id . 69))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 143)\n  (:start . 134) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 152)\n  (:start . 147) (:id . 72))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 157) (:start . 153)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 165)\n  (:start . 158) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s3.410) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500983@unknown@formal@none@1@S@repo>dTSC1dsRNA (D), repo>Rheb (H) and repo>deIF4E (I) brains contain normal numbers of glia.@(((:tag . "NNP") (:stem . "repo>dTSC1dsRNA") (:form . "repo>dTSC1dsRNA")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 17) (:start . 16)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "repo>Rheb") (:form . "repo>Rheb") (:end . 30)\n  (:start . 21) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 33) (:start . 32)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 34) (:start . 33)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "repo>deIF4E") (:form . "repo>deIF4E") (:end . 50)\n  (:start . 39) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . "NN") (:stem . "i") (:form . "I") (:end . 53) (:start . 52)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 54) (:start . 53)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 61)\n  (:start . 55) (:id . 56))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 69)\n  (:start . 62) (:id . 57))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 76)\n  (:start . 70) (:id . 58))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 84)\n  (:start . 77) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 60))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 92) (:start . 88)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.411) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500984@unknown@formal@none@1@S@Genotypes: (A) repo-Gal4 UAS-CD8GFP/+ (B) UAS-CD8GFP/+; repo-Gal4/UAS-dAktdsRNA (C) UAS-TorTED/UAS-CD8GFP; repo-Gal4/+ (D) UAS-CD8GFP/+; repo-Gal4/UAS-dTSC1dsRNA (E) UAS-dRaptordsRNA/UAS-CD8GFP; repo-Gal4/+ (F) UAS-CD8GFP/+; repo-Gal4/UAS-deIF4EdsRNA (G) UAS-dS6KdsRNA; UAS-CD8GFP/+; repo-Gal4/+ (H) UAS-CD8GFP/+; repo-Gal4/UAS-Rheb (I) UAS-CD8GFP//UAS-deIF4E; repo-Gal4/+. (8.83 MB TIF)@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotypes") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 24)\n  (:start . 15) (:id . 47))\n ((:tag . "JJ") (:stem . 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"H") (:form . "H") (:end . 298) (:start . 297)\n  (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 299) (:start . 298)\n  (:id . 89))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 312)\n  (:start . 300) (:id . 90))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 313) (:start . 312)\n  (:id . 91))\n ((:tag . "NN") (:stem . "repo-gal4/uas-rheb") (:form . "repo-Gal4/UAS-Rheb")\n  (:end . 332) (:start . 314) (:id . 92))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 334) (:start . 333)\n  (:id . 93))\n ((:tag . "NN") (:stem . "i") (:form . "I") (:end . 335) (:start . 334)\n  (:id . 94))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 336) (:start . 335)\n  (:id . 95))\n ((:tag . "NN") (:stem . "uas-cd8gfp//uas-deif4e")\n  (:form . "UAS-CD8GFP//UAS-deIF4E") (:end . 359) (:start . 337) (:id . 96))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 360) (:start . 359)\n  (:id . 97))\n ((:tag . "NNP") (:stem . "repo-Gal4/+.") (:form . "repo-Gal4/+.")\n  (:end . 373) (:start . 361) (:id . 98))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 375) (:start . 374)\n  (:id . 99))\n ((:tag . "CD") (:stem . "8.83") (:form . "8.83") (:end . 379) (:start . 375)\n  (:id . 100))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 382) (:start . 380)\n  (:id . 101))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 386) (:start . 383)\n  (:id . 102))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 387) (:start . 386)\n  (:id . 103)))@@@1@62@((:identifiers (:sid . :s3.412) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500985@unknown@formal@none@1@S@Figure S11 Validation of dsRNA constructs.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S11") (:form . "S11") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "validation") (:form . "Validation") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.413) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500986@unknown@formal@none@1@S@2 µm optical sections of larval brain hemispheres from wandering 3rd instar larvae.@(((:tag . "LS") (:stem . "2") (:form . "2") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . "µm") (:form . "µm") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "hemisphere") (:form . "hemispheres") (:end . 49)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "wander") (:form . "wandering") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "JJ") (:stem . "3rd") (:form . "3rd") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 75)\n  (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 82)\n  (:start . 76) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.414) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500987@unknown@formal@none@1@S@Frontal sections.@(((:tag . "JJ") (:stem . "frontal") (:form . "Frontal") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 44)))@@@1@3@((:identifiers (:sid . :s3.415) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500988@unknown@formal@none@1@S@Anterior up, midline to the left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "left") (:form . "left") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 33) (:start . 32)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s3.416) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500989@unknown@formal@none@1@S@Each individual staining pattern is shown alone (left panels) and with overlaid glial or neuronal markers (right panels).@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 47) (:start . 42)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "left") (:form . "left") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "overlaid") (:form . "overlaid") (:end . 79)\n  (:start . 71) (:id . 55))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 97)\n  (:start . 89) (:id . 58))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 105)\n  (:start . 98) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 112)\n  (:start . 107) (:id . 61))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 119)\n  (:start . 113) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.417) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500990@unknown@formal@none@1@S@Repo (blue) in (A–J) marks glial cell nuclei.@(((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 14) (:start . 12)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 16) (:start . 15)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "A–J") (:form . "A–J") (:end . 19) (:start . 16)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 20) (:start . 19)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "mark") (:form . "marks") (:end . 26) (:start . 21)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 32) (:start . 27)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 37) (:start . 33)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 44)\n  (:start . 38) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.418) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500991@unknown@formal@none@1@S@Glial cell bodies and membranes are labeled with CD8GFP (green) driven by repo-Gal4.@(((:tag . "JJ") (:stem . "glial") (:form . "Glial") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 17) (:start . 11)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 70)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 83)\n  (:start . 74) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.419) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500992@unknown@formal@none@1@S@In (K,L) an HRP counter-stain (blue) reveals neurons.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "K,L") (:form . "K,L") (:end . 7) (:start . 4)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 8) (:start . 7) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 11) (:start . 9)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 15) (:start . 12)\n  (:id . 47))\n ((:tag . "NN") (:stem . "counter-stain") (:form . "counter-stain")\n  (:end . 29) (:start . 16) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 49))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 35) (:start . 31)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 36) (:start . 35)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 44)\n  (:start . 37) (:id . 52))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 52)\n  (:start . 45) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.420) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500993@unknown@formal@none@1@S@Red marks histochemical stains for each indicated protein in repo>dEGFRλ;dp110CAAX (A,C,E,G,I,K) and repo>dEGFRλ;dp110CAAX with each indicated dsRNA construct (B,D,F,H,J,L).@(((:tag . "JJ") (:stem . "red") (:form . "Red") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mark") (:form . "marks") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "histochemical") (:form . "histochemical")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "stain") (:form . "stains") (:end . 30)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 49)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 82) (:start . 61) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "A,C,E,G,I,K") (:form . "A,C,E,G,I,K") (:end . 95)\n  (:start . 84) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 122) (:start . 101) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 127) (:start . 123)\n  (:id . 57))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 132) (:start . 128)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 142)\n  (:start . 133) (:id . 59))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 148)\n  (:start . 143) (:id . 60))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 158)\n  (:start . 149) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "B,D,F,H,J,L") (:form . "B,D,F,H,J,L") (:end . 171)\n  (:start . 160) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.421) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500994@unknown@formal@none@1@S@Each dsRNA construct was expressed with repo-Gal4 to yield glial-specific knock-down, which left protein expression in surrounding neuronal tissue intact.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 49)\n  (:start . 40) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "VB") (:stem . "yield") (:form . "yield") (:end . 58) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "glial-specific") (:form . "glial-specific")\n  (:end . 73) (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "knock-down") (:form . "knock-down") (:end . 84)\n  (:start . 74) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 91) (:start . 86)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "leave") (:form . "left") (:end . 96) (:start . 92)\n  (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 104)\n  (:start . 97) (:id . 56))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 115)\n  (:start . 105) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 118) (:start . 116)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "surround") (:form . "surrounding") (:end . 130)\n  (:start . 119) (:id . 59))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 139)\n  (:start . 131) (:id . 60))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 146)\n  (:start . 140) (:id . 61))\n ((:tag . "JJ") (:stem . "intact") (:form . "intact") (:end . 153)\n  (:start . 147) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.422) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500995@unknown@formal@none@1@S@For the nuclear protein PntP1, knock-down was verified by the lack of glial-specific staining in the presence of the pntdsRNA (B), although PntP1 is present within neighboring neurons (‘N’).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "pntp1") (:form . "PntP1") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "knock-down") (:form . "knock-down") (:end . 41)\n  (:start . 31) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "glial-specific") (:form . "glial-specific")\n  (:end . 84) (:start . 70) (:id . 55))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 93)\n  (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 109)\n  (:start . 101) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "pntdsRNA") (:form . "pntdsRNA") (:end . 125)\n  (:start . 117) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 66))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 139)\n  (:start . 131) (:id . 67))\n ((:tag . "NNP") (:stem . "PntP1") (:form . "PntP1") (:end . 145)\n  (:start . 140) (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 148) (:start . 146)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 156)\n  (:start . 149) (:id . 70))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 163)\n  (:start . 157) (:id . 71))\n ((:tag . "VBG") (:stem . "neighbor") (:form . "neighboring") (:end . 175)\n  (:start . 164) (:id . 72))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 183)\n  (:start . 176) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 74))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 186) (:start . 185)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 187) (:start . 186)\n  (:id . 76))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 188) (:start . 187)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s3.423) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500996@unknown@formal@none@1@S@For dAkt, deIF4E, and dS6K, gene knock-down was confirmed using antibodies for total protein.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "dakt") (:form . "dAkt") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "deif4e") (:form . "deIF4E") (:end . 16)\n  (:start . 10) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "NN") (:stem . "ds6k") (:form . "dS6K") (:end . 26) (:start . 22)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 49))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 32) (:start . 28)\n  (:id . 50))\n ((:tag . "NN") (:stem . "knock-down") (:form . "knock-down") (:end . 43)\n  (:start . 33) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 57)\n  (:start . 48) (:id . 53))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 63) (:start . 58)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 74)\n  (:start . 64) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 84) (:start . 79)\n  (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 92)\n  (:start . 85) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s3.424) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500997@unknown@formal@none@1@S@Glial-specific reduction in gene expression by dAktdsRNA and deIF4EdsRNA is highlighted by white outlines in (D) and (F).@(((:tag . "JJ") (:stem . "glial-specific") (:form . "Glial-specific")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 24)\n  (:start . 15) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 44))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 32) (:start . 28)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 43)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 46) (:start . 44)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "dAktdsRNA") (:form . "dAktdsRNA") (:end . 56)\n  (:start . 47) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "deIF4EdsRNA") (:form . "deIF4EdsRNA") (:end . 72)\n  (:start . 61) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 75) (:start . 73)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 87)\n  (:start . 76) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 90) (:start . 88)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 96) (:start . 91)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "outline") (:form . "outlines") (:end . 105)\n  (:start . 97) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 111) (:start . 110)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 119) (:start . 118)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s3.425) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500998@unknown@formal@none@1@S@dAkt protein is higher in neuronal tissue (‘N’) in both repo>dEGFRλ;dp110CAAX (C) and repo>dAktdsRNA;dEGFRλ;dp110CAAX (D).@(((:tag . "NN") (:stem . "dakt") (:form . "dAkt") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 22) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 46) (:start . 45)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 54))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 55) (:start . 51)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 77) (:start . 56) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "repo>dAktdsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>dAktdsRNA;dEGFRλ;dp110CAAX") (:end . 117) (:start . 86)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 119) (:start . 118)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.426) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5500999@unknown@formal@none@1@S@deIF4E is high in dEGFRλ;dp110CAAX glia (E) and low in neurons (E,F).@(((:tag . "NNP") (:stem . "deIF4E") (:form . "deIF4E") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 34) (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 62)\n  (:start . 55) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "E,F") (:form . "E,F") (:end . 67) (:start . 64)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s3.427) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501000@unknown@formal@none@1@S@repo>deIF4EdsRNA;dEGFRλ;dp110CAAX brains (F) have reduced glial eIF4E.@(((:tag . "NNP") (:stem . "repo>deIF4EdsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>deIF4EdsRNA;dEGFRλ;dp110CAAX") (:end . 33) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 40)\n  (:start . 34) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 44))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 43) (:start . 42)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 49) (:start . 45)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 57)\n  (:start . 50) (:id . 48))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 63) (:start . 58)\n  (:id . 49))\n ((:tag . "NN") (:stem . "eif4e") (:form . "eIF4E") (:end . 69) (:start . 64)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s3.428) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501001@unknown@formal@none@1@S@Reduced glial dS6K protein, which is diffusely cytoplasmic, is observed in repo>dS6KdsRNA;dEGFRλ;dp110CAAX brains (H) compared to repo>dEGFRλ;dp110CAAX (G).@(((:tag . "VBN") (:stem . "reduce") (:form . "Reduced") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "ds6k") (:form . "dS6K") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "RB") (:stem . "diffusely") (:form . "diffusely") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 58)\n  (:start . 47) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 71)\n  (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "repo>dS6KdsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>dS6KdsRNA;dEGFRλ;dp110CAAX") (:end . 106) (:start . 75)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 113)\n  (:start . 107) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 116) (:start . 115)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 117) (:start . 116)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 126)\n  (:start . 118) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 129) (:start . 127)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 151) (:start . 130) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 154) (:start . 153)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s3.429) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501002@unknown@formal@none@1@S@Reduced glial dMyc expression in repo>dMycdsRNA;dEGFRλ;dp110CAAX brains (J) is noted by white outlines, and the absence of purple nuclei in overlay (J, right panel), relative to repo>dEGFRλ;dp110CAAX (I, right panel).@(((:tag . "VBN") (:stem . "reduce") (:form . "Reduced") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "repo>dMycdsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>dMycdsRNA;dEGFRλ;dp110CAAX") (:end . 64) (:start . 33)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 71)\n  (:start . 65) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 74) (:start . 73)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 78) (:start . 76)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 84) (:start . 79)\n  (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 87) (:start . 85)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 93) (:start . 88)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "outline") (:form . "outlines") (:end . 102)\n  (:start . 94) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 119)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "purple") (:form . "purple") (:end . 129)\n  (:start . 123) (:id . 62))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 136)\n  (:start . 130) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 139) (:start . 137)\n  (:id . 64))\n ((:tag . "NN") (:stem . "overlay") (:form . "overlay") (:end . 147)\n  (:start . 140) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 149) (:start . 148)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 150) (:start . 149)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 157)\n  (:start . 152) (:id . 69))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 163)\n  (:start . 158) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 164) (:start . 163)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 174)\n  (:start . 166) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 177) (:start . 175)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 199) (:start . 178) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 201) (:start . 200)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "I") (:form . "I") (:end . 202) (:start . 201)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 203) (:start . 202)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 209)\n  (:start . 204) (:id . 79))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 215)\n  (:start . 210) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 216) (:start . 215)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s3.430) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501003@unknown@formal@none@1@S@dMyc is highly expressed in neuroblasts (‘NB’) in both samples (I, J), which do not express the dMycdsRNA.@(((:tag . "NN") (:stem . "dmyc") (:form . "dMyc") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 39)\n  (:start . 28) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "NB") (:form . "NB") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 53))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 54) (:start . 50)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 62)\n  (:start . 55) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n  (:id . 56))\n ((:tag . "NN") (:stem . "i") (:form . "I") (:end . 65) (:start . 64)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 68) (:start . 67)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 76) (:start . 71)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 79) (:start . 77)\n  (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 83) (:start . 80)\n  (:id . 64))\n ((:tag . "VB") (:stem . "express") (:form . "express") (:end . 91)\n  (:start . 84) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 66))\n ((:tag . "NN") (:stem . "dmycdsrna") (:form . "dMycdsRNA") (:end . 105)\n  (:start . 96) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s3.431) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501004@unknown@formal@none@1@S@Glial Rbf1 protein is absent in repo>dRbf1dsRNA;dEGFRλ;dp110CAAX brains (L) in contrast to neighboring neurons (‘N’) in ,repo>dEGFRλ;dp110CAAX brains (K).@(((:tag . "JJ") (:stem . "glial") (:form . "Glial") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Rbf1") (:form . "Rbf1") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "absent") (:form . "absent") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "repo>dRbf1dsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>dRbf1dsRNA;dEGFRλ;dp110CAAX") (:end . 64) (:start . 32)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 71)\n  (:start . 65) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "L") (:form . "L") (:end . 74) (:start . 73)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "neighbor") (:form . "neighboring") (:end . 102)\n  (:start . 91) (:id . 56))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 110)\n  (:start . 103) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 58))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 114) (:start . 113)\n  (:id . 60))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 63))\n ((:tag . "NNP") (:stem . ",repo>dEGFRλ;dp110CAAX")\n  (:form . ",repo>dEGFRλ;dp110CAAX") (:end . 142) (:start . 120) (:id . 64))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 149)\n  (:start . 143) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "K") (:form . "K") (:end . 152) (:start . 151)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.432) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5501006@unknown@formal@none@1@S@Figure S12 Phospho-MPM2 reveals increased S-phase and M-phase glia in repo>dRbf1dsRNA;dEGFRλ;dp110CAAX brains.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S12") (:form . "S12") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "phospho-mpm2") (:form . "Phospho-MPM2") (:end . 23)\n  (:start . 11) (:id . 44))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 31)\n  (:start . 24) (:id . 45))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 41)\n  (:start . 32) (:id . 46))\n ((:tag . "NNP") (:stem . "S-phase") (:form . "S-phase") (:end . 49)\n  (:start . 42) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "M-phase") (:form . "M-phase") (:end . 61)\n  (:start . 54) (:id . 49))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 66) (:start . 62)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "repo>dRbf1dsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>dRbf1dsRNA;dEGFRλ;dp110CAAX") (:end . 102) (:start . 70)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 109)\n  (:start . 103) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.434) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501007@unknown@formal@none@1@S@(A–C) phospho-MPM2 expression (red) in wild-type brains (A), repo>dEGFRλ;dp110CAAX brains (B), and repo>dRbf1dsRNA;dEGFRλ;dp110CAAX brains (C).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–C") (:form . "A–C") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NN") (:stem . "phospho-mpm2") (:form . "phospho-MPM2") (:end . 18)\n  (:start . 6) (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 48)\n  (:start . 39) (:id . 51))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 55)\n  (:start . 49) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 58) (:start . 57)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 59) (:start . 58)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 82) (:start . 61) (:id . 57))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 89)\n  (:start . 83) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 92) (:start . 91)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "repo>dRbf1dsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>dRbf1dsRNA;dEGFRλ;dp110CAAX") (:end . 131) (:start . 99)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 138)\n  (:start . 132) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 141) (:start . 140)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s3.435) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501008@unknown@formal@none@1@S@20 µm scale bars.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.436) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501009@unknown@formal@none@1@S@Anterior up, midline to the left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "left") (:form . "left") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 33) (:start . 32)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s3.437) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501010@unknown@formal@none@1@S@6 µm optical projections showing representative superficial dorsal regions enriched for mitotic glia.@(((:tag . "CD") (:stem . "6") (:form . "6") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 47) (:start . 33) (:id . 47))\n ((:tag . "JJ") (:stem . "superficial") (:form . "superficial") (:end . 59)\n  (:start . 48) (:id . 48))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 66)\n  (:start . 60) (:id . 49))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 74)\n  (:start . 67) (:id . 50))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 83)\n  (:start . 75) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 87) (:start . 84)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 95)\n  (:start . 88) (:id . 53))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 100) (:start . 96)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.438) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501011@unknown@formal@none@1@S@Phospho-MPM2 shown alone (left panels), overlaid with the Repo (blue, middle panels), and CD8GFP (green, right panels) glial markers.@(((:tag . "NNP") (:stem . "Phospho-MPM2") (:form . "Phospho-MPM2") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 18) (:start . 13)\n  (:id . 43))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 24) (:start . 19)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "left") (:form . "left") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "overlay") (:form . "overlaid") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "middle") (:form . "middle") (:end . 76)\n  (:start . 70) (:id . 57))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 83)\n  (:start . 77) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 96)\n  (:start . 90) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 103) (:start . 98)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 110)\n  (:start . 105) (:id . 66))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 117)\n  (:start . 111) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 124)\n  (:start . 119) (:id . 69))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 132)\n  (:start . 125) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s3.439) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501012@unknown@formal@none@1@S@Phospho-MPM2 nuclear foci are present in S-phase cells (arrows note examples).@(((:tag . "NN") (:stem . "phospho-mpm2") (:form . "Phospho-MPM2") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 20)\n  (:start . 13) (:id . 43))\n ((:tag . "NNS") (:stem . "focus") (:form . "foci") (:end . 25) (:start . 21)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "S-phase") (:form . "S-phase") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 54) (:start . 49)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "arrow") (:form . "arrows") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "note") (:form . "note") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 76)\n  (:start . 68) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.440) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501013@unknown@formal@none@1@S@S-phase glia are clearly visible in the middle panel as purple cells with MPM2 foci, which appear enriched in repo>dRbf1dsRNA;dEGFRλ;dp110CAAX brains (C) relative to repo>dEGFRλ;dp110CAAX brains (B).@(((:tag . "NNP") (:stem . "S-phase") (:form . "S-phase") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "visible") (:form . "visible") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "middle") (:form . "middle") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "purple") (:form . "purple") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "NN") (:stem . "mpm2") (:form . "MPM2") (:end . 78) (:start . 74)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "focus") (:form . "foci") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 90) (:start . 85)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 97)\n  (:start . 91) (:id . 59))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 106)\n  (:start . 98) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 109) (:start . 107)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "repo>dRbf1dsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>dRbf1dsRNA;dEGFRλ;dp110CAAX") (:end . 142) (:start . 110)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 149)\n  (:start . 143) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 162)\n  (:start . 154) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 165) (:start . 163)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 187) (:start . 166) (:id . 69))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 194)\n  (:start . 188) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 196) (:start . 195)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 197) (:start . 196)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 198) (:start . 197)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s3.441) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501014@unknown@formal@none@1@S@In all genotypes, high levels of phospho-MPM2 is also expressed in mitotic cells (asterisks note examples).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 29)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "phospho-mpm2") (:form . "phospho-MPM2") (:end . 45)\n  (:start . 33) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 74)\n  (:start . 67) (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 80) (:start . 75)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "asterisk") (:form . "asterisks") (:end . 91)\n  (:start . 82) (:id . 57))\n ((:tag . "VBP") (:stem . "note") (:form . "note") (:end . 96) (:start . 92)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 105)\n  (:start . 97) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s3.442) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501015@unknown@formal@none@1@S@Mitotic glia showed low levels of Repo (middle panels), but are clearly GFP-positive (right panels), suggesting that Repo protein expression is reduced upon mitosis in glia.@(((:tag . "JJ") (:stem . "mitotic") (:form . "Mitotic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 19) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "middle") (:form . "middle") (:end . 46)\n  (:start . 40) (:id . 50))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 53)\n  (:start . 47) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 59) (:start . 56)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 63) (:start . 60)\n  (:id . 55))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 71)\n  (:start . 64) (:id . 56))\n ((:tag . "JJ") (:stem . "gfp-positive") (:form . "GFP-positive") (:end . 84)\n  (:start . 72) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 91) (:start . 86)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 98)\n  (:start . 92) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 111)\n  (:start . 101) (:id . 63))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 121) (:start . 117)\n  (:id . 65))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 129)\n  (:start . 122) (:id . 66))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 140)\n  (:start . 130) (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 143) (:start . 141)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 151)\n  (:start . 144) (:id . 69))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 156) (:start . 152)\n  (:id . 70))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 164)\n  (:start . 157) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 167) (:start . 165)\n  (:id . 72))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 172) (:start . 168)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x3.443.1) (:span 101 111)))\n (:hscopes ((:id . :x3.443.1) (:span 101 172)))\n (:identifiers (:sid . :s3.443) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501016@unknown@formal@none@1@S@repo>dRbf1dsRNA;dEGFRλ;dp110CAAX brains (C) also show increased density of phospho-MPM2-positive mitotic glia compared to repo>dEGFRλ;dp110CAAX brains (B).@(((:tag . "NNP") (:stem . "repo>dRbf1dsRNA;dEGFRλ;dp110CAAX")\n  (:form . "repo>dRbf1dsRNA;dEGFRλ;dp110CAAX") (:end . 32) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 39)\n  (:start . 33) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 42) (:start . 41)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 48) (:start . 44)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 53) (:start . 49)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 63)\n  (:start . 54) (:id . 49))\n ((:tag . "NN") (:stem . "density") (:form . "density") (:end . 71)\n  (:start . 64) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "phospho-mpm2-positive")\n  (:form . "phospho-MPM2-positive") (:end . 96) (:start . 75) (:id . 52))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 104)\n  (:start . 97) (:id . 53))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 109) (:start . 105)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 118)\n  (:start . 110) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 121) (:start . 119)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "repo>dEGFRλ;dp110CAAX")\n  (:form . "repo>dEGFRλ;dp110CAAX") (:end . 143) (:start . 122) (:id . 57))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 150)\n  (:start . 144) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 152) (:start . 151)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 153) (:start . 152)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.444) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5501018@unknown@formal@none@1@S@Genotypes: (A) repo-Gal4 UAS-CD8GFP/+ (B) UAS-dEGFRλ UAS-dp110CAAX/+; UAS-CD8GFP/+; repo-Gal4/+ (C) UAS-dEGFRλ UAS-dp110CAAX/+; repo-Gal4 UAS-CD8GFP/UAS-Rbf1dsRNA. (8.99 MB TIF)@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotypes") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 24)\n  (:start . 15) (:id . 47))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 37)\n  (:start . 25) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 41) (:start . 40)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "UAS-dEGFRλ") (:form . "UAS-dEGFRλ") (:end . 52)\n  (:start . 42) (:id . 52))\n ((:tag . "JJ") (:stem . "uas-dp110caax/+") (:form . "UAS-dp110CAAX/+")\n  (:end . 68) (:start . 53) (:id . 53))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 82)\n  (:start . 70) (:id . 55))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "repo-gal4/+") (:form . "repo-Gal4/+") (:end . 95)\n  (:start . 84) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "UAS-dEGFRλ") (:form . "UAS-dEGFRλ") (:end . 110)\n  (:start . 100) (:id . 61))\n ((:tag . "JJ") (:stem . "uas-dp110caax/+") (:form . "UAS-dp110CAAX/+")\n  (:end . 126) (:start . 111) (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 127) (:start . 126)\n  (:id . 63))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 137)\n  (:start . 128) (:id . 64))\n ((:tag . "NN") (:stem . "uas-cd8gfp/uas-rbf1dsrna.")\n  (:form . "UAS-CD8GFP/UAS-Rbf1dsRNA.") (:end . 163) (:start . 138)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 165) (:start . 164)\n  (:id . 66))\n ((:tag . "CD") (:stem . "8.99") (:form . "8.99") (:end . 169) (:start . 165)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 172) (:start . 170)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 176) (:start . 173)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 177) (:start . 176)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s3.446) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501019@unknown@formal@none@1@S@Table S1 Overexpression of EGFR-Ras and PI3K-Akt pathways in Drosophila glia. (0.08 MB PDF)@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Overexpression") (:form . "Overexpression")\n  (:end . 23) (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "EGFR-Ras") (:form . "EGFR-Ras") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PI3K-Akt") (:form . "PI3K-Akt") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "glia.") (:form . "glia.") (:end . 77) (:start . 72)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 53))\n ((:tag . "CD") (:stem . "0.08") (:form . "0.08") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PDF") (:form . "PDF") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.447) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501020@unknown@formal@none@1@S@Table S2 Coactivation of EGFR and PI3K does not elicit neoplasia in all neural cell types. (0.08 MB PDF)@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Coactivation") (:form . "Coactivation") (:end . 21)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "EGFR") (:form . "EGFR") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PI3K") (:form . "PI3K") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "VB") (:stem . "elicit") (:form . "elicit") (:end . 54)\n  (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "neoplasia") (:form . "neoplasia") (:end . 64)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 78)\n  (:start . 72) (:id . 55))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "NN") (:stem . "types.") (:form . "types.") (:end . 90)\n  (:start . 84) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . "CD") (:stem . "0.08") (:form . "0.08") (:end . 96) (:start . 92)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 99) (:start . 97)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "PDF") (:form . "PDF") (:end . 103) (:start . 100)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.448) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501021@unknown@formal@none@1@S@Table S3 Genetic analysis of Akt, Tor, Myc, and CyclinD-Cdk4 pathways in neoplastic and normal glia. (0.10 MB PDF)@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "genetic") (:form . "Genetic") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Akt") (:form . "Akt") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Tor") (:form . "Tor") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Myc") (:form . "Myc") (:end . 42) (:start . 39)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cyclind-cdk4") (:form . "CyclinD-Cdk4") (:end . 60)\n  (:start . 48) (:id . 54))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 69)\n  (:start . 61) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "neoplastic") (:form . "neoplastic") (:end . 83)\n  (:start . 73) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 94)\n  (:start . 88) (:id . 59))\n ((:tag . "NN") (:stem . "glia.") (:form . "glia.") (:end . 100) (:start . 95)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "CD") (:stem . "0.10") (:form . "0.10") (:end . 106) (:start . 102)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 109) (:start . 107)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "PDF") (:form . "PDF") (:end . 113) (:start . 110)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.449) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501022@unknown@formal@none@1@S@Video S1 An animated 7.5 µm thick confocal z-stack of dEGFRλ; dp110CAAX tumor cells derived from transplanted larval glia, pictured in Figure 3D.@(((:tag . "JJ") (:stem . "video") (:form . "Video") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "An") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "animate") (:form . "animated") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "CD") (:stem . "7.5") (:form . "7.5") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "thick") (:form . "thick") (:end . 33) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 42)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "z-stack") (:form . "z-stack") (:end . 50)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 60)\n  (:start . 54) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 71)\n  (:start . 62) (:id . 54))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 83) (:start . 78)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 91)\n  (:start . 84) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 96) (:start . 92)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 109)\n  (:start . 97) (:id . 59))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 116)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 121) (:start . 117)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "picture") (:form . "pictured") (:end . 131)\n  (:start . 123) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 141)\n  (:start . 135) (:id . 65))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 144) (:start . 142)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.450) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501023@unknown@formal@none@1@S@The depth of each frame is noted in the upper left-hand corner.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "depth") (:form . "depth") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 45) (:start . 40)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "left-hand") (:form . "left-hand") (:end . 55)\n  (:start . 46) (:id . 52))\n ((:tag . "NN") (:stem . "corner") (:form . "corner") (:end . 62)\n  (:start . 56) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.451) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501024@unknown@formal@none@1@S@20 µm scale bar for x/y-axis.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "x/y-axis") (:form . "x/y-axis") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.452) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501025@unknown@formal@none@1@S@Transplanted mutant glia are labeled with membrane bound CD8GFP (green) and the Repo nuclear protein (blue).@(((:tag . "VBN") (:stem . "transplant") (:form . "Transplanted") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 19)\n  (:start . 13) (:id . 43))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 24) (:start . 20)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "VBD") (:stem . "bind") (:form . "bound") (:end . 56) (:start . 51)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 63)\n  (:start . 57) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 51))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 70) (:start . 65)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.453) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501026@unknown@formal@none@1@S@Actin staining (red, phalloidin) reveals abdominal anatomy of the host.@(((:tag . "NNP") (:stem . "Actin") (:form . "Actin") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "phalloidin") (:form . "phalloidin") (:end . 31)\n  (:start . 21) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 40)\n  (:start . 33) (:id . 49))\n ((:tag . "JJ") (:stem . "abdominal") (:form . "abdominal") (:end . 50)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "anatomy") (:form . "anatomy") (:end . 58)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.454) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501027@unknown@formal@none@1@S@Asterisks indicate trachea embedded in the pictured dEGFRλ;dp110CAAX tumor, visible as hollow actin-positive (red) tubules running through tissues.@(((:tag . "NNS") (:stem . "asterisk") (:form . "Asterisks") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 18)\n  (:start . 10) (:id . 43))\n ((:tag . "NN") (:stem . "trachea") (:form . "trachea") (:end . 26)\n  (:start . 19) (:id . 44))\n ((:tag . "VBN") (:stem . "embed") (:form . "embedded") (:end . 35)\n  (:start . 27) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "picture") (:form . "pictured") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 68) (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 74) (:start . 69)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "visible") (:form . "visible") (:end . 83)\n  (:start . 76) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 86) (:start . 84)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "hollow") (:form . "hollow") (:end . 93)\n  (:start . 87) (:id . 54))\n ((:tag . "JJ") (:stem . "actin-positive") (:form . "actin-positive")\n  (:end . 108) (:start . 94) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 113) (:start . 110)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "tubule") (:form . "tubules") (:end . 122)\n  (:start . 115) (:id . 59))\n ((:tag . "VBG") (:stem . "run") (:form . "running") (:end . 130)\n  (:start . 123) (:id . 60))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 138)\n  (:start . 131) (:id . 61))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 146)\n  (:start . 139) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s3.455) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501028@unknown@formal@none@1@S@Genotypes: Hosts were w1118 virgin females.@(((:tag . "NNPS") (:stem . "Genotype") (:form . "Genotypes") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "host") (:form . "Hosts") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "CD") (:stem . "w1118") (:form . "w1118") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "virgin") (:form . "virgin") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "female") (:form . "females") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s3.456) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501029@unknown@formal@none@1@S@Transplanted glia were UAS-dEGFRλ UAS-dp110CAAX/+; UAS-CD8GFP/+; repo-Gal4/+. (1.54 MB MOV)@(((:tag . "VBN") (:stem . "transplant") (:form . "Transplanted") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 17) (:start . 13)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "UAS-dEGFRλ") (:form . "UAS-dEGFRλ") (:end . 33)\n  (:start . 23) (:id . 45))\n ((:tag . "JJ") (:stem . "uas-dp110caax/+") (:form . "UAS-dp110CAAX/+")\n  (:end . 49) (:start . 34) (:id . 46))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 50) (:start . 49)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 63)\n  (:start . 51) (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 64) (:start . 63)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "repo-Gal4/+.") (:form . "repo-Gal4/+.") (:end . 77)\n  (:start . 65) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1.54") (:form . "1.54") (:end . 83) (:start . 79)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 86) (:start . 84)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "MOV") (:form . "MOV") (:end . 90) (:start . 87)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.457) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501030@unknown@formal@none@1@S@Video S2 An animated 27 µm thick confocal z-stack of dEGFRλ; dp110CAAX tumor cells derived from transplanted larval glia, pictured in Figure 3F.@(((:tag . "JJ") (:stem . "video") (:form . "Video") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "An") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "animate") (:form . "animated") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "thick") (:form . "thick") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "z-stack") (:form . "z-stack") (:end . 49)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "dEGFRλ") (:form . "dEGFRλ") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "dp110CAAX") (:form . "dp110CAAX") (:end . 70)\n  (:start . 61) (:id . 54))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 82) (:start . 77)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 90)\n  (:start . 83) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 108)\n  (:start . 96) (:id . 59))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 115)\n  (:start . 109) (:id . 60))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 120) (:start . 116)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "picture") (:form . "pictured") (:end . 130)\n  (:start . 122) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 133) (:start . 131)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 140)\n  (:start . 134) (:id . 65))\n ((:tag . "NN") (:stem . "3f") (:form . "3F") (:end . 143) (:start . 141)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s3.458) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501031@unknown@formal@none@1@S@The depth of each frame is noted in the upper left-hand corner.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "depth") (:form . "depth") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 45) (:start . 40)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "left-hand") (:form . "left-hand") (:end . 55)\n  (:start . 46) (:id . 52))\n ((:tag . "NN") (:stem . "corner") (:form . "corner") (:end . 62)\n  (:start . 56) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.459) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501032@unknown@formal@none@1@S@20 µm scale bar for x/y-axis.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "x/y-axis") (:form . "x/y-axis") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.460) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501033@unknown@formal@none@1@S@Transplanted mutant glia are labeled with membrane bound CD8GFP (green) and the Repo nuclear protein (blue).@(((:tag . "VBN") (:stem . "transplant") (:form . "Transplanted") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 19)\n  (:start . 13) (:id . 43))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 24) (:start . 20)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "VBD") (:stem . "bind") (:form . "bound") (:end . 56) (:start . 51)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 63)\n  (:start . 57) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 51))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 70) (:start . 65)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Repo") (:form . "Repo") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.461) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501034@unknown@formal@none@1@S@Actin staining (red, phalloidin) reveals abdominal anatomy of the host.@(((:tag . "NNP") (:stem . "Actin") (:form . "Actin") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "phalloidin") (:form . "phalloidin") (:end . 31)\n  (:start . 21) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 40)\n  (:start . 33) (:id . 49))\n ((:tag . "JJ") (:stem . "abdominal") (:form . "abdominal") (:end . 50)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "anatomy") (:form . "anatomy") (:end . 58)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.462) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501035@unknown@formal@none@1@S@Arrowheads in indicate dEGFRλ;dp110CAAX glial cells invading an ovary, distinguished by its characteristic actin staining (bright red).@(((:tag . "NNS") (:stem . "arrowhead") (:form . "Arrowheads") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "indicate") (:form . "indicate") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 39) (:start . 23) (:id . 45))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 45) (:start . 40)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 51) (:start . 46)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "invade") (:form . "invading") (:end . 60)\n  (:start . 52) (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 63) (:start . 61)\n  (:id . 49))\n ((:tag . "NN") (:stem . "ovary") (:form . "ovary") (:end . 69) (:start . 64)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "distinguish") (:form . "distinguished") (:end . 84)\n  (:start . 71) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 87) (:start . 85)\n  (:id . 53))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 91) (:start . 88)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 106) (:start . 92) (:id . 55))\n ((:tag . "NN") (:stem . "actin") (:form . "actin") (:end . 112)\n  (:start . 107) (:id . 56))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 121)\n  (:start . 113) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "bright") (:form . "bright") (:end . 129)\n  (:start . 123) (:id . 59))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 133) (:start . 130)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.463) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501036@unknown@formal@none@1@S@An asterisk indicates trachea embedded in this dEGFRλ;dp110CAAX tumor, visible as a hollow actin-positive (red) tubule running through the tissue.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "asterisk") (:form . "asterisk") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "trachea") (:form . "trachea") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "VBN") (:stem . "embed") (:form . "embedded") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "dEGFRλ;dp110CAAX") (:form . "dEGFRλ;dp110CAAX")\n  (:end . 63) (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "tumor") (:form . "tumor") (:end . 69) (:start . 64)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "visible") (:form . "visible") (:end . 78)\n  (:start . 71) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "hollow") (:form . "hollow") (:end . 90)\n  (:start . 84) (:id . 55))\n ((:tag . "JJ") (:stem . "actin-positive") (:form . "actin-positive")\n  (:end . 105) (:start . 91) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 110) (:start . 107)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 59))\n ((:tag . "NN") (:stem . "tubule") (:form . "tubule") (:end . 118)\n  (:start . 112) (:id . 60))\n ((:tag . "VBG") (:stem . "run") (:form . "running") (:end . 126)\n  (:start . 119) (:id . 61))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 134)\n  (:start . 127) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 63))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 145)\n  (:start . 139) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s3.464) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501037@unknown@formal@none@1@S@Genotypes: Hosts were w1118 virgin females.@(((:tag . "NNPS") (:stem . "Genotype") (:form . "Genotypes") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "host") (:form . "Hosts") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "CD") (:stem . "w1118") (:form . "w1118") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "virgin") (:form . "virgin") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "female") (:form . "females") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s3.465) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501038@unknown@formal@none@1@S@Transplanted glia were UAS-dEGFRλ UAS-dp110CAAX/+; UAS-CD8GFP/+; repo-Gal4/+. (1.16 MB MOV)@(((:tag . "VBN") (:stem . "transplant") (:form . "Transplanted") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "glia") (:form . "glia") (:end . 17) (:start . 13)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "UAS-dEGFRλ") (:form . "UAS-dEGFRλ") (:end . 33)\n  (:start . 23) (:id . 45))\n ((:tag . "JJ") (:stem . "uas-dp110caax/+") (:form . "UAS-dp110CAAX/+")\n  (:end . 49) (:start . 34) (:id . 46))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 50) (:start . 49)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "uas-cd8gfp/+") (:form . "UAS-CD8GFP/+") (:end . 63)\n  (:start . 51) (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 64) (:start . 63)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "repo-Gal4/+.") (:form . "repo-Gal4/+.") (:end . 77)\n  (:start . 65) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1.16") (:form . "1.16") (:end . 83) (:start . 79)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 86) (:start . 84)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "MOV") (:form . "MOV") (:end . 90) (:start . 87)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s3.466) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501039@unknown@formal@none@1@S@Video S3 An animated 88 µm thick confocal z-stack of a hs-FLP/FRT clone of dPTEN-/-;dRas85DV12 cells pictured in Figure 4E.@(((:tag . "JJ") (:stem . "video") (:form . "Video") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "An") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "animate") (:form . "animated") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "CD") (:stem . "88") (:form . "88") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "thick") (:form . "thick") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "z-stack") (:form . "z-stack") (:end . 49)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "hs-flp/frt") (:form . "hs-FLP/FRT") (:end . 65)\n  (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "clone") (:form . "clone") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "CD") (:stem . "dPTEN-/-;dRas85DV12")\n  (:form . "dPTEN-/-;dRas85DV12") (:end . 94) (:start . 75) (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 100) (:start . 95)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "picture") (:form . "pictured") (:end . 109)\n  (:start . 101) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 119)\n  (:start . 113) (:id . 60))\n ((:tag . "NN") (:stem . "4e") (:form . "4E") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.467) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501040@unknown@formal@none@1@S@The depth of each frame is noted in the upper left-hand corner.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "depth") (:form . "depth") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 45) (:start . 40)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "left-hand") (:form . "left-hand") (:end . 55)\n  (:start . 46) (:id . 52))\n ((:tag . "NN") (:stem . "corner") (:form . "corner") (:end . 62)\n  (:start . 56) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.468) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501041@unknown@formal@none@1@S@20 µm scale bar for x/y-axis.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "x/y-axis") (:form . "x/y-axis") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.469) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501042@unknown@formal@none@1@S@Approximately half of the affected brain is displayed, with the midline to the left.@(((:tag . "RB") (:stem . "approximately") (:form . "Approximately")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "half") (:form . "half") (:end . 18) (:start . 14)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "affect") (:form . "affected") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 40) (:start . 35)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "display") (:form . "displayed") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 71)\n  (:start . 64) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "left") (:form . "left") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s3.470) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501043@unknown@formal@none@1@S@The dPTEN-/-;dRas85DV12 mutant cells are labeled with membrane-bound CD8GFP (green) and penetrate through the entire depth of the brain, some of which is visible as red background.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "dPTEN-/-;dRas85DV12")\n  (:form . "dPTEN-/-;dRas85DV12") (:end . 23) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 30)\n  (:start . 24) (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 36) (:start . 31)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 48)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "membrane-bound") (:form . "membrane-bound")\n  (:end . 68) (:start . 54) (:id . 49))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 75)\n  (:start . 69) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 51))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 82) (:start . 77)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "penetrate") (:form . "penetrate") (:end . 97)\n  (:start . 88) (:id . 55))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 105)\n  (:start . 98) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 116)\n  (:start . 110) (:id . 58))\n ((:tag . "NN") (:stem . "depth") (:form . "depth") (:end . 122)\n  (:start . 117) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 61))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 135)\n  (:start . 130) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 63))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 141) (:start . 137)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 153) (:start . 151)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "visible") (:form . "visible") (:end . 161)\n  (:start . 154) (:id . 68))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 164) (:start . 162)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 168) (:start . 165)\n  (:id . 70))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 179)\n  (:start . 169) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.471) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501044@unknown@formal@none@1@S@These dPTEN-/-;dRas85DV12 cells appear to originate in the optic lobe (right) and extend variable tendrils into the central brain (middle, left).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "dPTEN-/-;dRas85DV12")\n  (:form . "dPTEN-/-;dRas85DV12") (:end . 25) (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 31) (:start . 26)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 38)\n  (:start . 32) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 46))\n ((:tag . "VB") (:stem . "originate") (:form . "originate") (:end . 51)\n  (:start . 42) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "optic") (:form . "optic") (:end . 64) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "lobe") (:form . "lobe") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "right") (:form . "right") (:end . 76) (:start . 71)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "extend") (:form . "extend") (:end . 88)\n  (:start . 82) (:id . 56))\n ((:tag . "JJ") (:stem . "variable") (:form . "variable") (:end . 97)\n  (:start . 89) (:id . 57))\n ((:tag . "NNS") (:stem . "tendril") (:form . "tendrils") (:end . 106)\n  (:start . 98) (:id . 58))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 111) (:start . 107)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 123)\n  (:start . 116) (:id . 61))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 129)\n  (:start . 124) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "middle") (:form . "middle") (:end . 137)\n  (:start . 131) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "left") (:form . "left") (:end . 143) (:start . 139)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x3.472.1) (:span 32 38)))\n (:hscopes ((:id . :x3.472.1) (:span 0 144)))\n (:identifiers (:sid . :s3.472) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501045@unknown@formal@none@1@S@Genotype: hs-flp1/+; FRT40A tubGal80/FRT40A PTEN2L117; repo-Gal4 UAS-CD8GFP/UAS-dRas85DV12. (1.06 MB MOV)@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotype") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "hs-flp1/+") (:form . "hs-flp1/+") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "FRT40A") (:form . "FRT40A") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "NNP") (:stem . "tubGal80/FRT40A") (:form . "tubGal80/FRT40A")\n  (:end . 43) (:start . 28) (:id . 47))\n ((:tag . "NNP") (:stem . "PTEN2L117") (:form . "PTEN2L117") (:end . 53)\n  (:start . 44) (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "repo-gal4") (:form . "repo-Gal4") (:end . 64)\n  (:start . 55) (:id . 50))\n ((:tag . "NNP") (:stem . "UAS-CD8GFP/UAS-dRas85DV12.")\n  (:form . "UAS-CD8GFP/UAS-dRas85DV12.") (:end . 91) (:start . 65) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n  (:id . 52))\n ((:tag . "CD") (:stem . "1.06") (:form . "1.06") (:end . 97) (:start . 93)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 100) (:start . 98)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "MOV") (:form . "MOV") (:end . 104) (:start . 101)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s3.473) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501046@unknown@formal@none@1@S@Video S4 An animated 16 µm thick confocal z-stack of a hs-FLP/FRT clone of wild-type cells pictured in Figure 4A.@(((:tag . "JJ") (:stem . "video") (:form . "Video") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "An") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "animate") (:form . "animated") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "thick") (:form . "thick") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "z-stack") (:form . "z-stack") (:end . 49)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "hs-flp/frt") (:form . "hs-FLP/FRT") (:end . 65)\n  (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "clone") (:form . "clone") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 84)\n  (:start . 75) (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "picture") (:form . "pictured") (:end . 99)\n  (:start . 91) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 109)\n  (:start . 103) (:id . 60))\n ((:tag . "NN") (:stem . "4a") (:form . "4A") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s3.474) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501047@unknown@formal@none@1@S@The depth of each frame is noted in the upper left-hand corner.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "depth") (:form . "depth") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 45) (:start . 40)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "left-hand") (:form . "left-hand") (:end . 55)\n  (:start . 46) (:id . 52))\n ((:tag . "NN") (:stem . "corner") (:form . "corner") (:end . 62)\n  (:start . 56) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s3.475) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501048@unknown@formal@none@1@S@20 µm scale bar for x/y-axis.@(((:tag . "CD") (:stem . "20") (:form . "20") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "x/y-axis") (:form . "x/y-axis") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s3.476) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501049@unknown@formal@none@1@S@Midline to the left.@(((:tag . "NNP") (:stem . "Midline") (:form . "Midline") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "left") (:form . "left") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 20) (:start . 19)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s3.477) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501050@unknown@formal@none@1@S@This clone of normal glia is labeled with membrane-bound CD8GFP (green) and shows cells in a cell-body rich region of the central brain adjacent to the optic lobe.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "clone") (:form . "clone") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "glia") (:form . "glia") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "membrane-bound") (:form . "membrane-bound")\n  (:end . 56) (:start . 42) (:id . 50))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 63)\n  (:start . 57) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 87) (:start . 82)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cell-body") (:form . "cell-body") (:end . 102)\n  (:start . 93) (:id . 60))\n ((:tag . "JJ") (:stem . "rich") (:form . "rich") (:end . 107) (:start . 103)\n  (:id . 61))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 114)\n  (:start . 108) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 129)\n  (:start . 122) (:id . 65))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 135)\n  (:start . 130) (:id . 66))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 144)\n  (:start . 136) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 147) (:start . 145)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "optic") (:form . "optic") (:end . 157)\n  (:start . 152) (:id . 70))\n ((:tag . "NN") (:stem . "lobe") (:form . "lobe") (:end . 162) (:start . 158)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s3.478) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501051@unknown@formal@none@1@S@The clone is composed of 2 cells with extensive cytoplasmic projections.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "clone") (:form . "clone") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 47)\n  (:start . 38) (:id . 50))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 59)\n  (:start . 48) (:id . 51))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 71)\n  (:start . 60) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s3.479) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501052@unknown@formal@none@1@S@Genotype: hs-flp1/+;FRTG13 tubGal80/FRTG13 UAS-CD8GFP; repo-Gal4/+. (0.24 MB MOV)@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotype") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "CD") (:stem . "hs-flp1/+;FRTG13") (:form . "hs-flp1/+;FRTG13")\n  (:end . 26) (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "tubgal80/frtg13") (:form . "tubGal80/FRTG13")\n  (:end . 42) (:start . 27) (:id . 45))\n ((:tag . "NNP") (:stem . "UAS-CD8GFP") (:form . "UAS-CD8GFP") (:end . 53)\n  (:start . 43) (:id . 46))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 54) (:start . 53)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "repo-Gal4/+.") (:form . "repo-Gal4/+.") (:end . 67)\n  (:start . 55) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 49))\n ((:tag . "CD") (:stem . "0.24") (:form . "0.24") (:end . 73) (:start . 69)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 76) (:start . 74)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "MOV") (:form . "MOV") (:end . 80) (:start . 77)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s3.480) (:did . :pmc2636203) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501053@unknown@formal@none@1@S@Kinesin-5–dependent Poleward Flux and Spindle Length Control in Drosophila Embryo Mitosis@(((:tag . "JJ") (:stem . "kinesin-5–dependent")\n  (:form . "Kinesin-5–dependent") (:end . 19) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Poleward") (:form . "Poleward") (:end . 28)\n  (:start . 20) (:id . 43))\n ((:tag . "NNP") (:stem . "Flux") (:form . "Flux") (:end . 33) (:start . 29)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Spindle") (:form . "Spindle") (:end . 45)\n  (:start . 38) (:id . 46))\n ((:tag . "NNP") (:stem . "Length") (:form . "Length") (:end . 52)\n  (:start . 46) (:id . 47))\n ((:tag . "NNP") (:stem . "Control") (:form . "Control") (:end . 60)\n  (:start . 53) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 74)\n  (:start . 64) (:id . 50))\n ((:tag . "NNP") (:stem . "Embryo") (:form . "Embryo") (:end . 81)\n  (:start . 75) (:id . 51))\n ((:tag . "NNP") (:stem . "Mitosis") (:form . "Mitosis") (:end . 89)\n  (:start . 82) (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.1) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5501054@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.2) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501055@unknown@formal@none@1@S@We used antibody microinjection and genetic manipulations to dissect the various roles of the homotetrameric kinesin-5, KLP61F, in astral, centrosome-controlled Drosophila embryo spindles and to test the hypothesis that it slides apart interpolar (ip) microtubules (MT), thereby controlling poleward flux and spindle length.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "microinjection") (:form . "microinjection")\n  (:end . 31) (:start . 17) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . "NNS") (:stem . "manipulation") (:form . "manipulations")\n  (:end . 57) (:start . 44) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 49))\n ((:tag . "VB") (:stem . "dissect") (:form . "dissect") (:end . 68)\n  (:start . 61) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 80)\n  (:start . 73) (:id . 52))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 86) (:start . 81)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "homotetrameric") (:form . "homotetrameric")\n  (:end . 108) (:start . 94) (:id . 56))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 118)\n  (:start . 109) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . 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"and") (:end . 191) (:start . 188)\n  (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 194) (:start . 192)\n  (:id . 69))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 199) (:start . 195)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n  (:id . 71))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 214)\n  (:start . 204) (:id . 72))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 219) (:start . 215)\n  (:id . 73))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 222) (:start . 220)\n  (:id . 74))\n ((:tag . "VBZ") (:stem . "slide") (:form . "slides") (:end . 229)\n  (:start . 223) (:id . 75))\n ((:tag . "RB") (:stem . "apart") (:form . "apart") (:end . 235)\n  (:start . 230) (:id . 76))\n ((:tag . "JJ") (:stem . "interpolar") (:form . "interpolar") (:end . 246)\n  (:start . 236) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 248) (:start . 247)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "ip") (:form . "ip") (:end . 250) (:start . 248)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 251) (:start . 250)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "microtubule") (:form . "microtubules") (:end . 264)\n  (:start . 252) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 266) (:start . 265)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "MT") (:form . "MT") (:end . 268) (:start . 266)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 269) (:start . 268)\n  (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 270) (:start . 269)\n  (:id . 85))\n ((:tag . "RB") (:stem . "thereby") (:form . "thereby") (:end . 278)\n  (:start . 271) (:id . 86))\n ((:tag . "VBG") (:stem . "control") (:form . "controlling") (:end . 290)\n  (:start . 279) (:id . 87))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 299)\n  (:start . 291) (:id . 88))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 304) (:start . 300)\n  (:id . 89))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 308) (:start . 305)\n  (:id . 90))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 316)\n  (:start . 309) (:id . 91))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 323)\n  (:start . 317) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 324) (:start . 323)\n  (:id . 93)))@@@1@52@((:hcues ((:id . :x4.3.1) (:span 204 214)))\n (:hscopes ((:id . :x4.3.1) (:span 204 323)))\n (:identifiers (:sid . :s4.3) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501056@unknown@formal@none@1@S@In wild-type and Ncd null mutant embryos, anti-KLP61F dissociated the motor from spindles, producing a spatial gradient in the KLP61F content of different spindles, which was visible in KLP61F-GFP transgenic embryos.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 32)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "anti-KLP61F") (:form . "anti-KLP61F") (:end . 53)\n  (:start . 42) (:id . 50))\n ((:tag . "VBD") (:stem . "dissociate") (:form . "dissociated") (:end . 65)\n  (:start . 54) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 75) (:start . 70)\n  (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 89)\n  (:start . 81) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 100)\n  (:start . 91) (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "spatial") (:form . "spatial") (:end . 110)\n  (:start . 103) (:id . 59))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 119)\n  (:start . 111) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 133)\n  (:start . 127) (:id . 63))\n ((:tag . "NN") (:stem . "content") (:form . "content") (:end . 141)\n  (:start . 134) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 154)\n  (:start . 145) (:id . 66))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 163)\n  (:start . 155) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 68))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 170)\n  (:start . 165) (:id . 69))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 174) (:start . 171)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "visible") (:form . "visible") (:end . 182)\n  (:start . 175) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 185) (:start . 183)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "KLP61F-GFP") (:form . "KLP61F-GFP") (:end . 196)\n  (:start . 186) (:id . 73))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 207)\n  (:start . 197) (:id . 74))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 215)\n  (:start . 208) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s4.4) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501057@unknown@formal@none@1@S@The resulting mitotic defects, supported by gene dosage experiments and time-lapse microscopy of living klp61f mutants, reveal that, after NEB, KLP61F drives persistent MT bundling and the outward sliding of antiparallel MTs, thereby contributing to several processes that all appear insensitive to cortical disruption.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 40)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . 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5501058@unknown@formal@none@1@S@KLP61F activity contributes to the poleward flux of both ipMTs and kinetochore MTs and to the length of the metaphase spindle.@(((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 15)\n  (:start . 7) (:id . 43))\n ((:tag . "VBZ") (:stem . "contribute") (:form . "contributes") (:end . 27)\n  (:start . 16) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "ipmt") (:form . "ipMTs") (:end . 62) (:start . 57)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "kinetochore") (:form . "kinetochore") (:end . 78)\n  (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 100)\n  (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 60))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 117)\n  (:start . 108) (:id . 61))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 125)\n  (:start . 118) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.6) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501059@unknown@formal@none@1@S@KLP61F activity maintains the prometaphase spindle by antagonizing Ncd and another unknown force-generator and drives anaphase B, although the rate of spindle elongation is relatively insensitive to the motor's concentration.@(((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 15)\n  (:start . 7) (:id . 43))\n ((:tag . "VBZ") (:stem . "maintain") (:form . "maintains") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 42)\n  (:start . 30) (:id . 46))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 50)\n  (:start . 43) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 53) (:start . 51)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "antagonize") (:form . "antagonizing") (:end . 66)\n  (:start . 54) (:id . 49))\n ((:tag . "NNP") (:stem . "Ncd") (:form . "Ncd") (:end . 70) (:start . 67)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 51))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 82)\n  (:start . 75) (:id . 52))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 90)\n  (:start . 83) (:id . 53))\n ((:tag . "NN") (:stem . "force-generator") (:form . "force-generator")\n  (:end . 106) (:start . 91) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "drive") (:form . "drives") (:end . 117)\n  (:start . 111) (:id . 56))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 126)\n  (:start . 118) (:id . 57))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 128) (:start . 127)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 59))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 138)\n  (:start . 130) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n  (:id . 61))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 147) (:start . 143)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 63))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 158)\n  (:start . 151) (:id . 64))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 169)\n  (:start . 159) (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 172) (:start . 170)\n  (:id . 66))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 183)\n  (:start . 173) (:id . 67))\n ((:tag . "JJ") (:stem . "insensitive") (:form . "insensitive") (:end . 195)\n  (:start . 184) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 198) (:start . 196)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 202) (:start . 199)\n  (:id . 70))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 208)\n  (:start . 203) (:id . 71))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 210) (:start . 208)\n  (:id . 72))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 224) (:start . 211) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s4.7) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501060@unknown@formal@none@1@S@Finally, KLP61F activity contributes to normal chromosome congression, kinetochore spacing, and anaphase A rates.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 15)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "VBZ") (:stem . "contribute") (:form . "contributes") (:end . 36)\n  (:start . 25) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 46)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "congression") (:form . "congression") (:end . 69)\n  (:start . 58) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "kinetochore") (:form . "kinetochore") (:end . 82)\n  (:start . 71) (:id . 52))\n ((:tag . "NN") (:stem . "spacing") (:form . "spacing") (:end . 90)\n  (:start . 83) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 55))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 104)\n  (:start . 96) (:id . 56))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 106) (:start . 105)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 112)\n  (:start . 107) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.8) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501061@unknown@formal@none@1@S@Thus, a KLP61F-driven sliding filament mechanism contributes to multiple aspects of mitosis in this system.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "klp61f-driven") (:form . "KLP61F-driven")\n  (:end . 21) (:start . 8) (:id . 45))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "filament") (:form . "filament") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . "VBZ") (:stem . "contribute") (:form . "contributes") (:end . 60)\n  (:start . 49) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 72)\n  (:start . 64) (:id . 51))\n ((:tag . "NNS") (:stem . "aspect") (:form . "aspects") (:end . 80)\n  (:start . 73) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 53))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 91)\n  (:start . 84) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n  (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 106)\n  (:start . 100) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s4.9) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501062@unknown@formal@none@1@S@INTRODUCTION@(((:tag . "NN") (:stem . "introduction") (:form . "INTRODUCTION") (:end . 12)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.10) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501063@unknown@formal@none@1@S@Mitosis, the process by which identical copies of the replicated genome are distributed to the products of each cell division, involves a highly dynamic sequence of coordinated motility events, mediated by a bipolar protein machine, the mitotic spindle (Karsenti and Vernos, 2001 ; Mitchison and Salmon, 2001 ; Gadde and Heald, 2004 ; Wadsworth and Khodjakov, 2004 ; Mogilner et al., 2006 ; Brust-Mascher and Scholey, 2007 ; Walczak and Heald, 2008 ).@(((:tag . "NNP") (:stem . "Mitosis") (:form . "Mitosis") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . 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5501064@unknown@formal@none@1@S@These motility events are driven by molecular-scale forces generated by mitotic kinesins and dyneins, together with dynamic microtubules (MTs), whose activities are controlled by a network of regulatory proteins, e.g., mitotic kinases, phosphatases, and proteolytic enzymes (Sharp et al., 2000c ; Bettencourt-Dias et al., 2004 ; Maiato and Sunkel, 2004 ; Rogers et al., 2005 ; Goshima et al., 2007 ).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "motility") (:form . "motility") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . 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5501066@unknown@formal@none@1@S@Purified kinesin-5 is a slow, modestly processive, plus-end–directed bipolar homotetramer capable of cross-linking adjacent MTs and sliding apart antiparallel MTs in motility assays (Sawin et al., 1992 ; Cole et al., 1994 ; Kashina et al., 1996a ; Kapitein et al., 2005 ; Tao et al., 2006 ; Valentine et al., 2006b ; Krzysiak et al., 2008 ; Van den Wildenberg et al., 2008 ).@(((:tag . "VBN") (:stem . "purify") (:form . "Purified") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "slow") (:form . "slow") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "RB") (:stem . 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5501067@unknown@formal@none@1@S@In yeast cells the homotetrameric structure of kinesin-5 appears to be essential for mitosis (Hildebrandt et al., 2006 ), and in Drosophila embryos KLP61F displays dynamic properties consistent with an association with spindle MTs (Cheerambathur et al., 2008 ) and forms presumptive MT–MT cross-bridges (Sharp et al., 1999a ).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "homotetrameric") (:form . "homotetrameric")\n  (:end . 33) (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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5501068@unknown@formal@none@1@S@These results suggest that ensembles of multiple kinesin-5 motors could serve as dynamic cross-links that organize spindle MTs into bundles and drive a sliding filament mechanism that pushes apart antiparallel spindle MTs (Sharp et al., 1999a ; Brust-Mascher et al., 2004 ), although alternative mechanisms of action for kinesin-5 motors have also been proposed (Kapoor and Mitchison, 2001 ; Tsai et al., 2006 ; Johansen and Johansen, 2007 ; Gardner et al., 2008 ).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "ensemble") (:form . "ensembles") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . 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5501069@unknown@formal@none@1@S@The most obvious and frequently observed consequence of loss of activity of kinesin-5 motors, induced by loss-of-function mutation, antibody inhibition, small molecule inhibition, or RNA interference, is the formation of abnormal monoastral spindles (Enos and Morris, 1990 ; Saunders and Hoyt, 1992 ; Sawin et al., 1992 ; Heck et al., 1993 ; Saunders et al., 1997 ; Cottingham et al., 1999 ; Mayer et al., 1999 ; Sharp et al., 1999b ; Sharp et al., 2000a ; Goshima and Vale, 2003 ).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . 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5501072@unknown@formal@none@1@S@It is clear that this activity is deployed differently in different systems, however.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "deploy") (:form . "deployed") (:end . 42)\n  (:start . 34) (:id . 49))\n ((:tag . "RB") (:stem . "differently") (:form . "differently") (:end . 54)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 67)\n  (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 75)\n  (:start . 68) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.20) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501073@unknown@formal@none@1@S@For example, kinesin-5 activity is required for initial spindle assembly in yeast but not in Drosophila embryos, whereas it is required for spindle maintenance in both systems (Saunders and Hoyt, 1992 ; Sharp et al., 1999b ).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 63)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 72)\n  (:start . 64) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 103)\n  (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 111)\n  (:start . 104) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 60))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 120)\n  (:start . 113) (:id . 61))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 126) (:start . 124)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 135)\n  (:start . 127) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 139) (:start . 136)\n  (:id . 65))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 147)\n  (:start . 140) (:id . 66))\n ((:tag . "NN") (:stem . "maintenance") (:form . "maintenance") (:end . 159)\n  (:start . 148) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 162) (:start . 160)\n  (:id . 68))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 167) (:start . 163)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 175)\n  (:start . 168) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Saunders") (:form . "Saunders") (:end . 185)\n  (:start . 177) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 189) (:start . 186)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Hoyt") (:form . "Hoyt") (:end . 194) (:start . 190)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n  (:id . 75))\n ((:tag . "CD") (:stem . "1992") (:form . "1992") (:end . 200) (:start . 196)\n  (:id . 76))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 202) (:start . 201)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Sharp") (:form . "Sharp") (:end . 208)\n  (:start . 203) (:id . 78))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 211) (:start . 209)\n  (:id . 79))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 215) (:start . 212)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 216) (:start . 215)\n  (:id . 81))\n ((:tag . "CD") (:stem . "1999b") (:form . "1999b") (:end . 222)\n  (:start . 217) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 224) (:start . 223)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s4.21) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501074@unknown@formal@none@1@S@Inhibition of kinesin-5 in different systems has also resulted in defects in poleward flux (Miyamoto et al., 2004 ; Cameron et al., 2006 ) and spindle pole organization (Gaglio et al., 1996 ).@(((:tag . "NNP") (:stem . "Inhibition") (:form . "Inhibition") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 53) (:start . 49)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "result") (:form . "resulted") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 73)\n  (:start . 66) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 85)\n  (:start . 77) (:id . 54))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 90) (:start . 86)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Miyamoto") (:form . "Miyamoto") (:end . 100)\n  (:start . 92) (:id . 57))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 103) (:start . 101)\n  (:id . 58))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Cameron") (:form . "Cameron") (:end . 123)\n  (:start . 116) (:id . 63))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 126) (:start . 124)\n  (:id . 64))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 130) (:start . 127)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 66))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 136) (:start . 132)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 69))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 150)\n  (:start . 143) (:id . 70))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 155) (:start . 151)\n  (:id . 71))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 168)\n  (:start . 156) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 170) (:start . 169)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Gaglio") (:form . "Gaglio") (:end . 176)\n  (:start . 170) (:id . 74))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 179) (:start . 177)\n  (:id . 75))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 183) (:start . 180)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 77))\n ((:tag . "CD") (:stem . "1996") (:form . "1996") (:end . 189) (:start . 185)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 191) (:start . 190)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s4.22) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501075@unknown@formal@none@1@S@However, in Drosophila S2 cells, perturbation of kinesin-5 levels did not interfere with metaphase spindle length (Goshima et al., 2005b ).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 22)\n  (:start . 12) (:id . 45))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "perturbation") (:form . "perturbation") (:end . 45)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 65)\n  (:start . 59) (:id . 52))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "VB") (:stem . "interfere") (:form . "interfere") (:end . 83)\n  (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 98)\n  (:start . 89) (:id . 57))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 106)\n  (:start . 99) (:id . 58))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 113)\n  (:start . 107) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Goshima") (:form . "Goshima") (:end . 122)\n  (:start . 115) (:id . 61))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 125) (:start . 123)\n  (:id . 62))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 129) (:start . 126)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . "LS") (:stem . "2005b") (:form . "2005b") (:end . 136)\n  (:start . 131) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.23) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501076@unknown@formal@none@1@S@In Caenorhabditis elegans, kinesin-5 was also found to exert a braking effect on the spindle midzone that governs the rate of spindle elongation mediated by cortical motors (Saunders et al., 2007 ).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Caenorhabditis") (:form . "Caenorhabditis")\n  (:end . 17) (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 25)\n  (:start . 18) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 51) (:start . 46)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "VB") (:stem . "exert") (:form . "exert") (:end . 60) (:start . 55)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "braking") (:form . "braking") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "midzone") (:form . "midzone") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "govern") (:form . "governs") (:end . 113)\n  (:start . 106) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 122) (:start . 118)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 63))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 133)\n  (:start . 126) (:id . 64))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 144)\n  (:start . 134) (:id . 65))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 153)\n  (:start . 145) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 156) (:start . 154)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "cortical") (:form . "cortical") (:end . 165)\n  (:start . 157) (:id . 68))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 172)\n  (:start . 166) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Saunder") (:form . "Saunders") (:end . 182)\n  (:start . 174) (:id . 71))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 185) (:start . 183)\n  (:id . 72))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 189) (:start . 186)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n  (:id . 74))\n ((:tag . "CD") (:stem . "2007") (:form . "2007") (:end . 195) (:start . 191)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 197) (:start . 196)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s4.24) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501077@unknown@formal@none@1@S@It is unclear if these findings are relevant to all spindles and if they all reflect the antiparallel MT sliding activity of kinesin-5, or if kinesin-5 functions differently in different systems as implied by the proposal that kinesin-5 functions as a MT depolymerase rather than a sliding motor to control chromosome congression in Saccharomyces cerevisiae (Gardner et al., 2008 ).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 13)\n  (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "VBP") (:stem . 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5501078@unknown@formal@none@1@S@To distinguish these possibilities, therefore, systematic studies of kinesin-5 function throughout mitosis are needed, but this is difficult because the most frequently observed effect of perturbing kinesin-5 function, spindle collapse, obscures later effects in mitosis.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "distinguish") (:form . "distinguish") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "possibility") (:form . "possibilities") (:end . 34)\n  (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 46))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 45)\n  (:start . 36) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "systematic") (:form . "systematic") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 65)\n  (:start . 58) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 78)\n  (:start . 69) (:id . 52))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 87)\n  (:start . 79) (:id . 53))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 98)\n  (:start . 88) (:id . 54))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 106)\n  (:start . 99) (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 110) (:start . 107)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "need") (:form . "needed") (:end . 117)\n  (:start . 111) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 58))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 122) (:start . 119)\n  (:id . 59))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 127) (:start . 123)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 130) (:start . 128)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 140)\n  (:start . 131) (:id . 62))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 148)\n  (:start . 141) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 64))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 157) (:start . 153)\n  (:id . 65))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 168)\n  (:start . 158) (:id . 66))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 177)\n  (:start . 169) (:id . 67))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 184)\n  (:start . 178) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "perturb") (:form . "perturbing") (:end . 198)\n  (:start . 188) (:id . 70))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 208)\n  (:start . 199) (:id . 71))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 217)\n  (:start . 209) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 218) (:start . 217)\n  (:id . 73))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 226)\n  (:start . 219) (:id . 74))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 235)\n  (:start . 227) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 236) (:start . 235)\n  (:id . 76))\n ((:tag . "VBZ") (:stem . "obscure") (:form . "obscures") (:end . 245)\n  (:start . 237) (:id . 77))\n ((:tag . "JJ") (:stem . "later") (:form . "later") (:end . 251)\n  (:start . 246) (:id . 78))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 259)\n  (:start . 252) (:id . 79))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 262) (:start . 260)\n  (:id . 80))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 270)\n  (:start . 263) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 271) (:start . 270)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s4.26) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501079@unknown@formal@none@1@S@In Drosophila embryos, where the centrosomes dictate the assembly of remarkably dynamic, fast-acting spindles (Megraw et al., 2001 ; Cheerambathur et al., 2007 ), inhibiting the function of the kinesin-5, KLP61F produced collapsed monoastral spindles at a specific stage during prometaphase, and this was rescued by loss of function of the kinesin-14, Ncd (Sharp et al., 1999b , 2000a ).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . 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5501080@unknown@formal@none@1@S@Biochemical evidence supports the idea that the prometaphase spindle is maintained by a KLP61F-Ncd force balance (Tao et al., 2006 ), but it is unclear if the monoastral spindles form by the drawing together of focused poles due to Ncd-induced inward MT sliding or by the disorganization of spindle MTs combined with the fusion of microtubule organizing centers (Goshima and Vale, 2003 ).@(((:tag . "JJ") (:stem . "biochemical") (:form . "Biochemical") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "VBZ") (:stem . "support") (:form . "supports") (:end . 29)\n  (:start . 21) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 45))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . 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5501081@unknown@formal@none@1@S@We previously proposed that the KLP61F-driven outward sliding of ipMTs drives pre-anaphase B poleward flux and anaphase B spindle elongation (Brust-Mascher and Scholey, 2002 ; Brust-Mascher et al., 2004 ).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "propose") (:form . "proposed") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "klp61f-driven") (:form . "KLP61F-driven")\n  (:end . 45) (:start . 32) (:id . 47))\n ((:tag . "JJ") (:stem . "outward") (:form . "outward") (:end . 53)\n  (:start . 46) (:id . 48))\n ((:tag . "NN") (:stem . "sliding") (:form . "sliding") (:end . 61)\n  (:start . 54) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "ipmt") (:form . "ipMTs") (:end . 70) (:start . 65)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "drive") (:form . "drives") (:end . 77)\n  (:start . 71) (:id . 52))\n ((:tag . "JJ") (:stem . "pre-anaphase") (:form . "pre-anaphase") (:end . 90)\n  (:start . 78) (:id . 53))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 92) (:start . 91)\n  (:id . 54))\n ((:tag . "NN") (:stem . "poleward") (:form . "poleward") (:end . 101)\n  (:start . 93) (:id . 55))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 106) (:start . 102)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 57))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 119)\n  (:start . 111) (:id . 58))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 121) (:start . 120)\n  (:id . 59))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 129)\n  (:start . 122) (:id . 60))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 140)\n  (:start . 130) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 155) (:start . 142) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Scholey") (:form . "Scholey") (:end . 167)\n  (:start . 160) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 66))\n ((:tag . "CD") (:stem . "2002") (:form . "2002") (:end . 173) (:start . 169)\n  (:id . 67))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 175) (:start . 174)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 189) (:start . 176) (:id . 69))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 192) (:start . 190)\n  (:id . 70))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 196) (:start . 193)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 72))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 202) (:start . 198)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 204) (:start . 203)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x4.29.1) (:span 14 22)))\n (:hscopes ((:id . :x4.29.1) (:span 14 140)))\n (:identifiers (:sid . :s4.29) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501082@unknown@formal@none@1@S@However, reductionist modeling (Brust-Mascher et al., 2004 ) and system level modeling (Wollman et al., 2008 ) surprisingly predicted that the rate of anaphase B pole–pole separation is insensitive to the KLP61F concentration and is controlled instead by the unloaded KLP61F MT sliding velocity together with a pole-associated MT depolymerase.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "reductionist") (:form . "reductionist") (:end . 21)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 45) (:start . 32) (:id . 47))\n ((:tag . "FW") (:stem . "et") (:form . 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5501083@unknown@formal@none@1@S@Although experimental evidence supports a requirement for KLP61F activity in anaphase B (Sharp et al., 2000a ), we had not tested the effect of changing its concentration on the rate of anaphase B or its contribution to poleward flux and metaphase spindle length.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 21)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 30)\n  (:start . 22) (:id . 44))\n ((:tag . "VBZ") (:stem . "support") (:form . "supports") (:end . 39)\n  (:start . 31) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n  (:id . 46))\n ((:tag . "NN") (:stem . "requirement") (:form . "requirement") (:end . 53)\n  (:start . 42) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 57) (:start . 54)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 64)\n  (:start . 58) (:id . 49))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 73)\n  (:start . 65) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 51))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 85)\n  (:start . 77) (:id . 52))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 87) (:start . 86)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sharp") (:form . "Sharp") (:end . 94) (:start . 89)\n  (:id . 55))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 97) (:start . 95)\n  (:id . 56))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 101) (:start . 98)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "NN") (:stem . "2000a") (:form . "2000a") (:end . 108)\n  (:start . 103) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 61))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 118) (:start . 115)\n  (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 122) (:start . 119)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 129)\n  (:start . 123) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 140)\n  (:start . 134) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "change") (:form . "changing") (:end . 152)\n  (:start . 144) (:id . 69))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 156) (:start . 153)\n  (:id . 70))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 170) (:start . 157) (:id . 71))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 173) (:start . 171)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 73))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 182) (:start . 178)\n  (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 185) (:start . 183)\n  (:id . 75))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 194)\n  (:start . 186) (:id . 76))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 196) (:start . 195)\n  (:id . 77))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 199) (:start . 197)\n  (:id . 78))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 203) (:start . 200)\n  (:id . 79))\n ((:tag . "NN") (:stem . "contribution") (:form . "contribution") (:end . 216)\n  (:start . 204) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 219) (:start . 217)\n  (:id . 81))\n ((:tag . "VB") (:stem . "poleward") (:form . "poleward") (:end . 228)\n  (:start . 220) (:id . 82))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 233) (:start . 229)\n  (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 237) (:start . 234)\n  (:id . 84))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 247)\n  (:start . 238) (:id . 85))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 255)\n  (:start . 248) (:id . 86))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 262)\n  (:start . 256) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 263) (:start . 262)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s4.31) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501084@unknown@formal@none@1@S@Furthermore, it is unclear if some of these activities also require the activity of the overlying cortex, e.g., via cortical motors pulling astral MTs outward.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 43) (:start . 38)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 54)\n  (:start . 44) (:id . 51))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 67)\n  (:start . 60) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 80)\n  (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "overlie") (:form . "overlying") (:end . 97)\n  (:start . 88) (:id . 58))\n ((:tag . "NN") (:stem . "cortex") (:form . "cortex") (:end . 104)\n  (:start . 98) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 110) (:start . 106)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 62))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 115) (:start . 112)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "cortical") (:form . "cortical") (:end . 124)\n  (:start . 116) (:id . 64))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 131)\n  (:start . 125) (:id . 65))\n ((:tag . "VBG") (:stem . "pull") (:form . "pulling") (:end . 139)\n  (:start . 132) (:id . 66))\n ((:tag . "JJ") (:stem . "astral") (:form . "astral") (:end . 146)\n  (:start . 140) (:id . 67))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 150) (:start . 147)\n  (:id . 68))\n ((:tag . "RB") (:stem . "outward") (:form . "outward") (:end . 158)\n  (:start . 151) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x4.32.1) (:span 27 29)) ((:id . :x4.32.2) (:span 19 26)))\n (:hscopes ((:id . :x4.32.1) (:span 27 158)) ((:id . :x4.32.2) (:span 19 158)))\n (:identifiers (:sid . :s4.32) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501085@unknown@formal@none@1@S@In the current study we addressed some of these uncertainties by undertaking a systematic investigation of the spectrum of mitotic functions of kinesin-5, through antibody-induced dissociation of KLP61F from Drosophila syncytial blastoderm-stage embryo spindles, using an experimental system where the extent of dissociation can be directly observed.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "address") (:form . "addressed") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "uncertainty") (:form . "uncertainties") (:end . 61)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "undertake") (:form . "undertaking") (:end . 76)\n  (:start . 65) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "systematic") (:form . "systematic") (:end . 89)\n  (:start . 79) (:id . 55))\n ((:tag . "NN") (:stem . "investigation") (:form . "investigation")\n  (:end . 103) (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . 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"using") (:end . 268) (:start . 263)\n  (:id . 78))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 271) (:start . 269)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 284)\n  (:start . 272) (:id . 80))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 291)\n  (:start . 285) (:id . 81))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 297)\n  (:start . 292) (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 301) (:start . 298)\n  (:id . 83))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 308)\n  (:start . 302) (:id . 84))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 311) (:start . 309)\n  (:id . 85))\n ((:tag . "NN") (:stem . "dissociation") (:form . "dissociation") (:end . 324)\n  (:start . 312) (:id . 86))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 328) (:start . 325)\n  (:id . 87))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 331) (:start . 329)\n  (:id . 88))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 340)\n  (:start . 332) (:id . 89))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 349)\n  (:start . 341) (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 350) (:start . 349)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s4.33) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501086@unknown@formal@none@1@S@This was complemented by studies of the effects of varying the KLP61F gene dosage in embryos and by the investigation of mutant spindles after depletion of the maternal load of KLP61F.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "complement") (:form . "complemented") (:end . 21)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "vary") (:form . "varying") (:end . 58)\n  (:start . 51) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "dosage") (:form . "dosage") (:end . 81)\n  (:start . 75) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 99) (:start . 97)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "NN") (:stem . "investigation") (:form . "investigation")\n  (:end . 117) (:start . 104) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 127)\n  (:start . 121) (:id . 63))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 136)\n  (:start . 128) (:id . 64))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 142)\n  (:start . 137) (:id . 65))\n ((:tag . "NN") (:stem . "depletion") (:form . "depletion") (:end . 152)\n  (:start . 143) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "maternal") (:form . "maternal") (:end . 168)\n  (:start . 160) (:id . 69))\n ((:tag . "NN") (:stem . "load") (:form . "load") (:end . 173) (:start . 169)\n  (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 183)\n  (:start . 177) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s4.34) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501087@unknown@formal@none@1@S@We find that kinesin-5 contributes to various aspects of mitosis in this system, some of which are novel and perhaps unexpected.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "VBZ") (:stem . "contribute") (:form . "contributes") (:end . 34)\n  (:start . 23) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "aspect") (:form . "aspects") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 64)\n  (:start . 57) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 79)\n  (:start . 73) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 94) (:start . 89)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 104) (:start . 99)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 116)\n  (:start . 109) (:id . 62))\n ((:tag . "JJ") (:stem . "unexpected") (:form . "unexpected") (:end . 127)\n  (:start . 117) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x4.35.1) (:span 109 116)))\n (:hscopes ((:id . :x4.35.1) (:span 109 127)))\n (:identifiers (:sid . :s4.35) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501088@unknown@formal@none@1@S@MATERIALS AND METHODS@(((:tag . "NNP") (:stem . "MATERIALS") (:form . "MATERIALS") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "AND") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "METHODS") (:form . "METHODS") (:end . 21)\n  (:start . 14) (:id . 44)))@@@1@3@((:identifiers (:sid . :s4.36) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501089@unknown@formal@none@1@S@Drosophila Stocks@(((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "stock") (:form . "Stocks") (:end . 17)\n  (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s4.37) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501090@unknown@formal@none@1@S@Flies were maintained and embryos were collected as described (Sharp et al., 1999 ).@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "maintain") (:form . "maintained") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 61)\n  (:start . 52) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Sharp") (:form . "Sharp") (:end . 68) (:start . 63)\n  (:id . 52))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s4.38) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501091@unknown@formal@none@1@S@Experiments were performed on embryos expressing green fluorescent protein (GFP)::tubulin or GFP::CNN (provided by Dr. Thomas Kaufman, Indiana University Bloomington) or GFP::CID, the Drosophila CENPA homolog (Henikoff et al., 2000 ), which is a stable and specific kinetochore marker (provided by Dr. Steven Henikoff, Fred Hutchinson Cancer Research), or KLP61F::GFP (Cheerambathur et al., 2008 ), as well as on Claret nondisjunctional (cand) and klp61f mutant embryos.@(((:tag . "NNS") (:stem . "experiment") (:form . "Experiments") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 26)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . 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(:end . 389) (:start . 386)\n  (:id . 107))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 390) (:start . 389)\n  (:id . 108))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 395) (:start . 391)\n  (:id . 109))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 397) (:start . 396)\n  (:id . 110))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 398) (:start . 397)\n  (:id . 111))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 401) (:start . 399)\n  (:id . 112))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 406) (:start . 402)\n  (:id . 113))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 409) (:start . 407)\n  (:id . 114))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 412) (:start . 410)\n  (:id . 115))\n ((:tag . "NNP") (:stem . "Claret") (:form . "Claret") (:end . 419)\n  (:start . 413) (:id . 116))\n ((:tag . "JJ") (:stem . "nondisjunctional") (:form . "nondisjunctional")\n  (:end . 436) (:start . 420) (:id . 117))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 438) (:start . 437)\n  (:id . 118))\n ((:tag . "NN") (:stem . "cand") (:form . "cand") (:end . 442) (:start . 438)\n  (:id . 119))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 443) (:start . 442)\n  (:id . 120))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 447) (:start . 444)\n  (:id . 121))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 454)\n  (:start . 448) (:id . 122))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 461)\n  (:start . 455) (:id . 123))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 469)\n  (:start . 462) (:id . 124))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 470) (:start . 469)\n  (:id . 125)))@@@1@84@((:identifiers (:sid . :s4.39) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501092@unknown@formal@none@1@S@Generation of klp61f Mutant Fly Lines Expressing GFP-Tubulin@(((:tag . "NNP") (:stem . "Generation") (:form . "Generation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "NNP") (:stem . "Mutant") (:form . "Mutant") (:end . 27)\n  (:start . 21) (:id . 45))\n ((:tag . "NNP") (:stem . "Fly") (:form . "Fly") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Lines") (:form . "Lines") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Expressing") (:form . "Expressing") (:end . 48)\n  (:start . 38) (:id . 48))\n ((:tag . "NNP") (:stem . "GFP-Tubulin") (:form . "GFP-Tubulin") (:end . 60)\n  (:start . 49) (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.40) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501093@unknown@formal@none@1@S@Standard genetic techniques were used to generate flies with GFP::tubulin on the second chromosome and these were then crossed into different alleles of klp61f mutants for genetic analyses.@(((:tag . "JJ") (:stem . "standard") (:form . "Standard") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "technique") (:form . "techniques") (:end . 27)\n  (:start . 17) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 32) (:start . 28)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 49)\n  (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "GFP::tubulin") (:form . "GFP::tubulin") (:end . 73)\n  (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 76) (:start . 74)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 87)\n  (:start . 81) (:id . 54))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 98)\n  (:start . 88) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 56))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 108)\n  (:start . 103) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 113) (:start . 109)\n  (:id . 58))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 118) (:start . 114)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "cross") (:form . "crossed") (:end . 126)\n  (:start . 119) (:id . 60))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 131) (:start . 127)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 141)\n  (:start . 132) (:id . 62))\n ((:tag . "NNS") (:stem . "allele") (:form . "alleles") (:end . 149)\n  (:start . 142) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n  (:id . 64))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 159)\n  (:start . 153) (:id . 65))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 167)\n  (:start . 160) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 171) (:start . 168)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 179)\n  (:start . 172) (:id . 68))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 188)\n  (:start . 180) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s4.41) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501094@unknown@formal@none@1@S@Briefly, we first crossed y[1] w[*]; P{w[+mC] = UASp-GFPS65C-alphaTub84B{14-6-II/P{w[+mC] = UASp-GFPS65C-alphaTub84B{14-6-II with yw;P{Act5C-Gal4{/CyO,y+ or w*; P{w[+mC] = matalpha4-GAL-VP16{V2H.@(((:tag . "RB") (:stem . "briefly") (:form . "Briefly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "cross") (:form . "crossed") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "CD") (:stem . "y[1") (:form . "y[1") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "SYM") (:stem . "w[*") (:form . "w[*") (:end . 34) (:start . 31)\n  (:id . 49))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 35) (:start . 34)\n  (:id . 50))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 36) (:start . 35)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "P{w[+mC") (:form . "P{w[+mC") (:end . 44)\n  (:start . 37) (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 45) (:start . 44)\n  (:id . 53))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 47) (:start . 46)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "UASp-GFPS65C-alphaTub84B{14-6-II/P{w[+mC")\n  (:form . "UASp-GFPS65C-alphaTub84B{14-6-II/P{w[+mC") (:end . 88)\n  (:start . 48) (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 89) (:start . 88)\n  (:id . 56))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "UASp-GFPS65C-alphaTub84B{14-6-II")\n  (:form . "UASp-GFPS65C-alphaTub84B{14-6-II") (:end . 124) (:start . 92)\n  (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 129) (:start . 125)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "yw;P{Act5C-Gal4{/CyO,y+")\n  (:form . "yw;P{Act5C-Gal4{/CyO,y+") (:end . 153) (:start . 130) (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 156) (:start . 154)\n  (:id . 61))\n ((:tag . "NN") (:stem . "w*") (:form . "w*") (:end . 159) (:start . 157)\n  (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 160) (:start . 159)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "P{w[+mC") (:form . "P{w[+mC") (:end . 168)\n  (:start . 161) (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 169) (:start . 168)\n  (:id . 65))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 171) (:start . 170)\n  (:id . 66))\n ((:tag . "FW") (:stem . "matalpha4-GAL-VP16{V2H")\n  (:form . "matalpha4-GAL-VP16{V2H") (:end . 194) (:start . 172) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x4.42.1) (:span 154 156)))\n (:hscopes ((:id . :x4.42.1) (:span 26 194)))\n (:identifiers (:sid . :s4.42) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501095@unknown@formal@none@1@S@We selected P{w[+mC] = UASp-GFPS65C-alphaTub84B{14-6-II/P{Act5C-Gal4{or P{w[+mC] = UASp-GFPS65C-alphaTub84B{14-6-II/P{w[+mC] = matalpha4-GAL-VP16{V2H females and crossed them with w; ln(2LR)Gla,wgGla-1Bc1/CyO males.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "P{w[+mC") (:form . "P{w[+mC") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "UASp-GFPS65C-alphaTub84B{14-6-II/P{Act5C-Gal4{or")\n  (:form . "UASp-GFPS65C-alphaTub84B{14-6-II/P{Act5C-Gal4{or") (:end . 71)\n  (:start . 23) (:id . 47))\n ((:tag . "NNP") (:stem . "P{w[+mC") (:form . "P{w[+mC") (:end . 79)\n  (:start . 72) (:id . 48))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 80) (:start . 79)\n  (:id . 49))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 82) (:start . 81)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "UASp-GFPS65C-alphaTub84B{14-6-II/P{w[+mC")\n  (:form . "UASp-GFPS65C-alphaTub84B{14-6-II/P{w[+mC") (:end . 123)\n  (:start . 83) (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 124) (:start . 123)\n  (:id . 52))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 126) (:start . 125)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "matalpha4-GAL-VP16{V2H")\n  (:form . "matalpha4-GAL-VP16{V2H") (:end . 149) (:start . 127) (:id . 54))\n ((:tag . "NNS") (:stem . "female") (:form . "females") (:end . 157)\n  (:start . 150) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "cross") (:form . "crossed") (:end . 169)\n  (:start . 162) (:id . 57))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 174) (:start . 170)\n  (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 179) (:start . 175)\n  (:id . 59))\n ((:tag . "NN") (:stem . "w") (:form . "w") (:end . 181) (:start . 180)\n  (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 182) (:start . 181)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "ln(2LR)Gla,wgGla-1Bc1/CyO")\n  (:form . "ln(2LR)Gla,wgGla-1Bc1/CyO") (:end . 208) (:start . 183)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "male") (:form . "males") (:end . 214)\n  (:start . 209) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x4.43.1) (:span 69 71)))\n (:hscopes ((:id . :x4.43.1) (:span 12 149)))\n (:identifiers (:sid . :s4.43) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501096@unknown@formal@none@1@S@We selected progeny in which recombination between the UAS-GFP-tubulin and the Gal4 driver had occurred by picking fluorescent larvae and used individual flies to make balanced stocks.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "progeny") (:form . "progeny") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n  (:end . 42) (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "UAS-GFP-tubulin") (:form . "UAS-GFP-tubulin")\n  (:end . 70) (:start . 55) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 52))\n ((:tag . "NN") (:stem . "gal4") (:form . "Gal4") (:end . 83) (:start . 79)\n  (:id . 53))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 90)\n  (:start . 84) (:id . 54))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 94) (:start . 91)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "occur") (:form . "occurred") (:end . 103)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 106) (:start . 104)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "pick") (:form . "picking") (:end . 114)\n  (:start . 107) (:id . 58))\n ((:tag . "JJ") (:stem . "fluorescent") (:form . "fluorescent") (:end . 126)\n  (:start . 115) (:id . 59))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 133)\n  (:start . 127) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 142) (:start . 138)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 153)\n  (:start . 143) (:id . 63))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 159) (:start . 154)\n  (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 162) (:start . 160)\n  (:id . 65))\n ((:tag . "VB") (:stem . "make") (:form . "make") (:end . 167) (:start . 163)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "balanced") (:form . "balanced") (:end . 176)\n  (:start . 168) (:id . 67))\n ((:tag . "NNS") (:stem . "stock") (:form . "stocks") (:end . 183)\n  (:start . 177) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.44) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501097@unknown@formal@none@1@S@All stocks were from the Bloomington Stock Center.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "stock") (:form . "stocks") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Bloomington") (:form . "Bloomington") (:end . 36)\n  (:start . 25) (:id . 47))\n ((:tag . "NNP") (:stem . "Stock") (:form . "Stock") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Center") (:form . "Center") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 50) (:start . 49)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s4.45) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501098@unknown@formal@none@1@S@To cross these balanced lines expressing GFP-tubulin under the Gal 4 driver with klp61f mutants (provided by Margarete Heck, University of Edinburgh; Andrea Pereira, University of Massachusetts; and Patricia Wilson, Georgia State University), we first crossed both lines with w; Sp/CyORoi; Ly/TM3Sbe flies (provided by Dr Jeanette Naetzle, University of California Davis), in which we had replaced the TM3 balancer with KrGFPTM3 or TM6 to distinguish homozygous from heterozygous embryos or larvae, respectively.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "cross") (:form . "cross") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "balanced") (:form . "balanced") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "NNP") (:stem . "GFP-tubulin") (:form . "GFP-tubulin") (:end . 52)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 58) (:start . 53)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "gal") (:form . "Gal") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 75)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 95)\n  (:start . 88) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 105)\n  (:start . 97) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Margarete") (:form . "Margarete") (:end . 118)\n  (:start . 109) (:id . 60))\n ((:tag . "NNP") (:stem . "Heck") (:form . "Heck") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "University") (:form . "University") (:end . 135)\n  (:start . 125) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Edinburgh") (:form . "Edinburgh") (:end . 148)\n  (:start . 139) (:id . 65))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 149) (:start . 148)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Andrea") (:form . "Andrea") (:end . 156)\n  (:start . 150) (:id . 67))\n ((:tag . "NNP") (:stem . "Pereira") (:form . "Pereira") (:end . 164)\n  (:start . 157) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "University") (:form . "University") (:end . 176)\n  (:start . 166) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 179) (:start . 177)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Massachusetts") (:form . "Massachusetts")\n  (:end . 193) (:start . 180) (:id . 72))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 194) (:start . 193)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 198) (:start . 195)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Patricia") (:form . "Patricia") (:end . 207)\n  (:start . 199) (:id . 75))\n ((:tag . "NNP") (:stem . "Wilson") (:form . "Wilson") (:end . 214)\n  (:start . 208) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 215) (:start . 214)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Georgia") (:form . "Georgia") (:end . 223)\n  (:start . 216) (:id . 78))\n ((:tag . "NNP") (:stem . "State") (:form . "State") (:end . 229)\n  (:start . 224) (:id . 79))\n ((:tag . "NNP") (:stem . "University") (:form . "University") (:end . 240)\n  (:start . 230) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 241) (:start . 240)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 242) (:start . 241)\n  (:id . 82))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 245) (:start . 243)\n  (:id . 83))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 251)\n  (:start . 246) (:id . 84))\n ((:tag . "VBD") (:stem . "cross") (:form . "crossed") (:end . 259)\n  (:start . 252) (:id . 85))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 264) (:start . 260)\n  (:id . 86))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 270)\n  (:start . 265) (:id . 87))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 275) (:start . 271)\n  (:id . 88))\n ((:tag . "NN") (:stem . "w") (:form . "w") (:end . 277) (:start . 276)\n  (:id . 89))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 278) (:start . 277)\n  (:id . 90))\n ((:tag . "NNP") (:stem . "Sp/CyORoi") (:form . "Sp/CyORoi") (:end . 288)\n  (:start . 279) (:id . 91))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 289) (:start . 288)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "Ly/TM3Sbe") (:form . "Ly/TM3Sbe") (:end . 299)\n  (:start . 290) (:id . 93))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 305) (:start . 300)\n  (:id . 94))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 307) (:start . 306)\n  (:id . 95))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 315)\n  (:start . 307) (:id . 96))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 318) (:start . 316)\n  (:id . 97))\n ((:tag . "NNP") (:stem . "Dr") (:form . "Dr") (:end . 321) (:start . 319)\n  (:id . 98))\n ((:tag . "NNP") (:stem . "Jeanette") (:form . "Jeanette") (:end . 330)\n  (:start . 322) (:id . 99))\n ((:tag . "NNP") (:stem . "Naetzle") (:form . "Naetzle") (:end . 338)\n  (:start . 331) (:id . 100))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 339) (:start . 338)\n  (:id . 101))\n ((:tag . "NNP") (:stem . "University") (:form . "University") (:end . 350)\n  (:start . 340) (:id . 102))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 353) (:start . 351)\n  (:id . 103))\n ((:tag . "NNP") (:stem . "California") (:form . "California") (:end . 364)\n  (:start . 354) (:id . 104))\n ((:tag . "NNP") (:stem . "Davis") (:form . "Davis") (:end . 370)\n  (:start . 365) (:id . 105))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 371) (:start . 370)\n  (:id . 106))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 372) (:start . 371)\n  (:id . 107))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 375) (:start . 373)\n  (:id . 108))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 381)\n  (:start . 376) (:id . 109))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 384) (:start . 382)\n  (:id . 110))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 388) (:start . 385)\n  (:id . 111))\n ((:tag . "VBN") (:stem . "replace") (:form . "replaced") (:end . 397)\n  (:start . 389) (:id . 112))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 401) (:start . 398)\n  (:id . 113))\n ((:tag . "NN") (:stem . "tm3") (:form . "TM3") (:end . 405) (:start . 402)\n  (:id . 114))\n ((:tag . "NN") (:stem . "balancer") (:form . "balancer") (:end . 414)\n  (:start . 406) (:id . 115))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 419) (:start . 415)\n  (:id . 116))\n ((:tag . "NNP") (:stem . "KrGFPTM3") (:form . "KrGFPTM3") (:end . 428)\n  (:start . 420) (:id . 117))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 431) (:start . 429)\n  (:id . 118))\n ((:tag . "NNP") (:stem . "TM6") (:form . "TM6") (:end . 435) (:start . 432)\n  (:id . 119))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 438) (:start . 436)\n  (:id . 120))\n ((:tag . "VB") (:stem . "distinguish") (:form . "distinguish") (:end . 450)\n  (:start . 439) (:id . 121))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 461)\n  (:start . 451) (:id . 122))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 466) (:start . 462)\n  (:id . 123))\n ((:tag . "JJ") (:stem . "heterozygous") (:form . "heterozygous") (:end . 479)\n  (:start . 467) (:id . 124))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 487)\n  (:start . 480) (:id . 125))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 490) (:start . 488)\n  (:id . 126))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 497)\n  (:start . 491) (:id . 127))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 498) (:start . 497)\n  (:id . 128))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 511)\n  (:start . 499) (:id . 129))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 512) (:start . 511)\n  (:id . 130)))@@@1@89@((:identifiers (:sid . :s4.46) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501099@unknown@formal@none@1@S@The klp61f alleles used (7012 and 7415) are null or severe hypomorphic, late larval lethals, obtained by P-element insertion in the untranslated region of KLP61F (Heck et al., 1993 ).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "allele") (:form . "alleles") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "CD") (:stem . "7012") (:form . "7012") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "CD") (:stem . "7415") (:form . "7415") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 39) (:start . 38)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 48) (:start . 44)\n  (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 51) (:start . 49)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 58)\n  (:start . 52) (:id . 54))\n ((:tag . "JJ") (:stem . "hypomorphic") (:form . "hypomorphic") (:end . 70)\n  (:start . 59) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 76) (:start . 72)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 83)\n  (:start . 77) (:id . 58))\n ((:tag . "NNS") (:stem . "lethal") (:form . "lethals") (:end . 91)\n  (:start . 84) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 101)\n  (:start . 93) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 104) (:start . 102)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "P-element") (:form . "P-element") (:end . 114)\n  (:start . 105) (:id . 63))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 124)\n  (:start . 115) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 127) (:start . 125)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "untranslated") (:form . "untranslated") (:end . 144)\n  (:start . 132) (:id . 67))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 151)\n  (:start . 145) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 161)\n  (:start . 155) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 163) (:start . 162)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Heck") (:form . "Heck") (:end . 167) (:start . 163)\n  (:id . 72))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 170) (:start . 168)\n  (:id . 73))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 174) (:start . 171)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 75))\n ((:tag . "CD") (:stem . "1993") (:form . "1993") (:end . 180) (:start . 176)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 182) (:start . 181)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s4.47) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501100@unknown@formal@none@1@S@Antibody Generation@(((:tag . "NN") (:stem . "antibody") (:form . "Antibody") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Generation") (:form . "Generation") (:end . 19)\n  (:start . 9) (:id . 43)))@@@1@2@((:identifiers (:sid . :s4.48) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501101@unknown@formal@none@1@S@KLP61F antibody was generated against amino acids 900-1066, which includes the BimC box containing a mutation in which the putative phosphorylation site, Threonine 933, was mutated to aspartic acid.@(((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 15)\n  (:start . 7) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 29)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 43) (:start . 38)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 49) (:start . 44)\n  (:id . 48))\n ((:tag . "CD") (:stem . "900-1066") (:form . "900-1066") (:end . 58)\n  (:start . 50) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 74)\n  (:start . 66) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "BimC") (:form . "BimC") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "box") (:form . "box") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 98)\n  (:start . 88) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 109)\n  (:start . 101) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 118)\n  (:start . 113) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 131)\n  (:start . 123) (:id . 62))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 147) (:start . 132) (:id . 63))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 152) (:start . 148)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Threonine") (:form . "Threonine") (:end . 163)\n  (:start . 154) (:id . 66))\n ((:tag . "CD") (:stem . "933") (:form . "933") (:end . 167) (:start . 164)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 172) (:start . 169)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 180)\n  (:start . 173) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 183) (:start . 181)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "aspartic") (:form . "aspartic") (:end . 192)\n  (:start . 184) (:id . 72))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 197) (:start . 193)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x4.49.1) (:span 123 131)))\n (:hscopes ((:id . :x4.49.1) (:span 123 152)))\n (:identifiers (:sid . :s4.49) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501102@unknown@formal@none@1@S@To generate this mutant, two sets of primers were used in three sequential PCR steps: two anchor primers, flanking the region of interest and containing BamHI and EcoRI restriction sites, and two mutagenic primers containing the T933D mutation.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 44)\n  (:start . 37) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 49) (:start . 45)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 54) (:start . 50)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 63) (:start . 58)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "sequential") (:form . "sequential") (:end . 74)\n  (:start . 64) (:id . 55))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 84) (:start . 79)\n  (:id . 57))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 89) (:start . 86)\n  (:id . 59))\n ((:tag . "NN") (:stem . "anchor") (:form . "anchor") (:end . 96)\n  (:start . 90) (:id . 60))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 104)\n  (:start . 97) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "flank") (:form . "flanking") (:end . 114)\n  (:start . 106) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 64))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 125)\n  (:start . 119) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n  (:id . 66))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 137)\n  (:start . 129) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 152)\n  (:start . 142) (:id . 69))\n ((:tag . "NNP") (:stem . "BamHI") (:form . "BamHI") (:end . 158)\n  (:start . 153) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "EcoRI") (:form . "EcoRI") (:end . 168)\n  (:start . 163) (:id . 72))\n ((:tag . "NN") (:stem . "restriction") (:form . "restriction") (:end . 180)\n  (:start . 169) (:id . 73))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 186)\n  (:start . 181) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 187) (:start . 186)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 191) (:start . 188)\n  (:id . 76))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 195) (:start . 192)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "mutagenic") (:form . "mutagenic") (:end . 205)\n  (:start . 196) (:id . 78))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 213)\n  (:start . 206) (:id . 79))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 224)\n  (:start . 214) (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 228) (:start . 225)\n  (:id . 81))\n ((:tag . "NN") (:stem . "t933d") (:form . "T933D") (:end . 234)\n  (:start . 229) (:id . 82))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 243)\n  (:start . 235) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s4.50) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501103@unknown@formal@none@1@S@To produce KLP61F antibody, PCR-amplified KLP61F (nt 2698-3201) containing the T933D mutation was subcloned into pGEX-JDK and the expressed protein was purified using glutathione-agarose affinity chromatography.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "pcr-amplified") (:form . "PCR-amplified")\n  (:end . 41) (:start . 28) (:id . 47))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 48)\n  (:start . 42) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "nt") (:form . "nt") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "CD") (:stem . "2698-3201") (:form . "2698-3201") (:end . 62)\n  (:start . 53) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 74)\n  (:start . 64) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "T933D") (:form . "T933D") (:end . 84) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 93)\n  (:start . 85) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 97) (:start . 94)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "subclone") (:form . "subcloned") (:end . 107)\n  (:start . 98) (:id . 58))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 112) (:start . 108)\n  (:id . 59))\n ((:tag . "NN") (:stem . "pgex-jdk") (:form . "pGEX-JDK") (:end . 121)\n  (:start . 113) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 139)\n  (:start . 130) (:id . 63))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 147)\n  (:start . 140) (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 151) (:start . 148)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 160)\n  (:start . 152) (:id . 66))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 166) (:start . 161)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "glutathione-agarose")\n  (:form . "glutathione-agarose") (:end . 186) (:start . 167) (:id . 68))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 195)\n  (:start . 187) (:id . 69))\n ((:tag . "NN") (:stem . "chromatography") (:form . "chromatography")\n  (:end . 210) (:start . 196) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s4.51) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501104@unknown@formal@none@1@S@Two rabbit polyclonal antibodies were generated using standard procedures and affinity-purified on GST-KLP61F columns.@(((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "rabbit") (:form . "rabbit") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "polyclonal") (:form . "polyclonal") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 32)\n  (:start . 22) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 47)\n  (:start . 38) (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 53) (:start . 48)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 62)\n  (:start . 54) (:id . 49))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 73)\n  (:start . 63) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "affinity-purified") (:form . "affinity-purified")\n  (:end . 95) (:start . 78) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 98) (:start . 96)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "GST-KLP61F") (:form . "GST-KLP61F") (:end . 109)\n  (:start . 99) (:id . 54))\n ((:tag . "NNS") (:stem . "column") (:form . "columns") (:end . 117)\n  (:start . 110) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.52) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501105@unknown@formal@none@1@S@The antibody was acid eluted, neutralized in Tris buffer, dialyzed into PBS buffer, and concentrated.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "elute") (:form . "eluted") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "neutralize") (:form . "neutralized") (:end . 41)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Tris") (:form . "Tris") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 56)\n  (:start . 50) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "dialyze") (:form . "dialyzed") (:end . 66)\n  (:start . 58) (:id . 53))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "PBS") (:form . "PBS") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 82)\n  (:start . 76) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "concentrate") (:form . "concentrated") (:end . 100)\n  (:start . 88) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.53) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501106@unknown@formal@none@1@S@For embryo injection, the concentration in the needle was 7–15 mg/ml.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 39) (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "needle") (:form . "needle") (:end . 53)\n  (:start . 47) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "CD") (:stem . "7–15") (:form . "7–15") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mg/ml") (:form . "mg/ml") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.54) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501107@unknown@formal@none@1@S@Time-Lapse and Fluorescent Speckle Microscopy of Embryos@(((:tag . "NNP") (:stem . "Time-Lapse") (:form . "Time-Lapse") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Fluorescent") (:form . "Fluorescent") (:end . 26)\n  (:start . 15) (:id . 44))\n ((:tag . "NNP") (:stem . "Speckle") (:form . "Speckle") (:end . 34)\n  (:start . 27) (:id . 45))\n ((:tag . "NNP") (:stem . "Microscopy") (:form . "Microscopy") (:end . 45)\n  (:start . 35) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Embryos") (:form . "Embryos") (:end . 56)\n  (:start . 49) (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.55) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501108@unknown@formal@none@1@S@Embryos were injected with rhodamine labeled tubulin (Cytoskeleton, Denver, CO).@(((:tag . "NNP") (:stem . "Embryo") (:form . "Embryos") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "rhodamine") (:form . "rhodamine") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Cytoskeleton") (:form . "Cytoskeleton") (:end . 66)\n  (:start . 54) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Denver") (:form . "Denver") (:end . 74)\n  (:start . 68) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "CO") (:form . "CO") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.56) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501109@unknown@formal@none@1@S@Time-lapse images were acquired with an Olympus (Melville, NY) microscope equipped with an Ultra-View spinning disk confocal head (Perkin Elmer-Cetus, Boston, MA) and a 100× 1.35 NA objective at time intervals of 1–3 s.@(((:tag . "NNP") (:stem . "Time-lapse") (:form . "Time-lapse") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 17)\n  (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "acquire") (:form . "acquired") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Olympus") (:form . "Olympus") (:end . 47)\n  (:start . 40) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Melville") (:form . "Melville") (:end . 57)\n  (:start . 49) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "NY") (:form . "NY") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "microscope") (:form . "microscope") (:end . 73)\n  (:start . 63) (:id . 54))\n ((:tag . "VBN") (:stem . "equip") (:form . "equipped") (:end . 82)\n  (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 87) (:start . 83)\n  (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "ultra-view") (:form . "Ultra-View") (:end . 101)\n  (:start . 91) (:id . 58))\n ((:tag . "NN") (:stem . "spinning") (:form . "spinning") (:end . 110)\n  (:start . 102) (:id . 59))\n ((:tag . "NN") (:stem . "disk") (:form . "disk") (:end . 115) (:start . 111)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 124)\n  (:start . 116) (:id . 61))\n ((:tag . "NN") (:stem . "head") (:form . "head") (:end . 129) (:start . 125)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Perkin") (:form . "Perkin") (:end . 137)\n  (:start . 131) (:id . 64))\n ((:tag . "NNP") (:stem . "Elmer-Cetus") (:form . "Elmer-Cetus") (:end . 149)\n  (:start . 138) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Boston") (:form . "Boston") (:end . 157)\n  (:start . 151) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "ma") (:form . "MA") (:end . 161) (:start . 159)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 168) (:start . 167)\n  (:id . 72))\n ((:tag . "CD") (:stem . "100×") (:form . "100×") (:end . 173) (:start . 169)\n  (:id . 73))\n ((:tag . "CD") (:stem . "1.35") (:form . "1.35") (:end . 178) (:start . 174)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "NA") (:form . "NA") (:end . 181) (:start . 179)\n  (:id . 75))\n ((:tag . "NN") (:stem . "objective") (:form . "objective") (:end . 191)\n  (:start . 182) (:id . 76))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 194) (:start . 192)\n  (:id . 77))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 199) (:start . 195)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 209)\n  (:start . 200) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 212) (:start . 210)\n  (:id . 80))\n ((:tag . "CD") (:stem . "1–3") (:form . "1–3") (:end . 216) (:start . 213)\n  (:id . 81))\n ((:tag . "NN") (:stem . "s") (:form . "s") (:end . 218) (:start . 217)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s4.57) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501110@unknown@formal@none@1@S@Images were analyzed with Metamorph Imaging software (Universal Imaging, West Chester, PA).@(((:tag . "NNS") (:stem . "image") (:form . "Images") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Metamorph") (:form . "Metamorph") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . "NNP") (:stem . "Imaging") (:form . "Imaging") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 52)\n  (:start . 44) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Universal") (:form . "Universal") (:end . 63)\n  (:start . 54) (:id . 50))\n ((:tag . "NNP") (:stem . "Imaging") (:form . "Imaging") (:end . 71)\n  (:start . 64) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "West") (:form . "West") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Chester") (:form . "Chester") (:end . 85)\n  (:start . 78) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PA") (:form . "PA") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s4.58) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501111@unknown@formal@none@1@S@No neighbors deconvolution or sharpen high filters followed by a low-pass filter were applied to all images.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "neighbor") (:form . "neighbors") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "deconvolution") (:form . "deconvolution")\n  (:end . 26) (:start . 13) (:id . 44))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "VB") (:stem . "sharpen") (:form . "sharpen") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "filter") (:form . "filters") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 59)\n  (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "low-pass") (:form . "low-pass") (:end . 73)\n  (:start . 65) (:id . 52))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 80)\n  (:start . 74) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 85) (:start . 81)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 107)\n  (:start . 101) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.59) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501112@unknown@formal@none@1@S@Pole-to-pole distance as a function of time was measured from the position of the poles in each image.@(((:tag . "NNP") (:stem . "Pole-to-pole") (:form . "Pole-to-pole") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 21)\n  (:start . 13) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 24) (:start . 22)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 87) (:start . 82)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "image") (:form . "image") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.60) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501113@unknown@formal@none@1@S@Kymography was used to quantify speckle movement.@(((:tag . "NNP") (:stem . "Kymography") (:form . "Kymography") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "VB") (:stem . "quantify") (:form . "quantify") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "speckle") (:form . "speckle") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "movement") (:form . "movement") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.61) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501114@unknown@formal@none@1@S@Calculations and statistical analyses were done on Microsoft Excel (Redmond, WA).@(((:tag . "NNS") (:stem . "calculation") (:form . "Calculations") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 28)\n  (:start . 17) (:id . 44))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 37)\n  (:start . 29) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 42) (:start . 38)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "do") (:form . "done") (:end . 47) (:start . 43)\n  (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Microsoft") (:form . "Microsoft") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . "NNP") (:stem . "Excel") (:form . "Excel") (:end . 66) (:start . 61)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Redmond") (:form . "Redmond") (:end . 75)\n  (:start . 68) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "WA") (:form . "WA") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.62) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501115@unknown@formal@none@1@S@To quantify the amount of motor on the spindle we measured the intensity of GFP and that of rhodamine on the spindle and subtracted background intensity and ratioed these two values.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "quantify") (:form . "quantify") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 46)\n  (:start . 39) (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "measure") (:form . "measured") (:end . 58)\n  (:start . 50) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 72)\n  (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 88) (:start . 84)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "NN") (:stem . "rhodamine") (:form . "rhodamine") (:end . 101)\n  (:start . 92) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 104) (:start . 102)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 62))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 116)\n  (:start . 109) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "subtract") (:form . "subtracted") (:end . 131)\n  (:start . 121) (:id . 65))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 142)\n  (:start . 132) (:id . 66))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 152)\n  (:start . 143) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "ratioe") (:form . "ratioed") (:end . 164)\n  (:start . 157) (:id . 69))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 170)\n  (:start . 165) (:id . 70))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 174) (:start . 171)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 181)\n  (:start . 175) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s4.63) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501116@unknown@formal@none@1@S@This allowed us to compare the amount of motor remaining on spindles within single embryos, but we cannot control the amount of injected rhodamine tubulin precisely enough to permit quantitative comparisons between different embryos.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "allow") (:form . "allowed") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 56)\n  (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 75)\n  (:start . 69) (:id . 54))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 82)\n  (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 90)\n  (:start . 83) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "cannot") (:form . "cannot") (:end . 105)\n  (:start . 99) (:id . 60))\n ((:tag . "VB") (:stem . "control") (:form . "control") (:end . 113)\n  (:start . 106) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 124)\n  (:start . 118) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 136)\n  (:start . 128) (:id . 65))\n ((:tag . "NN") (:stem . "rhodamine") (:form . "rhodamine") (:end . 146)\n  (:start . 137) (:id . 66))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 154)\n  (:start . 147) (:id . 67))\n ((:tag . "RB") (:stem . "precisely") (:form . "precisely") (:end . 164)\n  (:start . 155) (:id . 68))\n ((:tag . "RB") (:stem . "enough") (:form . "enough") (:end . 171)\n  (:start . 165) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 174) (:start . 172)\n  (:id . 70))\n ((:tag . "VB") (:stem . "permit") (:form . "permit") (:end . 181)\n  (:start . 175) (:id . 71))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 194)\n  (:start . 182) (:id . 72))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 206)\n  (:start . 195) (:id . 73))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 214)\n  (:start . 207) (:id . 74))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 224)\n  (:start . 215) (:id . 75))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 232)\n  (:start . 225) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 233) (:start . 232)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s4.64) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501117@unknown@formal@none@1@S@Time-Lapse Analysis of Mitosis in Late Embryos and Larval Brains@(((:tag . "NNP") (:stem . "Time-Lapse") (:form . "Time-Lapse") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Analysis") (:form . "Analysis") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Mitosis") (:form . "Mitosis") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Late") (:form . "Late") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Embryos") (:form . "Embryos") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Larval") (:form . "Larval") (:end . 57)\n  (:start . 51) (:id . 50))\n ((:tag . "NNP") (:stem . "Brains") (:form . "Brains") (:end . 64)\n  (:start . 58) (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.65) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501118@unknown@formal@none@1@S@Embryos were collected for 1 h and imaged after at least 7 h.@(((:tag . "NNP") (:stem . "Embryo") (:form . "Embryos") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "image") (:form . "imaged") (:end . 41)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s4.66) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501119@unknown@formal@none@1@S@Brains were dissected from wild-type larvae expressing G147-GFP (Bloomington Stock Center) or GFP-tubulin and from klp61f mutant second and third instar larvae expressing GFP-tubulin in D-22 (pH 6.7) insect medium (U.S. Biological, Swampscott, MA) supplemented with 7.5% fetal bovine serum and 0.5 mM ascorbic acid (Sigma, St. Louis, MO).@(((:tag . "NNS") (:stem . "brain") (:form . "Brains") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "dissect") (:form . "dissected") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 43)\n  (:start . 37) (:id . 47))\n ((:tag . "VBG") (:stem . "express") (:form . 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"NNP") (:stem . "Louis") (:form . "Louis") (:end . 332)\n  (:start . 327) (:id . 100))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 333) (:start . 332)\n  (:id . 101))\n ((:tag . "NNP") (:stem . "MO") (:form . "MO") (:end . 336) (:start . 334)\n  (:id . 102))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 337) (:start . 336)\n  (:id . 103))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 338) (:start . 337)\n  (:id . 104)))@@@1@63@((:identifiers (:sid . :s4.67) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501120@unknown@formal@none@1@S@The explanted brain was then moved carefully in a drop of medium onto a No. 1 coverslip placed on a special stainless steel slide with an indentation to allow observation of the sample.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "explante") (:form . "explanted") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "move") (:form . "moved") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "RB") (:stem . "carefully") (:form . "carefully") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "drop") (:form . "drop") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 64)\n  (:start . 58) (:id . 53))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 69) (:start . 65)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "no.") (:form . "No.") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 77) (:start . 76)\n  (:id . 57))\n ((:tag . "NN") (:stem . "coverslip") (:form . "coverslip") (:end . 87)\n  (:start . 78) (:id . 58))\n ((:tag . "VBN") (:stem . "place") (:form . "placed") (:end . 94)\n  (:start . 88) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 97) (:start . 95)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "special") (:form . "special") (:end . 107)\n  (:start . 100) (:id . 62))\n ((:tag . "JJ") (:stem . "stainless") (:form . "stainless") (:end . 117)\n  (:start . 108) (:id . 63))\n ((:tag . "NN") (:stem . "steel") (:form . "steel") (:end . 123)\n  (:start . 118) (:id . 64))\n ((:tag . "NN") (:stem . "slide") (:form . "slide") (:end . 129)\n  (:start . 124) (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 134) (:start . 130)\n  (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 137) (:start . 135)\n  (:id . 67))\n ((:tag . "NN") (:stem . "indentation") (:form . "indentation") (:end . 149)\n  (:start . 138) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 152) (:start . 150)\n  (:id . 69))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 158)\n  (:start . 153) (:id . 70))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 170)\n  (:start . 159) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 73))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 184)\n  (:start . 178) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s4.68) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501121@unknown@formal@none@1@S@The brain was pushed carefully into direct contact with the coverslip, and an additional coverslip was placed on top of the stainless steel slide to keep the medium in place and prevent dehydration of the sample.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "push") (:form . "pushed") (:end . 20) (:start . 14)\n  (:id . 45))\n ((:tag . "RB") (:stem . "carefully") (:form . "carefully") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "contact") (:form . "contact") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "coverslip") (:form . "coverslip") (:end . 69)\n  (:start . 60) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 88)\n  (:start . 78) (:id . 56))\n ((:tag . "NN") (:stem . "coverslip") (:form . "coverslip") (:end . 98)\n  (:start . 89) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "place") (:form . "placed") (:end . 109)\n  (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "NN") (:stem . "top") (:form . "top") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "stainless") (:form . "stainless") (:end . 133)\n  (:start . 124) (:id . 64))\n ((:tag . "NN") (:stem . "steel") (:form . "steel") (:end . 139)\n  (:start . 134) (:id . 65))\n ((:tag . "NN") (:stem . "slide") (:form . "slide") (:end . 145)\n  (:start . 140) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 67))\n ((:tag . "VB") (:stem . "keep") (:form . "keep") (:end . 153) (:start . 149)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n  (:id . 69))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 164)\n  (:start . 158) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 167) (:start . 165)\n  (:id . 71))\n ((:tag . "NN") (:stem . "place") (:form . "place") (:end . 173)\n  (:start . 168) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 177) (:start . 174)\n  (:id . 73))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 185)\n  (:start . 178) (:id . 74))\n ((:tag . "NN") (:stem . "dehydration") (:form . "dehydration") (:end . 197)\n  (:start . 186) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 200) (:start . 198)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 204) (:start . 201)\n  (:id . 77))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 211)\n  (:start . 205) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s4.69) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501122@unknown@formal@none@1@S@Late embryos and brains were imaged as above except that stacks of 14–18 confocal planes spaced 0.5 µm apart were taken at time intervals of 30 s.@(((:tag . "JJ") (:stem . "late") (:form . "Late") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "image") (:form . "imaged") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "IN") (:stem . "except") (:form . "except") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "stack") (:form . "stacks") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "CD") (:stem . "14–18") (:form . "14–18") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . "NNS") (:stem . "plane") (:form . "planes") (:end . 88)\n  (:start . 82) (:id . 56))\n ((:tag . "VBD") (:stem . "space") (:form . "spaced") (:end . 95)\n  (:start . 89) (:id . 57))\n ((:tag . "CD") (:stem . "0.5") (:form . "0.5") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . "RB") (:stem . "apart") (:form . "apart") (:end . 108)\n  (:start . 103) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 119)\n  (:start . 114) (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 127) (:start . 123)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 137)\n  (:start . 128) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n  (:id . 66))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 143) (:start . 141)\n  (:id . 67))\n ((:tag . "NN") (:stem . "s") (:form . "s") (:end . 145) (:start . 144)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.70) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501123@unknown@formal@none@1@S@Images were analyzed as above.@(((:tag . "NNS") (:stem . "image") (:form . "Images") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 30) (:start . 29)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s4.71) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501124@unknown@formal@none@1@S@Online Supplemental Material@(((:tag . "NNP") (:stem . "Online") (:form . "Online") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Supplemental") (:form . "Supplemental") (:end . 19)\n  (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "Material") (:form . "Material") (:end . 28)\n  (:start . 20) (:id . 44)))@@@1@3@((:identifiers (:sid . :s4.72) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501125@unknown@formal@none@1@S@Supplemental Video 1 shows a time-lapse movie of an embryo expressing KLP61F-GFP and injected with rhodamine tubulin and anti-KLP61F (see Figure 1).@(((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Video") (:form . "Video") (:end . 18) (:start . 13)\n  (:id . 43))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 20) (:start . 19)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "time-lapse") (:form . "time-lapse") (:end . 39)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "movie") (:form . "movie") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 58)\n  (:start . 52) (:id . 51))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 69)\n  (:start . 59) (:id . 52))\n ((:tag . "NNP") (:stem . "KLP61F-GFP") (:form . "KLP61F-GFP") (:end . 80)\n  (:start . 70) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 93)\n  (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 98) (:start . 94)\n  (:id . 56))\n ((:tag . "NN") (:stem . "rhodamine") (:form . "rhodamine") (:end . 108)\n  (:start . 99) (:id . 57))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 116)\n  (:start . 109) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 59))\n ((:tag . "NN") (:stem . "anti-klp61f") (:form . "anti-KLP61F") (:end . 132)\n  (:start . 121) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 61))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 137) (:start . 134)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 144)\n  (:start . 138) (:id . 63))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 146) (:start . 145)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.73) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501126@unknown@formal@none@1@S@Supplemental Video 2 shows a time-lapse movie of an embryo injected with rhodamine tubulin and anti-KLP61F (see Figure 2, A and C).@(((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Video") (:form . "Video") (:end . 18) (:start . 13)\n  (:id . 43))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 20) (:start . 19)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "time-lapse") (:form . "time-lapse") (:end . 39)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "movie") (:form . "movie") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 58)\n  (:start . 52) (:id . 51))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 67)\n  (:start . 59) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "NN") (:stem . "rhodamine") (:form . "rhodamine") (:end . 82)\n  (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 90)\n  (:start . 83) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . "anti-klp61f") (:form . "anti-KLP61F") (:end . 106)\n  (:start . 95) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 118)\n  (:start . 112) (:id . 60))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 123) (:start . 122)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.74) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501127@unknown@formal@none@1@S@Supplemental Video 3 shows a time-lapse movie of an embryo expressing GFP-CNN and injected with rhodamine tubulin and anti-KLP61F (see Figure 2, E–G).@(((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Video") (:form . "Video") (:end . 18) (:start . 13)\n  (:id . 43))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 20) (:start . 19)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "time-lapse") (:form . "time-lapse") (:end . 39)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "movie") (:form . "movie") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 58)\n  (:start . 52) (:id . 51))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 69)\n  (:start . 59) (:id . 52))\n ((:tag . "NNP") (:stem . "GFP-CNN") (:form . "GFP-CNN") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 90)\n  (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 95) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . "rhodamine") (:form . "rhodamine") (:end . 105)\n  (:start . 96) (:id . 57))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 113)\n  (:start . 106) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 59))\n ((:tag . "NN") (:stem . "anti-klp61f") (:form . "anti-KLP61F") (:end . 129)\n  (:start . 118) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 61))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 134) (:start . 131)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 141)\n  (:start . 135) (:id . 63))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 143) (:start . 142)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "E–G") (:form . "E–G") (:end . 148) (:start . 145)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s4.75) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501128@unknown@formal@none@1@S@(A) Microinjection of an anti-KLP61F antibody (designed to dissociate KLP61F from spindles) results in a gradient of antibody concentration and produces a gradient in the KLP61F content of different spindles.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "microinjection") (:form . "Microinjection")\n  (:end . 18) (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "anti-klp61f") (:form . "anti-KLP61F") (:end . 36)\n  (:start . 25) (:id . 48))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 45)\n  (:start . 37) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "VB") (:stem . "dissociate") (:form . "dissociate") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "klp61f") (:form . "KLP61F") (:end . 76)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 90)\n  (:start . 82) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 99)\n  (:start . 92) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 113)\n  (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 62))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 125)\n  (:start . 117) (:id . 63))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 139) (:start . 126) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "produce") (:form . "produces") (:end . 152)\n  (:start . 144) (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 154) (:start . 153)\n  (:id . 67))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 163)\n  (:start . 155) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 166) (:start . 164)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 177)\n  (:start . 171) (:id . 71))\n ((:tag . "NN") (:stem . "content") (:form . "content") (:end . 185)\n  (:start . 178) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 188) (:start . 186)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 198)\n  (:start . 189) (:id . 74))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 207)\n  (:start . 199) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s4.76) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501129@unknown@formal@none@1@S@Images from time-lapse movie of an embryo expressing KLP61F-GFP and injected with rhodamine tubulin and anti-KLP61F (see Supplemental Video 1).@(((:tag . "NNS") (:stem . "image") (:form . "Images") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "time-lapse") (:form . "time-lapse") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "movie") (:form . "movie") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . "NNP") (:stem . "KLP61F-GFP") (:form . "KLP61F-GFP") (:end . 63)\n  (:start . 53) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 76)\n  (:start . 68) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 81) (:start . 77)\n  (:id . 53))\n ((:tag . "NN") (:stem . "rhodamine") (:form . "rhodamine") (:end . 91)\n  (:start . 82) (:id . 54))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 99)\n  (:start . 92) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 56))\n ((:tag . "NN") (:stem . "anti-klp61f") (:form . "anti-KLP61F") (:end . 115)\n  (:start . 104) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 58))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 120) (:start . 117)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 133)\n  (:start . 121) (:id . 60))\n ((:tag . "NNP") (:stem . "Video") (:form . "Video") (:end . 139)\n  (:start . 134) (:id . 61))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 141) (:start . 140)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s4.77) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501130@unknown@formal@none@1@S@Time in each frame is given in seconds from NEB.@(((:tag . "NNP") (:stem . "Time") (:form . "Time") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "second") (:form . "seconds") (:end . 38)\n  (:start . 31) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 43) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "NEB") (:form . "NEB") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 48) (:start . 47)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.78) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501131@unknown@formal@none@1@S@Bar, 10 µm.@(((:tag . "NNP") (:stem . "Bar") (:form . "Bar") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 7) (:start . 5)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 10) (:start . 8)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 11) (:start . 10)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s4.79) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501132@unknown@formal@none@1@S@The injection site was close to the top of the embryo (arrow), KLP61F-GFP forms immunoprecipitates, and most KLP61F-GFP is depleted from the spindles.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "RB") (:stem . "close") (:form . "close") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "top") (:form . "top") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 53)\n  (:start . 47) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "arrow") (:form . "arrow") (:end . 60) (:start . 55)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "KLP61F-GFP") (:form . "KLP61F-GFP") (:end . 73)\n  (:start . 63) (:id . 57))\n ((:tag . "NNS") (:stem . "form") (:form . "forms") (:end . 79) (:start . 74)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "immunoprecipitate") (:form . "immunoprecipitates")\n  (:end . 98) (:start . 80) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 61))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "KLP61F-GFP") (:form . "KLP61F-GFP") (:end . 119)\n  (:start . 109) (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 122) (:start . 120)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "deplete") (:form . "depleted") (:end . 131)\n  (:start . 123) (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 136) (:start . 132)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 149)\n  (:start . 141) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.80) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501133@unknown@formal@none@1@S@These spindles collapse, as seen at 247 s.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "CD") (:stem . "247") (:form . "247") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "s") (:form . "s") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.81) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501134@unknown@formal@none@1@S@Toward the bottom of the embryo, KLP61F-GFP is still present on the spindles and consequently these spindles assemble, though they may exhibit defects.@(((:tag . "IN") (:stem . "toward") (:form . "Toward") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "bottom") (:form . "bottom") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "KLP61F-GFP") (:form . "KLP61F-GFP") (:end . 43)\n  (:start . 33) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 52) (:start . 47)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 60)\n  (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 76)\n  (:start . 68) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "RB") (:stem . "consequently") (:form . "consequently") (:end . 93)\n  (:start . 81) (:id . 57))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 99) (:start . 94)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 108)\n  (:start . 100) (:id . 59))\n ((:tag . "VBP") (:stem . "assemble") (:form . "assemble") (:end . 117)\n  (:start . 109) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 125)\n  (:start . 119) (:id . 62))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 130) (:start . 126)\n  (:id . 63))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 134) (:start . 131)\n  (:id . 64))\n ((:tag . "VB") (:stem . "exhibit") (:form . "exhibit") (:end . 142)\n  (:start . 135) (:id . 65))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 150)\n  (:start . 143) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x4.82.1) (:span 131 134)))\n (:hscopes ((:id . :x4.82.1) (:span 131 150)))\n (:identifiers (:sid . :s4.82) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501135@unknown@formal@none@1@S@(B) Graph of pole–pole distance as a function of time (left) and quantification of KLP61F remaining on these spindles (right).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Graph") (:form . "Graph") (:end . 9) (:start . 4)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pole–pole") (:form . "pole–pole") (:end . 22)\n  (:start . 13) (:id . 47))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 31)\n  (:start . 23) (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 45)\n  (:start . 37) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 52))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 53) (:start . 49)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 54))\n ((:tag . "NN") (:stem . "left") (:form . "left") (:end . 59) (:start . 55)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 57))\n ((:tag . "NN") (:stem . "quantification") (:form . "quantification")\n  (:end . 79) (:start . 65) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 89)\n  (:start . 83) (:id . 60))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 99)\n  (:start . 90) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 102) (:start . 100)\n  (:id . 62))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 108)\n  (:start . 103) (:id . 63))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 117)\n  (:start . 109) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 119) (:start . 118)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 124)\n  (:start . 119) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s4.83) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501136@unknown@formal@none@1@S@The normalized ratio of KLP61F-GFP to rhodamine tubulin is used to compare the amount of motor remaining on each spindle at different time points.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "normalized") (:form . "normalized") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "KLP61F-GFP") (:form . "KLP61F-GFP") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "rhodamine") (:form . "rhodamine") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 63) (:start . 59)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 74)\n  (:start . 67) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 85)\n  (:start . 79) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 94) (:start . 89)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 104)\n  (:start . 95) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 112) (:start . 108)\n  (:id . 60))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 120)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 133)\n  (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 138) (:start . 134)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 145)\n  (:start . 139) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.84) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501137@unknown@formal@none@1@S@Spindles that collapse have practically no motor on them, whereas spindles that do not collapse or recover from partial collapse have at least 40% remaining.@(((:tag . "NNS") (:stem . "spindle") (:form . "Spindles") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "RB") (:stem . "practically") (:form . "practically") (:end . 39)\n  (:start . 28) (:id . 46))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 86) (:start . 83)\n  (:id . 56))\n ((:tag . "VB") (:stem . "collapse") (:form . "collapse") (:end . 95)\n  (:start . 87) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 98) (:start . 96)\n  (:id . 58))\n ((:tag . "VB") (:stem . "recover") (:form . "recover") (:end . 106)\n  (:start . 99) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 111) (:start . 107)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 119)\n  (:start . 112) (:id . 61))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 128)\n  (:start . 120) (:id . 62))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 133) (:start . 129)\n  (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 136) (:start . 134)\n  (:id . 64))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 142)\n  (:start . 137) (:id . 65))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 145) (:start . 143)\n  (:id . 66))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 146) (:start . 145)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 156)\n  (:start . 147) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.85) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501138@unknown@formal@none@1@S@(A) Two time points from a wild-type embryo injected with anti-KLP61F antibody showing a gradient of defects (see Supplemental Video 2).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 12) (:start . 8)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 19)\n  (:start . 13) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 24) (:start . 20)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 36)\n  (:start . 27) (:id . 50))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 43)\n  (:start . 37) (:id . 51))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 52)\n  (:start . 44) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 57) (:start . 53)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "anti-klp61f") (:form . "anti-KLP61F") (:end . 69)\n  (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 78)\n  (:start . 70) (:id . 55))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 86)\n  (:start . 79) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 88) (:start . 87)\n  (:id . 57))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 97)\n  (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 108)\n  (:start . 101) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 113) (:start . 110)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 126)\n  (:start . 114) (:id . 63))\n ((:tag . "NNP") (:stem . "Video") (:form . "Video") (:end . 132)\n  (:start . 127) (:id . 64))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 135) (:start . 134)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.86) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501139@unknown@formal@none@1@S@Bar, 10 µm.@(((:tag . "NNP") (:stem . "Bar") (:form . "Bar") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 7) (:start . 5)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 10) (:start . 8)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 11) (:start . 10)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s4.87) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501140@unknown@formal@none@1@S@(B) Two time points from an Ncd null embryo injected with anti-KLP61F antibody showing more disorganized spindles due to the loss of two motors.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 12) (:start . 8)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 19)\n  (:start . 13) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 24) (:start . 20)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 27) (:start . 25)\n  (:id . 49))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 31) (:start . 28)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 36) (:start . 32)\n  (:id . 51))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 43)\n  (:start . 37) (:id . 52))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 52)\n  (:start . 44) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 57) (:start . 53)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "anti-klp61f") (:form . "anti-KLP61F") (:end . 69)\n  (:start . 58) (:id . 55))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 78)\n  (:start . 70) (:id . 56))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 86)\n  (:start . 79) (:id . 57))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 91) (:start . 87)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "disorganized") (:form . "disorganized") (:end . 104)\n  (:start . 92) (:id . 59))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 113)\n  (:start . 105) (:id . 60))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 120) (:start . 118)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n  (:id . 63))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 129) (:start . 125)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 136) (:start . 133)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 143)\n  (:start . 137) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s4.88) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501141@unknown@formal@none@1@S@Bar, 10 µm.@(((:tag . "NNP") (:stem . "Bar") (:form . "Bar") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 7) (:start . 5)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 10) (:start . 8)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 11) (:start . 10)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s4.89) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501142@unknown@formal@none@1@S@(C) Graph of pole–pole distance as a function of time for the embryo shown in A.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Graph") (:form . "Graph") (:end . 9) (:start . 4)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pole–pole") (:form . "pole–pole") (:end . 22)\n  (:start . 13) (:id . 47))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 31)\n  (:start . 23) (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 45)\n  (:start . 37) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 52))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 53) (:start . 49)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 57) (:start . 54)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 55))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 68)\n  (:start . 62) (:id . 56))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 74) (:start . 69)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 58))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 79) (:start . 78)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.90) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501143@unknown@formal@none@1@S@Close to the injection site spindles collapse (see s1 and s3), and other spindles shorten but remain small (see s2).@(((:tag . "NN") (:stem . "close") (:form . "Close") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "s1") (:form . "s1") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "s3") (:form . "s3") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 72) (:start . 67)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 81)\n  (:start . 73) (:id . 58))\n ((:tag . "VBP") (:stem . "shorten") (:form . "shorten") (:end . 89)\n  (:start . 82) (:id . 59))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 93) (:start . 90)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "remain") (:form . "remain") (:end . 100)\n  (:start . 94) (:id . 61))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 106)\n  (:start . 101) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 63))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 111) (:start . 108)\n  (:id . 64))\n ((:tag . "NN") (:stem . "s2") (:form . "s2") (:end . 114) (:start . 112)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.91) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501144@unknown@formal@none@1@S@Further away from the injection site, spindles do not elongate during prometaphase (s5, and the most distal spindles exhibit anaphase elongation (s6, s7, and s8).@(((:tag . "RB") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 46)\n  (:start . 38) (:id . 49))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "VB") (:stem . "elongate") (:form . "elongate") (:end . 62)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 82)\n  (:start . 70) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "s5") (:form . "s5") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "distal") (:form . "distal") (:end . 107)\n  (:start . 101) (:id . 61))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 116)\n  (:start . 108) (:id . 62))\n ((:tag . "VBP") (:stem . "exhibit") (:form . "exhibit") (:end . 124)\n  (:start . 117) (:id . 63))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 133)\n  (:start . 125) (:id . 64))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 144)\n  (:start . 134) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n  (:id . 66))\n ((:tag . "NN") (:stem . "s6") (:form . "s6") (:end . 148) (:start . 146)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 68))\n ((:tag . "NN") (:stem . "s7") (:form . "s7") (:end . 152) (:start . 150)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 71))\n ((:tag . "NN") (:stem . "s8") (:form . "s8") (:end . 160) (:start . 158)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s4.92) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501145@unknown@formal@none@1@S@For comparison, we show graphs from a wild-type embryo (purple) and most severe effect (an embryo injected with enough antibody to collapse all spindles within the field of view; red).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "graph") (:form . "graphs") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 47)\n  (:start . 38) (:id . 50))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 54)\n  (:start . 48) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "purple") (:form . "purple") (:end . 62)\n  (:start . 56) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 72) (:start . 68)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 79)\n  (:start . 73) (:id . 57))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 86)\n  (:start . 80) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 59))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 90) (:start . 88)\n  (:id . 60))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 97)\n  (:start . 91) (:id . 61))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 106)\n  (:start . 98) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 111) (:start . 107)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "enough") (:form . "enough") (:end . 118)\n  (:start . 112) (:id . 64))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 127)\n  (:start . 119) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n  (:id . 66))\n ((:tag . "VB") (:stem . "collapse") (:form . "collapse") (:end . 139)\n  (:start . 131) (:id . 67))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 143) (:start . 140)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 152)\n  (:start . 144) (:id . 69))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 159)\n  (:start . 153) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 71))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 169)\n  (:start . 164) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 172) (:start . 170)\n  (:id . 73))\n ((:tag . "NN") (:stem . "view") (:form . "view") (:end . 177) (:start . 173)\n  (:id . 74))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 178) (:start . 177)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 182) (:start . 179)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s4.93) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501146@unknown@formal@none@1@S@(D) Spindle length as a function of time for the Ncd null embryo shown in B.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Spindle") (:form . "Spindle") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 18)\n  (:start . 12) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 21) (:start . 19)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 48))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 32)\n  (:start . 24) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 50))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 40) (:start . 36)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 44) (:start . 41)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 53))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 52) (:start . 49)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 57) (:start . 53)\n  (:id . 55))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 64)\n  (:start . 58) (:id . 56))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 70) (:start . 65)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 75) (:start . 74)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.94) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501147@unknown@formal@none@1@S@For comparison graphs of wild-type embryos (purple), Ncd null embryos (dark blue), and Ncd null embryos injected with a high concentration of anti-KLP61F (red) are shown.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "graph") (:form . "graphs") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 42)\n  (:start . 35) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "purple") (:form . "purple") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 69)\n  (:start . 62) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "dark") (:form . "dark") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 80) (:start . 76)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 60))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 90) (:start . 87)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 95) (:start . 91)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 103)\n  (:start . 96) (:id . 63))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 112)\n  (:start . 104) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 117) (:start . 113)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 119) (:start . 118)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 124) (:start . 120)\n  (:id . 67))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 138) (:start . 125) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 141) (:start . 139)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "anti-KLP61F") (:form . "anti-KLP61F") (:end . 153)\n  (:start . 142) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 71))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 158) (:start . 155)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 73))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 163) (:start . 160)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 169)\n  (:start . 164) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s4.95) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501148@unknown@formal@none@1@S@The gradient of concentration of antibody leads to a gradient of spindle pole lengths.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 29) (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 47) (:start . 42)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 61)\n  (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "length") (:form . "lengths") (:end . 85)\n  (:start . 78) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.96) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501149@unknown@formal@none@1@S@A high inhibition of KLP61F leads to spindle collapse; lower concentrations lead to less severe defects.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "VB") (:stem . "spindle") (:form . "spindle") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 75) (:start . 61) (:id . 53))\n ((:tag . "VBP") (:stem . "lead") (:form . "lead") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n  (:id . 55))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 95)\n  (:start . 89) (:id . 57))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 103)\n  (:start . 96) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.97) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501150@unknown@formal@none@1@S@At a certain concentration the spindle maintains a steady length (light purple).@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 26) (:start . 13) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "VBZ") (:stem . "maintain") (:form . "maintains") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "steady") (:form . "steady") (:end . 57)\n  (:start . 51) (:id . 50))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 64)\n  (:start . 58) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "light") (:form . "light") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "purple") (:form . "purple") (:end . 78)\n  (:start . 72) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.98) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501151@unknown@formal@none@1@S@(E) Anti-KLP61F antibody causes spindle collapse at prometaphase without apparent disruption of centrosomes or spindle poles.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Anti-KLP61F") (:form . "Anti-KLP61F") (:end . 15)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 64)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 72)\n  (:start . 65) (:id . 52))\n ((:tag . "JJ") (:stem . "apparent") (:form . "apparent") (:end . 81)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "disruption") (:form . "disruption") (:end . 92)\n  (:start . 82) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "centrosome") (:form . "centrosomes") (:end . 107)\n  (:start . 96) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 110) (:start . 108)\n  (:id . 57))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 118)\n  (:start . 111) (:id . 58))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 124)\n  (:start . 119) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.99) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501152@unknown@formal@none@1@S@Images from time-lapse movie of an embryo expressing GFP-CNN (green) and injected with rhodamine tubulin (red) and anti-KLP61F (see Supplemental Video 3).@(((:tag . "NNS") (:stem . "image") (:form . "Images") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "time-lapse") (:form . "time-lapse") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "movie") (:form . "movie") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . "NNP") (:stem . "GFP-CNN") (:form . "GFP-CNN") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . "NN") (:stem . "rhodamine") (:form . "rhodamine") (:end . 96)\n  (:start . 87) (:id . 57))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 104)\n  (:start . 97) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "anti-KLP61F") (:form . "anti-KLP61F") (:end . 126)\n  (:start . 115) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 131) (:start . 128)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 144)\n  (:start . 132) (:id . 66))\n ((:tag . "NNP") (:stem . "Video") (:form . "Video") (:end . 150)\n  (:start . 145) (:id . 67))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 152) (:start . 151)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s4.100) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501153@unknown@formal@none@1@S@Time in each frame is given in seconds.@(((:tag . "NNP") (:stem . "Time") (:form . "Time") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "second") (:form . "seconds") (:end . 38)\n  (:start . 31) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 39) (:start . 38)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s4.101) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501154@unknown@formal@none@1@S@Bar, 10 µm.@(((:tag . "NNP") (:stem . "Bar") (:form . "Bar") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 7) (:start . 5)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 10) (:start . 8)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 11) (:start . 10)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s4.102) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501155@unknown@formal@none@1@S@Note how the centrosomes move toward each other, but do not appear disorganized.@(((:tag . "VB") (:stem . "note") (:form . "Note") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "centrosome") (:form . "centrosomes") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "VBP") (:stem . "move") (:form . "move") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "toward") (:form . "toward") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 66)\n  (:start . 60) (:id . 54))\n ((:tag . "VBN") (:stem . "disorganize") (:form . "disorganized") (:end . 79)\n  (:start . 67) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.103) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501156@unknown@formal@none@1@S@(F) Tubulin fluorescence in the central spindle increases as the spindle collapses.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Tubulin") (:form . "Tubulin") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 24)\n  (:start . 12) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 39)\n  (:start . 32) (:id . 49))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 57)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 72)\n  (:start . 65) (:id . 54))\n ((:tag . "NNS") (:stem . "collapse") (:form . "collapses") (:end . 82)\n  (:start . 73) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.104) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501157@unknown@formal@none@1@S@Normalized spindle length (filled symbols) and fluorescent tubulin intensity at the equator (empty symbols) as a function of time for wild-type (black) and KLP61F inhibited spindles (red).@(((:tag . "VBN") (:stem . "normalize") (:form . "Normalized") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 18)\n  (:start . 11) (:id . 43))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 25)\n  (:start . 19) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "fill") (:form . "filled") (:end . 33) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "symbol") (:form . "symbols") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "fluorescent") (:form . "fluorescent") (:end . 58)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 76)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "equator") (:form . "equator") (:end . 91)\n  (:start . 84) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "empty") (:form . "empty") (:end . 98) (:start . 93)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "symbol") (:form . "symbols") (:end . 106)\n  (:start . 99) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 121)\n  (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 129) (:start . 125)\n  (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 133) (:start . 130)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 143)\n  (:start . 134) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 150)\n  (:start . 145) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 155) (:start . 152)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 162)\n  (:start . 156) (:id . 71))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 172)\n  (:start . 163) (:id . 72))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 181)\n  (:start . 173) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 183) (:start . 182)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 186) (:start . 183)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s4.105) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501158@unknown@formal@none@1@S@After KLP61F inhibition spindles collapse with a correlated increase in tubulin intensity, suggesting that MTs are sliding inward and not depolymerizing.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 12)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "spindle") (:form . "spindles") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 41)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "correlated") (:form . "correlated") (:end . 59)\n  (:start . 49) (:id . 49))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 68)\n  (:start . 60) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 79)\n  (:start . 72) (:id . 52))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 89)\n  (:start . 80) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 101)\n  (:start . 91) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 106) (:start . 102)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 110) (:start . 107)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 114) (:start . 111)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 122)\n  (:start . 115) (:id . 59))\n ((:tag . "RB") (:stem . "inward") (:form . "inward") (:end . 129)\n  (:start . 123) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 61))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 137) (:start . 134)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "depolymerize") (:form . "depolymerizing")\n  (:end . 152) (:start . 138) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x4.106.1) (:span 91 101)))\n (:hscopes ((:id . :x4.106.1) (:span 91 152)))\n (:identifiers (:sid . :s4.106) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501159@unknown@formal@none@1@S@The increase is much higher than that observed in wild-type spindles, indicating that it is not due to a normal increase in tubulin.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 27) (:start . 21)\n  (:id . 46))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 46)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 59)\n  (:start . 50) (:id . 51))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 68)\n  (:start . 60) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 80)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 104) (:start . 103)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 111)\n  (:start . 105) (:id . 62))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 120)\n  (:start . 112) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 131)\n  (:start . 124) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x4.107.1) (:span 70 85)))\n (:hscopes ((:id . :x4.107.1) (:span 70 131)))\n (:identifiers (:sid . :s4.107) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501160@unknown@formal@none@1@S@(G) Linescans of fluorescent tubulin intensity along a single ipMT bundle at different time points during the collapse.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "linescan") (:form . "Linescans") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "fluorescent") (:form . "fluorescent") (:end . 28)\n  (:start . 17) (:id . 47))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "ipmt") (:form . "ipMT") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "bundle") (:form . "bundle") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 86)\n  (:start . 77) (:id . 56))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 91) (:start . 87)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 98)\n  (:start . 92) (:id . 58))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 105)\n  (:start . 99) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 118)\n  (:start . 110) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.108) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501161@unknown@formal@none@1@S@The intensity increases as the spindle collapses.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "NNS") (:stem . "collapse") (:form . "collapses") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.109) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501162@unknown@formal@none@1@S@RESULTS@(((:tag . "NNS") (:stem . "results") (:form . "RESULTS") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.110) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501163@unknown@formal@none@1@S@Injection of Anti-KLP61F Antibody into the Drosophila Syncytial Embryo Causes a Gradient of Mitotic Defects@(((:tag . "NN") (:stem . "injection") (:form . "Injection") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Anti-KLP61F") (:form . "Anti-KLP61F") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "NNP") (:stem . "Antibody") (:form . "Antibody") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 53)\n  (:start . 43) (:id . 48))\n ((:tag . "JJ") (:stem . "syncytial") (:form . "Syncytial") (:end . 63)\n  (:start . 54) (:id . 49))\n ((:tag . "NN") (:stem . "embryo") (:form . "Embryo") (:end . 70)\n  (:start . 64) (:id . 50))\n ((:tag . "VBZ") (:stem . "cause") (:form . "Causes") (:end . 77)\n  (:start . 71) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 79) (:start . 78)\n  (:id . 52))\n ((:tag . "NN") (:stem . "gradient") (:form . "Gradient") (:end . 88)\n  (:start . 80) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "Mitotic") (:end . 99)\n  (:start . 92) (:id . 55))\n ((:tag . "NNPS") (:stem . "Defect") (:form . "Defects") (:end . 107)\n  (:start . 100) (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.111) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501164@unknown@formal@none@1@S@We raised new rabbit affinity-purified polyclonal antibodies to the C-terminal tail domain of KLP61F.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "raise") (:form . "raised") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "rabbit") (:form . "rabbit") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "JJ") (:stem . "affinity-purified") (:form . "affinity-purified")\n  (:end . 38) (:start . 21) (:id . 46))\n ((:tag . "JJ") (:stem . "polyclonal") (:form . "polyclonal") (:end . 49)\n  (:start . 39) (:id . 47))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 60)\n  (:start . 50) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 78)\n  (:start . 68) (:id . 51))\n ((:tag . "NN") (:stem . "tail") (:form . "tail") (:end . 83) (:start . 79)\n  (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 90)\n  (:start . 84) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 100)\n  (:start . 94) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.112) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501165@unknown@formal@none@1@S@Studies using transient transfection with Eg5 mutants in cultured Xenopus cells (Sawin and Mitchison, 1995 ), with KLP61F mutants in live Drosophila embryos (Cheerambathur et al., 2008 ) and using antibodies raised against phospho- and unphospho-epitopes in Drosophila embryos (Sharp et al., 1999a ) suggest that the cyclin-dependent kinase-mediated phosphorylation of a conserved Thr-933 residue in the bimC box of kinesin-5 is critical for its localization to the spindle.@(((:tag . "NNS") (:stem . "study") (:form . "Studies") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "transient") (:form . "transient") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 36)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . 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"bimc") (:form . "bimC") (:end . 408) (:start . 404)\n  (:id . 106))\n ((:tag . "NN") (:stem . "box") (:form . "box") (:end . 412) (:start . 409)\n  (:id . 107))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 415) (:start . 413)\n  (:id . 108))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 425)\n  (:start . 416) (:id . 109))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 428) (:start . 426)\n  (:id . 110))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 437)\n  (:start . 429) (:id . 111))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 441) (:start . 438)\n  (:id . 112))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 445) (:start . 442)\n  (:id . 113))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 458)\n  (:start . 446) (:id . 114))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 461) (:start . 459)\n  (:id . 115))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 465) (:start . 462)\n  (:id . 116))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 473)\n  (:start . 466) (:id . 117))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 474) (:start . 473)\n  (:id . 118)))@@@1@77@((:hcues ((:id . :x4.113.1) (:span 300 307)))\n (:hscopes ((:id . :x4.113.1) (:span 300 473)))\n (:identifiers (:sid . :s4.113) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501166@unknown@formal@none@1@S@We reasoned that antibodies to the phosphorylated form of this domain would competitively inhibit the binding of native phosphorylated KLP61F to the spindle and, by displacing the motor from its site of action, would inhibit its function.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "reason") (:form . "reasoned") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "phosphorylated") (:form . "phosphorylated")\n  (:end . 49) (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 69)\n  (:start . 63) (:id . 52))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 75) (:start . 70)\n  (:id . 53))\n ((:tag . "RB") (:stem . "competitively") (:form . "competitively")\n  (:end . 89) (:start . 76) (:id . 54))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 97)\n  (:start . 90) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 56))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 109)\n  (:start . 102) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 119)\n  (:start . 113) (:id . 59))\n ((:tag . "VBN") (:stem . "phosphorylate") (:form . "phosphorylated")\n  (:end . 134) (:start . 120) (:id . 60))\n ((:tag . "NN") (:stem . "klp61f") (:form . "KLP61F") (:end . 141)\n  (:start . 135) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 144) (:start . 142)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 63))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 156)\n  (:start . 149) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 164) (:start . 162)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "displace") (:form . "displacing") (:end . 175)\n  (:start . 165) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 69))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 185)\n  (:start . 180) (:id . 70))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 190) (:start . 186)\n  (:id . 71))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 194) (:start . 191)\n  (:id . 72))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 199) (:start . 195)\n  (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 202) (:start . 200)\n  (:id . 74))\n ((:tag . "NN") (:stem . "action") (:form . "action") (:end . 209)\n  (:start . 203) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 210) (:start . 209)\n  (:id . 76))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 216)\n  (:start . 211) (:id . 77))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 224)\n  (:start . 217) (:id . 78))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 228) (:start . 225)\n  (:id . 79))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 237)\n  (:start . 229) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s4.114) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501167@unknown@formal@none@1@S@Accordingly antibodies were raised against a tail domain fragment in which the Thr-933 residue was changed to an aspartate phospho-mimic by site-directed mutagenesis (Materials and Methods).@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 22)\n  (:start . 12) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 27) (:start . 23)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "raise") (:form . "raised") (:end . 34)\n  (:start . 28) (:id . 45))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 42)\n  (:start . 35) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 47))\n ((:tag . "NN") (:stem . "tail") (:form . "tail") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 56)\n  (:start . 50) (:id . 49))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 65)\n  (:start . 57) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "NN") (:stem . "thr-933") (:form . "Thr-933") (:end . 86)\n  (:start . 79) (:id . 54))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 94)\n  (:start . 87) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 98) (:start . 95)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "change") (:form . "changed") (:end . 106)\n  (:start . 99) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 109) (:start . 107)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 112) (:start . 110)\n  (:id . 59))\n ((:tag . "NN") (:stem . "aspartate") (:form . "aspartate") (:end . 122)\n  (:start . 113) (:id . 60))\n ((:tag . "JJ") (:stem . "phospho-mimic") (:form . "phospho-mimic")\n  (:end . 136) (:start . 123) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 139) (:start . 137)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "site-directed") (:form . "site-directed")\n  (:end . 153) (:start . 140) (:id . 63))\n ((:tag . "NN") (:stem . "mutagenesis") (:form . "mutagenesis") (:end . 165)\n  (:start . 154) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 65))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 176)\n  (:start . 167) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 180) (:start . 177)\n  (:id . 67))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 188)\n  (:start . 181) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s4.115) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501168@unknown@formal@none@1@S@These antibodies react with a single polypeptide of appropriate molecular weight on immunoblots of embryonic extracts and have been shown to stain mitotic spindles by immunofluorescence (our unpublished results and Silverman-Gavrila and Wilde, 2006 ), consistent with our previous results (Sharp et al., 1999a ; Cheerambathur et al., 2008 ).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "react") (:form . "react") (:end . 22) (:start . 17)\n  (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "polypeptide") (:form . "polypeptide") (:end . 48)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 63)\n  (:start . 52) (:id . 50))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 73)\n  (:start . 64) (:id . 51))\n ((:tag . "NN") (:stem . "weight") (:form . "weight") (:end . 80)\n  (:start . 74) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 83) (:start . 81)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "immunoblot") (:form . "immunoblots") (:end . 95)\n  (:start . 84) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 108)\n  (:start . 99) (:id . 56))\n ((:tag . "NNS") (:stem . "extract") (:form . "extracts") (:end . 117)\n  (:start . 109) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . 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"(") (:end . 187) (:start . 186)\n  (:id . 68))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 190) (:start . 187)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "unpublished") (:form . "unpublished") (:end . 202)\n  (:start . 191) (:id . 70))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 210)\n  (:start . 203) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 214) (:start . 211)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Silverman-Gavrila") (:form . "Silverman-Gavrila")\n  (:end . 232) (:start . 215) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 236) (:start . 233)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Wilde") (:form . "Wilde") (:end . 242)\n  (:start . 237) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 243) (:start . 242)\n  (:id . 76))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 248) (:start . 244)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 250) (:start . 249)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 251) (:start . 250)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 262)\n  (:start . 252) (:id . 80))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 267) (:start . 263)\n  (:id . 81))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 271) (:start . 268)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 280)\n  (:start . 272) (:id . 83))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 288)\n  (:start . 281) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 290) (:start . 289)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "Sharp") (:form . "Sharp") (:end . 295)\n  (:start . 290) (:id . 86))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 298) (:start . 296)\n  (:id . 87))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 302) (:start . 299)\n  (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 303) (:start . 302)\n  (:id . 89))\n ((:tag . "CD") (:stem . "1999a") (:form . "1999a") (:end . 309)\n  (:start . 304) (:id . 90))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 311) (:start . 310)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "Cheerambathur") (:form . "Cheerambathur")\n  (:end . 325) (:start . 312) (:id . 92))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 328) (:start . 326)\n  (:id . 93))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 332) (:start . 329)\n  (:id . 94))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 333) (:start . 332)\n  (:id . 95))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 338) (:start . 334)\n  (:id . 96))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 340) (:start . 339)\n  (:id . 97))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 341) (:start . 340)\n  (:id . 98)))@@@1@57@((:identifiers (:sid . :s4.116) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501169@unknown@formal@none@1@S@As reported previously, the microinjection of affinity-purified antibody into the syncytial blastoderm embryo blocked mitosis and produced monoastral arrays of microtubules (Sharp et al., 1999b , 2000a ) similar to those seen in fixed loss-of-function klp61f mutants after depletion of the maternal load in larvae (Heck et al., 1993 ; see below).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "microinjection") (:form . "microinjection")\n  (:end . 42) (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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"JJ") (:stem . "loss-of-function") (:form . "loss-of-function")\n  (:end . 251) (:start . 235) (:id . 79))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 258)\n  (:start . 252) (:id . 80))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 266)\n  (:start . 259) (:id . 81))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 272)\n  (:start . 267) (:id . 82))\n ((:tag . "NN") (:stem . "depletion") (:form . "depletion") (:end . 282)\n  (:start . 273) (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 285) (:start . 283)\n  (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 289) (:start . 286)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "maternal") (:form . "maternal") (:end . 298)\n  (:start . 290) (:id . 86))\n ((:tag . "NN") (:stem . "load") (:form . "load") (:end . 303) (:start . 299)\n  (:id . 87))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 306) (:start . 304)\n  (:id . 88))\n ((:tag . "NNS") (:stem . 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(:stem . ".") (:form . ".") (:end . 346) (:start . 345)\n  (:id . 100)))@@@1@59@((:identifiers (:sid . :s4.117) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501170@unknown@formal@none@1@S@To directly visualize the extent of the anti-KLP61F induced dissociation of KLP61F from mitotic spindles in the injected embryos, we coinjected fluorescent tubulin and anti-KLP61F into stable transgenic strains of Drosophila that express functional KLP61F-GFP (Cheerambathur et al., 2008 ; Figure 1; Supplemental Video 1).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "VB") (:stem . "visualize") (:form . "visualize") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . 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"into") (:end . 184) (:start . 180)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "stable") (:form . "stable") (:end . 191)\n  (:start . 185) (:id . 69))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 202)\n  (:start . 192) (:id . 70))\n ((:tag . "NNS") (:stem . "strain") (:form . "strains") (:end . 210)\n  (:start . 203) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 213) (:start . 211)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 224)\n  (:start . 214) (:id . 73))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 229) (:start . 225)\n  (:id . 74))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 237)\n  (:start . 230) (:id . 75))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 248)\n  (:start . 238) (:id . 76))\n ((:tag . "NNP") (:stem . "KLP61F-GFP") (:form . "KLP61F-GFP") (:end . 259)\n  (:start . 249) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . 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"Supplemental") (:end . 312)\n  (:start . 300) (:id . 88))\n ((:tag . "NNP") (:stem . "Video") (:form . "Video") (:end . 318)\n  (:start . 313) (:id . 89))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 320) (:start . 319)\n  (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 321) (:start . 320)\n  (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 322) (:start . 321)\n  (:id . 92)))@@@1@51@((:identifiers (:sid . :s4.118) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501171@unknown@formal@none@1@S@The antibody rapidly displaced KLP61F from spindles and formed visible, fluorescent immunoprecipitates in the adjacent cytoplasm (Figure 1, arrow).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "displace") (:form . "displaced") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "klp61f") (:form . "KLP61F") (:end . 37)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "form") (:form . "formed") (:end . 62) (:start . 56)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "visible") (:form . "visible") (:end . 70)\n  (:start . 63) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "fluorescent") (:form . "fluorescent") (:end . 83)\n  (:start . 72) (:id . 53))\n ((:tag . "NNS") (:stem . "immunoprecipitate") (:form . "immunoprecipitates")\n  (:end . 102) (:start . 84) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 118)\n  (:start . 110) (:id . 57))\n ((:tag . "NN") (:stem . "cytoplasm") (:form . "cytoplasm") (:end . 128)\n  (:start . 119) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 136)\n  (:start . 130) (:id . 60))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 138) (:start . 137)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 62))\n ((:tag . "NN") (:stem . "arrow") (:form . "arrow") (:end . 145)\n  (:start . 140) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.119) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501172@unknown@formal@none@1@S@Moreover this experiment provided clear visual evidence of the formation of a spatial gradient of inhibition of the target antigen throughout the syncytial blastoderm, as had been inferred indirectly from the effects of inhibitory antibody microinjection in previous studies (Sharp et al., 2000b ; Blower and Karpen, 2001 ; Kwon et al., 2004 ).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "provide") (:form . "provided") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 39) (:start . 34)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "visual") (:form . "visual") (:end . 46)\n  (:start . 40) (:id . 47))\n ((:tag . "NN") (:stem . 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5501173@unknown@formal@none@1@S@Proximal to the antibody microinjection site, where the anti-KLP61F concentration is highest, KLP61F is completely dissociated from spindles and consequently spindles form monoasters.@(((:tag . "JJ") (:stem . "proximal") (:form . "Proximal") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "microinjection") (:form . "microinjection")\n  (:end . 39) (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 44) (:start . 40)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 51) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "anti-klp61f") (:form . "anti-KLP61F") (:end . 67)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 81) (:start . 68) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 84) (:start . 82)\n  (:id . 53))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 92)\n  (:start . 85) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 100)\n  (:start . 94) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 114)\n  (:start . 104) (:id . 58))\n ((:tag . "VBN") (:stem . "dissociate") (:form . "dissociated") (:end . 126)\n  (:start . 115) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 131) (:start . 127)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 140)\n  (:start . 132) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n  (:id . 62))\n ((:tag . "RB") (:stem . "consequently") (:form . "consequently") (:end . 157)\n  (:start . 145) (:id . 63))\n ((:tag . "VBZ") (:stem . "spindle") (:form . "spindles") (:end . 166)\n  (:start . 158) (:id . 64))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 171) (:start . 167)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "monoaster") (:form . "monoasters") (:end . 182)\n  (:start . 172) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.121) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501174@unknown@formal@none@1@S@The injected antibody diffuses through the cytoplasm, setting up a concentration gradient, highest at the injection site and decreasing at increasingly distal sites.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "diffus") (:form . "diffuses") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cytoplasm") (:form . "cytoplasm") (:end . 52)\n  (:start . 43) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "set") (:form . "setting") (:end . 61) (:start . 54)\n  (:id . 50))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 80) (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 98)\n  (:start . 91) (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 101) (:start . 99)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 58))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 115)\n  (:start . 106) (:id . 59))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 120) (:start . 116)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "decrease") (:form . "decreasing") (:end . 135)\n  (:start . 125) (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 138) (:start . 136)\n  (:id . 63))\n ((:tag . "RB") (:stem . "increasingly") (:form . "increasingly") (:end . 151)\n  (:start . 139) (:id . 64))\n ((:tag . "JJ") (:stem . "distal") (:form . "distal") (:end . 158)\n  (:start . 152) (:id . 65))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 164)\n  (:start . 159) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.122) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501175@unknown@formal@none@1@S@Accordingly, moving away from the injection site, the extent of depletion of KLP61F from spindles decreases, and increasingly higher concentrations of fluorescent motor are retained on spindles (Figure 1).@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "move") (:form . "moving") (:end . 19) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 60)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "depletion") (:form . "depletion") (:end . 73)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 83)\n  (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 97)\n  (:start . 89) (:id . 58))\n ((:tag . "VBZ") (:stem . "decrease") (:form . "decreases") (:end . 107)\n  (:start . 98) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 61))\n ((:tag . "RB") (:stem . "increasingly") (:form . "increasingly") (:end . 125)\n  (:start . 113) (:id . 62))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 132)\n  (:start . 126) (:id . 63))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 147) (:start . 133) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "fluorescent") (:form . "fluorescent") (:end . 162)\n  (:start . 151) (:id . 66))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 168)\n  (:start . 163) (:id . 67))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 172) (:start . 169)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "retain") (:form . "retained") (:end . 181)\n  (:start . 173) (:id . 69))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 184) (:start . 182)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 193)\n  (:start . 185) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 195) (:start . 194)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 201)\n  (:start . 195) (:id . 73))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 203) (:start . 202)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 204) (:start . 203)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s4.123) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501176@unknown@formal@none@1@S@Thus at distal sites, spindles do not form monoasters but display less severe defects, producing a range of “phenotypes” analogous to an allelic series of genetic mutants (Figure 1).@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "distal") (:form . "distal") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "monoaster") (:form . "monoasters") (:end . 53)\n  (:start . 43) (:id . 51))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 65)\n  (:start . 58) (:id . 53))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 77)\n  (:start . 71) (:id . 55))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 85)\n  (:start . 78) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 96)\n  (:start . 87) (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 104) (:start . 99)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 61))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "phenotypes") (:form . "phenotypes") (:end . 119)\n  (:start . 109) (:id . 63))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 120) (:start . 119)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "analogous") (:form . "analogous") (:end . 130)\n  (:start . 121) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 133) (:start . 131)\n  (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 136) (:start . 134)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "allelic") (:form . "allelic") (:end . 144)\n  (:start . 137) (:id . 68))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 151)\n  (:start . 145) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 162)\n  (:start . 155) (:id . 71))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 170)\n  (:start . 163) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 178)\n  (:start . 172) (:id . 74))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 180) (:start . 179)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 181) (:start . 180)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s4.124) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501177@unknown@formal@none@1@S@We quantified the amount of KLP61F present on spindles at different sites within this gradient by measuring the fluorescence intensity ratio of KLP61F-GFP to injected rhodamine tubulin, which allows us to compare spindles within a single embryo, but not between multiple embryos, due to small variations in the amount of injected tubulin.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "quantify") (:form . "quantified") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 67)\n  (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 73) (:start . 68)\n  (:id . 53))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 80)\n  (:start . 74) (:id . 54))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 94)\n  (:start . 86) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "measure") (:form . 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"to") (:end . 286) (:start . 284)\n  (:id . 88))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 292)\n  (:start . 287) (:id . 89))\n ((:tag . "NNS") (:stem . "variation") (:form . "variations") (:end . 303)\n  (:start . 293) (:id . 90))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 306) (:start . 304)\n  (:id . 91))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 310) (:start . 307)\n  (:id . 92))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 317)\n  (:start . 311) (:id . 93))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 320) (:start . 318)\n  (:id . 94))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 329)\n  (:start . 321) (:id . 95))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 337)\n  (:start . 330) (:id . 96))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 338) (:start . 337)\n  (:id . 97)))@@@1@56@((:identifiers (:sid . :s4.125) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501178@unknown@formal@none@1@S@As shown in Figure 1B, the severity of spindle pole separation defects correlates reasonably well with the extent of depletion of KLP61F from the spindle, so that spindles containing maximal levels of KLP61F-GFP (arbitrarily assigned a value 1.0) displayed spindle pole separation profiles similar to uninjected controls, spindles containing only 0–10% residual KLP61F-GFP collapsed into monoasters, and those containing intermediate levels of the motor (50–70%) displayed spindle length defects but completed mitosis nonetheless.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "1b") (:form . 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"only") (:end . 346) (:start . 342)\n  (:id . 96))\n ((:tag . "CD") (:stem . "0–10") (:form . "0–10") (:end . 351) (:start . 347)\n  (:id . 97))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 352) (:start . 351)\n  (:id . 98))\n ((:tag . "JJ") (:stem . "residual") (:form . "residual") (:end . 361)\n  (:start . 353) (:id . 99))\n ((:tag . "NNP") (:stem . "KLP61F-GFP") (:form . "KLP61F-GFP") (:end . 372)\n  (:start . 362) (:id . 100))\n ((:tag . "VBD") (:stem . "collapse") (:form . "collapsed") (:end . 382)\n  (:start . 373) (:id . 101))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 387) (:start . 383)\n  (:id . 102))\n ((:tag . "NNS") (:stem . "monoaster") (:form . "monoasters") (:end . 398)\n  (:start . 388) (:id . 103))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 399) (:start . 398)\n  (:id . 104))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 403) (:start . 400)\n  (:id . 105))\n ((:tag . "DT") (:stem . "those") (:form . 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")") (:end . 462) (:start . 461)\n  (:id . 116))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 472)\n  (:start . 463) (:id . 117))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 480)\n  (:start . 473) (:id . 118))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 487)\n  (:start . 481) (:id . 119))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 495)\n  (:start . 488) (:id . 120))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 499) (:start . 496)\n  (:id . 121))\n ((:tag . "VBN") (:stem . "complete") (:form . "completed") (:end . 509)\n  (:start . 500) (:id . 122))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 517)\n  (:start . 510) (:id . 123))\n ((:tag . "RB") (:stem . "nonetheless") (:form . "nonetheless") (:end . 529)\n  (:start . 518) (:id . 124))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 530) (:start . 529)\n  (:id . 125)))@@@1@84@((:identifiers (:sid . :s4.126) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501179@unknown@formal@none@1@S@Spindle Pole Separation Defects Produced by Varying Levels of KLP61F Depletion in Wild-Type Versus Ncd Null Mutant Embryos@(((:tag . "NNP") (:stem . "Spindle") (:form . "Spindle") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Pole") (:form . "Pole") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Separation") (:form . "Separation") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "NNPS") (:stem . "Defect") (:form . "Defects") (:end . 31)\n  (:start . 24) (:id . 45))\n ((:tag . "VBN") (:stem . "produce") (:form . "Produced") (:end . 40)\n  (:start . 32) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "vary") (:form . "Varying") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "NNS") (:stem . "level") (:form . "Levels") (:end . 58)\n  (:start . 52) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 68)\n  (:start . 62) (:id . 51))\n ((:tag . "NNP") (:stem . "Depletion") (:form . "Depletion") (:end . 78)\n  (:start . 69) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Wild-Type") (:form . "Wild-Type") (:end . 91)\n  (:start . 82) (:id . 54))\n ((:tag . "NNP") (:stem . "Versus") (:form . "Versus") (:end . 98)\n  (:start . 92) (:id . 55))\n ((:tag . "NNP") (:stem . "Ncd") (:form . "Ncd") (:end . 102) (:start . 99)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Null") (:form . "Null") (:end . 107) (:start . 103)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Mutant") (:form . "Mutant") (:end . 114)\n  (:start . 108) (:id . 58))\n ((:tag . "NNP") (:stem . "Embryos") (:form . "Embryos") (:end . 122)\n  (:start . 115) (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.127) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501180@unknown@formal@none@1@S@In previous studies, we reported that prometaphase spindles collapse into monoasters after KLP61F inhibition and are “rescued” in Ncd null mutants, but the behavior of spindles containing intermediate levels of KLP61F was not systematically examined.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "report") (:form . "reported") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 50)\n  (:start . 38) (:id . 49))\n ((:tag . "VBZ") (:stem . "spindle") (:form . "spindles") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "monoaster") (:form . "monoasters") (:end . 84)\n  (:start . 74) (:id . 53))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 90) (:start . 85)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 97)\n  (:start . 91) (:id . 55))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 108)\n  (:start . 98) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 116) (:start . 113)\n  (:id . 58))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 118) (:start . 117)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "rescued") (:form . "rescued") (:end . 125)\n  (:start . 118) (:id . 60))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 126) (:start . 125)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 62))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 133) (:start . 130)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 138) (:start . 134)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 146)\n  (:start . 139) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 66))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 151) (:start . 148)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 68))\n ((:tag . "NN") (:stem . "behavior") (:form . "behavior") (:end . 164)\n  (:start . 156) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 167) (:start . 165)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 176)\n  (:start . 168) (:id . 71))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 187)\n  (:start . 177) (:id . 72))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 200)\n  (:start . 188) (:id . 73))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 207)\n  (:start . 201) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 210) (:start . 208)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 217)\n  (:start . 211) (:id . 76))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 221) (:start . 218)\n  (:id . 77))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 225) (:start . 222)\n  (:id . 78))\n ((:tag . "RB") (:stem . "systematically") (:form . "systematically")\n  (:end . 240) (:start . 226) (:id . 79))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 249)\n  (:start . 241) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 250) (:start . 249)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s4.128) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501181@unknown@formal@none@1@S@Results presented in the previous section now permit us to do so.@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "present") (:form . "presented") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "permit") (:form . "permit") (:end . 52)\n  (:start . 46) (:id . 49))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "VB") (:stem . "do") (:form . "do") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.129) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501182@unknown@formal@none@1@S@In wild-type embryos, we observed that, at increasing distances from the injection site, the extent of perturbation of spindle length, as characterized by changes in pole–pole spacing versus time, decreases in parallel with the decrease in extent of depletion of KLP61F from spindles (Figures 1B and 2C).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . 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5501183@unknown@formal@none@1@S@The most severe effect, prometaphase spindle collapse, occurred at a rate of 0.06 µm/s (Figure 1B, spindles s5 and s6), although some spindles close by retained sufficient levels of KLP61F to slow down the rate of collapse (Figure 2C, spindles s1–s4).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 36)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "collapse") (:form . 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5501184@unknown@formal@none@1@S@Further away, spindles were observed to shorten somewhat, but did not collapse and instead maintained a short prometaphase length, and then elongated at anaphase B (Figures 1B, s3 and s4, and 2C, s5).@(((:tag . "RB") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "VB") (:stem . "shorten") (:form . "shorten") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "RB") (:stem . "somewhat") (:form . "somewhat") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 78)\n  (:start . 70) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "RB") (:stem . "instead") (:form . "instead") (:end . 90)\n  (:start . 83) (:id . 57))\n ((:tag . "VBD") (:stem . "maintain") (:form . "maintained") (:end . 101)\n  (:start . 91) (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 109)\n  (:start . 104) (:id . 60))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 122)\n  (:start . 110) (:id . 61))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 129)\n  (:start . 123) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 64))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 139) (:start . 135)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "elongate") (:form . "elongated") (:end . 149)\n  (:start . 140) (:id . 66))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 152) (:start . 150)\n  (:id . 67))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 161)\n  (:start . 153) (:id . 68))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 163) (:start . 162)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 165) (:start . 164)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 172)\n  (:start . 165) (:id . 71))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 175) (:start . 173)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 176) (:start . 175)\n  (:id . 73))\n ((:tag . "NN") (:stem . "s3") (:form . "s3") (:end . 179) (:start . 177)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 183) (:start . 180)\n  (:id . 75))\n ((:tag . "NN") (:stem . "s4") (:form . "s4") (:end . 186) (:start . 184)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 187) (:start . 186)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 191) (:start . 188)\n  (:id . 78))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 194) (:start . 192)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n  (:id . 80))\n ((:tag . "NN") (:stem . "s5") (:form . "s5") (:end . 198) (:start . 196)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s4.132) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501185@unknown@formal@none@1@S@Even further away, spindles did not elongate during prometaphase, or did so only slightly, but then elongated at approximately wild-type rates during anaphase B sometimes after a slight delay (Figures 1B, s1 and s2, and 2C, s6–s8).@(((:tag . "RB") (:stem . "even") (:form . "Even") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "VB") (:stem . "elongate") (:form . "elongate") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 64)\n  (:start . 52) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 89)\n  (:start . 81) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 99) (:start . 95)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "elongate") (:form . "elongated") (:end . 109)\n  (:start . 100) (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 126) (:start . 113) (:id . 63))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 136)\n  (:start . 127) (:id . 64))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 142)\n  (:start . 137) (:id . 65))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 149)\n  (:start . 143) (:id . 66))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 158)\n  (:start . 150) (:id . 67))\n ((:tag . "NN") (:stem . "b") (:form . "B") (:end . 160) (:start . 159)\n  (:id . 68))\n ((:tag . "RB") (:stem . "sometimes") (:form . "sometimes") (:end . 170)\n  (:start . 161) (:id . 69))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 176)\n  (:start . 171) (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 178) (:start . 177)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "slight") (:form . "slight") (:end . 185)\n  (:start . 179) (:id . 72))\n ((:tag . "NN") (:stem . "delay") (:form . "delay") (:end . 191)\n  (:start . 186) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 193) (:start . 192)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 200)\n  (:start . 193) (:id . 75))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 203) (:start . 201)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 204) (:start . 203)\n  (:id . 77))\n ((:tag . "NN") (:stem . "s1") (:form . "s1") (:end . 207) (:start . 205)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 211) (:start . 208)\n  (:id . 79))\n ((:tag . "NN") (:stem . "s2") (:form . "s2") (:end . 214) (:start . 212)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 215) (:start . 214)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 219) (:start . 216)\n  (:id . 82))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 222) (:start . 220)\n  (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 223) (:start . 222)\n  (:id . 84))\n ((:tag . "NN") (:stem . "s6–s8") (:form . "s6–s8") (:end . 229)\n  (:start . 224) (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 230) (:start . 229)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s4.133) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501186@unknown@formal@none@1@S@Thus, particularly noteworthy features of the spindles that do not collapse after partial loss of KLP61F are their short lengths during metaphase and anaphase A and their relatively normal rates of anaphase B spindle elongation.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 18)\n  (:start . 6) (:id . 44))\n ((:tag . "JJ") (:stem . "noteworthy") (:form . "noteworthy") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 75)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 89)\n  (:start . 82) (:id . 55))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 104)\n  (:start . 98) (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 114)\n  (:start . 109) (:id . 60))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 120)\n  (:start . 115) (:id . 61))\n ((:tag . "NNS") (:stem . "length") (:form . "lengths") (:end . 128)\n  (:start . 121) (:id . 62))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 135)\n  (:start . 129) (:id . 63))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 145)\n  (:start . 136) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 149) (:start . 146)\n  (:id . 65))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 158)\n  (:start . 150) (:id . 66))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 160) (:start . 159)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n  (:id . 68))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 170)\n  (:start . 165) (:id . 69))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 181)\n  (:start . 171) (:id . 70))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 188)\n  (:start . 182) (:id . 71))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 194)\n  (:start . 189) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 197) (:start . 195)\n  (:id . 73))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 206)\n  (:start . 198) (:id . 74))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 208) (:start . 207)\n  (:id . 75))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 216)\n  (:start . 209) (:id . 76))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 227)\n  (:start . 217) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s4.134) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501187@unknown@formal@none@1@S@The latter result was intriguing because we had previously proposed that KLP61F-driven ipMT sliding drives anaphase B, yet in studying the gradient of intermediate phenotypes (Figures 1B and 2C), we did not observe spindles that circumvented the prometaphase collapse but then failed to elongate normally during subsequent anaphase B.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "intrigue") (:form . "intriguing") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . 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5501188@unknown@formal@none@1@S@This is, in fact, consistent with mathematical modeling predicting that the rate of anaphase spindle elongation is independent of the number of motors, at least above a low threshold number (Brust-Mascher et al., 2004 ; Wollman et al., 2008 ).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 16) (:start . 12)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 28)\n  (:start . 18) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 33) (:start . 29)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "mathematical") (:form . "mathematical") (:end . 46)\n  (:start . 34) (:id . 50))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . "VBG") (:stem . "predict") (:form . "predicting") (:end . 66)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 92)\n  (:start . 84) (:id . 57))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 111)\n  (:start . 101) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 126)\n  (:start . 115) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 63))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 140)\n  (:start . 134) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 150)\n  (:start . 144) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n  (:id . 67))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 154) (:start . 152)\n  (:id . 68))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 160)\n  (:start . 155) (:id . 69))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 166)\n  (:start . 161) (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 168) (:start . 167)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 172) (:start . 169)\n  (:id . 72))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 182)\n  (:start . 173) (:id . 73))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 189)\n  (:start . 183) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 191) (:start . 190)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 204) (:start . 191) (:id . 76))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 207) (:start . 205)\n  (:id . 77))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 211) (:start . 208)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 212) (:start . 211)\n  (:id . 79))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 217) (:start . 213)\n  (:id . 80))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 219) (:start . 218)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Wollman") (:form . "Wollman") (:end . 227)\n  (:start . 220) (:id . 82))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 230) (:start . 228)\n  (:id . 83))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 234) (:start . 231)\n  (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 235) (:start . 234)\n  (:id . 85))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 240) (:start . 236)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 242) (:start . 241)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 88)))@@@1@47@((:hcues ((:id . :x4.136.1) (:span 56 66)))\n (:hscopes ((:id . :x4.136.1) (:span 56 189)))\n (:identifiers (:sid . :s4.136) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501189@unknown@formal@none@1@S@We hypothesized that spindles containing sufficient KLP61F motor to circumvent collapse and progress through prometaphase might also contain enough motor to elongate the spindle at normal rates during anaphase B.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "hypothesize") (:form . "hypothesized") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 51)\n  (:start . 41) (:id . 47))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 58)\n  (:start . 52) (:id . 48))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 64) (:start . 59)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 50))\n ((:tag . "VB") (:stem . "circumvent") (:form . "circumvent") (:end . 78)\n  (:start . 68) (:id . 51))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 87)\n  (:start . 79) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 53))\n ((:tag . "NN") (:stem . "progress") (:form . "progress") (:end . 100)\n  (:start . 92) (:id . 54))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 108)\n  (:start . 101) (:id . 55))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 121)\n  (:start . 109) (:id . 56))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 127)\n  (:start . 122) (:id . 57))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 132) (:start . 128)\n  (:id . 58))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 140)\n  (:start . 133) (:id . 59))\n ((:tag . "JJ") (:stem . "enough") (:form . "enough") (:end . 147)\n  (:start . 141) (:id . 60))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 153)\n  (:start . 148) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 156) (:start . 154)\n  (:id . 62))\n ((:tag . "VB") (:stem . "elongate") (:form . "elongate") (:end . 165)\n  (:start . 157) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n  (:id . 64))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 177)\n  (:start . 170) (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 180) (:start . 178)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 187)\n  (:start . 181) (:id . 67))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 193)\n  (:start . 188) (:id . 68))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 200)\n  (:start . 194) (:id . 69))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 209)\n  (:start . 201) (:id . 70))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 211) (:start . 210)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x4.137.1) (:span 122 127)) ((:id . :x4.137.2) (:span 3 15)))\n (:hscopes ((:id . :x4.137.1) (:span 122 211))\n  ((:id . :x4.137.2) (:span 3 211)))\n (:identifiers (:sid . :s4.137) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501190@unknown@formal@none@1@S@We further reasoned that, because Ncd generates an inward force capable of antagonizing KLP61F (Sharp et al., 2000a ; Tao et al., 2006 ), in the absence of Ncd function, we might improve our chances of encountering spindles with sufficient KLP61F to proceed through prometaphase but below the threshold level of KLP61F needed to drive normal rates of anaphase B.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "reason") (:form . "reasoned") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "NNP") (:stem . "Ncd") (:form . 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(:end . 362) (:start . 361)\n  (:id . 108)))@@@1@67@((:hcues ((:id . :x4.138.1) (:span 173 178)))\n (:hscopes ((:id . :x4.138.1) (:span 173 361)))\n (:identifiers (:sid . :s4.138) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501191@unknown@formal@none@1@S@In such spindles, a decreased rate of anaphase B spindle elongation should be observed.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "decrease") (:form . "decreased") (:end . 29)\n  (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 56)\n  (:start . 49) (:id . 52))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 67)\n  (:start . 57) (:id . 53))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 74)\n  (:start . 68) (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x4.139.1) (:span 68 74)))\n (:hscopes ((:id . :x4.139.1) (:span 18 86)))\n (:identifiers (:sid . :s4.139) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501192@unknown@formal@none@1@S@Accordingly, we inhibited KLP61F in Ncd null mutant embryos, which totally lack kinesin-14 function, in order to circumvent prometaphase spindle collapse and to study the role of KLP61F during spindle elongation.@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 59)\n  (:start . 52) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 66) (:start . 61)\n  (:id . 53))\n ((:tag . "RB") (:stem . "totally") (:form . "totally") (:end . 74)\n  (:start . 67) (:id . 54))\n ((:tag . "VBP") (:stem . "lack") (:form . "lack") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "kinesin-14") (:form . "kinesin-14") (:end . 90)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 99)\n  (:start . 91) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 109)\n  (:start . 104) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "VB") (:stem . "circumvent") (:form . "circumvent") (:end . 123)\n  (:start . 113) (:id . 62))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 136)\n  (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 144)\n  (:start . 137) (:id . 64))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 153)\n  (:start . 145) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 160) (:start . 158)\n  (:id . 67))\n ((:tag . "VB") (:stem . "study") (:form . "study") (:end . 166)\n  (:start . 161) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 69))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 175) (:start . 171)\n  (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 178) (:start . 176)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 185)\n  (:start . 179) (:id . 72))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 192)\n  (:start . 186) (:id . 73))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 200)\n  (:start . 193) (:id . 74))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 211)\n  (:start . 201) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s4.140) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501193@unknown@formal@none@1@S@In uninjected mutants, pole–pole separation occurred prematurely from prometaphase onward, supporting our hypothesis that Ncd serves as a “brake” that exerts an inward force on spindle poles, antagonistic to KLP61F (Figure 2D, dark blue).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "uninjected") (:form . "uninjected") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "pole–pole") (:form . "pole–pole") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "VBD") (:stem . "occur") (:form . "occurred") (:end . 52)\n  (:start . 44) (:id . 48))\n ((:tag . "RB") (:stem . "prematurely") (:form . "prematurely") (:end . 64)\n  (:start . 53) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 69) (:start . 65)\n  (:id . 50))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 82)\n  (:start . 70) (:id . 51))\n ((:tag . "RB") (:stem . "onward") (:form . "onward") (:end . 89)\n  (:start . 83) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "support") (:form . "supporting") (:end . 101)\n  (:start . 91) (:id . 54))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 105) (:start . 102)\n  (:id . 55))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 116)\n  (:start . 106) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 121) (:start . 117)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Ncd") (:form . "Ncd") (:end . 125) (:start . 122)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "serve") (:form . "serves") (:end . 132)\n  (:start . 126) (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 135) (:start . 133)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 137) (:start . 136)\n  (:id . 61))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 139) (:start . 138)\n  (:id . 62))\n ((:tag . "NN") (:stem . "brake") (:form . "brake") (:end . 144)\n  (:start . 139) (:id . 63))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 145) (:start . 144)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 150) (:start . 146)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "exert") (:form . "exerts") (:end . 157)\n  (:start . 151) (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 160) (:start . 158)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "inward") (:form . "inward") (:end . 167)\n  (:start . 161) (:id . 68))\n ((:tag . "NN") (:stem . "force") (:form . "force") (:end . 173)\n  (:start . 168) (:id . 69))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 176) (:start . 174)\n  (:id . 70))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 184)\n  (:start . 177) (:id . 71))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 190)\n  (:start . 185) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "antagonistic") (:form . "antagonistic") (:end . 204)\n  (:start . 192) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 207) (:start . 205)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 214)\n  (:start . 208) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 216) (:start . 215)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 222)\n  (:start . 216) (:id . 78))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 225) (:start . 223)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 226) (:start . 225)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "dark") (:form . "dark") (:end . 231) (:start . 227)\n  (:id . 81))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 236) (:start . 232)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 237) (:start . 236)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x4.141.1) (:span 106 116)))\n (:hscopes ((:id . :x4.141.1) (:span 106 214)))\n (:identifiers (:sid . :s4.141) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501194@unknown@formal@none@1@S@Pole–pole separation in Ncd null embryos occurs shortly after nuclear envelope breakdown (NEB), earlier than in wild-type embryos, suggesting that normally Ncd's braking activity is turned on throughout prometaphase.@(((:tag . "NNP") (:stem . "Pole–pole") (:form . "Pole–pole") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 20)\n  (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 47)\n  (:start . 41) (:id . 48))\n ((:tag . "RB") (:stem . "shortly") (:form . "shortly") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 61) (:start . 56)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 69)\n  (:start . 62) (:id . 51))\n ((:tag . "NN") (:stem . "envelope") (:form . "envelope") (:end . 78)\n  (:start . 70) (:id . 52))\n ((:tag . "NN") (:stem . "breakdown") (:form . "breakdown") (:end . 88)\n  (:start . 79) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "NEB") (:form . "NEB") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 94) (:start . 93)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . "RBR") (:stem . "earlier") (:form . "earlier") (:end . 103)\n  (:start . 96) (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 121)\n  (:start . 112) (:id . 61))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 129)\n  (:start . 122) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 141)\n  (:start . 131) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 146) (:start . 142)\n  (:id . 65))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 155)\n  (:start . 147) (:id . 66))\n ((:tag . "NNP") (:stem . "Ncd") (:form . "Ncd") (:end . 159) (:start . 156)\n  (:id . 67))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 161) (:start . 159)\n  (:id . 68))\n ((:tag . "NN") (:stem . "braking") (:form . "braking") (:end . 169)\n  (:start . 162) (:id . 69))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 178)\n  (:start . 170) (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 181) (:start . 179)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "turn") (:form . "turned") (:end . 188)\n  (:start . 182) (:id . 72))\n ((:tag . "RP") (:stem . "on") (:form . "on") (:end . 191) (:start . 189)\n  (:id . 73))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 202)\n  (:start . 192) (:id . 74))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 215)\n  (:start . 203) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x4.142.1) (:span 131 141)))\n (:hscopes ((:id . :x4.142.1) (:span 131 215)))\n (:identifiers (:sid . :s4.142) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501195@unknown@formal@none@1@S@Anti-KLP61F injection into Ncd null mutant embryos produced a gradient of defects (Figure 2D), where the most severe effect was spindle collapse.@(((:tag . "JJ") (:stem . "anti-klp61f") (:form . "Anti-KLP61F") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 21)\n  (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 26) (:start . 22)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 42)\n  (:start . 36) (:id . 47))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 59)\n  (:start . 51) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 50))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 70)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 81)\n  (:start . 74) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 89)\n  (:start . 83) (:id . 55))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 100)\n  (:start . 95) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 109) (:start . 105)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 116)\n  (:start . 110) (:id . 62))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 123)\n  (:start . 117) (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 135)\n  (:start . 128) (:id . 65))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 144)\n  (:start . 136) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.143) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501196@unknown@formal@none@1@S@This was not observed in our previous studies (Sharp et al., 1999b , 2000a ) because more antibody is needed to collapse the spindle in an Ncd null background than in a wild-type background.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sharp") (:form . "Sharp") (:end . 52) (:start . 47)\n  (:id . 51))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . "CD") (:stem . "1999b") (:form . "1999b") (:end . 66) (:start . 61)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 56))\n ((:tag . "CD") (:stem . "2000a") (:form . "2000a") (:end . 74) (:start . 69)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n  (:id . 58))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 84)\n  (:start . 77) (:id . 59))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 89) (:start . 85)\n  (:id . 60))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 98)\n  (:start . 90) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 101) (:start . 99)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "need") (:form . "needed") (:end . 108)\n  (:start . 102) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n  (:id . 64))\n ((:tag . "VB") (:stem . "collapse") (:form . "collapse") (:end . 120)\n  (:start . 112) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n  (:id . 66))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 132)\n  (:start . 125) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 68))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 138) (:start . 136)\n  (:id . 69))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 142) (:start . 139)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 147) (:start . 143)\n  (:id . 71))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 158)\n  (:start . 148) (:id . 72))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 163) (:start . 159)\n  (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 166) (:start . 164)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 168) (:start . 167)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 178)\n  (:start . 169) (:id . 76))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 189)\n  (:start . 179) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s4.144) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501197@unknown@formal@none@1@S@This result suggests that, when KLP61F and Ncd function are both missing, another inward force-generator must drive pole–pole collapse.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Ncd") (:form . "Ncd") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "missing") (:form . "missing") (:end . 72)\n  (:start . 65) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 81)\n  (:start . 74) (:id . 56))\n ((:tag . "JJ") (:stem . "inward") (:form . "inward") (:end . 88)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "force-generator") (:form . "force-generator")\n  (:end . 104) (:start . 89) (:id . 58))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 109) (:start . 105)\n  (:id . 59))\n ((:tag . "VB") (:stem . "drive") (:form . "drive") (:end . 115)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "pole–pole") (:form . "pole–pole") (:end . 125)\n  (:start . 116) (:id . 61))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 134)\n  (:start . 126) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x4.145.1) (:span 12 20)))\n (:hscopes ((:id . :x4.145.1) (:span 12 134)))\n (:identifiers (:sid . :s4.145) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501198@unknown@formal@none@1@S@In addition, spindles lacking the function of both motors are disorganized (Figure 2B), suggesting that these motors contribute to spindle organization by cross-linking MTs throughout the spindle, in agreement with their localization in these cells.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "VBG") (:stem . "lack") (:form . "lacking") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 57)\n  (:start . 51) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "disorganize") (:form . "disorganized") (:end . 74)\n  (:start . 62) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 82)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "2b") (:form . "2B") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 98)\n  (:start . 88) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 103) (:start . 99)\n  (:id . 60))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 109)\n  (:start . 104) (:id . 61))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 116)\n  (:start . 110) (:id . 62))\n ((:tag . "VBP") (:stem . "contribute") (:form . "contribute") (:end . 127)\n  (:start . 117) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n  (:id . 64))\n ((:tag . "VB") (:stem . "spindle") (:form . "spindle") (:end . 138)\n  (:start . 131) (:id . 65))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 151)\n  (:start . 139) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "cross-linking") (:form . "cross-linking")\n  (:end . 168) (:start . 155) (:id . 68))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 172) (:start . 169)\n  (:id . 69))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 183)\n  (:start . 173) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 187) (:start . 184)\n  (:id . 71))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 195)\n  (:start . 188) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n  (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 199) (:start . 197)\n  (:id . 74))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 209)\n  (:start . 200) (:id . 75))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 214) (:start . 210)\n  (:id . 76))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 220)\n  (:start . 215) (:id . 77))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 233)\n  (:start . 221) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 236) (:start . 234)\n  (:id . 79))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 242)\n  (:start . 237) (:id . 80))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 248)\n  (:start . 243) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 249) (:start . 248)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x4.146.1) (:span 88 98)))\n (:hscopes ((:id . :x4.146.1) (:span 88 248)))\n (:identifiers (:sid . :s4.146) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501199@unknown@formal@none@1@S@Significantly, at more distal sites where spindles retain partial KLP61F function but Ncd function is missing, the spindles do not collapse and either do not elongate at all (Figure 2D, s1) or elongate after a significant delay (Figure 2D, s2–s6).@(((:tag . "RB") (:stem . "significantly") (:form . "Significantly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "distal") (:form . "distal") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "spindle") (:form . 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5501200@unknown@formal@none@1@S@This failure to elongate was not observed in anti-KLP61F–injected wild-type embryos, and it supports the hypothesis that KLP61F is necessary for anaphase B.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "failure") (:form . "failure") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VB") (:stem . "elongate") (:form . "elongate") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "anti-klp61f–injected")\n  (:form . "anti-KLP61F–injected") (:end . 65) (:start . 45) (:id . 50))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 75)\n  (:start . 66) (:id . 51))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 83)\n  (:start . 76) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "support") (:form . "supports") (:end . 100)\n  (:start . 92) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 57))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 115)\n  (:start . 105) (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 120) (:start . 116)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 127)\n  (:start . 121) (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 130) (:start . 128)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 140)\n  (:start . 131) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 144) (:start . 141)\n  (:id . 63))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 153)\n  (:start . 145) (:id . 64))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 155) (:start . 154)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x4.148.1) (:span 105 115)))\n (:hscopes ((:id . :x4.148.1) (:span 105 155)))\n (:identifiers (:sid . :s4.148) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501201@unknown@formal@none@1@S@The Collapse Observed after Strong Inhibition of KLP61F Is Due to the Drawing Together of Intact, Organized Spindle Poles by Inward MT Sliding@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Collapse") (:form . "Collapse") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "observe") (:form . "Observed") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "strong") (:form . "Strong") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . "NNP") (:stem . "Inhibition") (:form . "Inhibition") (:end . 45)\n  (:start . 35) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 55)\n  (:start . 49) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "due") (:form . "Due") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Drawing") (:form . "Drawing") (:end . 77)\n  (:start . 70) (:id . 54))\n ((:tag . "NNP") (:stem . "Together") (:form . "Together") (:end . 86)\n  (:start . 78) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Intact") (:form . "Intact") (:end . 96)\n  (:start . 90) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Organized") (:form . "Organized") (:end . 107)\n  (:start . 98) (:id . 59))\n ((:tag . "NNP") (:stem . "Spindle") (:form . "Spindle") (:end . 115)\n  (:start . 108) (:id . 60))\n ((:tag . "NNPS") (:stem . "Pole") (:form . "Poles") (:end . 121)\n  (:start . 116) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 124) (:start . 122)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "inward") (:form . "Inward") (:end . 131)\n  (:start . 125) (:id . 63))\n ((:tag . "NNP") (:stem . "MT") (:form . "MT") (:end . 134) (:start . 132)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "slide") (:form . "Sliding") (:end . 142)\n  (:start . 135) (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.149) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501202@unknown@formal@none@1@S@We wanted to better understand if the spindle length defects we observe after loss of kinesin-5 function reflect defects in spindle pole separation (Saunders et al., 1997 ; Sharp et al., 2000a ) or in spindle pole focusing (Gaglio et al., 1996 ; Goshima and Vale, 2003 ).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "want") (:form . "wanted") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "RBR") (:stem . "well") (:form . "better") (:end . 19) (:start . 13)\n  (:id . 45))\n ((:tag . "VB") (:stem . "understand") (:form . "understand") (:end . 30)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "spindle") (:form . 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5501203@unknown@formal@none@1@S@To simultaneously observe the behavior of MTs and spindle poles and see if anti-KLP61F has any detectable effect on pole organization, we microinjected anti-KLP61F with rhodamine-labeled tubulin into embryos expressing GFP-centrosomin (CNN), an integral component of the mitotic centrosome (Megraw et al., 2002 ; Figure 2E; Supplemental Video 3).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n  (:end . 17) (:start . 3) (:id . 43))\n ((:tag . "VB") (:stem . "observe") (:form . "observe") (:end . 25)\n  (:start . 18) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "behavior") (:form . "behavior") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "mt") (:form . 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5501204@unknown@formal@none@1@S@During collapse, intact spindle poles steadily moved toward one another at a rate of ~0.06 µm/s, and the appearance of focused, radial sets of fluorescent MTs projecting from discrete centrosomes persisted throughout the collapse (Figure 2E).@(((:tag . "IN") (:stem . "during") (:form . "During") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 15)\n  (:start . 7) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "intact") (:form . "intact") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "RB") (:stem . "steadily") (:form . "steadily") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "VBD") (:stem . "move") (:form . "moved") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . "IN") (:stem . "toward") (:form . "toward") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . "CD") (:stem . "~0.06") (:form . "~0.06") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "µm/") (:form . "µm/s") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 61))\n ((:tag . "NN") (:stem . "appearance") (:form . "appearance") (:end . 115)\n  (:start . 105) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "focus") (:form . "focused") (:end . 126)\n  (:start . 119) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "radial") (:form . "radial") (:end . 134)\n  (:start . 128) (:id . 66))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 139) (:start . 135)\n  (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "fluorescent") (:form . "fluorescent") (:end . 154)\n  (:start . 143) (:id . 69))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 158) (:start . 155)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "project") (:form . "projecting") (:end . 169)\n  (:start . 159) (:id . 71))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 174) (:start . 170)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "discrete") (:form . "discrete") (:end . 183)\n  (:start . 175) (:id . 73))\n ((:tag . "NNS") (:stem . "centrosome") (:form . "centrosomes") (:end . 195)\n  (:start . 184) (:id . 74))\n ((:tag . "VBD") (:stem . "persist") (:form . "persisted") (:end . 205)\n  (:start . 196) (:id . 75))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 216)\n  (:start . 206) (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 220) (:start . 217)\n  (:id . 77))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 229)\n  (:start . 221) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 231) (:start . 230)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 237)\n  (:start . 231) (:id . 80))\n ((:tag . "NN") (:stem . "2e") (:form . "2E") (:end . 240) (:start . 238)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 241) (:start . 240)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 242) (:start . 241)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s4.152) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501205@unknown@formal@none@1@S@There was no obvious disorganization of the spindle poles, although some MT bundles appeared to “splay” laterally, projecting from the pole into the adjacent cytoplasm.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "disorganization") (:form . "disorganization")\n  (:end . 36) (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 67)\n  (:start . 59) (:id . 52))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "MT") (:form . "MT") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "bundle") (:form . "bundles") (:end . 83)\n  (:start . 76) (:id . 55))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "splay") (:form . "splay") (:end . 102) (:start . 97)\n  (:id . 59))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "RB") (:stem . "laterally") (:form . "laterally") (:end . 113)\n  (:start . 104) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "project") (:form . "projecting") (:end . 125)\n  (:start . 115) (:id . 63))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 130) (:start . 126)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n  (:id . 65))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 139) (:start . 135)\n  (:id . 66))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 144) (:start . 140)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 157)\n  (:start . 149) (:id . 69))\n ((:tag . "NN") (:stem . "cytoplasm") (:form . "cytoplasm") (:end . 167)\n  (:start . 158) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x4.153.1) (:span 84 92)))\n (:hscopes ((:id . :x4.153.1) (:span 68 167)))\n (:identifiers (:sid . :s4.153) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501206@unknown@formal@none@1@S@Injection of a high concentration of antibody caused all observed spindles to collapse, and this was accompanied by a concomitant increase in the fluorescent intensity of tubulin in the central spindle (Figure 2F) as seen in linescans along the pole–pole axis of the collapsing spindles (Figure 2G).@(((:tag . "NN") (:stem . "injection") (:form . "Injection") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 33) (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "antibody") (:form . 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5501207@unknown@formal@none@1@S@This indicates that ipMT bundles become thicker during the collapse, consistent with spindle shortening being due to an inward sliding of adjacent, antiparallel ipMTs, although serial section electron microscopy (EM) done at time intervals during the collapse, which is probably not feasible, would be required to establish this.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ipmt") (:form . "ipMT") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "bundle") (:form . "bundles") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "VBP") (:stem . "become") (:form . "become") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "thicker") (:form . 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5501208@unknown@formal@none@1@S@Genetic Evidence for a Role of KLP61F in Driving Spindle Pole Separation@(((:tag . "JJ") (:stem . "genetic") (:form . "Genetic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "evidence") (:form . "Evidence") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Role") (:form . "Role") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Driving") (:form . "Driving") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "NNP") (:stem . "Spindle") (:form . "Spindle") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "NNP") (:stem . "Pole") (:form . "Pole") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Separation") (:form . "Separation") (:end . 72)\n  (:start . 62) (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.156) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501209@unknown@formal@none@1@S@Loss-of-function mutants provide a complementary method to antibody inhibition for probing motor protein function (Scholey, 1998 ; Figure 3).@(((:tag . "NNP") (:stem . "Loss-of-function") (:form . "Loss-of-function")\n  (:end . 16) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 24)\n  (:start . 17) (:id . 43))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 32)\n  (:start . 25) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "complementary") (:form . "complementary")\n  (:end . 48) (:start . 35) (:id . 46))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 55)\n  (:start . 49) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 48))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 67)\n  (:start . 59) (:id . 49))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 78)\n  (:start . 68) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 82) (:start . 79)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "probe") (:form . "probing") (:end . 90)\n  (:start . 83) (:id . 52))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 96) (:start . 91)\n  (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 104)\n  (:start . 97) (:id . 54))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 113)\n  (:start . 105) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Scholey") (:form . "Scholey") (:end . 122)\n  (:start . 115) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1998") (:form . "1998") (:end . 128) (:start . 124)\n  (:id . 59))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 130) (:start . 129)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 137)\n  (:start . 131) (:id . 61))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 139) (:start . 138)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s4.157) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501210@unknown@formal@none@1@S@Homozygous klp61f mutants undergo mitosis in embryos due to the maternal load of KLP61F but display late larval lethality due to mitotic defects that arise when the maternal load of KLP61F is depleted (Heck et al., 1993 ).@(((:tag . "JJ") (:stem . "homozygous") (:form . "Homozygous") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 17)\n  (:start . 11) (:id . 43))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 25)\n  (:start . 18) (:id . 44))\n ((:tag . "VBP") (:stem . "undergo") (:form . "undergo") (:end . 33)\n  (:start . 26) (:id . 45))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 41)\n  (:start . 34) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "maternal") (:form . "maternal") (:end . 72)\n  (:start . 64) (:id . 52))\n ((:tag . "NN") (:stem . "load") (:form . "load") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 99)\n  (:start . 92) (:id . 57))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 104) (:start . 100)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 111)\n  (:start . 105) (:id . 59))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 121)\n  (:start . 112) (:id . 60))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 136)\n  (:start . 129) (:id . 63))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 144)\n  (:start . 137) (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 149) (:start . 145)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "arise") (:form . "arise") (:end . 155)\n  (:start . 150) (:id . 66))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 160) (:start . 156)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 164) (:start . 161)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "maternal") (:form . "maternal") (:end . 173)\n  (:start . 165) (:id . 69))\n ((:tag . "NN") (:stem . "load") (:form . "load") (:end . 178) (:start . 174)\n  (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 181) (:start . 179)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 188)\n  (:start . 182) (:id . 72))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 191) (:start . 189)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "deplete") (:form . "depleted") (:end . 200)\n  (:start . 192) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 202) (:start . 201)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Heck") (:form . "Heck") (:end . 206) (:start . 202)\n  (:id . 76))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 209) (:start . 207)\n  (:id . 77))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 213) (:start . 210)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 214) (:start . 213)\n  (:id . 79))\n ((:tag . "CD") (:stem . "1993") (:form . "1993") (:end . 219) (:start . 215)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s4.158) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501211@unknown@formal@none@1@S@Fixed larval neuroblasts were previously found to contain abnormal monoastral spindles, consistent with our antibody inhibition results (Heck et al., 1993 ).@(((:tag . "VBN") (:stem . "fix") (:form . "Fixed") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 46) (:start . 41)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 66)\n  (:start . 58) (:id . 50))\n ((:tag . "JJ") (:stem . "monoastral") (:form . "monoastral") (:end . 77)\n  (:start . 67) (:id . 51))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 86)\n  (:start . 78) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 98)\n  (:start . 88) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 103) (:start . 99)\n  (:id . 55))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 107) (:start . 104)\n  (:id . 56))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 116)\n  (:start . 108) (:id . 57))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 127)\n  (:start . 117) (:id . 58))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 135)\n  (:start . 128) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Heck") (:form . "Heck") (:end . 141) (:start . 137)\n  (:id . 61))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 144) (:start . 142)\n  (:id . 62))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 148) (:start . 145)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 64))\n ((:tag . "CD") (:stem . "1993") (:form . "1993") (:end . 154) (:start . 150)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.159) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501212@unknown@formal@none@1@S@However, in the absence of real-time studies, it is unclear if these monoasters arise from an initial failure in spindle pole separation, from a collapse of assembled bipolar spindles, or from the fixation of transiently collapsing structures.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "real-time") (:form . "real-time") (:end . 36)\n  (:start . 27) (:id . 48))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 59)\n  (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 68) (:start . 63)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "monoaster") (:form . "monoasters") (:end . 79)\n  (:start . 69) (:id . 56))\n ((:tag . "VBP") (:stem . "arise") (:form . "arise") (:end . 85) (:start . 80)\n  (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 90) (:start . 86)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 101)\n  (:start . 94) (:id . 60))\n ((:tag . "NN") (:stem . "failure") (:form . "failure") (:end . 109)\n  (:start . 102) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 120)\n  (:start . 113) (:id . 63))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 125) (:start . 121)\n  (:id . 64))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 136)\n  (:start . 126) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 142) (:start . 138)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 144) (:start . 143)\n  (:id . 68))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 153)\n  (:start . 145) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 156) (:start . 154)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "assemble") (:form . "assembled") (:end . 166)\n  (:start . 157) (:id . 71))\n ((:tag . "JJ") (:stem . "bipolar") (:form . "bipolar") (:end . 174)\n  (:start . 167) (:id . 72))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 183)\n  (:start . 175) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 187) (:start . 185)\n  (:id . 75))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 192) (:start . 188)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 77))\n ((:tag . "NN") (:stem . "fixation") (:form . "fixation") (:end . 205)\n  (:start . 197) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 208) (:start . 206)\n  (:id . 79))\n ((:tag . "RB") (:stem . "transiently") (:form . "transiently") (:end . 220)\n  (:start . 209) (:id . 80))\n ((:tag . "VBG") (:stem . "collapse") (:form . "collapsing") (:end . 231)\n  (:start . 221) (:id . 81))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 242)\n  (:start . 232) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x4.160.1) (:span 185 187)) ((:id . :x4.160.2) (:span 60 62))\n  ((:id . :x4.160.3) (:span 52 59)))\n (:hscopes ((:id . :x4.160.1) (:span 86 242))\n  ((:id . :x4.160.2) (:span 60 242)) ((:id . :x4.160.3) (:span 52 242)))\n (:identifiers (:sid . :s4.160) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501213@unknown@formal@none@1@S@To study this problem, we created klp61f mutant flies (Heck et al., 1993 ) expressing GFP-tubulin using laborious genetic crosses (Materials and Methods).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "study") (:form . "study") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "problem") (:form . "problem") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "create") (:form . "created") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 40)\n  (:start . 34) (:id . 49))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 47)\n  (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Heck") (:form . "Heck") (:end . 59) (:start . 55)\n  (:id . 53))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1993") (:form . "1993") (:end . 72) (:start . 68)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 85)\n  (:start . 75) (:id . 59))\n ((:tag . "NNP") (:stem . "GFP-tubulin") (:form . "GFP-tubulin") (:end . 97)\n  (:start . 86) (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 103) (:start . 98)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "laborious") (:form . "laborious") (:end . 113)\n  (:start . 104) (:id . 62))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 121)\n  (:start . 114) (:id . 63))\n ((:tag . "NNS") (:stem . "crosse") (:form . "crosses") (:end . 129)\n  (:start . 122) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 65))\n ((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 140)\n  (:start . 131) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n  (:id . 67))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 152)\n  (:start . 145) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s4.161) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501214@unknown@formal@none@1@S@(A) Still images from real-time recordings of spindle pole separation dynamics in klp61f7012 mutant embryos expressing GFP-tubulin.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Still") (:form . "Still") (:end . 9) (:start . 4)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 16)\n  (:start . 10) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 21) (:start . 17)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "real-time") (:form . "real-time") (:end . 31)\n  (:start . 22) (:id . 48))\n ((:tag . "NNS") (:stem . "recording") (:form . "recordings") (:end . 42)\n  (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 53)\n  (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . "NNS") (:stem . "dynamic") (:form . "dynamics") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "klp61f7012") (:form . "klp61f7012") (:end . 92)\n  (:start . 82) (:id . 56))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 99)\n  (:start . 93) (:id . 57))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 107)\n  (:start . 100) (:id . 58))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 118)\n  (:start . 108) (:id . 59))\n ((:tag . "NNP") (:stem . "GFP-tubulin") (:form . "GFP-tubulin") (:end . 130)\n  (:start . 119) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s4.162) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501215@unknown@formal@none@1@S@Top row, spindle in wild-type embryo.@(((:tag . "JJ") (:stem . "top") (:form . "Top") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "row") (:form . "row") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 16)\n  (:start . 9) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 29)\n  (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 37) (:start . 36)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.163) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501216@unknown@formal@none@1@S@Second row, a monoastral spindle that becomes bipolar.@(((:tag . "JJ") (:stem . "second") (:form . "Second") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "row") (:form . "row") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "monoastral") (:form . "monoastral") (:end . 24)\n  (:start . 14) (:id . 46))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "become") (:form . "becomes") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "JJ") (:stem . "bipolar") (:form . "bipolar") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.164) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501217@unknown@formal@none@1@S@Third row, a spindle that collapses to form a permanent monoaster.@(((:tag . "JJ") (:stem . "third") (:form . "Third") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "row") (:form . "row") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 20)\n  (:start . 13) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "collapse") (:form . "collapses") (:end . 35)\n  (:start . 26) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 43) (:start . 39)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "permanent") (:form . "permanent") (:end . 55)\n  (:start . 46) (:id . 52))\n ((:tag . "NN") (:stem . "monoaster") (:form . "monoaster") (:end . 65)\n  (:start . 56) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.165) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501218@unknown@formal@none@1@S@Arrows mark the poles.@(((:tag . "NNS") (:stem . "arrow") (:form . "Arrows") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "mark") (:form . "mark") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 22) (:start . 21)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s4.166) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501219@unknown@formal@none@1@S@Fourth row, monoaster that does not change during observation time.@(((:tag . "JJ") (:stem . "fourth") (:form . "Fourth") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "row") (:form . "row") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "monoaster") (:form . "monoaster") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "VB") (:stem . "change") (:form . "change") (:end . 42)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 49)\n  (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 61)\n  (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.167) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501220@unknown@formal@none@1@S@Bar, 5 µm.@(((:tag . "NNP") (:stem . "Bar") (:form . "Bar") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 6) (:start . 5)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 9) (:start . 7)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 10) (:start . 9)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s4.168) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501221@unknown@formal@none@1@S@(B) Still images from real-time recordings of spindle pole separation dynamics in wild-type and klp61f7415 mutants expressing GFP-tubulin.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Still") (:form . "Still") (:end . 9) (:start . 4)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 16)\n  (:start . 10) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 21) (:start . 17)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "real-time") (:form . "real-time") (:end . 31)\n  (:start . 22) (:id . 48))\n ((:tag . "NNS") (:stem . "recording") (:form . "recordings") (:end . 42)\n  (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 53)\n  (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . "NNS") (:stem . "dynamic") (:form . "dynamics") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 91)\n  (:start . 82) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "NN") (:stem . "klp61f7415") (:form . "klp61f7415") (:end . 106)\n  (:start . 96) (:id . 58))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 114)\n  (:start . 107) (:id . 59))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 125)\n  (:start . 115) (:id . 60))\n ((:tag . "NNP") (:stem . "GFP-tubulin") (:form . "GFP-tubulin") (:end . 137)\n  (:start . 126) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.169) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501222@unknown@formal@none@1@S@Top row, a wild-type neuroblast.@(((:tag . "JJ") (:stem . "top") (:form . "Top") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "row") (:form . "row") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 20)\n  (:start . 11) (:id . 46))\n ((:tag . "NN") (:stem . "neuroblast") (:form . "neuroblast") (:end . 31)\n  (:start . 21) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 32) (:start . 31)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.170) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501223@unknown@formal@none@1@S@Second row, a mutant neuroblast with separated spindle poles that transiently collapse, then recover and separate fully.@(((:tag . "JJ") (:stem . "second") (:form . "Second") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "row") (:form . "row") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 20)\n  (:start . 14) (:id . 46))\n ((:tag . "NN") (:stem . "neuroblast") (:form . "neuroblast") (:end . 31)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 60) (:start . 55)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "RB") (:stem . "transiently") (:form . "transiently") (:end . 77)\n  (:start . 66) (:id . 53))\n ((:tag . "VBP") (:stem . "collapse") (:form . "collapse") (:end . 86)\n  (:start . 78) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . "VB") (:stem . "recover") (:form . "recover") (:end . 100)\n  (:start . 93) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "VB") (:stem . "separate") (:form . "separate") (:end . 113)\n  (:start . 105) (:id . 59))\n ((:tag . "RB") (:stem . "fully") (:form . "fully") (:end . 119)\n  (:start . 114) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s4.171) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501224@unknown@formal@none@1@S@Third row, a mutant larval spindle that collapses to form a permanent monoaster.@(((:tag . "JJ") (:stem . "third") (:form . "Third") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "row") (:form . "row") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 19)\n  (:start . 13) (:id . 46))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 26)\n  (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 34)\n  (:start . 27) (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "collapse") (:form . "collapses") (:end . 49)\n  (:start . 40) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "permanent") (:form . "permanent") (:end . 69)\n  (:start . 60) (:id . 54))\n ((:tag . "NN") (:stem . "monoaster") (:form . "monoaster") (:end . 79)\n  (:start . 70) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.172) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501225@unknown@formal@none@1@S@Bar, 5 µm.@(((:tag . "NNP") (:stem . "Bar") (:form . "Bar") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 6) (:start . 5)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 9) (:start . 7)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 10) (:start . 9)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s4.173) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501226@unknown@formal@none@1@S@(C) Differences in spindle pole separation due to varying KLP61F gene dosage.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "difference") (:form . "Differences") (:end . 15)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 26)\n  (:start . 19) (:id . 47))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 42)\n  (:start . 32) (:id . 49))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "vary") (:form . "varying") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 64)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 69) (:start . 65)\n  (:id . 54))\n ((:tag . "NN") (:stem . "dosage") (:form . "dosage") (:end . 76)\n  (:start . 70) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.174) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501227@unknown@formal@none@1@S@Left, embryos from heterozygous mothers have a shorter metaphase length than wild-type embryos.@(((:tag . "VBN") (:stem . "leave") (:form . "Left") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 13)\n  (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "heterozygous") (:form . "heterozygous") (:end . 31)\n  (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "mother") (:form . "mothers") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "JJR") (:stem . "short") (:form . "shorter") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 71)\n  (:start . 65) (:id . 52))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 86)\n  (:start . 77) (:id . 54))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 94)\n  (:start . 87) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.175) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501228@unknown@formal@none@1@S@Right, klp61f mutant embryos rescued with two copies of a KLP61F-GFP transgene have a longer metaphase spindle length than those rescued with one copy.@(((:tag . "RB") (:stem . "right") (:form . "Right") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "copy") (:form . "copies") (:end . 52) (:start . 46)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "KLP61F-GFP") (:form . "KLP61F-GFP") (:end . 68)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 78)\n  (:start . 69) (:id . 54))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "JJR") (:stem . "long") (:form . "longer") (:end . 92) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 102)\n  (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 110)\n  (:start . 103) (:id . 59))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 117)\n  (:start . 111) (:id . 60))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 122) (:start . 118)\n  (:id . 61))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 128)\n  (:start . 123) (:id . 62))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 136)\n  (:start . 129) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 141) (:start . 137)\n  (:id . 64))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 145) (:start . 142)\n  (:id . 65))\n ((:tag . "NN") (:stem . "copy") (:form . "copy") (:end . 150) (:start . 146)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.176) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501229@unknown@formal@none@1@S@In one allele (klp61f7012), larvae have smaller brains than wild types and spindles are rare.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "klp61f7012") (:form . "klp61f7012") (:end . 25)\n  (:start . 15) (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 34)\n  (:start . 28) (:id . 49))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 39) (:start . 35)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 47)\n  (:start . 40) (:id . 51))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 59) (:start . 55)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 64) (:start . 60)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 70) (:start . 65)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 83)\n  (:start . 75) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "rare") (:form . "rare") (:end . 92) (:start . 88)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.177) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501230@unknown@formal@none@1@S@In these mutants, spindles start collapsing in mitotic domains of the late embryo (Figure 3A), where we observed that some spindles collapse into stable monoasters that fail to complete mitosis.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "VBP") (:stem . "start") (:form . "start") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "collapse") (:form . "collapsing") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 62)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 81)\n  (:start . 75) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 89)\n  (:start . 83) (:id . 57))\n ((:tag . "NN") (:stem . "3a") (:form . "3A") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 60))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 100)\n  (:start . 95) (:id . 61))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 103) (:start . 101)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 112)\n  (:start . 104) (:id . 63))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 117) (:start . 113)\n  (:id . 64))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 122) (:start . 118)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 131)\n  (:start . 123) (:id . 66))\n ((:tag . "VBP") (:stem . "collapse") (:form . "collapse") (:end . 140)\n  (:start . 132) (:id . 67))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 145) (:start . 141)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "stable") (:form . "stable") (:end . 152)\n  (:start . 146) (:id . 69))\n ((:tag . "NNS") (:stem . "monoaster") (:form . "monoasters") (:end . 163)\n  (:start . 153) (:id . 70))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 168) (:start . 164)\n  (:id . 71))\n ((:tag . "VBP") (:stem . "fail") (:form . "fail") (:end . 173) (:start . 169)\n  (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 176) (:start . 174)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 185)\n  (:start . 177) (:id . 74))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 193)\n  (:start . 186) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s4.178) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501231@unknown@formal@none@1@S@Other monoasters seem to form monoastral bipolar spindles, which may assemble via a chromosome-directed pathway in which KLP61F activity is required to focus the anastral spindle pole as proposed for S2 cells (Goshima and Vale, 2003 ).@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "monoaster") (:form . "monoasters") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "seem") (:form . "seem") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "monoastral") (:form . "monoastral") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "JJ") (:stem . "bipolar") (:form . "bipolar") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 64) (:start . 59)\n  (:id . 51))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "VB") (:stem . "assemble") (:form . "assemble") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "chromosome-directed")\n  (:form . "chromosome-directed") (:end . 103) (:start . 84) (:id . 56))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 111)\n  (:start . 104) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 120)\n  (:start . 115) (:id . 59))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 127)\n  (:start . 121) (:id . 60))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 136)\n  (:start . 128) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 139) (:start . 137)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 148)\n  (:start . 140) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 151) (:start . 149)\n  (:id . 64))\n ((:tag . "VB") (:stem . "focus") (:form . "focus") (:end . 157)\n  (:start . 152) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "anastral") (:form . "anastral") (:end . 170)\n  (:start . 162) (:id . 67))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 178)\n  (:start . 171) (:id . 68))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 183) (:start . 179)\n  (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 186) (:start . 184)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 195)\n  (:start . 187) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 199) (:start . 196)\n  (:id . 72))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 202) (:start . 200)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 208)\n  (:start . 203) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 210) (:start . 209)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Goshima") (:form . "Goshima") (:end . 217)\n  (:start . 210) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 221) (:start . 218)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Vale") (:form . "Vale") (:end . 226) (:start . 222)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 227) (:start . 226)\n  (:id . 79))\n ((:tag . "CD") (:stem . "2003") (:form . "2003") (:end . 232) (:start . 228)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 234) (:start . 233)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 235) (:start . 234)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x4.179.1) (:span 65 68)))\n (:hscopes ((:id . :x4.179.1) (:span 65 208)))\n (:identifiers (:sid . :s4.179) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501232@unknown@formal@none@1@S@Such monoastral bipolar spindles were not observed in our antibody inhibition experiments in syncytial embryos, but they have previously been observed in fixed larval brains and gonial cells of klp61f mutants (Wilson et al., 1997 ).@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "monoastral") (:form . "monoastral") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "bipolar") (:form . "bipolar") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 66)\n  (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 77)\n  (:start . 67) (:id . 52))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 89)\n  (:start . 78) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "syncytial") (:form . "syncytial") (:end . 102)\n  (:start . 93) (:id . 55))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 110)\n  (:start . 103) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 115) (:start . 112)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 120) (:start . 116)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 125) (:start . 121)\n  (:id . 60))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 136)\n  (:start . 126) (:id . 61))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 141) (:start . 137)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 150)\n  (:start . 142) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 153) (:start . 151)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 159) (:start . 154)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 166)\n  (:start . 160) (:id . 66))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 173)\n  (:start . 167) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 177) (:start . 174)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "gonial") (:form . "gonial") (:end . 184)\n  (:start . 178) (:id . 69))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 190)\n  (:start . 185) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 193) (:start . 191)\n  (:id . 71))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 200)\n  (:start . 194) (:id . 72))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 208)\n  (:start . 201) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 210) (:start . 209)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Wilson") (:form . "Wilson") (:end . 216)\n  (:start . 210) (:id . 75))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 219) (:start . 217)\n  (:id . 76))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 223) (:start . 220)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 224) (:start . 223)\n  (:id . 78))\n ((:tag . "CD") (:stem . "1997") (:form . "1997") (:end . 229) (:start . 225)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 231) (:start . 230)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s4.180) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501233@unknown@formal@none@1@S@These observations are consistent with the idea that KLP61F is required for the separation of spindle poles in the rapid, centrosome-dominant mitoses of the syncytial embryo, but as development proceeds, mitosis slows down (see below) and centrosomes become less dominant, so that KLP61F plays increasingly important roles in anastral spindle pole focusing.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 18)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 33)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . 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"pole") (:end . 347) (:start . 343)\n  (:id . 98))\n ((:tag . "NN") (:stem . "focusing") (:form . "focusing") (:end . 356)\n  (:start . 348) (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 357) (:start . 356)\n  (:id . 100)))@@@1@59@((:hcues ((:id . :x4.181.1) (:span 43 47)))\n (:hscopes ((:id . :x4.181.1) (:span 43 356)))\n (:identifiers (:sid . :s4.181) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501234@unknown@formal@none@1@S@In a different allele (klp61f7415), homozygous larvae had brains of normal size, and we could follow the progression of living mutant cells through mitosis (Figure 3B).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 14)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "klp61f7415") (:form . "klp61f7415") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 46)\n  (:start . 36) (:id . 50))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 53)\n  (:start . 47) (:id . 51))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 64)\n  (:start . 58) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 74)\n  (:start . 68) (:id . 55))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 79) (:start . 75)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 93) (:start . 88)\n  (:id . 60))\n ((:tag . "VB") (:stem . "follow") (:form . "follow") (:end . 100)\n  (:start . 94) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 62))\n ((:tag . "NN") (:stem . "progression") (:form . "progression") (:end . 116)\n  (:start . 105) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "live") (:form . "living") (:end . 126)\n  (:start . 120) (:id . 65))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 133)\n  (:start . 127) (:id . 66))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 139)\n  (:start . 134) (:id . 67))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 147)\n  (:start . 140) (:id . 68))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 155)\n  (:start . 148) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 163)\n  (:start . 157) (:id . 71))\n ((:tag . "NN") (:stem . "3b") (:form . "3B") (:end . 166) (:start . 164)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s4.182) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501235@unknown@formal@none@1@S@We observed collapsing spindles with similar pole–pole separation defects to those seen in anti-KLP61F–injected embryos.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "VBG") (:stem . "collapse") (:form . "collapsing") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "NN") (:stem . "pole–pole") (:form . "pole–pole") (:end . 54)\n  (:start . 45) (:id . 48))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 65)\n  (:start . 55) (:id . 49))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 73)\n  (:start . 66) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n  (:id . 51))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 82) (:start . 77)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 87) (:start . 83)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "anti-klp61f–injected")\n  (:form . "anti-KLP61F–injected") (:end . 111) (:start . 91) (:id . 55))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 119)\n  (:start . 112) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s4.183) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501236@unknown@formal@none@1@S@In wild-type brains we never observed such collapsing or shortening spindles.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "RB") (:stem . "never") (:form . "never") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "collapse") (:form . "collapsing") (:end . 53)\n  (:start . 43) (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "shorten") (:form . "shortening") (:end . 67)\n  (:start . 57) (:id . 51))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 76)\n  (:start . 68) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.184) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501237@unknown@formal@none@1@S@Figure 3B shows the dynamics of spindle pole separation in a wild-type neuroblast spindle (Figure 3B, top row), a mutant spindle that initially separates its poles then collapses into a stable monoaster (Figure 3B, bottom), and a mutant spindle that transiently collapses and then recovers (Figure 3B, center).@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "3b") (:form . "3B") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "dynamic") (:form . "dynamics") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "spindle") (:form . 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"RB") (:stem . "transiently") (:form . "transiently") (:end . 261)\n  (:start . 250) (:id . 90))\n ((:tag . "VBZ") (:stem . "collapse") (:form . "collapses") (:end . 271)\n  (:start . 262) (:id . 91))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 275) (:start . 272)\n  (:id . 92))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 280) (:start . 276)\n  (:id . 93))\n ((:tag . "VBZ") (:stem . "recover") (:form . "recovers") (:end . 289)\n  (:start . 281) (:id . 94))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 291) (:start . 290)\n  (:id . 95))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 297)\n  (:start . 291) (:id . 96))\n ((:tag . "NN") (:stem . "3b") (:form . "3B") (:end . 300) (:start . 298)\n  (:id . 97))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 301) (:start . 300)\n  (:id . 98))\n ((:tag . "NN") (:stem . "center") (:form . "center") (:end . 308)\n  (:start . 302) (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . 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5501238@unknown@formal@none@1@S@Careful 3D observations and measurements confirm that we were indeed visualizing spindle pole separation dynamics and not simply changes in the orientation of the spindle.@(((:tag . "JJ") (:stem . "careful") (:form . "Careful") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 23)\n  (:start . 11) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "measurement") (:form . "measurements") (:end . 40)\n  (:start . 28) (:id . 46))\n ((:tag . "VBP") (:stem . "confirm") (:form . "confirm") (:end . 48)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 56) (:start . 54)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 61) (:start . 57)\n  (:id . 50))\n ((:tag . "RB") (:stem . "indeed") (:form . "indeed") (:end . 68)\n  (:start . 62) (:id . 51))\n ((:tag . "VBG") (:stem . "visualize") (:form . "visualizing") (:end . 80)\n  (:start . 69) (:id . 52))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 88)\n  (:start . 81) (:id . 53))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 93) (:start . 89)\n  (:id . 54))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 104)\n  (:start . 94) (:id . 55))\n ((:tag . "NNS") (:stem . "dynamic") (:form . "dynamics") (:end . 113)\n  (:start . 105) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 121) (:start . 118)\n  (:id . 58))\n ((:tag . "VB") (:stem . "simply") (:form . "simply") (:end . 128)\n  (:start . 122) (:id . 59))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 136)\n  (:start . 129) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 139) (:start . 137)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 62))\n ((:tag . "NN") (:stem . "orientation") (:form . "orientation") (:end . 155)\n  (:start . 144) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n  (:id . 65))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 170)\n  (:start . 163) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.186) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501239@unknown@formal@none@1@S@The results are consistent with a complete and partial depletion of the maternal load of KLP61F giving rise to permanent and transient spindle collapse, respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "depletion") (:form . "depletion") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "maternal") (:form . "maternal") (:end . 80)\n  (:start . 72) (:id . 54))\n ((:tag . "NN") (:stem . "load") (:form . "load") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 95)\n  (:start . 89) (:id . 57))\n ((:tag . "VBG") (:stem . "give") (:form . "giving") (:end . 102)\n  (:start . 96) (:id . 58))\n ((:tag . "NN") (:stem . "rise") (:form . "rise") (:end . 107) (:start . 103)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "permanent") (:form . "permanent") (:end . 120)\n  (:start . 111) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "transient") (:form . "transient") (:end . 134)\n  (:start . 125) (:id . 63))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 142)\n  (:start . 135) (:id . 64))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 151)\n  (:start . 143) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 66))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 165)\n  (:start . 153) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s4.187) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501240@unknown@formal@none@1@S@Because the mutants examined are recessive lethal (Heck et al., 1993 ), this result makes it extremely unlikely that the collapse of prometaphase spindles seen after severe antibody inhibition is due to dominant effects of the antibody.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "recessive") (:form . "recessive") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "JJ") (:stem . "lethal") (:form . "lethal") (:end . 49)\n  (:start . 43) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Heck") (:form . "Heck") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1993") (:form . "1993") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 76) (:start . 72)\n  (:id . 57))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 83)\n  (:start . 77) (:id . 58))\n ((:tag . "VBZ") (:stem . "make") (:form . "makes") (:end . 89) (:start . 84)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 92) (:start . 90)\n  (:id . 60))\n ((:tag . "RB") (:stem . "extremely") (:form . "extremely") (:end . 102)\n  (:start . 93) (:id . 61))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 111)\n  (:start . 103) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 64))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 129)\n  (:start . 121) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 66))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 145)\n  (:start . 133) (:id . 67))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 154)\n  (:start . 146) (:id . 68))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 159) (:start . 155)\n  (:id . 69))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 165)\n  (:start . 160) (:id . 70))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 172)\n  (:start . 166) (:id . 71))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 181)\n  (:start . 173) (:id . 72))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 192)\n  (:start . 182) (:id . 73))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 195) (:start . 193)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 199) (:start . 196)\n  (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 202) (:start . 200)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 211)\n  (:start . 203) (:id . 77))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 219)\n  (:start . 212) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 222) (:start . 220)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 226) (:start . 223)\n  (:id . 80))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 235)\n  (:start . 227) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 236) (:start . 235)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x4.188.1) (:span 103 111)))\n (:hscopes ((:id . :x4.188.1) (:span 103 235)))\n (:identifiers (:sid . :s4.188) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501241@unknown@formal@none@1@S@Interestingly, the rate of spindle pole separation in late embryos and neuroblasts is slower than in syncytial embryos; the time from NEB to telophase takes 10–15 min in late embryos and ~20 min in neuroblasts compared with 4–6 min in the syncytial embryo.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 50)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 66)\n  (:start . 59) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 82)\n  (:start . 71) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "JJR") (:stem . "slow") (:form . "slower") (:end . 92) (:start . 86)\n  (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 97) (:start . 93)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "syncytial") (:form . "syncytial") (:end . 110)\n  (:start . 101) (:id . 59))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 118)\n  (:start . 111) (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 119) (:start . 118)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 62))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 128) (:start . 124)\n  (:id . 63))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 133) (:start . 129)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "NEB") (:form . "NEB") (:end . 137) (:start . 134)\n  (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 140) (:start . 138)\n  (:id . 66))\n ((:tag . "NN") (:stem . "telophase") (:form . "telophase") (:end . 150)\n  (:start . 141) (:id . 67))\n ((:tag . "VBZ") (:stem . "take") (:form . "takes") (:end . 156)\n  (:start . 151) (:id . 68))\n ((:tag . "CD") (:stem . "10–15") (:form . "10–15") (:end . 162)\n  (:start . 157) (:id . 69))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 166) (:start . 163)\n  (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 169) (:start . 167)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 174) (:start . 170)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 182)\n  (:start . 175) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 186) (:start . 183)\n  (:id . 74))\n ((:tag . "CD") (:stem . "~20") (:form . "~20") (:end . 190) (:start . 187)\n  (:id . 75))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 194) (:start . 191)\n  (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 197) (:start . 195)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "neuroblast") (:form . "neuroblasts") (:end . 209)\n  (:start . 198) (:id . 78))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 218)\n  (:start . 210) (:id . 79))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 223) (:start . 219)\n  (:id . 80))\n ((:tag . "CD") (:stem . "4–6") (:form . "4–6") (:end . 227) (:start . 224)\n  (:id . 81))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 231) (:start . 228)\n  (:id . 82))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 234) (:start . 232)\n  (:id . 83))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 238) (:start . 235)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "syncytial") (:form . "syncytial") (:end . 248)\n  (:start . 239) (:id . 85))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 255)\n  (:start . 249) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 256) (:start . 255)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s4.189) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501242@unknown@formal@none@1@S@However, whether this difference in time reflects differences in the balance of forces operating in the spindles of different cell types or some other unknown factors is unclear.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "reflect") (:form . "reflects") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 61)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "balance") (:form . "balance") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "force") (:form . "forces") (:end . 86)\n  (:start . 80) (:id . 55))\n ((:tag . "VBG") (:stem . "operate") (:form . "operating") (:end . 96)\n  (:start . 87) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 112)\n  (:start . 104) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 125)\n  (:start . 116) (:id . 61))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 130) (:start . 126)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 136)\n  (:start . 131) (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 139) (:start . 137)\n  (:id . 64))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 144) (:start . 140)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 158)\n  (:start . 151) (:id . 67))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 166)\n  (:start . 159) (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 169) (:start . 167)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 177)\n  (:start . 170) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x4.190.2) (:span 170 177))\n  ((:id . :x4.190.1) (:span 137 139)) ((:id . :x4.190.3) (:span 9 16)))\n (:hscopes ((:id . :x4.190.1) (:span 50 166)) ((:id . :x4.190.3) (:span 9 166))\n  ((:id . :x4.190.2) (:span 9 177)))\n (:identifiers (:sid . :s4.190) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501243@unknown@formal@none@1@S@Further evidence in support of the idea that KLP61F exerts outward forces on spindle poles was obtained by examining embryos carrying varying “doses” of the KLP61F gene (Figure 3C).@(((:tag . "JJ") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "VBZ") (:stem . "exert") (:form . "exerts") (:end . 58)\n  (:start . 52) (:id . 51))\n ((:tag . "JJ") (:stem . "outward") (:form . "outward") (:end . 66)\n  (:start . 59) (:id . 52))\n ((:tag . "NNS") (:stem . "force") (:form . "forces") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 90) (:start . 85)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 94) (:start . 91)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 103)\n  (:start . 95) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "examine") (:form . "examining") (:end . 116)\n  (:start . 107) (:id . 60))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 124)\n  (:start . 117) (:id . 61))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 133)\n  (:start . 125) (:id . 62))\n ((:tag . "VBG") (:stem . "vary") (:form . "varying") (:end . 141)\n  (:start . 134) (:id . 63))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 143) (:start . 142)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "doses") (:form . "doses") (:end . 148)\n  (:start . 143) (:id . 65))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 149) (:start . 148)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 163)\n  (:start . 157) (:id . 69))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 168) (:start . 164)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 170) (:start . 169)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 176)\n  (:start . 170) (:id . 72))\n ((:tag . "NN") (:stem . "3c") (:form . "3C") (:end . 179) (:start . 177)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x4.191.1) (:span 35 39)))\n (:hscopes ((:id . :x4.191.1) (:span 35 90)))\n (:identifiers (:sid . :s4.191) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501244@unknown@formal@none@1@S@For example, during prometaphase wild types harboring two copies of the KLP61F gene separated their spindle poles further than klp61f mutant heterozygotes containing a single copy, suggesting that the predicted increase in the concentration of the motor increases the outward force that pushes apart the poles (Figure 3C, left).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 32)\n  (:start . 20) (:id . 46))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "type") (:form . 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5501245@unknown@formal@none@1@S@In addition, the viability of klp61f mutants could be rescued with one or two copies of a KLP61F-GFP transgene that express the expected amount of protein based on immunoblotting (Cheerambathur et al., 2008 ).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "copy") (:form . "copies") (:end . 84) (:start . 78)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 89) (:start . 88)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "KLP61F-GFP") (:form . "KLP61F-GFP") (:end . 100)\n  (:start . 90) (:id . 60))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 110)\n  (:start . 101) (:id . 61))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 115) (:start . 111)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 123)\n  (:start . 116) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 136)\n  (:start . 128) (:id . 65))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 143)\n  (:start . 137) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 146) (:start . 144)\n  (:id . 67))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 154)\n  (:start . 147) (:id . 68))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 160)\n  (:start . 155) (:id . 69))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 163) (:start . 161)\n  (:id . 70))\n ((:tag . "NN") (:stem . "immunoblotting") (:form . "immunoblotting")\n  (:end . 178) (:start . 164) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 180) (:start . 179)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Cheerambathur") (:form . "Cheerambathur")\n  (:end . 193) (:start . 180) (:id . 73))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 196) (:start . 194)\n  (:id . 74))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 200) (:start . 197)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 201) (:start . 200)\n  (:id . 76))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 206) (:start . 202)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 208) (:start . 207)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x4.193.1) (:span 45 50)))\n (:hscopes ((:id . :x4.193.1) (:span 13 178)))\n (:identifiers (:sid . :s4.193) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501246@unknown@formal@none@1@S@Measurement of pole–pole distances in these embryos also showed that two copies of the GFP transgene supported faster prometaphase spindle elongation and the formation of longer metaphase spindles than did a single copy of the transgene (Figure 3C, right), again consistent with the gradient observed after antibody inhibition.@(((:tag . "NNP") (:stem . "Measurement") (:form . "Measurement") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "NN") (:stem . "pole–pole") (:form . "pole–pole") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "distance") (:form . "distances") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 43) (:start . 38)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "embryo") (:form . 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5501247@unknown@formal@none@1@S@KLP61F Is Required for Poleward Flux and Normal Metaphase Spindle Length@(((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Required") (:form . "Required") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Poleward") (:form . "Poleward") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "NNP") (:stem . "Flux") (:form . "Flux") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Normal") (:form . "Normal") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "NNP") (:stem . "Metaphase") (:form . "Metaphase") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "NNP") (:stem . "Spindle") (:form . "Spindle") (:end . 65)\n  (:start . 58) (:id . 51))\n ((:tag . "NNP") (:stem . "Length") (:form . "Length") (:end . 72)\n  (:start . 66) (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.195) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501248@unknown@formal@none@1@S@The gradient of defects elicited by antibody inhibition experiments revealed additional roles for KLP61F in embryos.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "VBN") (:stem . "elicit") (:form . "elicited") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 55)\n  (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 67)\n  (:start . 56) (:id . 50))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 76)\n  (:start . 68) (:id . 51))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 87)\n  (:start . 77) (:id . 52))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 93) (:start . 88)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 97) (:start . 94)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 104)\n  (:start . 98) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 115)\n  (:start . 108) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s4.196) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501249@unknown@formal@none@1@S@On the basis of comparisons of the rates of poleward flux within ipMT bundles and the rates of MT sliding induced by purified KLP61F, as well as the observation that poleward flux stops at the onset of anaphase B, we previously proposed that KLP61F drives poleward flux in Drosophila embryos, but this had not been tested in vivo (Cole et al., 1994 ; Brust-Mascher and Scholey, 2002 ; Brust-Mascher et al., 2004 ; Tao et al., 2006 ).@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 27)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . 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"not") (:end . 309) (:start . 306)\n  (:id . 98))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 314) (:start . 310)\n  (:id . 99))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 321)\n  (:start . 315) (:id . 100))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 324) (:start . 322)\n  (:id . 101))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 329) (:start . 325)\n  (:id . 102))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 331) (:start . 330)\n  (:id . 103))\n ((:tag . "NNP") (:stem . "Cole") (:form . "Cole") (:end . 335) (:start . 331)\n  (:id . 104))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 338) (:start . 336)\n  (:id . 105))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 342) (:start . 339)\n  (:id . 106))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 343) (:start . 342)\n  (:id . 107))\n ((:tag . "CD") (:stem . "1994") (:form . "1994") (:end . 348) (:start . 344)\n  (:id . 108))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 350) (:start . 349)\n  (:id . 109))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 364) (:start . 351) (:id . 110))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 368) (:start . 365)\n  (:id . 111))\n ((:tag . "NNP") (:stem . "Scholey") (:form . "Scholey") (:end . 376)\n  (:start . 369) (:id . 112))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 377) (:start . 376)\n  (:id . 113))\n ((:tag . "CD") (:stem . "2002") (:form . "2002") (:end . 382) (:start . 378)\n  (:id . 114))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 384) (:start . 383)\n  (:id . 115))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 398) (:start . 385) (:id . 116))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 401) (:start . 399)\n  (:id . 117))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 405) (:start . 402)\n  (:id . 118))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 406) (:start . 405)\n  (:id . 119))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 411) (:start . 407)\n  (:id . 120))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 413) (:start . 412)\n  (:id . 121))\n ((:tag . "NNP") (:stem . "Tao") (:form . "Tao") (:end . 417) (:start . 414)\n  (:id . 122))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 420) (:start . 418)\n  (:id . 123))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 424) (:start . 421)\n  (:id . 124))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 425) (:start . 424)\n  (:id . 125))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 430) (:start . 426)\n  (:id . 126))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 432) (:start . 431)\n  (:id . 127))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 433) (:start . 432)\n  (:id . 128)))@@@1@87@((:hcues ((:id . :x4.197.1) (:span 228 236)))\n (:hscopes ((:id . :x4.197.1) (:span 228 291)))\n (:identifiers (:sid . :s4.197) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501250@unknown@formal@none@1@S@If we classify the gradient induced by KLP61F antibody injection by analyzing spindle pole length, we find as stated above that the most severe effect is spindle collapse.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "classify") (:form . "classify") (:end . 14)\n  (:start . 6) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "analyze") (:form . "analyzing") (:end . 77)\n  (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 85)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 90) (:start . 86)\n  (:id . 55))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 97)\n  (:start . 91) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 101) (:start . 99)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 109) (:start . 107)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "state") (:form . "stated") (:end . 116)\n  (:start . 110) (:id . 61))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 122)\n  (:start . 117) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 127) (:start . 123)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 64))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 136) (:start . 132)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 143)\n  (:start . 137) (:id . 66))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 150)\n  (:start . 144) (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 153) (:start . 151)\n  (:id . 68))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 161)\n  (:start . 154) (:id . 69))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 170)\n  (:start . 162) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s4.198) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501251@unknown@formal@none@1@S@The next most severe effect is partial spindle shortening followed by a steady-state length that is smaller than the pole spacing at NEB.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "shortening") (:form . "shortening") (:end . 57)\n  (:start . 47) (:id . 50))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 66)\n  (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "steady-state") (:form . "steady-state") (:end . 84)\n  (:start . 72) (:id . 54))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 91)\n  (:start . 85) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 96) (:start . 92)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 107)\n  (:start . 100) (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 112) (:start . 108)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 121) (:start . 117)\n  (:id . 61))\n ((:tag . "NN") (:stem . "spacing") (:form . "spacing") (:end . 129)\n  (:start . 122) (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "NEB") (:form . "NEB") (:end . 136) (:start . 133)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.199) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501252@unknown@formal@none@1@S@Other spindles maintained the characteristic NEB pole spacing until anaphase B or displayed only a small prometaphase elongation.@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "maintain") (:form . "maintained") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 44) (:start . 30) (:id . 46))\n ((:tag . "NNP") (:stem . "NEB") (:form . "NEB") (:end . 48) (:start . 45)\n  (:id . 47))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 53) (:start . 49)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "space") (:form . "spacing") (:end . 61)\n  (:start . 54) (:id . 49))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 67) (:start . 62)\n  (:id . 50))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 76)\n  (:start . 68) (:id . 51))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 78) (:start . 77)\n  (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 91)\n  (:start . 82) (:id . 54))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 96) (:start . 92)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 98) (:start . 97)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 104) (:start . 99)\n  (:id . 57))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 117)\n  (:start . 105) (:id . 58))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 128)\n  (:start . 118) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s4.200) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501253@unknown@formal@none@1@S@In these spindles we measured the steady-state length and the rate of poleward flux during these periods of steady spindle length maintenance (i.e., metaphase and anaphase A).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "measure") (:form . "measured") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "steady-state") (:form . "steady-state") (:end . 46)\n  (:start . 34) (:id . 48))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 90)\n  (:start . 84) (:id . 56))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "period") (:form . "periods") (:end . 104)\n  (:start . 97) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "steady") (:form . "steady") (:end . 114)\n  (:start . 108) (:id . 60))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 122)\n  (:start . 115) (:id . 61))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 129)\n  (:start . 123) (:id . 62))\n ((:tag . "NN") (:stem . "maintenance") (:form . "maintenance") (:end . 141)\n  (:start . 130) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 64))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 147) (:start . 143)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 66))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 158)\n  (:start . 149) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 68))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 171)\n  (:start . 163) (:id . 69))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 173) (:start . 172)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 174) (:start . 173)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s4.201) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501254@unknown@formal@none@1@S@The average metaphase length decreased from 11.8 ± 0.08 to 8.8 ± 1.4 µm (Table 1), and poleward flux was significantly inhibited both within ipMTs and kinetochore (k) MTs (Figure 4).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "VBD") (:stem . "decrease") (:form . "decreased") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "CD") (:stem . "11.8") (:form . "11.8") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "±") (:form . "±") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "CD") (:stem . "0.08") (:form . "0.08") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "CD") (:stem . "8.8") (:form . "8.8") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "HYPH") (:stem . "±") (:form . "±") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1.4") (:form . "1.4") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 78) (:start . 73)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 95)\n  (:start . 87) (:id . 62))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 100) (:start . 96)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 104) (:start . 101)\n  (:id . 64))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 118) (:start . 105) (:id . 65))\n ((:tag . "VBN") (:stem . "inhibit") (:form . "inhibited") (:end . 128)\n  (:start . 119) (:id . 66))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 133) (:start . 129)\n  (:id . 67))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 140)\n  (:start . 134) (:id . 68))\n ((:tag . "NNS") (:stem . "ipmt") (:form . "ipMTs") (:end . 146)\n  (:start . 141) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 70))\n ((:tag . "NN") (:stem . "kinetochore") (:form . "kinetochore") (:end . 162)\n  (:start . 151) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n  (:id . 72))\n ((:tag . "NN") (:stem . "k") (:form . "k") (:end . 165) (:start . 164)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 170) (:start . 167)\n  (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 178)\n  (:start . 172) (:id . 77))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 180) (:start . 179)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 181) (:start . 180)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s4.202) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501255@unknown@formal@none@1@S@The average rate of flux was 0.01 ± 0.02 µm/s in KLP61F inhibited embryos compared with 0.05 ± 0.02 µm/s in control embryos (Figure 4; Table 1).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "CD") (:stem . "0.01") (:form . "0.01") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "IN") (:stem . "±") (:form . "±") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "CD") (:stem . "0.02") (:form . "0.02") (:end . 40) (:start . 36)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "µm/") (:form . "µm/s") (:end . 45) (:start . 41)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 55)\n  (:start . 49) (:id . 53))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 65)\n  (:start . 56) (:id . 54))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 73)\n  (:start . 66) (:id . 55))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 82)\n  (:start . 74) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 87) (:start . 83)\n  (:id . 57))\n ((:tag . "CD") (:stem . "0.05") (:form . "0.05") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . "HYPH") (:stem . "±") (:form . "±") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "CD") (:stem . "0.02") (:form . "0.02") (:end . 99) (:start . 95)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "µm/") (:form . "µm/s") (:end . 104) (:start . 100)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 62))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 115)\n  (:start . 108) (:id . 63))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 123)\n  (:start . 116) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 131)\n  (:start . 125) (:id . 66))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 133) (:start . 132)\n  (:id . 67))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 134) (:start . 133)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 140)\n  (:start . 135) (:id . 69))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 142) (:start . 141)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s4.203) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501256@unknown@formal@none@1@S@This indicates that KLP61F-driven MT sliding is necessary to achieve the wild-type metaphase spindle length and that it also contributes to poleward flux in both ipMTs and kMTs.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "klp61f-driven") (:form . "KLP61F-driven")\n  (:end . 33) (:start . 20) (:id . 45))\n ((:tag . "NNP") (:stem . "MT") (:form . "MT") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "VB") (:stem . "achieve") (:form . "achieve") (:end . 68)\n  (:start . 61) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 92)\n  (:start . 83) (:id . 54))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 100)\n  (:start . 93) (:id . 55))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 107)\n  (:start . 101) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 119) (:start . 117)\n  (:id . 59))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 124) (:start . 120)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "contribute") (:form . "contributes") (:end . 136)\n  (:start . 125) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n  (:id . 62))\n ((:tag . "VB") (:stem . "poleward") (:form . "poleward") (:end . 148)\n  (:start . 140) (:id . 63))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 153) (:start . 149)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 156) (:start . 154)\n  (:id . 65))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 161) (:start . 157)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "ipmt") (:form . "ipMTs") (:end . 167)\n  (:start . 162) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "kmt") (:form . "kMTs") (:end . 176) (:start . 172)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x4.204.1) (:span 5 19)))\n (:hscopes ((:id . :x4.204.1) (:span 5 176)))\n (:identifiers (:sid . :s4.204) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501257@unknown@formal@none@1@S@Interestingly, 17% of our flux measurements were negative (Figure 4C).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 30) (:start . 26)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "measurement") (:form . "measurements") (:end . 43)\n  (:start . 31) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 65)\n  (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "4c") (:form . "4C") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s4.205) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501258@unknown@formal@none@1@S@A possible source of negative flux numbers, especially close to zero, is noise in the measurements.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "RB") (:stem . "especially") (:form . "especially") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "RB") (:stem . "close") (:form . "close") (:end . 60) (:start . 55)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "CD") (:stem . "zero") (:form . "zero") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 78) (:start . 73)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "measurement") (:form . "measurements") (:end . 98)\n  (:start . 86) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x4.206.1) (:span 2 10)))\n (:hscopes ((:id . :x4.206.1) (:span 2 42)))\n (:identifiers (:sid . :s4.206) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501259@unknown@formal@none@1@S@A more interesting possibility is that they represent speckles on ipMTs associated with one pole that slide inward as the spindle transiently shortens, bringing them closer to the pole in the opposite half spindle.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "interesting") (:form . "interesting") (:end . 18)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 30)\n  (:start . 19) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "speckle") (:form . "speckles") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "ipmt") (:form . "ipMTs") (:end . 71) (:start . 66)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 82)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 87) (:start . 83)\n  (:id . 54))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 96) (:start . 92)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 101) (:start . 97)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "slide") (:form . "slide") (:end . 107)\n  (:start . 102) (:id . 58))\n ((:tag . "RB") (:stem . "inward") (:form . "inward") (:end . 114)\n  (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 61))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 129)\n  (:start . 122) (:id . 62))\n ((:tag . "RB") (:stem . "transiently") (:form . "transiently") (:end . 141)\n  (:start . 130) (:id . 63))\n ((:tag . "VBZ") (:stem . "shorten") (:form . "shortens") (:end . 150)\n  (:start . 142) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "bring") (:form . "bringing") (:end . 160)\n  (:start . 152) (:id . 66))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 165) (:start . 161)\n  (:id . 67))\n ((:tag . "RBR") (:stem . "closer") (:form . "closer") (:end . 172)\n  (:start . 166) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 175) (:start . 173)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 70))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 184) (:start . 180)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 187) (:start . 185)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "opposite") (:form . "opposite") (:end . 200)\n  (:start . 192) (:id . 74))\n ((:tag . "JJ") (:stem . "half") (:form . "half") (:end . 205) (:start . 201)\n  (:id . 75))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 213)\n  (:start . 206) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x4.207.1) (:span 19 30)))\n (:hscopes ((:id . :x4.207.1) (:span 19 213)))\n (:identifiers (:sid . :s4.207) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501260@unknown@formal@none@1@S@Such a speckle would flux toward the first pole but away from the second, now closer, pole, and this would be measured as negative flux.@(((:tag . "PDT") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "speckle") (:form . "speckle") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "VB") (:stem . "flux") (:form . "flux") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "IN") (:stem . "toward") (:form . "toward") (:end . 32)\n  (:start . 26) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 72)\n  (:start . 66) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "RBR") (:stem . "closer") (:form . "closer") (:end . 84)\n  (:start . 78) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 59))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 90) (:start . 86)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 62))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 100) (:start . 96)\n  (:id . 63))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 106)\n  (:start . 101) (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 109) (:start . 107)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 118)\n  (:start . 110) (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 121) (:start . 119)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 130)\n  (:start . 122) (:id . 68))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 135) (:start . 131)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x4.208.1) (:span 101 106)) ((:id . :x4.208.2) (:span 15 20)))\n (:hscopes ((:id . :x4.208.1) (:span 96 135))\n  ((:id . :x4.208.2) (:span 15 90)))\n (:identifiers (:sid . :s4.208) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501261@unknown@formal@none@1@S@Partial inhibition of KLP61F decreases the rates of flux and anaphase A chromosome to pole movement as well as the metaphase spindle length and kinetochore-kinetochore distance@(((:tag . "JJ") (:stem . "partial") (:form . "Partial") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "VBZ") (:stem . "decrease") (:form . "decreases") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 69)\n  (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 82)\n  (:start . 72) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 90) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "movement") (:form . "movement") (:end . 99)\n  (:start . 91) (:id . 57))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 102) (:start . 100)\n  (:id . 58))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 107) (:start . 103)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 61))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 124)\n  (:start . 115) (:id . 62))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 132)\n  (:start . 125) (:id . 63))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 139)\n  (:start . 133) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 65))\n ((:tag . "NN") (:stem . "kinetochore-kinetochore")\n  (:form . "kinetochore-kinetochore") (:end . 167) (:start . 144) (:id . 66))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 176)\n  (:start . 168) (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.209) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5501262@unknown@formal@none@1@S@Poleward flux requires the function of KLP61F.@(((:tag . "JJ") (:stem . "poleward") (:form . "Poleward") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.210) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501263@unknown@formal@none@1@S@(A) In wild-type embryos kymographs show that tubulin speckles flux toward the poles during the metaphase–anaphase A steady state, but move at the same rate as the poles during anaphase B. (Brust-Mascher and Scholey, 2002 ).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "In") (:end . 6) (:start . 4)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 16)\n  (:start . 7) (:id . 46))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 24)\n  (:start . 17) (:id . 47))\n ((:tag . "NNS") (:stem . "kymograph") (:form . "kymographs") (:end . 35)\n  (:start . 25) (:id . 48))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 53)\n  (:start . 46) (:id . 51))\n ((:tag . "NNS") (:stem . "speckle") (:form . "speckles") (:end . 62)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "IN") (:stem . "toward") (:form . "toward") (:end . 74)\n  (:start . 68) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 84) (:start . 79)\n  (:id . 56))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 91)\n  (:start . 85) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "NN") (:stem . "metaphase–anaphase") (:form . "metaphase–anaphase")\n  (:end . 114) (:start . 96) (:id . 59))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 116) (:start . 115)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "steady") (:form . "steady") (:end . 123)\n  (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 129)\n  (:start . 124) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 134) (:start . 131)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "move") (:form . "move") (:end . 139) (:start . 135)\n  (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 142) (:start . 140)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 151) (:start . 147)\n  (:id . 68))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 156) (:start . 152)\n  (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 159) (:start . 157)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 169)\n  (:start . 164) (:id . 72))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 176)\n  (:start . 170) (:id . 73))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 185)\n  (:start . 177) (:id . 74))\n ((:tag . "NNP") (:stem . "B.") (:form . "B.") (:end . 188) (:start . 186)\n  (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 190) (:start . 189)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 203) (:start . 190) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 207) (:start . 204)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Scholey") (:form . "Scholey") (:end . 215)\n  (:start . 208) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 216) (:start . 215)\n  (:id . 80))\n ((:tag . "CD") (:stem . "2002") (:form . "2002") (:end . 221) (:start . 217)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 223) (:start . 222)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s4.211) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501264@unknown@formal@none@1@S@(B) In embryos injected with anti-KLP61F antibody, kymographs obtained from spindles that did not collapse but maintained a steady length show that tubulin speckles do not flux toward the pole, indicating that the function of KLP61F is required for this movement (see Supplemental Video 2 for speckled movie).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "In") (:end . 6) (:start . 4)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 14)\n  (:start . 7) (:id . 46))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 23)\n  (:start . 15) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "JJ") (:stem . 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5501265@unknown@formal@none@1@S@(C) Histogram of all the flux data obtained on spindles that did not collapse after KLP61F inhibition.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Histogram") (:form . "Histogram") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 20) (:start . 17)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 48))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 29) (:start . 25)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 34) (:start . 30)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 43)\n  (:start . 35) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 46) (:start . 44)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 55)\n  (:start . 47) (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 60) (:start . 56)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 64) (:start . 61)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 68) (:start . 65)\n  (:id . 56))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 77)\n  (:start . 69) (:id . 57))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 83) (:start . 78)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 90)\n  (:start . 84) (:id . 59))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 101)\n  (:start . 91) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s4.213) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501266@unknown@formal@none@1@S@Congression Is Defective, Kinetochore Spacing and the Rate of Anaphase A Are Reduced, and the Relative Timing of Anaphase A and B Is Perturbed in Spindles Partially Depleted of KLP61F@(((:tag . "NNP") (:stem . "Congression") (:form . "Congression") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "defective") (:form . "Defective") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Kinetochore") (:form . "Kinetochore") (:end . 37)\n  (:start . 26) (:id . 46))\n ((:tag . "NNP") (:stem . "Spacing") (:form . "Spacing") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Rate") (:form . "Rate") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Anaphase") (:form . "Anaphase") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 72) (:start . 71)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "Are") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "reduce") (:form . "Reduced") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "relative") (:form . "Relative") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . "NN") (:stem . "timing") (:form . "Timing") (:end . 109)\n  (:start . 103) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Anaphase") (:form . "Anaphase") (:end . 121)\n  (:start . 113) (:id . 62))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 123) (:start . 122)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 132) (:start . 130)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Perturbed") (:form . "Perturbed") (:end . 142)\n  (:start . 133) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 145) (:start . 143)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Spindles") (:form . "Spindles") (:end . 154)\n  (:start . 146) (:id . 69))\n ((:tag . "NNP") (:stem . "Partially") (:form . "Partially") (:end . 164)\n  (:start . 155) (:id . 70))\n ((:tag . "NNP") (:stem . "Depleted") (:form . "Depleted") (:end . 173)\n  (:start . 165) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 183)\n  (:start . 177) (:id . 73)))@@@1@32@((:identifiers (:sid . :s4.214) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501267@unknown@formal@none@1@S@In those spindles that retain sufficient KLP61F to maintain pole–pole spacing and resist prometaphase spindle collapse, we were also able to study congression and measure the subsequent rate of anaphase A in transgenic embryos expressing GFP-CID that were injected with rhodamine tubulin and anti-KLP61F (Figure 5).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "retain") (:form . "retain") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "klp61f") (:form . 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"GFP-CID") (:end . 245)\n  (:start . 238) (:id . 78))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 250) (:start . 246)\n  (:id . 79))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 255) (:start . 251)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 264)\n  (:start . 256) (:id . 81))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 269) (:start . 265)\n  (:id . 82))\n ((:tag . "NN") (:stem . "rhodamine") (:form . "rhodamine") (:end . 279)\n  (:start . 270) (:id . 83))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 287)\n  (:start . 280) (:id . 84))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 291) (:start . 288)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "anti-KLP61F") (:form . "anti-KLP61F") (:end . 303)\n  (:start . 292) (:id . 86))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 305) (:start . 304)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 311)\n  (:start . 305) (:id . 88))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 313) (:start . 312)\n  (:id . 89))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 314) (:start . 313)\n  (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 315) (:start . 314)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s4.215) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501268@unknown@formal@none@1@S@In spindles that shorten or do not undergo prometaphase-to-metaphase elongation, but then proceed through anaphase, we find that congression is defective.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "shorten") (:form . "shorten") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "VB") (:stem . "undergo") (:form . "undergo") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "JJ") (:stem . "prometaphase-to-metaphase")\n  (:form . "prometaphase-to-metaphase") (:end . 68) (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 79)\n  (:start . 69) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 84) (:start . 81)\n  (:id . 53))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 89) (:start . 85)\n  (:id . 54))\n ((:tag . "VB") (:stem . "proceed") (:form . "proceed") (:end . 97)\n  (:start . 90) (:id . 55))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 105)\n  (:start . 98) (:id . 56))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 114)\n  (:start . 106) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 118) (:start . 116)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 123) (:start . 119)\n  (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 128) (:start . 124)\n  (:id . 61))\n ((:tag . "NN") (:stem . "congression") (:form . "congression") (:end . 140)\n  (:start . 129) (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 143) (:start . 141)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "defective") (:form . "defective") (:end . 153)\n  (:start . 144) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.216) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501269@unknown@formal@none@1@S@Kinetochores occupy a larger area around the equator compared with wild-type spindles, revealing subtle defects in chromosome positioning on the metaphase plate (Figure 5B).@(((:tag . "NNP") (:stem . "Kinetochore") (:form . "Kinetochores") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "occupy") (:form . "occupy") (:end . 19)\n  (:start . 13) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 21) (:start . 20)\n  (:id . 44))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "equator") (:form . "equator") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 76)\n  (:start . 67) (:id . 52))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 85)\n  (:start . 77) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "reveal") (:form . "revealing") (:end . 96)\n  (:start . 87) (:id . 55))\n ((:tag . "JJ") (:stem . "subtle") (:form . "subtle") (:end . 103)\n  (:start . 97) (:id . 56))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 111)\n  (:start . 104) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 58))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 125)\n  (:start . 115) (:id . 59))\n ((:tag . "VBG") (:stem . "position") (:form . "positioning") (:end . 137)\n  (:start . 126) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 140) (:start . 138)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 62))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 154)\n  (:start . 145) (:id . 63))\n ((:tag . "NN") (:stem . "plate") (:form . "plate") (:end . 160)\n  (:start . 155) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 168)\n  (:start . 162) (:id . 66))\n ((:tag . "NN") (:stem . "5b") (:form . "5B") (:end . 171) (:start . 169)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s4.217) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501270@unknown@formal@none@1@S@Interestingly, kinetochore–kinetochore distance is reduced from 1.31 ± 0.22 µm in wild type to 0.77 ± 0.20 µm in KLP61F-inhibited spindles (Table 1), indicating a reduction in the magnitude of poleward forces acting on the kinetochores.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "kinetochore–kinetochore")\n  (:form . "kinetochore–kinetochore") (:end . 38) (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 47)\n  (:start . 39) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 58)\n  (:start . 51) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 63) (:start . 59)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1.31") (:form . "1.31") (:end . 68) (:start . 64)\n  (:id . 49))\n ((:tag . "HYPH") (:stem . "±") (:form . "±") (:end . 70) (:start . 69)\n  (:id . 50))\n ((:tag . "CD") (:stem . "0.22") (:form . "0.22") (:end . 75) (:start . 71)\n  (:id . 51))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 78) (:start . 76)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 91) (:start . 87)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "CD") (:stem . "0.77") (:form . "0.77") (:end . 99) (:start . 95)\n  (:id . 57))\n ((:tag . "HYPH") (:stem . "±") (:form . "±") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "CD") (:stem . "0.20") (:form . "0.20") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 109) (:start . 107)\n  (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "klp61f-inhibited") (:form . "KLP61F-inhibited")\n  (:end . 129) (:start . 113) (:id . 62))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 138)\n  (:start . 130) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 145)\n  (:start . 140) (:id . 65))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 147) (:start . 146)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 160)\n  (:start . 150) (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 162) (:start . 161)\n  (:id . 70))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 172)\n  (:start . 163) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 175) (:start . 173)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 73))\n ((:tag . "NN") (:stem . "magnitude") (:form . "magnitude") (:end . 189)\n  (:start . 180) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 192) (:start . 190)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 201)\n  (:start . 193) (:id . 76))\n ((:tag . "NNS") (:stem . "force") (:form . "forces") (:end . 208)\n  (:start . 202) (:id . 77))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 215)\n  (:start . 209) (:id . 78))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 218) (:start . 216)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 222) (:start . 219)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "kinetochore") (:form . "kinetochores") (:end . 235)\n  (:start . 223) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 236) (:start . 235)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s4.218) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501271@unknown@formal@none@1@S@Subsequently, the average rate of kinetochore-to-pole movement is 0.06 ± 0.02 µm/s (144 kinetochores in 37 spindles) compared with 0.11 ± 0.02 µm/s for wild-type anaphase A movement (Figure 5; Table 1).@(((:tag . "RB") (:stem . "subsequently") (:form . "Subsequently") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "kinetochore-to-pole")\n  (:form . "kinetochore-to-pole") (:end . 53) (:start . 34) (:id . 48))\n ((:tag . "NN") (:stem . "movement") (:form . "movement") (:end . 62)\n  (:start . 54) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "CD") (:stem . "0.06") (:form . "0.06") (:end . 70) (:start . 66)\n  (:id . 51))\n ((:tag . "IN") (:stem . "±") (:form . "±") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "CD") (:stem . "0.02") (:form . "0.02") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "µm/") (:form . "µm/s") (:end . 82) (:start . 78)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "CD") (:stem . "144") (:form . "144") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "kinetochore") (:form . "kinetochores") (:end . 100)\n  (:start . 88) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 58))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 115)\n  (:start . 107) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 125)\n  (:start . 117) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 130) (:start . 126)\n  (:id . 63))\n ((:tag . "CD") (:stem . "0.11") (:form . "0.11") (:end . 135) (:start . 131)\n  (:id . 64))\n ((:tag . "HYPH") (:stem . "±") (:form . "±") (:end . 137) (:start . 136)\n  (:id . 65))\n ((:tag . "CD") (:stem . "0.02") (:form . "0.02") (:end . 142) (:start . 138)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "µm/") (:form . "µm/s") (:end . 147) (:start . 143)\n  (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 151) (:start . 148)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 161)\n  (:start . 152) (:id . 69))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 170)\n  (:start . 162) (:id . 70))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 172) (:start . 171)\n  (:id . 71))\n ((:tag . "NN") (:stem . "movement") (:form . "movement") (:end . 181)\n  (:start . 173) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 183) (:start . 182)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 189)\n  (:start . 183) (:id . 74))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 191) (:start . 190)\n  (:id . 75))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 192) (:start . 191)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 198)\n  (:start . 193) (:id . 77))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 200) (:start . 199)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 201) (:start . 200)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s4.219) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501272@unknown@formal@none@1@S@Some spindles that maintained a reduced but steady pole–pole spacing displayed no kinetochore-to-pole movement and a single nucleus reformed around the unsegregated parental chromosomes.@(((:tag . "DT") (:stem . "some") (:form . "Some") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "maintain") (:form . "maintained") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "steady") (:form . "steady") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "pole–pole") (:form . "pole–pole") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . "NN") (:stem . "spacing") (:form . "spacing") (:end . 68)\n  (:start . 61) (:id . 51))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 78)\n  (:start . 69) (:id . 52))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "NN") (:stem . "kinetochore-to-pole")\n  (:form . "kinetochore-to-pole") (:end . 101) (:start . 82) (:id . 54))\n ((:tag . "NN") (:stem . "movement") (:form . "movement") (:end . 110)\n  (:start . 102) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 116) (:start . 115)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 123)\n  (:start . 117) (:id . 58))\n ((:tag . "NN") (:stem . "nucleus") (:form . "nucleus") (:end . 131)\n  (:start . 124) (:id . 59))\n ((:tag . "VBD") (:stem . "reform") (:form . "reformed") (:end . 140)\n  (:start . 132) (:id . 60))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 147)\n  (:start . 141) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "unsegregated") (:form . "unsegregated") (:end . 164)\n  (:start . 152) (:id . 63))\n ((:tag . "JJ") (:stem . "parental") (:form . "parental") (:end . 173)\n  (:start . 165) (:id . 64))\n ((:tag . "NNS") (:stem . "chromosome") (:form . "chromosomes") (:end . 185)\n  (:start . 174) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s4.220) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501273@unknown@formal@none@1@S@Such spindles were excluded from our calculations of the average rate.@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "calculation") (:form . "calculations") (:end . 49)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 64)\n  (:start . 57) (:id . 51))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 69) (:start . 65)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.221) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501274@unknown@formal@none@1@S@Chromosome congression and anaphase A are perturbed by partial KLP61F inhibition.@(((:tag . "NN") (:stem . "chromosome") (:form . "Chromosome") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "congression") (:form . "congression") (:end . 22)\n  (:start . 11) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 44))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 35)\n  (:start . 27) (:id . 45))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 37) (:start . 36)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "perturb") (:form . "perturbed") (:end . 51)\n  (:start . 42) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 62)\n  (:start . 55) (:id . 50))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 69)\n  (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 80)\n  (:start . 70) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.222) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501275@unknown@formal@none@1@S@(A) Time-lapse images of one spindle in an embryo expressing GFP-CID injected with rhodamine tubulin and anti-KLP61F antibody.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Time-lapse") (:form . "Time-lapse") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 21)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 36)\n  (:start . 29) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 42) (:start . 40)\n  (:id . 51))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 49)\n  (:start . 43) (:id . 52))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 60)\n  (:start . 50) (:id . 53))\n ((:tag . "NNP") (:stem . "GFP-CID") (:form . "GFP-CID") (:end . 68)\n  (:start . 61) (:id . 54))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 77)\n  (:start . 69) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 82) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "rhodamine") (:form . "rhodamine") (:end . 92)\n  (:start . 83) (:id . 57))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "anti-klp61f") (:form . "anti-KLP61F") (:end . 116)\n  (:start . 105) (:id . 60))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 125)\n  (:start . 117) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.223) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501276@unknown@formal@none@1@S@The spindle shortens slightly (compare 215 with 126) but does not collapse after KLP61F inhibition.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "shorten") (:form . "shortens") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "compare") (:form . "compare") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "CD") (:stem . "215") (:form . "215") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "CD") (:stem . "126") (:form . "126") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 74)\n  (:start . 66) (:id . 55))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 87)\n  (:start . 81) (:id . 57))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 98)\n  (:start . 88) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.224) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501277@unknown@formal@none@1@S@Kinetochores move to the poles albeit slower than in control spindles.@(((:tag . "NNP") (:stem . "Kinetochore") (:form . "Kinetochores") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "move") (:form . "move") (:end . 17) (:start . 13)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "albeit") (:form . "albeit") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "JJR") (:stem . "slow") (:form . "slower") (:end . 44) (:start . 38)\n  (:id . 48))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 69)\n  (:start . 61) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s4.225) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501278@unknown@formal@none@1@S@Time in each frame is given in seconds from NEB.@(((:tag . "NNP") (:stem . "Time") (:form . "Time") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "second") (:form . "seconds") (:end . 38)\n  (:start . 31) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 43) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "NEB") (:form . "NEB") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 48) (:start . 47)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.226) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501279@unknown@formal@none@1@S@Bar, 5 µm.@(((:tag . "NNP") (:stem . "Bar") (:form . "Bar") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 6) (:start . 5)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 9) (:start . 7)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 10) (:start . 9)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s4.227) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501280@unknown@formal@none@1@S@(B) Positions of the center of kinetochore pairs in wild-type (black) and KLP61F-inhibited (red) spindles.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "position") (:form . "Positions") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 47))\n ((:tag . "NN") (:stem . "center") (:form . "center") (:end . 27)\n  (:start . 21) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "NN") (:stem . "kinetochore") (:form . "kinetochore") (:end . 42)\n  (:start . 31) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 48) (:start . 43)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 61)\n  (:start . 52) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 68) (:start . 63)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "klp61f-inhibited") (:form . "KLP61F-inhibited")\n  (:end . 90) (:start . 74) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 95) (:start . 92)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 105)\n  (:start . 97) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s4.228) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501281@unknown@formal@none@1@S@In anti-KLP61F–inhibited spindles, kinetochores do not congress as tightly as in controls, and they exhibit a larger displacement around the equator.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "anti-klp61f–inhibited")\n  (:form . "anti-KLP61F–inhibited") (:end . 24) (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 33)\n  (:start . 25) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "kinetochore") (:form . "kinetochores") (:end . 47)\n  (:start . 35) (:id . 46))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 50) (:start . 48)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 54) (:start . 51)\n  (:id . 48))\n ((:tag . "VB") (:stem . "congress") (:form . "congress") (:end . 63)\n  (:start . 55) (:id . 49))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 66) (:start . 64)\n  (:id . 50))\n ((:tag . "RB") (:stem . "tightly") (:form . "tightly") (:end . 74)\n  (:start . 67) (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 77) (:start . 75)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 99) (:start . 95)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "exhibit") (:form . "exhibit") (:end . 107)\n  (:start . 100) (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 116)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "displacement") (:form . "displacement") (:end . 129)\n  (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 136)\n  (:start . 130) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 63))\n ((:tag . "NN") (:stem . "equator") (:form . "equator") (:end . 148)\n  (:start . 141) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.229) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501282@unknown@formal@none@1@S@Triangles mark the average positions of the poles.@(((:tag . "NNS") (:stem . "triangle") (:form . "Triangles") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "mark") (:form . "mark") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 50) (:start . 49)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s4.230) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501283@unknown@formal@none@1@S@(C) Pole–pole distance and kinetochore-to-pole distances for the spindle shown in A (averages in Table 1).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Pole–pole") (:form . "Pole–pole") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 22)\n  (:start . 14) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "kinetochore-to-pole")\n  (:form . "kinetochore-to-pole") (:end . 46) (:start . 27) (:id . 48))\n ((:tag . "NNS") (:stem . "distance") (:form . "distances") (:end . 56)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 72)\n  (:start . 65) (:id . 52))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 78) (:start . 73)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "average") (:form . "averages") (:end . 93)\n  (:start . 85) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 102) (:start . 97)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.231) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501284@unknown@formal@none@1@S@Significantly, the lower rate of 0.06 µm/s parallels the observed lack of poleward flux (previous section) and supports the idea that anaphase A is driven by a combined “flux-pacman” mechanism in Drosophila embryos (Brust-Mascher and Scholey, 2002 ; Maddox et al., 2002 ; Rogers et al., 2004 ).@(((:tag . "RB") (:stem . "significantly") (:form . "Significantly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "CD") (:stem . "0.06") (:form . "0.06") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "µm/") (:form . "µm/s") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "parallel") (:form . "parallels") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 65)\n  (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 70) (:start . 66)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 82)\n  (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 87) (:start . 83)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 97)\n  (:start . 89) (:id . 58))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 105)\n  (:start . 98) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "support") (:form . "supports") (:end . 119)\n  (:start . 111) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 128) (:start . 124)\n  (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 133) (:start . 129)\n  (:id . 65))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 142)\n  (:start . 134) (:id . 66))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 144) (:start . 143)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 147) (:start . 145)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 154)\n  (:start . 148) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 157) (:start . 155)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 159) (:start . 158)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "combined") (:form . "combined") (:end . 168)\n  (:start . 160) (:id . 72))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 170) (:start . 169)\n  (:id . 73))\n ((:tag . "NN") (:stem . "flux-pacman") (:form . "flux-pacman") (:end . 181)\n  (:start . 170) (:id . 74))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 182) (:start . 181)\n  (:id . 75))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 192)\n  (:start . 183) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 195) (:start . 193)\n  (:id . 77))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 206)\n  (:start . 196) (:id . 78))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 214)\n  (:start . 207) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 216) (:start . 215)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 229) (:start . 216) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 233) (:start . 230)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Scholey") (:form . "Scholey") (:end . 241)\n  (:start . 234) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 242) (:start . 241)\n  (:id . 84))\n ((:tag . "CD") (:stem . "2002") (:form . "2002") (:end . 247) (:start . 243)\n  (:id . 85))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 249) (:start . 248)\n  (:id . 86))\n ((:tag . "NNP") (:stem . "Maddox") (:form . "Maddox") (:end . 256)\n  (:start . 250) (:id . 87))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 259) (:start . 257)\n  (:id . 88))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 263) (:start . 260)\n  (:id . 89))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 264) (:start . 263)\n  (:id . 90))\n ((:tag . "CD") (:stem . "2002") (:form . "2002") (:end . 269) (:start . 265)\n  (:id . 91))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 271) (:start . 270)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "Rogers") (:form . "Rogers") (:end . 278)\n  (:start . 272) (:id . 93))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 281) (:start . 279)\n  (:id . 94))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 285) (:start . 282)\n  (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 286) (:start . 285)\n  (:id . 96))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 291) (:start . 287)\n  (:id . 97))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 293) (:start . 292)\n  (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 294) (:start . 293)\n  (:id . 99)))@@@1@58@((:hcues ((:id . :x4.232.1) (:span 124 128)))\n (:hscopes ((:id . :x4.232.1) (:span 124 214)))\n (:identifiers (:sid . :s4.232) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501285@unknown@formal@none@1@S@Interestingly, we noticed that in many of these spindles, kinetochore-to-pole movement occurs at the same time as pole–pole separation, whereas in wild-type spindles, anaphase A always precedes anaphase B.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "notice") (:form . "noticed") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 56)\n  (:start . 48) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "NN") (:stem . "kinetochore-to-pole")\n  (:form . "kinetochore-to-pole") (:end . 77) (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "movement") (:form . "movement") (:end . 86)\n  (:start . 78) (:id . 54))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 93)\n  (:start . 87) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 105) (:start . 101)\n  (:id . 58))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 110) (:start . 106)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "NN") (:stem . "pole–pole") (:form . "pole–pole") (:end . 123)\n  (:start . 114) (:id . 61))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 134)\n  (:start . 124) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 63))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 143)\n  (:start . 136) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 156)\n  (:start . 147) (:id . 66))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 165)\n  (:start . 157) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 68))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 175)\n  (:start . 167) (:id . 69))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 177) (:start . 176)\n  (:id . 70))\n ((:tag . "RB") (:stem . "always") (:form . "always") (:end . 184)\n  (:start . 178) (:id . 71))\n ((:tag . "VBZ") (:stem . "precede") (:form . "precedes") (:end . 193)\n  (:start . 185) (:id . 72))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 202)\n  (:start . 194) (:id . 73))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 204) (:start . 203)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s4.233) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501286@unknown@formal@none@1@S@How loss of kinesin-5 function could lead to changes in the temporal relationship between chromosome-to-pole motility and spindle elongation during anaphase is unclear.@(((:tag . "WRB") (:stem . "how") (:form . "How") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "VB") (:stem . "lead") (:form . "lead") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 81)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 89)\n  (:start . 82) (:id . 55))\n ((:tag . "NN") (:stem . "chromosome-to-pole") (:form . "chromosome-to-pole")\n  (:end . 108) (:start . 90) (:id . 56))\n ((:tag . "NN") (:stem . "motility") (:form . "motility") (:end . 117)\n  (:start . 109) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 58))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 129)\n  (:start . 122) (:id . 59))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 140)\n  (:start . 130) (:id . 60))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 147)\n  (:start . 141) (:id . 61))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 156)\n  (:start . 148) (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 159) (:start . 157)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 167)\n  (:start . 160) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x4.234.1) (:span 160 167)))\n (:hscopes ((:id . :x4.234.1) (:span 0 167)))\n (:identifiers (:sid . :s4.234) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501287@unknown@formal@none@1@S@As predicted (Sharp et al., 2000a ; Brust-Mascher et al., 2004 ) the rate of anaphase B is relatively insensitive to KLP61F concentration to a certain point: spindles that exhibited a partial collapse and had a metaphase length of <7 µm elongated at a slower rate, but spindles that maintained at least the NEB length elongated at approximately wild-type rates.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sharp") (:form . "Sharp") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "CD") (:stem . "2000a") (:form . "2000a") (:end . 33) (:start . 28)\n  (:id . 49))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 35) (:start . 34)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 49) (:start . 36) (:id . 51))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 52) (:start . 50)\n  (:id . 52))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 54))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 62) (:start . 58)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 64) (:start . 63)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 57))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 73) (:start . 69)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . 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"JJR") (:stem . "slow") (:form . "slower") (:end . 258)\n  (:start . 252) (:id . 90))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 263) (:start . 259)\n  (:id . 91))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 264) (:start . 263)\n  (:id . 92))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 268) (:start . 265)\n  (:id . 93))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 277)\n  (:start . 269) (:id . 94))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 282) (:start . 278)\n  (:id . 95))\n ((:tag . "VBD") (:stem . "maintain") (:form . "maintained") (:end . 293)\n  (:start . 283) (:id . 96))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 296) (:start . 294)\n  (:id . 97))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 302)\n  (:start . 297) (:id . 98))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 306) (:start . 303)\n  (:id . 99))\n ((:tag . "NNP") (:stem . "NEB") (:form . "NEB") (:end . 310) (:start . 307)\n  (:id . 100))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 317)\n  (:start . 311) (:id . 101))\n ((:tag . "VBN") (:stem . "elongate") (:form . "elongated") (:end . 327)\n  (:start . 318) (:id . 102))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 330) (:start . 328)\n  (:id . 103))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 344) (:start . 331) (:id . 104))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 354)\n  (:start . 345) (:id . 105))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 360)\n  (:start . 355) (:id . 106))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 361) (:start . 360)\n  (:id . 107)))@@@1@66@((:identifiers (:sid . :s4.235) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501288@unknown@formal@none@1@S@Influence of Cortical Organization on KLP61F-dependent Mitotic Events@(((:tag . "NN") (:stem . "influence") (:form . "Influence") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "cortical") (:form . "Cortical") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "NNP") (:stem . "Organization") (:form . "Organization") (:end . 34)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "klp61f-dependent") (:form . "KLP61F-dependent")\n  (:end . 54) (:start . 38) (:id . 47))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "Mitotic") (:end . 62)\n  (:start . 55) (:id . 48))\n ((:tag . "NNS") (:stem . "event") (:form . "Events") (:end . 69)\n  (:start . 63) (:id . 49)))@@@1@8@((:identifiers (:sid . :s4.236) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501289@unknown@formal@none@1@S@Cortical pulling forces could complement the outward sliding of ipMTs to control pole–pole spacing.@(((:tag . "JJ") (:stem . "cortical") (:form . "Cortical") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBG") (:stem . "pull") (:form . "pulling") (:end . 16) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "force") (:form . "forces") (:end . 23)\n  (:start . 17) (:id . 44))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 29) (:start . 24)\n  (:id . 45))\n ((:tag . "VB") (:stem . "complement") (:form . "complement") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "outward") (:form . "outward") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "NN") (:stem . "sliding") (:form . "sliding") (:end . 60)\n  (:start . 53) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "ipmt") (:form . "ipMTs") (:end . 69) (:start . 64)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "VB") (:stem . "control") (:form . "control") (:end . 80)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "pole–pole") (:form . "pole–pole") (:end . 90)\n  (:start . 81) (:id . 54))\n ((:tag . "NN") (:stem . "spacing") (:form . "spacing") (:end . 98)\n  (:start . 91) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x4.237.1) (:span 24 29)))\n (:hscopes ((:id . :x4.237.1) (:span 24 98)))\n (:identifiers (:sid . :s4.237) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501290@unknown@formal@none@1@S@To examine this, we measured spindle pole dynamics and MT speckle movements in two mutants that have severely disrupted actin cortices surrounding the nucleus.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "measure") (:form . "measured") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "dynamic") (:form . "dynamics") (:end . 50)\n  (:start . 42) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "mt") (:form . "MT") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "speckle") (:form . "speckle") (:end . 65)\n  (:start . 58) (:id . 53))\n ((:tag . "NNS") (:stem . "movement") (:form . "movements") (:end . 75)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 90)\n  (:start . 83) (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "RB") (:stem . "severely") (:form . "severely") (:end . 109)\n  (:start . 101) (:id . 60))\n ((:tag . "VBN") (:stem . "disrupt") (:form . "disrupted") (:end . 119)\n  (:start . 110) (:id . 61))\n ((:tag . "NN") (:stem . "actin") (:form . "actin") (:end . 125)\n  (:start . 120) (:id . 62))\n ((:tag . "NNS") (:stem . "cortex") (:form . "cortices") (:end . 134)\n  (:start . 126) (:id . 63))\n ((:tag . "VBG") (:stem . "surround") (:form . "surrounding") (:end . 146)\n  (:start . 135) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n  (:id . 65))\n ((:tag . "NN") (:stem . "nucleus") (:form . "nucleus") (:end . 158)\n  (:start . 151) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.238) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501291@unknown@formal@none@1@S@In the Drosophila syncytial embryo, actin caps are normally formed over each nucleus and a furrow is formed around the spindle during metaphase (Cytrynbaum et al., 2005 ).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "JJ") (:stem . "syncytial") (:form . "syncytial") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "actin") (:form . "actin") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cap") (:form . "caps") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 59)\n  (:start . 51) (:id . 51))\n ((:tag . "VBN") (:stem . "form") (:form . "formed") (:end . 66) (:start . 60)\n  (:id . 52))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "nucleus") (:form . "nucleus") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "furrow") (:form . "furrow") (:end . 97)\n  (:start . 91) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "form") (:form . "formed") (:end . 107)\n  (:start . 101) (:id . 60))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 114)\n  (:start . 108) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 62))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 126)\n  (:start . 119) (:id . 63))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 133)\n  (:start . 127) (:id . 64))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 143)\n  (:start . 134) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Cytrynbaum") (:form . "Cytrynbaum") (:end . 155)\n  (:start . 145) (:id . 67))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 158) (:start . 156)\n  (:id . 68))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 162) (:start . 159)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 70))\n ((:tag . "CD") (:stem . "2005") (:form . "2005") (:end . 168) (:start . 164)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s4.239) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501292@unknown@formal@none@1@S@The cortex-defective Scrambled (sced; Stevenson et al., 2001 ) and Sponge (spg; Postner et al., 1992 ) mutants have highly reduced actin caps and no metaphase furrows (Supplemental Figure S1).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "cortex-defective") (:form . "cortex-defective")\n  (:end . 20) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Scrambled") (:form . "Scrambled") (:end . 30)\n  (:start . 21) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "sce") (:form . "sced") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Stevenson") (:form . "Stevenson") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sponge") (:form . "Sponge") (:end . 73)\n  (:start . 67) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "spg") (:form . "spg") (:end . 78) (:start . 75)\n  (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 79) (:start . 78)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Postner") (:form . "Postner") (:end . 87)\n  (:start . 80) (:id . 59))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 90) (:start . 88)\n  (:id . 60))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 94) (:start . 91)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 62))\n ((:tag . "CD") (:stem . "1992") (:form . "1992") (:end . 100) (:start . 96)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 110)\n  (:start . 103) (:id . 65))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 115) (:start . 111)\n  (:id . 66))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 122)\n  (:start . 116) (:id . 67))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 130)\n  (:start . 123) (:id . 68))\n ((:tag . "NN") (:stem . "actin") (:form . "actin") (:end . 136)\n  (:start . 131) (:id . 69))\n ((:tag . "NNS") (:stem . "cap") (:form . "caps") (:end . 141) (:start . 137)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 71))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 148) (:start . 146)\n  (:id . 72))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 158)\n  (:start . 149) (:id . 73))\n ((:tag . "VBZ") (:stem . "furrow") (:form . "furrows") (:end . 166)\n  (:start . 159) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 168) (:start . 167)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 180)\n  (:start . 168) (:id . 76))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 187)\n  (:start . 181) (:id . 77))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 190) (:start . 188)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 191) (:start . 190)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s4.240) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501293@unknown@formal@none@1@S@If cortical dynein or cortical MT depolymerases play a significant role in pulling spindle poles apart by sliding astral MTs outward relative to the actin cortex, this activity should be reduced or eliminated due to the depletion of actin caps and furrows in these mutants.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "cortical") (:form . "cortical") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "dynein") (:form . "dynein") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "cortical") (:form . "cortical") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "mt") (:form . "MT") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "depolymeras") (:form . "depolymerases") (:end . 47)\n  (:start . 34) (:id . 48))\n ((:tag . "VBP") (:stem . 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(:end . 273) (:start . 272)\n  (:id . 88)))@@@1@47@((:hcues ((:id . :x4.241.1) (:span 177 183)))\n (:hscopes ((:id . :x4.241.1) (:span 163 272)))\n (:identifiers (:sid . :s4.241) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501294@unknown@formal@none@1@S@Plots of pole–pole separation dynamics (Supplemental Figure S1) show that the rate of separation during prometaphase is slower in these mutants, but during anaphase B there is no significant difference.@(((:tag . "NNS") (:stem . "plot") (:form . "Plots") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "pole–pole") (:form . "pole–pole") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "dynamic") (:form . "dynamics") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "supplemental") (:form . "Supplemental") (:end . 52)\n  (:start . 40) (:id . 48))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 59)\n  (:start . 53) (:id . 49))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 96)\n  (:start . 86) (:id . 57))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 116)\n  (:start . 104) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 119) (:start . 117)\n  (:id . 60))\n ((:tag . "JJR") (:stem . "slow") (:form . "slower") (:end . 126)\n  (:start . 120) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 62))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 135)\n  (:start . 130) (:id . 63))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 143)\n  (:start . 136) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 65))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 148) (:start . 145)\n  (:id . 66))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 155)\n  (:start . 149) (:id . 67))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 164)\n  (:start . 156) (:id . 68))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 166) (:start . 165)\n  (:id . 69))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 172)\n  (:start . 167) (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 178) (:start . 176)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 190)\n  (:start . 179) (:id . 73))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 201)\n  (:start . 191) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s4.242) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501295@unknown@formal@none@1@S@Using fluorescence speckle microscopy, we examined the rate of movement of tubulin speckles away from the equator during metaphase and anaphase.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 18)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "speckle") (:form . "speckle") (:end . 26)\n  (:start . 19) (:id . 44))\n ((:tag . "NN") (:stem . "microscopy") (:form . "microscopy") (:end . 37)\n  (:start . 27) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "movement") (:form . "movement") (:end . 71)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "tubulin") (:form . "tubulin") (:end . 82)\n  (:start . 75) (:id . 54))\n ((:tag . "NNS") (:stem . "speckle") (:form . "speckles") (:end . 91)\n  (:start . 83) (:id . 55))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 96) (:start . 92)\n  (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 101) (:start . 97)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 58))\n ((:tag . "NN") (:stem . "equator") (:form . "equator") (:end . 113)\n  (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 120)\n  (:start . 114) (:id . 60))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 130)\n  (:start . 121) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 62))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 143)\n  (:start . 135) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s4.243) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501296@unknown@formal@none@1@S@This could reflect the sliding apart of MTs either by outward ipMT sliding by KLP61F or, during anaphase B, by outward pulling by cortical forces.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VB") (:stem . "reflect") (:form . "reflect") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "apart") (:form . "apart") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "outward") (:form . "outward") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "ipmt") (:form . "ipMT") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 74)\n  (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 84)\n  (:start . 78) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 58))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 95)\n  (:start . 89) (:id . 59))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 104)\n  (:start . 96) (:id . 60))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 106) (:start . 105)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 110) (:start . 108)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "outward") (:form . "outward") (:end . 118)\n  (:start . 111) (:id . 64))\n ((:tag . "NN") (:stem . "pulling") (:form . "pulling") (:end . 126)\n  (:start . 119) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 129) (:start . 127)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "cortical") (:form . "cortical") (:end . 138)\n  (:start . 130) (:id . 67))\n ((:tag . "NNS") (:stem . "force") (:form . "forces") (:end . 145)\n  (:start . 139) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x4.244.1) (:span 44 50 85 87)))\n (:hscopes ((:id . :x4.244.1) (:span 44 145)))\n (:identifiers (:sid . :s4.244) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501297@unknown@formal@none@1@S@In wild-type spindles, speckles move at a rate of 0.05 ± 0.02 µm/s, in spg mutants they move at 0.05 ± 0.02 µm/s, and in sced mutants at 0.06 ± 0.02 µm/s (Supplemental Figure S1), indicating that outward pulling by cortical forces is not significant throughout metaphase and anaphase.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "speckle") (:form . "speckles") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "VBP") (:stem . "move") (:form . "move") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . 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5501298@unknown@formal@none@1@S@Together these results are consistent with the hypothesis that cortical forces augment ipMT sliding to contribute to spindle elongation during the prometaphase-to-metaphase transition, for example, via cortical dynein activity (Sharp et al., 2000a ).@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "cortical") (:form . "cortical") (:end . 71)\n  (:start . 63) (:id . 51))\n ((:tag . "NNS") (:stem . "force") (:form . "forces") (:end . 78)\n  (:start . 72) (:id . 52))\n ((:tag . "VBP") (:stem . "augment") (:form . "augment") (:end . 86)\n  (:start . 79) (:id . 53))\n ((:tag . "NN") (:stem . "ipmt") (:form . "ipMT") (:end . 91) (:start . 87)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 99)\n  (:start . 92) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 102) (:start . 100)\n  (:id . 56))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 113)\n  (:start . 103) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 116) (:start . 114)\n  (:id . 58))\n ((:tag . "VB") (:stem . "spindle") (:form . "spindle") (:end . 124)\n  (:start . 117) (:id . 59))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 135)\n  (:start . 125) (:id . 60))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 142)\n  (:start . 136) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "prometaphase-to-metaphase")\n  (:form . "prometaphase-to-metaphase") (:end . 172) (:start . 147)\n  (:id . 63))\n ((:tag . "NN") (:stem . "transition") (:form . "transition") (:end . 183)\n  (:start . 173) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 188) (:start . 185)\n  (:id . 66))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 196)\n  (:start . 189) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 68))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 201) (:start . 198)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "cortical") (:form . "cortical") (:end . 210)\n  (:start . 202) (:id . 70))\n ((:tag . "NN") (:stem . "dynein") (:form . "dynein") (:end . 217)\n  (:start . 211) (:id . 71))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 226)\n  (:start . 218) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 228) (:start . 227)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Sharp") (:form . "Sharp") (:end . 233)\n  (:start . 228) (:id . 74))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 236) (:start . 234)\n  (:id . 75))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 240) (:start . 237)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 241) (:start . 240)\n  (:id . 77))\n ((:tag . "LS") (:stem . "2000a") (:form . "2000a") (:end . 247)\n  (:start . 242) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 249) (:start . 248)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 250) (:start . 249)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s4.246) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501299@unknown@formal@none@1@S@However, cortical pulling forces apparently do not play a significant role after metaphase onset, whereupon KLP61F becomes the major force generator for the outward sliding of ipMTs that underlies poleward flux and anaphase spindle elongation.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "cortical") (:form . "cortical") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "VBG") (:stem . "pull") (:form . "pulling") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "force") (:form . "forces") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "RB") (:stem . "apparently") (:form . "apparently") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 46) (:start . 44)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 69)\n  (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 74) (:start . 70)\n  (:id . 53))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 80) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 90)\n  (:start . 81) (:id . 55))\n ((:tag . "NN") (:stem . "onset") (:form . "onset") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 57))\n ((:tag . "IN") (:stem . "whereupon") (:form . "whereupon") (:end . 107)\n  (:start . 98) (:id . 58))\n ((:tag . "NN") (:stem . "klp61f") (:form . "KLP61F") (:end . 114)\n  (:start . 108) (:id . 59))\n ((:tag . "VBZ") (:stem . "become") (:form . "becomes") (:end . 122)\n  (:start . 115) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 132)\n  (:start . 127) (:id . 62))\n ((:tag . "NN") (:stem . "force") (:form . "force") (:end . 138)\n  (:start . 133) (:id . 63))\n ((:tag . "NN") (:stem . "generator") (:form . "generator") (:end . 148)\n  (:start . 139) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 152) (:start . 149)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "outward") (:form . "outward") (:end . 164)\n  (:start . 157) (:id . 67))\n ((:tag . "NN") (:stem . "sliding") (:form . "sliding") (:end . 172)\n  (:start . 165) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 175) (:start . 173)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "ipmt") (:form . "ipMTs") (:end . 181)\n  (:start . 176) (:id . 70))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 186) (:start . 182)\n  (:id . 71))\n ((:tag . "VBZ") (:stem . "underlie") (:form . "underlies") (:end . 196)\n  (:start . 187) (:id . 72))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 205)\n  (:start . 197) (:id . 73))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 210) (:start . 206)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 214) (:start . 211)\n  (:id . 75))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 223)\n  (:start . 215) (:id . 76))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 231)\n  (:start . 224) (:id . 77))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 242)\n  (:start . 232) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x4.247.1) (:span 33 43)))\n (:hscopes ((:id . :x4.247.1) (:span 33 96)))\n (:identifiers (:sid . :s4.247) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501300@unknown@formal@none@1@S@DISCUSSION@(((:tag . "NN") (:stem . "discussion") (:form . "DISCUSSION") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.248) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501301@unknown@formal@none@1@S@This study exploits our ability to create and directly visualize the KLP61F concentration gradient produced by the microinjection of an antibody to the motor's spindle targeting domain in wild-type and Ncd null mutant Drosophila syncytial blastoderm embryos in order to examine the spectrum of functions of kinesin-5.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "exploit") (:form . "exploits") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "VB") (:stem . "create") (:form . 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5501302@unknown@formal@none@1@S@The work suggests that MT–MT crosslinking and sliding by KLP61F contributes to 1) the maintenance of prometaphase spindles as chromosomes are captured; 2) poleward flux in ipMTs and kMTs; 3) the bundling and organization of MTs throughout the spindle; 4) the control of pre-anaphase B spindle length; 5) tight congression, kinetochore–kinetochore spacing and the rate of anaphase A chromatid-to-pole motility; and 6) the elongation of the anaphase B spindle in a manner that is relatively insensitive to the KLP61F concentration (Figure 6).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "MT–MT") (:form . 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5501303@unknown@formal@none@1@S@The hypothesis that KLP61F drives MT sliding from NEB through anaphase B to push apart spindle poles was also supported by gene dosage experiments in embryos and real-time fluorescence microscopy of transgenic late embryonic/larval klp61f mutants expressing GFP-tubulin.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "VBZ") (:stem . "drive") (:form . "drives") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "mt") (:form . "MT") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "NEB") (:form . "NEB") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 72) (:start . 71)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "VB") (:stem . "push") (:form . "push") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "RP") (:stem . "apart") (:form . "apart") (:end . 86) (:start . 81)\n  (:id . 56))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 94)\n  (:start . 87) (:id . 57))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 100) (:start . 95)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 119)\n  (:start . 110) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 127) (:start . 123)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dosage") (:form . "dosage") (:end . 134)\n  (:start . 128) (:id . 64))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 146)\n  (:start . 135) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 157)\n  (:start . 150) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "real-time") (:form . "real-time") (:end . 171)\n  (:start . 162) (:id . 69))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 184)\n  (:start . 172) (:id . 70))\n ((:tag . "NN") (:stem . "microscopy") (:form . "microscopy") (:end . 195)\n  (:start . 185) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 198) (:start . 196)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 209)\n  (:start . 199) (:id . 73))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 214) (:start . 210)\n  (:id . 74))\n ((:tag . "NN") (:stem . "embryonic/larval") (:form . "embryonic/larval")\n  (:end . 231) (:start . 215) (:id . 75))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 238)\n  (:start . 232) (:id . 76))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 246)\n  (:start . 239) (:id . 77))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 257)\n  (:start . 247) (:id . 78))\n ((:tag . "NNP") (:stem . "GFP-tubulin") (:form . "GFP-tubulin") (:end . 269)\n  (:start . 258) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x4.251.1) (:span 4 14)))\n (:hscopes ((:id . :x4.251.1) (:span 4 100)))\n (:identifiers (:sid . :s4.251) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501304@unknown@formal@none@1@S@The latter studies also revealed monoastral bipolar spindles that were never seen in syncytial embryos, suggesting that chromosome-directed spindle assembly becomes more evident as embryonic and larval development proceeds and mitosis slows down.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "JJ") (:stem . "monoastral") (:form . "monoastral") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "JJ") (:stem . "bipolar") (:form . "bipolar") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 60)\n  (:start . 52) (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 65) (:start . 61)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 70) (:start . 66)\n  (:id . 51))\n ((:tag . "RB") (:stem . "never") (:form . "never") (:end . 76) (:start . 71)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 81) (:start . 77)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "syncytial") (:form . "syncytial") (:end . 94)\n  (:start . 85) (:id . 55))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 102)\n  (:start . 95) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 114)\n  (:start . 104) (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 119) (:start . 115)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "chromosome-directed")\n  (:form . "chromosome-directed") (:end . 139) (:start . 120) (:id . 60))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 147)\n  (:start . 140) (:id . 61))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 156)\n  (:start . 148) (:id . 62))\n ((:tag . "VBZ") (:stem . "become") (:form . "becomes") (:end . 164)\n  (:start . 157) (:id . 63))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 169) (:start . 165)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "evident") (:form . "evident") (:end . 177)\n  (:start . 170) (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 180) (:start . 178)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 190)\n  (:start . 181) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 201)\n  (:start . 195) (:id . 69))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 213)\n  (:start . 202) (:id . 70))\n ((:tag . "NNS") (:stem . "proceed") (:form . "proceeds") (:end . 222)\n  (:start . 214) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 226) (:start . 223)\n  (:id . 72))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 234)\n  (:start . 227) (:id . 73))\n ((:tag . "VBZ") (:stem . "slow") (:form . "slows") (:end . 240)\n  (:start . 235) (:id . 74))\n ((:tag . "RB") (:stem . "down") (:form . "down") (:end . 245) (:start . 241)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x4.252.1) (:span 104 114)))\n (:hscopes ((:id . :x4.252.1) (:span 104 245)))\n (:identifiers (:sid . :s4.252) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501305@unknown@formal@none@1@S@Model for the multiple roles of KLP61F in Drosophila syncytial embryo mitosis.@(((:tag . "NNP") (:stem . "Model") (:form . "Model") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . "JJ") (:stem . "syncytial") (:form . "syncytial") (:end . 62)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 69)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.253) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501306@unknown@formal@none@1@S@We propose that kinesin-5 motors function as ensembles of dynamic, transient, MT crosslinkers throughout the spindle (Sharp et al., 1999a ; Cheerambathur et al., 2008 ), organizing parallel MTs into bundles (inset i) and sliding apart antiparallel MTs (inset ii), in accordance with the biochemical properties of KLP61F (e.g., Cole et al., 1994 ; Kashina et al., 1996a ; Tao et al., 2006 ; Van den Wildenberg et al., 2008 ).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "propose") (:form . "propose") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "VBP") (:stem . "function") (:form . 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5501307@unknown@formal@none@1@S@The results suggest that KLP61F-driven MT-MT sliding is required to oppose an inward force (ii, brown arrows) and maintain the spindle during early prometaphase, as well as to elongate it to the metaphase steady state length.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "klp61f-driven") (:form . "KLP61F-driven")\n  (:end . 38) (:start . 25) (:id . 46))\n ((:tag . "NNP") (:stem . "MT-MT") (:form . "MT-MT") (:end . 44) (:start . 39)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 55) (:start . 53)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "VB") (:stem . "oppose") (:form . "oppose") (:end . 74)\n  (:start . 68) (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "inward") (:form . "inward") (:end . 84)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "force") (:form . "force") (:end . 90) (:start . 85)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . "ii") (:form . "ii") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "brown") (:form . "brown") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 108)\n  (:start . 102) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "maintain") (:form . "maintain") (:end . 122)\n  (:start . 114) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 64))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 134)\n  (:start . 127) (:id . 65))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 141)\n  (:start . 135) (:id . 66))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 147)\n  (:start . 142) (:id . 67))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 160)\n  (:start . 148) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 69))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 164) (:start . 162)\n  (:id . 70))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 169) (:start . 165)\n  (:id . 71))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 172) (:start . 170)\n  (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 175) (:start . 173)\n  (:id . 73))\n ((:tag . "VB") (:stem . "elongate") (:form . "elongate") (:end . 184)\n  (:start . 176) (:id . 74))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 187) (:start . 185)\n  (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 190) (:start . 188)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 194) (:start . 191)\n  (:id . 77))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 204)\n  (:start . 195) (:id . 78))\n ((:tag . "JJ") (:stem . "steady") (:form . "steady") (:end . 211)\n  (:start . 205) (:id . 79))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 217)\n  (:start . 212) (:id . 80))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 224)\n  (:start . 218) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x4.255.1) (:span 12 19)))\n (:hscopes ((:id . :x4.255.1) (:span 12 224)))\n (:identifiers (:sid . :s4.255) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501308@unknown@formal@none@1@S@In preanaphase B (i.e. metaphase and anaphase A) spindles, KLP61F driven ipMT outward sliding (blue solid arrows) is required for poleward flux in both kMT and ipMT bundles and for anaphase A chromosome movement.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "preanaphase") (:form . "preanaphase") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "b") (:form . "B") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 32)\n  (:start . 23) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 45)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 57)\n  (:start . 49) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "klp61f") (:form . "KLP61F") (:end . 65)\n  (:start . 59) (:id . 54))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 72)\n  (:start . 66) (:id . 55))\n ((:tag . "NN") (:stem . "ipmt") (:form . "ipMT") (:end . 77) (:start . 73)\n  (:id . 56))\n ((:tag . "RB") (:stem . "outward") (:form . "outward") (:end . 85)\n  (:start . 78) (:id . 57))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 93)\n  (:start . 86) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 99) (:start . 95)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "solid") (:form . "solid") (:end . 105)\n  (:start . 100) (:id . 61))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 112)\n  (:start . 106) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 116) (:start . 114)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 125)\n  (:start . 117) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 129) (:start . 126)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 138)\n  (:start . 130) (:id . 67))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 143) (:start . 139)\n  (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n  (:id . 69))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 151) (:start . 147)\n  (:id . 70))\n ((:tag . "NN") (:stem . "kmt") (:form . "kMT") (:end . 155) (:start . 152)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 72))\n ((:tag . "NN") (:stem . "ipmt") (:form . "ipMT") (:end . 164) (:start . 160)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "bundle") (:form . "bundles") (:end . 172)\n  (:start . 165) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n  (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 180) (:start . 177)\n  (:id . 76))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 189)\n  (:start . 181) (:id . 77))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 191) (:start . 190)\n  (:id . 78))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 202)\n  (:start . 192) (:id . 79))\n ((:tag . "NN") (:stem . "movement") (:form . "movement") (:end . 211)\n  (:start . 203) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s4.256) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501309@unknown@formal@none@1@S@The kMTs may be slid poleward (dashed blue arrows) via crosslinks to the actively sliding antiparallel ipMTs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "kmt") (:form . "kMTs") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "slid") (:form . "slid") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "poleward") (:form . "poleward") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "dash") (:form . "dashed") (:end . 37) (:start . 31)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 49)\n  (:start . 43) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 52))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 54) (:start . 51)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "crosslink") (:form . "crosslinks") (:end . 65)\n  (:start . 55) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "RB") (:stem . "actively") (:form . "actively") (:end . 81)\n  (:start . 73) (:id . 57))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 89)\n  (:start . 82) (:id . 58))\n ((:tag . "JJ") (:stem . "antiparallel") (:form . "antiparallel") (:end . 102)\n  (:start . 90) (:id . 59))\n ((:tag . "NNS") (:stem . "ipmt") (:form . "ipMTs") (:end . 108)\n  (:start . 103) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x4.257.1) (:span 9 12)))\n (:hscopes ((:id . :x4.257.1) (:span 0 108)))\n (:identifiers (:sid . :s4.257) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501310@unknown@formal@none@1@S@Finally, KLP61F drives spindle elongation during anaphase B.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 15)\n  (:start . 9) (:id . 44))\n ((:tag . "VBZ") (:stem . "drive") (:form . "drives") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 48)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 59) (:start . 58)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.258) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501311@unknown@formal@none@1@S@This model is proposed only for Drosophila embryos (see Discussion).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Discussion") (:form . "Discussion") (:end . 66)\n  (:start . 56) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s4.259) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501312@unknown@formal@none@1@S@Experimental Strategy@(((:tag . "NNP") (:stem . "Experimental") (:form . "Experimental") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Strategy") (:form . "Strategy") (:end . 21)\n  (:start . 13) (:id . 43)))@@@1@2@((:identifiers (:sid . :s4.260) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501313@unknown@formal@none@1@S@Several methods are currently available for inhibiting target proteins in cells, including mutants, injection of dominant negative protein fragments, chemical inhibitors, RNA interference, and inhibitory antibody microinjection.@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 29)\n  (:start . 20) (:id . 45))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 39)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "inhibit") (:form . "inhibiting") (:end . 54)\n  (:start . 44) (:id . 48))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 61)\n  (:start . 55) (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 70)\n  (:start . 62) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 79) (:start . 74)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 90)\n  (:start . 81) (:id . 54))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 98)\n  (:start . 91) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 56))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 109)\n  (:start . 100) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 121)\n  (:start . 113) (:id . 59))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 130)\n  (:start . 122) (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 138)\n  (:start . 131) (:id . 61))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 148)\n  (:start . 139) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "chemical") (:form . "chemical") (:end . 158)\n  (:start . 150) (:id . 64))\n ((:tag . "NNS") (:stem . "inhibitor") (:form . "inhibitors") (:end . 169)\n  (:start . 159) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 170) (:start . 169)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 174) (:start . 171)\n  (:id . 67))\n ((:tag . "NN") (:stem . "interference") (:form . "interference") (:end . 187)\n  (:start . 175) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 188) (:start . 187)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 192) (:start . 189)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 203)\n  (:start . 193) (:id . 71))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 212)\n  (:start . 204) (:id . 72))\n ((:tag . "NN") (:stem . "microinjection") (:form . "microinjection")\n  (:end . 227) (:start . 213) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s4.261) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501314@unknown@formal@none@1@S@In the current study, microinjected antibody to the spindle-targeting phospho-tail domain on kinesin-5 (Sawin and Mitchison, 1995 ; Sharp et al., 1999a ; Cheerambathur et al., 2008 ) rapidly dissociated KP61F from mitotic spindles.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "microinjecte") (:form . "microinjected")\n  (:end . 35) (:start . 22) (:id . 47))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "spindle-targeting") (:form . "spindle-targeting")\n  (:end . 69) (:start . 52) (:id . 51))\n ((:tag . "JJ") (:stem . "phospho-tail") (:form . "phospho-tail") (:end . 82)\n  (:start . 70) (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 89)\n  (:start . 83) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 92) (:start . 90)\n  (:id . 54))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 102)\n  (:start . 93) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Sawin") (:form . "Sawin") (:end . 109)\n  (:start . 104) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Mitchison") (:form . "Mitchison") (:end . 123)\n  (:start . 114) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 129) (:start . 125)\n  (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 131) (:start . 130)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Sharp") (:form . "Sharp") (:end . 137)\n  (:start . 132) (:id . 63))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 140) (:start . 138)\n  (:id . 64))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 144) (:start . 141)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . "CD") (:stem . "1999a") (:form . "1999a") (:end . 151)\n  (:start . 146) (:id . 67))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Cheerambathur") (:form . "Cheerambathur")\n  (:end . 167) (:start . 154) (:id . 69))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 170) (:start . 168)\n  (:id . 70))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 174) (:start . 171)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 72))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 180) (:start . 176)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 182) (:start . 181)\n  (:id . 74))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 190)\n  (:start . 183) (:id . 75))\n ((:tag . "VBD") (:stem . "dissociate") (:form . "dissociated") (:end . 202)\n  (:start . 191) (:id . 76))\n ((:tag . "NN") (:stem . "kp61f") (:form . "KP61F") (:end . 208)\n  (:start . 203) (:id . 77))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 213) (:start . 209)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 221)\n  (:start . 214) (:id . 79))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 230)\n  (:start . 222) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s4.262) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501315@unknown@formal@none@1@S@By utilizing stable transgenic embryos that express GFP-tagged KLP61F, we were able to directly visualize the extent of dissociation of the target antigen from spindles in different regions of the syncytium relative to the injection site.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "utilize") (:form . "utilizing") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "stable") (:form . "stable") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "JJ") (:stem . "gfp-tagged") (:form . "GFP-tagged") (:end . 62)\n  (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "klp61f") (:form . "KLP61F") (:end . 69)\n  (:start . 63) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 78) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 95)\n  (:start . 87) (:id . 56))\n ((:tag . "VB") (:stem . "visualize") (:form . "visualize") (:end . 105)\n  (:start . 96) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 58))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 116)\n  (:start . 110) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 60))\n ((:tag . "NN") (:stem . "dissociation") (:form . "dissociation") (:end . 132)\n  (:start . 120) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 63))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 146)\n  (:start . 140) (:id . 64))\n ((:tag . "NN") (:stem . "antigen") (:form . "antigen") (:end . 154)\n  (:start . 147) (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 159) (:start . 155)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 168)\n  (:start . 160) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 171) (:start . 169)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 181)\n  (:start . 172) (:id . 69))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 189)\n  (:start . 182) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 192) (:start . 190)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 72))\n ((:tag . "NN") (:stem . "syncytium") (:form . "syncytium") (:end . 206)\n  (:start . 197) (:id . 73))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 215)\n  (:start . 207) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 218) (:start . 216)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 222) (:start . 219)\n  (:id . 76))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 232)\n  (:start . 223) (:id . 77))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 237) (:start . 233)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s4.263) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501316@unknown@formal@none@1@S@This in turn allowed us to correlate the extent of KLP61F depletion with the mitotic perturbation observed, which permitted an exploration of the range of mitotic functions of KLP61F, in addition to the unseparated/collapsed spindle pole phenotype seen after severe inhibition or loss of function (Heck et al., 1993 ; Sharp et al., 1999b ).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "turn") (:form . "turn") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "allow") (:form . "allowed") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VB") (:stem . "correlate") (:form . 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5501317@unknown@formal@none@1@S@Our results with respect to spindle pole spacing were confirmed by the observation of similar defects in klp61f mutants, including spindle collapse into monoasters after severe loss of KLP61F function and the observation that spindles depleted of ~30–50% of KLP61F by antibody injection, like those in embryos carrying half the normal dose of the corresponding gene, are shorter than normal at metaphase, but complete anaphase successfully (Figures 1 and 3).@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VB") (:stem . 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5501318@unknown@formal@none@1@S@Relation to Previous Experimental Studies of Kinesin-5 in Drosophila Syncytial Embryos@(((:tag . "NN") (:stem . "relation") (:form . "Relation") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "previous") (:form . "Previous") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "JJ") (:stem . "experimental") (:form . "Experimental") (:end . 33)\n  (:start . 21) (:id . 45))\n ((:tag . "NNS") (:stem . "study") (:form . "Studies") (:end . 41)\n  (:start . 34) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Kinesin-5") (:form . "Kinesin-5") (:end . 54)\n  (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 68)\n  (:start . 58) (:id . 50))\n ((:tag . "JJ") (:stem . "syncytial") (:form . "Syncytial") (:end . 78)\n  (:start . 69) (:id . 51))\n ((:tag . "NNP") (:stem . "Embryo") (:form . "Embryos") (:end . 86)\n  (:start . 79) (:id . 52)))@@@1@11@((:identifiers (:sid . :s4.266) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501319@unknown@formal@none@1@S@The results support previous studies suggesting that KLP61F is dispensable for the assembly of astral syncytial embryo spindles but is essential for prometaphase spindle maintenance where it is antagonized by Ncd (Sharp et al., 1999b ; Sharp et al., 2000a ; Tao et al., 2006 ), and it further implicates the action of an additional, unknown, inward motor, possibly the MT depolymerase, KLP10A.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "VBG") (:stem . "suggest") (:form . 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5501320@unknown@formal@none@1@S@Previously, we had predicted that KLP61F has a role in driving poleward flux and that the rate of anaphase B is insensitive to changes in the concentration of KLP61F (Brust-Mascher et al., 2004 ; Wollman et al., 2008 ).@(((:tag . "RB") (:stem . "previously") (:form . "Previously") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "drive") (:form . "driving") (:end . 62)\n  (:start . 55) (:id . 53))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 71)\n  (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 94) (:start . 90)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 60))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 106)\n  (:start . 98) (:id . 61))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 108) (:start . 107)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 111) (:start . 109)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "insensitive") (:form . "insensitive") (:end . 123)\n  (:start . 112) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 126) (:start . 124)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 134)\n  (:start . 127) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 137) (:start . 135)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 68))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 155) (:start . 142) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 165)\n  (:start . 159) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 180) (:start . 167) (:id . 73))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 183) (:start . 181)\n  (:id . 74))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 187) (:start . 184)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 188) (:start . 187)\n  (:id . 76))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 193) (:start . 189)\n  (:id . 77))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 195) (:start . 194)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Wollman") (:form . "Wollman") (:end . 203)\n  (:start . 196) (:id . 79))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 206) (:start . 204)\n  (:id . 80))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 210) (:start . 207)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 211) (:start . 210)\n  (:id . 82))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 216) (:start . 212)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 218) (:start . 217)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s4.268) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501321@unknown@formal@none@1@S@Here, we confirmed these predictions experimentally and also obtained evidence for new roles in controlling the length of the metaphase spindle, the tightness of chromosome congression, the distance between sister kinetochores, the rate of anaphase A chromatid-to-pole motility, and the relative timing of anaphase A and B, none of which have been reported previously.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 18)\n  (:start . 9) (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 36)\n  (:start . 25) (:id . 47))\n ((:tag . "RB") (:stem . 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5501322@unknown@formal@none@1@S@For example, in spindles lacking Ncd function, spindle collapse driven by the inward force-generators can be circumvented and the results, specifically the failure or delay of spindle elongation, then reveal a role for KLP61F-driven sliding in anaphase B.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "VBG") (:stem . "lack") (:form . "lacking") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 45)\n  (:start . 37) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 70)\n  (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "inward") (:form . "inward") (:end . 84)\n  (:start . 78) (:id . 56))\n ((:tag . "NNS") (:stem . "force-generator") (:form . "force-generators")\n  (:end . 101) (:start . 85) (:id . 57))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 105) (:start . 102)\n  (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "circumvent") (:form . "circumvented") (:end . 121)\n  (:start . 109) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 137)\n  (:start . 130) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 64))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 151)\n  (:start . 139) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 66))\n ((:tag . "NN") (:stem . "failure") (:form . "failure") (:end . 163)\n  (:start . 156) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 166) (:start . 164)\n  (:id . 68))\n ((:tag . "NN") (:stem . "delay") (:form . "delay") (:end . 172)\n  (:start . 167) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 175) (:start . 173)\n  (:id . 70))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 183)\n  (:start . 176) (:id . 71))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 194)\n  (:start . 184) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n  (:id . 73))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 200) (:start . 196)\n  (:id . 74))\n ((:tag . "VBP") (:stem . "reveal") (:form . "reveal") (:end . 207)\n  (:start . 201) (:id . 75))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 209) (:start . 208)\n  (:id . 76))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 214) (:start . 210)\n  (:id . 77))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 218) (:start . 215)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "klp61f-driven") (:form . "KLP61F-driven")\n  (:end . 232) (:start . 219) (:id . 79))\n ((:tag . "NN") (:stem . "sliding") (:form . "sliding") (:end . 240)\n  (:start . 233) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 243) (:start . 241)\n  (:id . 81))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 252)\n  (:start . 244) (:id . 82))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 254) (:start . 253)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 255) (:start . 254)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x4.270.1) (:span 102 105)))\n (:hscopes ((:id . :x4.270.1) (:span 47 121)))\n (:identifiers (:sid . :s4.270) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501323@unknown@formal@none@1@S@In the spindles that fail to elongate, we propose that there is enough KLP61F to prevent spindle collapse but not enough to drive anaphase B (Figure 2).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 15)\n  (:start . 7) (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "fail") (:form . "fail") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "VB") (:stem . "elongate") (:form . "elongate") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "propose") (:form . "propose") (:end . 49)\n  (:start . 42) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 54) (:start . 50)\n  (:id . 52))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 60) (:start . 55)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "enough") (:form . "enough") (:end . 70)\n  (:start . 64) (:id . 55))\n ((:tag . "NN") (:stem . "klp61f") (:form . "KLP61F") (:end . 77)\n  (:start . 71) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 88)\n  (:start . 81) (:id . 58))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 96)\n  (:start . 89) (:id . 59))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 105)\n  (:start . 97) (:id . 60))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 109) (:start . 106)\n  (:id . 61))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 113) (:start . 110)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "enough") (:form . "enough") (:end . 120)\n  (:start . 114) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . "VB") (:stem . "drive") (:form . "drive") (:end . 129)\n  (:start . 124) (:id . 65))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 138)\n  (:start . 130) (:id . 66))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 140) (:start . 139)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 148)\n  (:start . 142) (:id . 69))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 150) (:start . 149)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x4.271.1) (:span 42 49)))\n (:hscopes ((:id . :x4.271.1) (:span 42 140)))\n (:identifiers (:sid . :s4.271) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501324@unknown@formal@none@1@S@An outward, KLP61F-driven ipMT sliding, coupled to MT depolymerization at the poles, could also underlie KLP61F's contribution to poleward flux as predicted, but not previously tested (Brust-Mascher and Scholey, 2002 ).@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "outward") (:form . "outward") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "klp61f-driven") (:form . "KLP61F-driven")\n  (:end . 25) (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "ipmt") (:form . "ipMT") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "couple") (:form . "coupled") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "mt") (:form . "MT") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "depolymerization") (:form . "depolymerization")\n  (:end . 70) (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "VB") (:stem . "underlie") (:form . "underlie") (:end . 104)\n  (:start . 96) (:id . 59))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 111)\n  (:start . 105) (:id . 60))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "NN") (:stem . "contribution") (:form . "contribution") (:end . 126)\n  (:start . 114) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . "VB") (:stem . "poleward") (:form . "poleward") (:end . 138)\n  (:start . 130) (:id . 64))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 143) (:start . 139)\n  (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 146) (:start . 144)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 156)\n  (:start . 147) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n  (:id . 68))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 161) (:start . 158)\n  (:id . 69))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 165) (:start . 162)\n  (:id . 70))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 176)\n  (:start . 166) (:id . 71))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 183)\n  (:start . 177) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 198) (:start . 185) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 202) (:start . 199)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Scholey") (:form . "Scholey") (:end . 210)\n  (:start . 203) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 211) (:start . 210)\n  (:id . 77))\n ((:tag . "CD") (:stem . "2002") (:form . "2002") (:end . 216) (:start . 212)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 218) (:start . 217)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x4.272.1) (:span 85 90)))\n (:hscopes ((:id . :x4.272.1) (:span 85 183)))\n (:identifiers (:sid . :s4.272) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501325@unknown@formal@none@1@S@Perhaps surprisingly, after partial KLP61F inhibition, flux is slowed down in all MT bundles, suggesting that all bundles are interconnected.@(((:tag . "RB") (:stem . "perhaps") (:form . "Perhaps") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "surprisingly") (:form . "surprisingly") (:end . 20)\n  (:start . 8) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 44))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 42)\n  (:start . 36) (:id . 47))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 53)\n  (:start . 43) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "slow") (:form . "slowed") (:end . 69) (:start . 63)\n  (:id . 52))\n ((:tag . "RP") (:stem . "down") (:form . "down") (:end . 74) (:start . 70)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "MT") (:form . "MT") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "bundle") (:form . "bundles") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 104)\n  (:start . 94) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 113) (:start . 110)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "bundle") (:form . "bundles") (:end . 121)\n  (:start . 114) (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "interconnect") (:form . "interconnected")\n  (:end . 140) (:start . 126) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x4.273.1) (:span 94 104)) ((:id . :x4.273.2) (:span 0 7)))\n (:hscopes ((:id . :x4.273.1) (:span 94 140)) ((:id . :x4.273.2) (:span 0 20)))\n (:identifiers (:sid . :s4.273) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501326@unknown@formal@none@1@S@We propose that the sliding apart of ipMTs by KLP61F would also push kMTs poleward, if the kMTs are mechanically coupled to the sliding ipMTs by KLP61F (or other) MT–MT cross-linkers (Figure 6; Sharp et al., 1999a ; Cheerambathur et al., 2008 ).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "propose") (:form . "propose") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "apart") (:form . "apart") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "ipmt") (:form . 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")") (:end . 244) (:start . 243)\n  (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 245) (:start . 244)\n  (:id . 92)))@@@1@51@((:hcues ((:id . :x4.274.1) (:span 53 58)) ((:id . :x4.274.2) (:span 3 10)))\n (:hscopes ((:id . :x4.274.1) (:span 53 82)) ((:id . :x4.274.2) (:span 3 182)))\n (:identifiers (:sid . :s4.274) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501327@unknown@formal@none@1@S@Depolymerization of ipMTs and kMTs at the poles would then create KLP61F-dependent poleward flux.@(((:tag . "NN") (:stem . "depolymerization") (:form . "Depolymerization")\n  (:end . 16) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "ipmt") (:form . "ipMTs") (:end . 25) (:start . 20)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "kmt") (:form . "kMTs") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "VB") (:stem . "create") (:form . "create") (:end . 65)\n  (:start . 59) (:id . 52))\n ((:tag . "JJ") (:stem . "klp61f-dependent") (:form . "KLP61F-dependent")\n  (:end . 82) (:start . 66) (:id . 53))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 91)\n  (:start . 83) (:id . 54))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 96) (:start . 92)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x4.275.1) (:span 48 53)))\n (:hscopes ((:id . :x4.275.1) (:span 48 96)))\n (:identifiers (:sid . :s4.275) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501328@unknown@formal@none@1@S@The slowing down of anaphase A chromatid-to-pole motility resulting from KLP61F inhibition could be explained by the loss of flux because it has been shown that in Drosophila embryos, anaphase A is driven by a combined flux-pacman mechanism (Rogers et al., 2004 ).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "slow") (:form . "slowing") (:end . 11) (:start . 4)\n  (:id . 43))\n ((:tag . "RP") (:stem . "down") (:form . "down") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "chromatid-to-pole") (:form . "chromatid-to-pole")\n  (:end . 48) (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "motility") (:form . "motility") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 67)\n  (:start . 58) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 72) (:start . 68)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 79)\n  (:start . 73) (:id . 52))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 90)\n  (:start . 80) (:id . 53))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 96) (:start . 91)\n  (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 99) (:start . 97)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "explain") (:form . "explained") (:end . 109)\n  (:start . 100) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 112) (:start . 110)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 58))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 121) (:start . 117)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 60))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 129) (:start . 125)\n  (:id . 61))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 137)\n  (:start . 130) (:id . 62))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 140) (:start . 138)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 144) (:start . 141)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 149) (:start . 145)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 155)\n  (:start . 150) (:id . 66))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 160) (:start . 156)\n  (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 163) (:start . 161)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 174)\n  (:start . 164) (:id . 69))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 182)\n  (:start . 175) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 71))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 192)\n  (:start . 184) (:id . 72))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 194) (:start . 193)\n  (:id . 73))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 197) (:start . 195)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 204)\n  (:start . 198) (:id . 75))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 207) (:start . 205)\n  (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 209) (:start . 208)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "combined") (:form . "combined") (:end . 218)\n  (:start . 210) (:id . 78))\n ((:tag . "JJ") (:stem . "flux-pacman") (:form . "flux-pacman") (:end . 230)\n  (:start . 219) (:id . 79))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 240)\n  (:start . 231) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 242) (:start . 241)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Rogers") (:form . "Rogers") (:end . 248)\n  (:start . 242) (:id . 82))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 251) (:start . 249)\n  (:id . 83))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 255) (:start . 252)\n  (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 256) (:start . 255)\n  (:id . 85))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 261) (:start . 257)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 263) (:start . 262)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 264) (:start . 263)\n  (:id . 88)))@@@1@47@((:hcues ((:id . :x4.276.1) (:span 91 96)))\n (:hscopes ((:id . :x4.276.1) (:span 0 240)))\n (:identifiers (:sid . :s4.276) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501329@unknown@formal@none@1@S@Surprisingly, we also observed a loss of tension between sister kinetochores and a loss of congression.@(((:tag . "RB") (:stem . "surprisingly") (:form . "Surprisingly") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "tension") (:form . "tension") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "sister") (:form . "sister") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "NNS") (:stem . "kinetochore") (:form . "kinetochores") (:end . 76)\n  (:start . 64) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 87) (:start . 83)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "congression") (:form . "congression") (:end . 102)\n  (:start . 91) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.277) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501330@unknown@formal@none@1@S@This may also be due to the loss of flux; i.e., normally as MTs slide outward, they generate a pulling force on the kinetochores.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 48))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 32) (:start . 28)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 50))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 40) (:start . 36)\n  (:id . 51))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 41) (:start . 40)\n  (:id . 52))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 46) (:start . 42)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 54))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 56)\n  (:start . 48) (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 59) (:start . 57)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "MT") (:form . "MTs") (:end . 63) (:start . 60)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "slide") (:form . "slide") (:end . 69) (:start . 64)\n  (:id . 58))\n ((:tag . "RB") (:stem . "outward") (:form . "outward") (:end . 77)\n  (:start . 70) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 83) (:start . 79)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "generate") (:form . "generate") (:end . 92)\n  (:start . 84) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "pull") (:form . "pulling") (:end . 102)\n  (:start . 95) (:id . 64))\n ((:tag . "NN") (:stem . "force") (:form . "force") (:end . 108)\n  (:start . 103) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 111) (:start . 109)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "kinetochore") (:form . "kinetochores") (:end . 128)\n  (:start . 116) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x4.278.1) (:span 5 8)))\n (:hscopes ((:id . :x4.278.1) (:span 5 40)))\n (:identifiers (:sid . :s4.278) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501331@unknown@formal@none@1@S@This force maintains the tension between sister kinetochores so that the loss of this outward sliding leads to a decrease in the distance between sisters.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "force") (:form . "force") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "maintain") (:form . "maintains") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "tension") (:form . "tension") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "sister") (:form . "sister") (:end . 47)\n  (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "kinetochore") (:form . "kinetochores") (:end . 60)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "outward") (:form . "outward") (:end . 93)\n  (:start . 86) (:id . 56))\n ((:tag . "NN") (:stem . "sliding") (:form . "sliding") (:end . 101)\n  (:start . 94) (:id . 57))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 107)\n  (:start . 102) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 112) (:start . 111)\n  (:id . 60))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 121)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 124) (:start . 122)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n  (:id . 63))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 137)\n  (:start . 129) (:id . 64))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 145)\n  (:start . 138) (:id . 65))\n ((:tag . "NNS") (:stem . "sister") (:form . "sisters") (:end . 153)\n  (:start . 146) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.279) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501332@unknown@formal@none@1@S@Relation to Experimental Studies of Kinesin-5 Function in Other Systems@(((:tag . "NN") (:stem . "relation") (:form . "Relation") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "experimental") (:form . "Experimental") (:end . 24)\n  (:start . 12) (:id . 44))\n ((:tag . "NNPS") (:stem . "Study") (:form . "Studies") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Kinesin-5") (:form . "Kinesin-5") (:end . 45)\n  (:start . 36) (:id . 47))\n ((:tag . "NNP") (:stem . "Function") (:form . "Function") (:end . 54)\n  (:start . 46) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Other") (:form . "Other") (:end . 63) (:start . 58)\n  (:id . 50))\n ((:tag . "NNPS") (:stem . "Systems") (:form . "Systems") (:end . 71)\n  (:start . 64) (:id . 51)))@@@1@10@((:identifiers (:sid . :s4.280) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501333@unknown@formal@none@1@S@A comprehensive review of the diverse roles of kinesin-5 in different systems is beyond the scope of this article (see Valentine et al., 2006a ; Civelekoglu-Scholey and Scholey, 2007 ), but a brief comparison between Drosophila syncytial embryos and other systems is appropriate.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "comprehensive") (:form . "comprehensive")\n  (:end . 15) (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "review") (:form . "review") (:end . 22)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "IN") (:stem . 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5501334@unknown@formal@none@1@S@Live imaging of klp61f mutant late embryos and larvae (Figure 3) revealed that bipolar spindles collapse into monoasters, as observed in syncytial embryos, and also revealed the formation of functional bipolar, monoastral spindles, as observed previously in studies of fixed larval brains and testis (Wilson et al., 1997 ) but not in anti-KLP61F–injected embryos.@(((:tag . "JJ") (:stem . "live") (:form . "Live") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "imaging") (:form . "imaging") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "klp61f") (:form . "klp61f") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "embryo") (:form . 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5501335@unknown@formal@none@1@S@It is plausible that this reflects the formation of bipolar monoastral spindles by chromosome-directed, KLP61F-mediated acentrosomal pole focusing as proposed for Drosophila S2 cells, based on RNA interference (RNAi) experiments (Goshima and Vale, 2003 ).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "plausible") (:form . "plausible") (:end . 15)\n  (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "reflect") (:form . "reflects") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 48)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "bipolar") (:form . "bipolar") (:end . 59)\n  (:start . 52) (:id . 51))\n ((:tag . "JJ") (:stem . "monoastral") (:form . "monoastral") (:end . 70)\n  (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "chromosome-directed")\n  (:form . "chromosome-directed") (:end . 102) (:start . 83) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "klp61f-mediated") (:form . "KLP61F-mediated")\n  (:end . 119) (:start . 104) (:id . 57))\n ((:tag . "JJ") (:stem . "acentrosomal") (:form . "acentrosomal") (:end . 132)\n  (:start . 120) (:id . 58))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 137) (:start . 133)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "focus") (:form . "focusing") (:end . 146)\n  (:start . 138) (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 149) (:start . 147)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 158)\n  (:start . 150) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 162) (:start . 159)\n  (:id . 63))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 173)\n  (:start . 163) (:id . 64))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 176) (:start . 174)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 182)\n  (:start . 177) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 189)\n  (:start . 184) (:id . 68))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 192) (:start . 190)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 196) (:start . 193)\n  (:id . 70))\n ((:tag . "NN") (:stem . "interference") (:form . "interference") (:end . 209)\n  (:start . 197) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 211) (:start . 210)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 215) (:start . 211)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 216) (:start . 215)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 228)\n  (:start . 217) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 230) (:start . 229)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Goshima") (:form . "Goshima") (:end . 237)\n  (:start . 230) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 241) (:start . 238)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Vale") (:form . "Vale") (:end . 246) (:start . 242)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 247) (:start . 246)\n  (:id . 80))\n ((:tag . "CD") (:stem . "2003") (:form . "2003") (:end . 252) (:start . 248)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 254) (:start . 253)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 255) (:start . 254)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s4.283) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501336@unknown@formal@none@1@S@We hypothesize that the syncytial embryo spindles that we study are adapted for rapid mitoses (Civelekoglu-Scholey et al., 2006 ) and consequently their assembly and function is dominated by the centrosome-directed pathway so that, unlike in larvae, S2 cells and many other cells, the chromosome-directed spindle assembly pathway plays a lesser role (Heald et al., 1997 ; Megraw et al., 2001 ).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "hypothesize") (:form . "hypothesize") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "syncytial") (:form . "syncytial") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "embryo") (:form . 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"CD") (:stem . "2001") (:form . "2001") (:end . 391) (:start . 387)\n  (:id . 110))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 393) (:start . 392)\n  (:id . 111))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 394) (:start . 393)\n  (:id . 112)))@@@1@71@((:hcues ((:id . :x4.284.1) (:span 3 14)))\n (:hscopes ((:id . :x4.284.1) (:span 3 349)))\n (:identifiers (:sid . :s4.284) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501337@unknown@formal@none@1@S@The relative importance of centrosome- versus chromosome-directed spindle organization may be a key factor influencing how kinesin-5 is deployed in different spindles, e.g., in spindle pole focusing versus spindle pole separation, though it is obviously not the only factor.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "centrosome-") (:form . "centrosome-") (:end . 38)\n  (:start . 27) (:id . 46))\n ((:tag . "CC") (:stem . "versus") (:form . "versus") (:end . 45)\n  (:start . 39) (:id . 47))\n ((:tag . "JJ") (:stem . "chromosome-directed")\n  (:form . "chromosome-directed") (:end . 65) (:start . 46) (:id . 48))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 73)\n  (:start . 66) (:id . 49))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 86)\n  (:start . 74) (:id . 50))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 90) (:start . 87)\n  (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 93) (:start . 91)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 95) (:start . 94)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 99) (:start . 96)\n  (:id . 54))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 106)\n  (:start . 100) (:id . 55))\n ((:tag . "VBG") (:stem . "influence") (:form . "influencing") (:end . 118)\n  (:start . 107) (:id . 56))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 122) (:start . 119)\n  (:id . 57))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 132)\n  (:start . 123) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 135) (:start . 133)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "deploy") (:form . "deployed") (:end . 144)\n  (:start . 136) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 147) (:start . 145)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 157)\n  (:start . 148) (:id . 62))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 166)\n  (:start . 158) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 64))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 172) (:start . 168)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 176) (:start . 174)\n  (:id . 67))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 184)\n  (:start . 177) (:id . 68))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 189) (:start . 185)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "focus") (:form . "focusing") (:end . 198)\n  (:start . 190) (:id . 70))\n ((:tag . "IN") (:stem . "versus") (:form . "versus") (:end . 205)\n  (:start . 199) (:id . 71))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 213)\n  (:start . 206) (:id . 72))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 218) (:start . 214)\n  (:id . 73))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 229)\n  (:start . 219) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 230) (:start . 229)\n  (:id . 75))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 237)\n  (:start . 231) (:id . 76))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 240) (:start . 238)\n  (:id . 77))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 243) (:start . 241)\n  (:id . 78))\n ((:tag . "RB") (:stem . "obviously") (:form . "obviously") (:end . 253)\n  (:start . 244) (:id . 79))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 257) (:start . 254)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 261) (:start . 258)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 266) (:start . 262)\n  (:id . 82))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 273)\n  (:start . 267) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 274) (:start . 273)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x4.285.1) (:span 87 90)))\n (:hscopes ((:id . :x4.285.1) (:span 87 273)))\n (:identifiers (:sid . :s4.285) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501338@unknown@formal@none@1@S@Our results showing that KLP61F appears to contribute to the length of pre-anaphase B spindles in living embryos differ from the results obtained in fixed S2 cells where, above the critical concentration required for bipolar spindle assembly, increasing concentrations of KLP61F did not influence metaphase spindle length (Goshima et al., 2005b ).@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . 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5501339@unknown@formal@none@1@S@Although we cannot rule out an influence of technical differences between the two studies, we suspect that they reflect genuine system-specific differences, akin to the different consequences of loss of Ncd function in embryos versus cultured cells of Drosophila (Sharp et al., 2000a ; Goshima et al., 2005a ; Morales-Mulia and Scholey, 2005 ).@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "cannot") (:form . "cannot") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "VB") (:stem . "rule") (:form . "rule") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "influence") (:form . 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5501340@unknown@formal@none@1@S@The Drosophila embryo spindle differs from that of S. cerevisiae in using only one, rather than two kinesin-5 motors.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "VBZ") (:stem . "differ") (:form . "differs") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 64)\n  (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 73) (:start . 68)\n  (:id . 53))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 90)\n  (:start . 84) (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 109)\n  (:start . 100) (:id . 60))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 116)\n  (:start . 110) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s4.288) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501341@unknown@formal@none@1@S@In both these systems, kinesin-5 function is required to prevent kinesin-14–induced prometaphase spindle collapse, but only in yeast is it essential for de novo spindle assembly (Saunders and Hoyt, 1992 ).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PDT") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 32)\n  (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . "JJ") (:stem . "kinesin-14–induced") (:form . "kinesin-14–induced")\n  (:end . 83) (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 96)\n  (:start . 84) (:id . 54))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 104)\n  (:start . 97) (:id . 55))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 113)\n  (:start . 105) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 123) (:start . 119)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 126) (:start . 124)\n  (:id . 60))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 132)\n  (:start . 127) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 135) (:start . 133)\n  (:id . 62))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 138) (:start . 136)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 148)\n  (:start . 139) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 152) (:start . 149)\n  (:id . 65))\n ((:tag . "FW") (:stem . "de") (:form . "de") (:end . 155) (:start . 153)\n  (:id . 66))\n ((:tag . "FW") (:stem . "novo") (:form . "novo") (:end . 160) (:start . 156)\n  (:id . 67))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 168)\n  (:start . 161) (:id . 68))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 177)\n  (:start . 169) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 179) (:start . 178)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Saunder") (:form . "Saunders") (:end . 187)\n  (:start . 179) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 191) (:start . 188)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Hoyt") (:form . "Hoyt") (:end . 196) (:start . 192)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 74))\n ((:tag . "CD") (:stem . "1992") (:form . "1992") (:end . 202) (:start . 198)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 204) (:start . 203)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s4.289) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5501343@unknown@formal@none@1@S@In some respects, therefore, the manner in which kinesin-5 is deployed in Drosophila embryos resembles yeast more closely than S2 cells, again possibly reflecting the relative dominance of centrosomes and spindle pole bodies.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "respect") (:form . "respects") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 39)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 48) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 58)\n  (:start . 49) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "deploy") (:form . "deployed") (:end . 70)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 84)\n  (:start . 74) (:id . 56))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "VBZ") (:stem . "resemble") (:form . "resembles") (:end . 102)\n  (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 108)\n  (:start . 103) (:id . 59))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 113) (:start . 109)\n  (:id . 60))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 121)\n  (:start . 114) (:id . 61))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 126) (:start . 122)\n  (:id . 62))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 135)\n  (:start . 130) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 65))\n ((:tag . "RB") (:stem . "again") (:form . "again") (:end . 142)\n  (:start . 137) (:id . 66))\n ((:tag . "RB") (:stem . "possibly") (:form . "possibly") (:end . 151)\n  (:start . 143) (:id . 67))\n ((:tag . "VBG") (:stem . "reflect") (:form . "reflecting") (:end . 162)\n  (:start . 152) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 175)\n  (:start . 167) (:id . 70))\n ((:tag . "NN") (:stem . "dominance") (:form . "dominance") (:end . 185)\n  (:start . 176) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 188) (:start . 186)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "centrosome") (:form . "centrosomes") (:end . 200)\n  (:start . 189) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 204) (:start . 201)\n  (:id . 74))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 212)\n  (:start . 205) (:id . 75))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 217) (:start . 213)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 224)\n  (:start . 218) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x4.291.1) (:span 143 151)))\n (:hscopes ((:id . :x4.291.1) (:span 143 224)))\n (:identifiers (:sid . :s4.291) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501344@unknown@formal@none@1@S@In other respects the two systems may differ significantly; for instance, although kinesin-5 contributes to congression in Drosophila embryos and yeast, the proposed underlying mechanisms are very different (Figure 6 and Gardner et al., 2008 ).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "respect") (:form . "respects") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "VB") (:stem . "differ") (:form . "differ") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 58) (:start . 45) (:id . 50))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 59) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 82)\n  (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 92)\n  (:start . 83) (:id . 56))\n ((:tag . "VBZ") (:stem . "contribute") (:form . "contributes") (:end . 104)\n  (:start . 93) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "NN") (:stem . "congression") (:form . "congression") (:end . 119)\n  (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 122) (:start . 120)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 133)\n  (:start . 123) (:id . 61))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 141)\n  (:start . 134) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 63))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 151)\n  (:start . 146) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 165)\n  (:start . 157) (:id . 67))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 176)\n  (:start . 166) (:id . 68))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 187)\n  (:start . 177) (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 191) (:start . 188)\n  (:id . 70))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 196) (:start . 192)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 206)\n  (:start . 197) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 208) (:start . 207)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 214)\n  (:start . 208) (:id . 74))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 216) (:start . 215)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 220) (:start . 217)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Gardner") (:form . "Gardner") (:end . 228)\n  (:start . 221) (:id . 77))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 231) (:start . 229)\n  (:id . 78))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 235) (:start . 232)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 236) (:start . 235)\n  (:id . 80))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 241) (:start . 237)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 243) (:start . 242)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x4.292.1) (:span 34 37)))\n (:hscopes ((:id . :x4.292.1) (:span 34 58)))\n (:identifiers (:sid . :s4.292) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501345@unknown@formal@none@1@S@The kinesin-5 inhibitor, monastrol, unfortunately does not interfere with purified kinesin-5 motility or mitosis in Drosophila (our unpublished observations), but it has been used extensively to probe the diverse functions of vertebrate kinesin-5.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "inhibitor") (:form . "inhibitor") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "monastrol") (:form . "monastrol") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "RB") (:stem . "unfortunately") (:form . "unfortunately")\n  (:end . 49) (:start . 36) (:id . 48))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 58) (:start . 55)\n  (:id . 50))\n ((:tag . "VB") (:stem . "interfere") (:form . "interfere") (:end . 68)\n  (:start . 59) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 82)\n  (:start . 74) (:id . 53))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 92)\n  (:start . 83) (:id . 54))\n ((:tag . "NN") (:stem . "motility") (:form . "motility") (:end . 101)\n  (:start . 93) (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 104) (:start . 102)\n  (:id . 56))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 112)\n  (:start . 105) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 58))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 126)\n  (:start . 116) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 131) (:start . 128)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "unpublished") (:form . "unpublished") (:end . 143)\n  (:start . 132) (:id . 62))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 156)\n  (:start . 144) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 65))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 162) (:start . 159)\n  (:id . 66))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 165) (:start . 163)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 169) (:start . 166)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 174) (:start . 170)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 179) (:start . 175)\n  (:id . 70))\n ((:tag . "RB") (:stem . "extensively") (:form . "extensively") (:end . 191)\n  (:start . 180) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 194) (:start . 192)\n  (:id . 72))\n ((:tag . "VB") (:stem . "probe") (:form . "probe") (:end . 200)\n  (:start . 195) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 204) (:start . 201)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 212)\n  (:start . 205) (:id . 75))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 222)\n  (:start . 213) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 225) (:start . 223)\n  (:id . 77))\n ((:tag . "NN") (:stem . "vertebrate") (:form . "vertebrate") (:end . 236)\n  (:start . 226) (:id . 78))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 246)\n  (:start . 237) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 247) (:start . 246)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s4.293) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501346@unknown@formal@none@1@S@This work, together with complementary approaches, has revealed multiple roles for kinesin-5 in early spindle assembly, in spindle maintenance (in Xenopus but not cultured cells), in the sorting out of antiparallel chromosome nucleated MTs, and in the proper biorientation of chromosomes (Gaglio et al., 1996 ; Walczak et al., 1998 ; Kapoor et al., 2000 ; Uteng et al., 2008 ).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 19)\n  (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "complementary") (:form . "complementary")\n  (:end . 38) (:start . 25) (:id . 47))\n ((:tag . 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5501347@unknown@formal@none@1@S@Roles for kinesin-5 in driving poleward flux and controlling metaphase spindle length were proposed previously for Xenopus extract spindles (Miyamoto et al., 2004 ; Shirasu-Hiza et al., 2004 ) as we report here for Drosophila embryo spindles.@(((:tag . "NNS") (:stem . "role") (:form . "Roles") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "drive") (:form . "driving") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "control") (:form . "controlling") (:end . 60)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "metaphase") (:form . "metaphase") (:end . 70)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 78)\n  (:start . 71) (:id . 52))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 85)\n  (:start . 79) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 90) (:start . 86)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 99)\n  (:start . 91) (:id . 55))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 110)\n  (:start . 100) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 114) (:start . 111)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Xenopus") (:form . "Xenopus") (:end . 122)\n  (:start . 115) (:id . 58))\n ((:tag . "NN") (:stem . "extract") (:form . "extract") (:end . 130)\n  (:start . 123) (:id . 59))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 139)\n  (:start . 131) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Miyamoto") (:form . "Miyamoto") (:end . 149)\n  (:start . 141) (:id . 62))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 152) (:start . 150)\n  (:id . 63))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 156) (:start . 153)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n  (:id . 65))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 162) (:start . 158)\n  (:id . 66))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 164) (:start . 163)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Shirasu-Hiza") (:form . "Shirasu-Hiza")\n  (:end . 177) (:start . 165) (:id . 68))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 180) (:start . 178)\n  (:id . 69))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 184) (:start . 181)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 71))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 190) (:start . 186)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 192) (:start . 191)\n  (:id . 73))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 195) (:start . 193)\n  (:id . 74))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 198) (:start . 196)\n  (:id . 75))\n ((:tag . "VBP") (:stem . "report") (:form . "report") (:end . 205)\n  (:start . 199) (:id . 76))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 210) (:start . 206)\n  (:id . 77))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 214) (:start . 211)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 225)\n  (:start . 215) (:id . 79))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 232)\n  (:start . 226) (:id . 80))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 241)\n  (:start . 233) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 242) (:start . 241)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s4.295) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501348@unknown@formal@none@1@S@In vertebrate cultured cells, in contrast, the inhibition of Eg5 function led to only a 25% decrease in the rate of poleward flux while spindle length remained normal, suggesting only minor contributions from kinesin-5 (Cameron et al., 2006 ).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "vertebrate") (:form . "vertebrate") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 57)\n  (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "eg5") (:form . "Eg5") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 73)\n  (:start . 65) (:id . 54))\n ((:tag . "VBD") (:stem . "lead") (:form . "led") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 91) (:start . 90)\n  (:id . 60))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 100)\n  (:start . 92) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 63))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 112) (:start . 108)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 124)\n  (:start . 116) (:id . 66))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 129) (:start . 125)\n  (:id . 67))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 135)\n  (:start . 130) (:id . 68))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 143)\n  (:start . 136) (:id . 69))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 150)\n  (:start . 144) (:id . 70))\n ((:tag . "VBD") (:stem . "remain") (:form . "remained") (:end . 159)\n  (:start . 151) (:id . 71))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 166)\n  (:start . 160) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 178)\n  (:start . 168) (:id . 74))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 183) (:start . 179)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "minor") (:form . "minor") (:end . 189)\n  (:start . 184) (:id . 76))\n ((:tag . "NNS") (:stem . "contribution") (:form . "contributions")\n  (:end . 203) (:start . 190) (:id . 77))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 208) (:start . 204)\n  (:id . 78))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 218)\n  (:start . 209) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 220) (:start . 219)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Cameron") (:form . "Cameron") (:end . 227)\n  (:start . 220) (:id . 81))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 230) (:start . 228)\n  (:id . 82))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 234) (:start . 231)\n  (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 235) (:start . 234)\n  (:id . 84))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 240) (:start . 236)\n  (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 242) (:start . 241)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 87)))@@@1@46@((:hcues ((:id . :x4.296.1) (:span 168 178)))\n (:hscopes ((:id . :x4.296.1) (:span 168 218)))\n (:identifiers (:sid . :s4.296) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501349@unknown@formal@none@1@S@The latter authors also reported a small decrease in kinetochore–kinetochore spacing after Eg5 inhibition, supporting the notion that kinesin-5 may contribute to the exertion of poleward tension on kinetochores in some systems, including the Drosophila embryo (Figure 5).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "author") (:form . "authors") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "report") (:form . "reported") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "kinetochore–kinetochore")\n  (:form . "kinetochore–kinetochore") (:end . 76) (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "spacing") (:form . "spacing") (:end . 84)\n  (:start . 77) (:id . 52))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 90) (:start . 85)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Eg5") (:form . "Eg5") (:end . 94) (:start . 91)\n  (:id . 54))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 105)\n  (:start . 95) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "support") (:form . "supporting") (:end . 117)\n  (:start . 107) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 58))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 128)\n  (:start . 122) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 133) (:start . 129)\n  (:id . 60))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 143)\n  (:start . 134) (:id . 61))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 147) (:start . 144)\n  (:id . 62))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 158)\n  (:start . 148) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 161) (:start . 159)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 65))\n ((:tag . "NN") (:stem . "exertion") (:form . "exertion") (:end . 174)\n  (:start . 166) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "poleward") (:form . "poleward") (:end . 186)\n  (:start . 178) (:id . 68))\n ((:tag . "NN") (:stem . "tension") (:form . "tension") (:end . 194)\n  (:start . 187) (:id . 69))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 197) (:start . 195)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "kinetochore") (:form . "kinetochores") (:end . 210)\n  (:start . 198) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 213) (:start . 211)\n  (:id . 72))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 218) (:start . 214)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 226)\n  (:start . 219) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 227) (:start . 226)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 237)\n  (:start . 228) (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 241) (:start . 238)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 252)\n  (:start . 242) (:id . 78))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 259)\n  (:start . 253) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 261) (:start . 260)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 267)\n  (:start . 261) (:id . 81))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 269) (:start . 268)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 270) (:start . 269)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 271) (:start . 270)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x4.297.1) (:span 144 147)))\n (:hscopes ((:id . :x4.297.1) (:span 144 259)))\n (:identifiers (:sid . :s4.297) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501350@unknown@formal@none@1@S@Thus kinesin-5 motors have diverse, often essential mitotic functions in many systems including the Drosophila embryo.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 69)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 85)\n  (:start . 78) (:id . 54))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 95)\n  (:start . 86) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 110)\n  (:start . 100) (:id . 57))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 117)\n  (:start . 111) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s4.298) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501351@unknown@formal@none@1@S@However, in Dictyostelium amoebae and C. elegans embryos, kinesin-5 motors play relatively minor mitotic roles, and they appear to be dispensable for mitosis (Saunders et al., 2007 ; Tikhonenko et al., 2008 ).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dictyostelium") (:form . "Dictyostelium")\n  (:end . 25) (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "amoeba") (:form . "amoebae") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 67)\n  (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 74)\n  (:start . 68) (:id . 53))\n ((:tag . "VBP") (:stem . "play") (:form . "play") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 90)\n  (:start . 80) (:id . 55))\n ((:tag . "JJ") (:stem . "minor") (:form . "minor") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 104)\n  (:start . 97) (:id . 57))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 110)\n  (:start . 105) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 120) (:start . 116)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 127)\n  (:start . 121) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n  (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 133) (:start . 131)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "dispensable") (:form . "dispensable") (:end . 145)\n  (:start . 134) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 149) (:start . 146)\n  (:id . 66))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 157)\n  (:start . 150) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Saunder") (:form . "Saunders") (:end . 167)\n  (:start . 159) (:id . 69))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 170) (:start . 168)\n  (:id . 70))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 174) (:start . 171)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 72))\n ((:tag . "CD") (:stem . "2007") (:form . "2007") (:end . 180) (:start . 176)\n  (:id . 73))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 182) (:start . 181)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Tikhonenko") (:form . "Tikhonenko") (:end . 193)\n  (:start . 183) (:id . 75))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 196) (:start . 194)\n  (:id . 76))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 200) (:start . 197)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 201) (:start . 200)\n  (:id . 78))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 206) (:start . 202)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 208) (:start . 207)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x4.299.1) (:span 121 127)))\n (:hscopes ((:id . :x4.299.1) (:span 116 157)))\n (:identifiers (:sid . :s4.299) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501352@unknown@formal@none@1@S@Thus, mitotic motors can be deployed to carry out very different functions in different types of spindles, presenting a challenge for the formulation of general, integrated models of kinesin-5 function.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 13)\n  (:start . 6) (:id . 44))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "deploy") (:form . "deployed") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "VB") (:stem . "carry") (:form . "carry") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 54) (:start . 50)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 64)\n  (:start . 55) (:id . 53))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 74)\n  (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 87)\n  (:start . 78) (:id . 56))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 105)\n  (:start . 97) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "present") (:form . "presenting") (:end . 117)\n  (:start . 107) (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 119) (:start . 118)\n  (:id . 62))\n ((:tag . "NN") (:stem . "challenge") (:form . "challenge") (:end . 129)\n  (:start . 120) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 133) (:start . 130)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 65))\n ((:tag . "NN") (:stem . "formulation") (:form . "formulation") (:end . 149)\n  (:start . 138) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 160)\n  (:start . 153) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "integrated") (:form . "integrated") (:end . 172)\n  (:start . 162) (:id . 70))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 179)\n  (:start . 173) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 182) (:start . 180)\n  (:id . 72))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 192)\n  (:start . 183) (:id . 73))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 201)\n  (:start . 193) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x4.300.1) (:span 21 24)))\n (:hscopes ((:id . :x4.300.1) (:span 6 105)))\n (:identifiers (:sid . :s4.300) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501353@unknown@formal@none@1@S@Relation to Studies of the Mechanism of Kinesin-5 Action@(((:tag . "NN") (:stem . "relation") (:form . "Relation") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "study") (:form . "Studies") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mechanism") (:form . "Mechanism") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Kinesin-5") (:form . "Kinesin-5") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "NNP") (:stem . "Action") (:form . "Action") (:end . 56)\n  (:start . 50) (:id . 50)))@@@1@9@((:identifiers (:sid . :s4.301) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501354@unknown@formal@none@1@S@The multiple mitotic functions of KLP61F in Drosophila syncytial embryos can be explained by a model in which KLP61F cross-links adjacent MTs throughout the spindle (Figure 6), in accordance with the biochemical properties of the purified native embryonic or recombinant baculovirus-expressed motor (Cole et al., 1994 ; Kashina et al., 1996a ; Kashina et al., 1996b ; Tao et al., 2006 ; Van den Wildenberg et al., 2008 ), its immunolocalization (Sharp et al., 1999a ), and its localization and dynamics in living cells (Cheerambathur et al., 2008 ).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . 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5501355@unknown@formal@none@1@S@By cross-linking parallel MTs, KLP61F would “zip” together adjacent MTs to bundle and organize spindle MTs but would generate no force on them.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "cross-linking") (:form . "cross-linking")\n  (:end . 16) (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "parallel") (:form . "parallel") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "VB") (:stem . "zip") (:form . "zip") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 58)\n  (:start . 50) (:id . 52))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 67)\n  (:start . 59) (:id . 53))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "VB") (:stem . "bundle") (:form . "bundle") (:end . 81)\n  (:start . 75) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 57))\n ((:tag . "VB") (:stem . "organize") (:form . "organize") (:end . 94)\n  (:start . 86) (:id . 58))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 102)\n  (:start . 95) (:id . 59))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 116)\n  (:start . 111) (:id . 62))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 125)\n  (:start . 117) (:id . 63))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 128) (:start . 126)\n  (:id . 64))\n ((:tag . "NN") (:stem . "force") (:form . "force") (:end . 134)\n  (:start . 129) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 137) (:start . 135)\n  (:id . 66))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 142) (:start . 138)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x4.303.1) (:span 111 116)) ((:id . :x4.303.2) (:span 38 43)))\n (:hscopes ((:id . :x4.303.1) (:span 111 142))\n  ((:id . :x4.303.2) (:span 38 106)))\n (:identifiers (:sid . :s4.303) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501356@unknown@formal@none@1@S@By cross-linking and moving toward the plus ends of antiparallel ipMTs, however, it would persistently slide them apart to drive poleward flux when ipMT sliding is balanced by ipMT depolymerization at spindle poles, or to exert outward forces on spindles poles when ipMT depolymerization is turned off (McIntosh et al., 1969 ; Sharp et al., 1999a ; Van den Wildenberg et al., 2008 ).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "cross-linke") (:form . "cross-linking") (:end . 16)\n  (:start . 3) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "move") (:form . "moving") (:end . 27) (:start . 21)\n  (:id . 45))\n ((:tag . "IN") (:stem . "toward") (:form . "toward") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . 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5501357@unknown@formal@none@1@S@In the current study, this KLP61F-driven, outward ipMT sliding was directly visualized by monitoring fluorescent tubulin speckle behavior (Brust-Mascher and Scholey, 2002 ; Brust-Mascher et al., 2004 ), and it appeared to be antagonized by the inward sliding of ipMTs during prometaphase.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "klp61f-driven") (:form . "KLP61F-driven")\n  (:end . 40) (:start . 27) (:id . 48))\n ((:tag . ",") (:stem . 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5501358@unknown@formal@none@1@S@In support of this, the decrease in pole–pole separation after KLP61F inhibition occurs without spindle pole disorganization, as documented in embryos expressing GFP-CNN, and is accompanied by an increase in microtubule density, as revealed by an increase in fluorescent tubulin intensity at the central spindle, consistent with the proposed sliding filament mechanism (Figure 2).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "NN") (:stem . "decrease") (:form . 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5501360@unknown@formal@none@1@S@This is consistent with the hypothesis that KLP61F-driven outward sliding of ipMTs, augmented at specific stages by other ipMT-bound proteins such as KLP3A (Kwon et al., 2004 ), plays a central role.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "klp61f-driven") (:form . "KLP61F-driven")\n  (:end . 57) (:start . 44) (:id . 49))\n ((:tag . "JJ") (:stem . "outward") (:form . "outward") (:end . 65)\n  (:start . 58) (:id . 50))\n ((:tag . "NN") (:stem . "sliding") (:form . "sliding") (:end . 73)\n  (:start . 66) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "ipmt") (:form . "ipMTs") (:end . 82) (:start . 77)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "augment") (:form . "augmented") (:end . 93)\n  (:start . 84) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 105)\n  (:start . 97) (:id . 57))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 112)\n  (:start . 106) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 115) (:start . 113)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 121)\n  (:start . 116) (:id . 60))\n ((:tag . "JJ") (:stem . "ipmt-bound") (:form . "ipMT-bound") (:end . 132)\n  (:start . 122) (:id . 61))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 141)\n  (:start . 133) (:id . 62))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 146) (:start . 142)\n  (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 149) (:start . 147)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "KLP3A") (:form . "KLP3A") (:end . 155)\n  (:start . 150) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Kwon") (:form . "Kwon") (:end . 161) (:start . 157)\n  (:id . 67))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 164) (:start . 162)\n  (:id . 68))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 168) (:start . 165)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 70))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 174) (:start . 170)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 73))\n ((:tag . "VBZ") (:stem . "play") (:form . "plays") (:end . 183)\n  (:start . 178) (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 185) (:start . 184)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 193)\n  (:start . 186) (:id . 76))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 198) (:start . 194)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x4.308.1) (:span 28 38)))\n (:hscopes ((:id . :x4.308.1) (:span 28 198)))\n (:identifiers (:sid . :s4.308) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501361@unknown@formal@none@1@S@We do not want to extrapolate our sliding filament model for kinesin-5 function in Drosophila syncytial embryos (Figure 6) to other systems where the molecular mechanism of action of kinesin-5 may be different (e.g., Kapoor and Mitchison, 2001 ; Gardner et al., 2008 ).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "VB") (:stem . "want") (:form . "want") (:end . 14) (:start . 10)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "VB") (:stem . "extrapolate") (:form . "extrapolate") (:end . 29)\n  (:start . 18) (:id . 47))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "slide") (:form . 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5501362@unknown@formal@none@1@S@The slow, plus-end–directed motility of kinesin-5 was first observed using recombinant motor domain subfragments of Eg5 (Sawin et al., 1992 ), and subsequently, in elegant, pioneering work, full-length recombinant Eg5 was shown to cross-link and slide adjacent MTs (Kapitein et al., 2005 ).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "slow") (:form . "slow") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "plus-end–directed") (:form . "plus-end–directed")\n  (:end . 27) (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "motility") (:form . "motility") (:end . 36)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 49)\n  (:start . 40) (:id . 48))\n ((:tag . 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5501363@unknown@formal@none@1@S@The dynamic behavior of Eg5 in spindles is also consistent with it driving MT–MT sliding (Uteng et al., 2008 ), but to our knowledge, the ultrastructure of Eg5 and the properties of the purified native protein have not been studied.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "dynamic") (:form . "dynamic") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "behavior") (:form . "behavior") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "eg5") (:form . "Eg5") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 58)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "drive") (:form . "driving") (:end . 74)\n  (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "mt–mt") (:form . "MT–MT") (:end . 80) (:start . 75)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 88)\n  (:start . 81) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Uteng") (:form . "Uteng") (:end . 95) (:start . 90)\n  (:id . 58))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 64))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 115) (:start . 112)\n  (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 118) (:start . 116)\n  (:id . 66))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 122) (:start . 119)\n  (:id . 67))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 132)\n  (:start . 123) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 70))\n ((:tag . "NN") (:stem . "ultrastructure") (:form . "ultrastructure")\n  (:end . 152) (:start . 138) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Eg5") (:form . "Eg5") (:end . 159) (:start . 156)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 163) (:start . 160)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 178)\n  (:start . 168) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 181) (:start . 179)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n  (:id . 78))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 194)\n  (:start . 186) (:id . 79))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 201)\n  (:start . 195) (:id . 80))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 209)\n  (:start . 202) (:id . 81))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 214) (:start . 210)\n  (:id . 82))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 218) (:start . 215)\n  (:id . 83))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 223) (:start . 219)\n  (:id . 84))\n ((:tag . "VBN") (:stem . "study") (:form . "studied") (:end . 231)\n  (:start . 224) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s4.311) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501364@unknown@formal@none@1@S@The yeast kinesin-5, Kip1, has a bipolar ultrastructure, like the Drosophila embryo protein, but its motility properties have not been described (Gordon and Roof, 1999 ).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Kip1") (:form . "Kip1") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "bipolar") (:form . "bipolar") (:end . 40)\n  (:start . 33) (:id . 50))\n ((:tag . "NN") (:stem . "ultrastructure") (:form . "ultrastructure")\n  (:end . 55) (:start . 41) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 76)\n  (:start . 66) (:id . 55))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 83)\n  (:start . 77) (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 91)\n  (:start . 84) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "NN") (:stem . "motility") (:form . "motility") (:end . 109)\n  (:start . 101) (:id . 61))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 120)\n  (:start . 110) (:id . 62))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 125) (:start . 121)\n  (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 129) (:start . 126)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 134) (:start . 130)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 144)\n  (:start . 135) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Gordon") (:form . "Gordon") (:end . 152)\n  (:start . 146) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Roof") (:form . "Roof") (:end . 161) (:start . 157)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 71))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 167) (:start . 163)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s4.312) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501365@unknown@formal@none@1@S@Elsewhere, many kinesin-5 motors have not been purified and studied biochemically, so it is possible that some kinesin-5 motors may act differently, e.g., serving as MT depolymerases (Gardner et al., 2008 ) or sliding MTs relative to a spindle matrix (Kapoor and Mitchison, 2001 ).@(((:tag . "RB") (:stem . "elsewhere") (:form . "Elsewhere") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "VBN") (:stem . 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5501366@unknown@formal@none@1@S@Purified kinesin-5 motors have been shown to slide MTs over inert surfaces but not to depolymerize MTs (Sawin et al., 1992 ; Tao et al., 2006 ).@(((:tag . "VBN") (:stem . "purify") (:form . "Purified") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 25)\n  (:start . 19) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "VB") (:stem . "slide") (:form . "slide") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "inert") (:form . "inert") (:end . 65) (:start . 60)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "surface") (:form . "surfaces") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "VB") (:stem . "depolymerize") (:form . "depolymerize") (:end . 98)\n  (:start . 86) (:id . 57))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Sawin") (:form . "Sawin") (:end . 109)\n  (:start . 104) (:id . 60))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . "CD") (:stem . "1992") (:form . "1992") (:end . 122) (:start . 118)\n  (:id . 64))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 124) (:start . 123)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Tao") (:form . "Tao") (:end . 128) (:start . 125)\n  (:id . 66))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 131) (:start . 129)\n  (:id . 67))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 135) (:start . 132)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 69))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 141) (:start . 137)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s4.314) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501367@unknown@formal@none@1@S@Further biochemical studies on the mechanism of action of purified kinesin-5 from multiple systems would obviously be fruitful.@(((:tag . "JJ") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "biochemical") (:form . "biochemical") (:end . 19)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 27)\n  (:start . 20) (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 44)\n  (:start . 35) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "NN") (:stem . "action") (:form . "action") (:end . 54)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 66)\n  (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 76)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 81) (:start . 77)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 90)\n  (:start . 82) (:id . 54))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 98)\n  (:start . 91) (:id . 55))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 104) (:start . 99)\n  (:id . 56))\n ((:tag . "RB") (:stem . "obviously") (:form . "obviously") (:end . 114)\n  (:start . 105) (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 117) (:start . 115)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "fruitful") (:form . "fruitful") (:end . 126)\n  (:start . 118) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x4.315.1) (:span 99 104)))\n (:hscopes ((:id . :x4.315.1) (:span 0 126)))\n (:identifiers (:sid . :s4.315) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501368@unknown@formal@none@1@S@Relation to Quantitative Force-Balance Models for Mitosis@(((:tag . "NN") (:stem . "relation") (:form . "Relation") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "Quantitative") (:end . 24)\n  (:start . 12) (:id . 44))\n ((:tag . "NNP") (:stem . "Force-Balance") (:form . "Force-Balance")\n  (:end . 38) (:start . 25) (:id . 45))\n ((:tag . "NNP") (:stem . "Model") (:form . "Models") (:end . 45)\n  (:start . 39) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Mitosis") (:form . "Mitosis") (:end . 57)\n  (:start . 50) (:id . 48)))@@@1@7@((:identifiers (:sid . :s4.316) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501369@unknown@formal@none@1@S@System level and reductionist models have been used to describe spindle pole separation after NEB in Drosophila (Brust-Mascher et al., 2004 ; Goshima et al., 2005b ; Wollman et al., 2008 ; Civelekoglu-Scholey, Tao, Wollman, Brust-Mascher, and Scholey, unpublished data).@(((:tag . "NNP") (:stem . "System") (:form . "System") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "reductionist") (:form . "reductionist") (:end . 29)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 36)\n  (:start . 30) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "VBN") (:stem . 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5501370@unknown@formal@none@1@S@In Wollman et al. (2008) a system level search was undertaken to find the integration of force generator activity that best explains spindle pole separation versus time in embryos, using experimental data to constrain the number of plausible models.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Wollman") (:form . "Wollman") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 23) (:start . 19)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 24) (:start . 23)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 49))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 33)\n  (:start . 27) (:id . 50))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 39) (:start . 34)\n  (:id . 51))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 46)\n  (:start . 40) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 50) (:start . 47)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "undertake") (:form . "undertaken") (:end . 61)\n  (:start . 51) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 55))\n ((:tag . "VB") (:stem . "find") (:form . "find") (:end . 69) (:start . 65)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 57))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 85)\n  (:start . 74) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 59))\n ((:tag . "NN") (:stem . "force") (:form . "force") (:end . 94) (:start . 89)\n  (:id . 60))\n ((:tag . "NN") (:stem . "generator") (:form . "generator") (:end . 104)\n  (:start . 95) (:id . 61))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 113)\n  (:start . 105) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 118) (:start . 114)\n  (:id . 63))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 123) (:start . 119)\n  (:id . 64))\n ((:tag . "VBZ") (:stem . "explain") (:form . "explains") (:end . 132)\n  (:start . 124) (:id . 65))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 140)\n  (:start . 133) (:id . 66))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 145) (:start . 141)\n  (:id . 67))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 156)\n  (:start . 146) (:id . 68))\n ((:tag . "IN") (:stem . "versus") (:form . "versus") (:end . 163)\n  (:start . 157) (:id . 69))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 168) (:start . 164)\n  (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 171) (:start . 169)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 179)\n  (:start . 172) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 186) (:start . 181)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 199)\n  (:start . 187) (:id . 75))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 204)\n  (:start . 200) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 207) (:start . 205)\n  (:id . 77))\n ((:tag . "VB") (:stem . "constrain") (:form . "constrain") (:end . 217)\n  (:start . 208) (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 221) (:start . 218)\n  (:id . 79))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 228)\n  (:start . 222) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 231) (:start . 229)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "plausible") (:form . "plausible") (:end . 241)\n  (:start . 232) (:id . 82))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 248)\n  (:start . 242) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 249) (:start . 248)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s4.318) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501371@unknown@formal@none@1@S@Although ~1000 models emerged from the search, these models fall into only six groups, which fit the experimental data, including most of the data on spindle pole separation presented here, remarkably well.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "CD") (:stem . "~1000") (:form . "~1000") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "VBD") (:stem . "emerge") (:form . "emerged") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 59)\n  (:start . 53) (:id . 51))\n ((:tag . "VBP") (:stem . "fall") (:form . "fall") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 85)\n  (:start . 79) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 92) (:start . 87)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "fit") (:form . "fit") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 113)\n  (:start . 101) (:id . 61))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 118)\n  (:start . 114) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 129)\n  (:start . 120) (:id . 64))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 134) (:start . 130)\n  (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 146)\n  (:start . 142) (:id . 68))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 149) (:start . 147)\n  (:id . 69))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 157)\n  (:start . 150) (:id . 70))\n ((:tag . "NN") (:stem . "pole") (:form . "pole") (:end . 162) (:start . 158)\n  (:id . 71))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 173)\n  (:start . 163) (:id . 72))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 183)\n  (:start . 174) (:id . 73))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 188) (:start . 184)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 75))\n ((:tag . "RB") (:stem . "remarkably") (:form . "remarkably") (:end . 200)\n  (:start . 190) (:id . 76))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 205) (:start . 201)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s4.319) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501372@unknown@formal@none@1@S@Some discrepancies remain, e.g., the timing of activation of Ncd, but this is perhaps not surprising, given the inherent assumptions in such a broad theoretical approach.@(((:tag . "DT") (:stem . "some") (:form . "Some") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "discrepancy") (:form . "discrepancies") (:end . 18)\n  (:start . 5) (:id . 43))\n ((:tag . "VBP") (:stem . "remain") (:form . "remain") (:end . 25)\n  (:start . 19) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "timing") (:form . "timing") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 57)\n  (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Ncd") (:form . "Ncd") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 74) (:start . 70)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 77) (:start . 75)\n  (:id . 57))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 85)\n  (:start . 78) (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 89) (:start . 86)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "surprising") (:form . "surprising") (:end . 100)\n  (:start . 90) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 107)\n  (:start . 102) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "inherent") (:form . "inherent") (:end . 120)\n  (:start . 112) (:id . 64))\n ((:tag . "NNS") (:stem . "assumption") (:form . "assumptions") (:end . 132)\n  (:start . 121) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 66))\n ((:tag . "PDT") (:stem . "such") (:form . "such") (:end . 140) (:start . 136)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 142) (:start . 141)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "broad") (:form . "broad") (:end . 148)\n  (:start . 143) (:id . 69))\n ((:tag . "JJ") (:stem . "theoretical") (:form . "theoretical") (:end . 160)\n  (:start . 149) (:id . 70))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 169)\n  (:start . 161) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x4.320.1) (:span 78 85)))\n (:hscopes ((:id . :x4.320.1) (:span 70 100)))\n (:identifiers (:sid . :s4.320) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501373@unknown@formal@none@1@S@Reductionist models were developed for Drosophila S2 cells (Goshima et al., 2005b ) and for embryos (Brust-Mascher et al., 2004 ; Civelekoglu-Scholey, G., Tao, L., Wollman, R., Brust-Mascher, I., and Scholey, J.M., unpublished data).@(((:tag . "NN") (:stem . "reductionist") (:form . "Reductionist") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 19)\n  (:start . 13) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "develop") (:form . "developed") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 49)\n  (:start . 39) (:id . 47))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 52) (:start . 50)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . 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5501374@unknown@formal@none@1@S@In the former model, which complemented novel high throughput microscopy and RNAi experiments, coupling of outward ipMT sliding to MT depolymerization at the poles was introduced to account for the lack of effect of KLP61F concentration on spindle length.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "former") (:form . "former") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 26) (:start . 21)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "complement") (:form . "complemented") (:end . 39)\n  (:start . 27) (:id . 48))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "throughput") (:form . "throughput") (:end . 61)\n  (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "microscopy") (:form . "microscopy") (:end . 72)\n  (:start . 62) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 81) (:start . 77)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 93)\n  (:start . 82) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "couple") (:form . "coupling") (:end . 103)\n  (:start . 95) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "outward") (:form . "outward") (:end . 114)\n  (:start . 107) (:id . 59))\n ((:tag . "NN") (:stem . "ipmt") (:form . "ipMT") (:end . 119) (:start . 115)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 127)\n  (:start . 120) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "MT") (:form . "MT") (:end . 133) (:start . 131)\n  (:id . 63))\n ((:tag . "NN") (:stem . "depolymerization") (:form . "depolymerization")\n  (:end . 150) (:start . 134) (:id . 64))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 153) (:start . 151)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 163)\n  (:start . 158) (:id . 67))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 167) (:start . 164)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "introduce") (:form . "introduced") (:end . 178)\n  (:start . 168) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 181) (:start . 179)\n  (:id . 70))\n ((:tag . "VB") (:stem . "account") (:form . "account") (:end . 189)\n  (:start . 182) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 193) (:start . 190)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n  (:id . 73))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 202) (:start . 198)\n  (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n  (:id . 75))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 212)\n  (:start . 206) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 215) (:start . 213)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 222)\n  (:start . 216) (:id . 78))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 236) (:start . 223) (:id . 79))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 239) (:start . 237)\n  (:id . 80))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 247)\n  (:start . 240) (:id . 81))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 254)\n  (:start . 248) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 255) (:start . 254)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s4.322) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501375@unknown@formal@none@1@S@We now understand that this model contains a physically unrealistic assumption in which an inward motion of the poles through increased depolymerization, coupled to decreased sliding, occurs in the absence of an associated force to drive this movement.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "understand") (:form . "understand") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "RB") (:stem . "physically") (:form . "physically") (:end . 55)\n  (:start . 45) (:id . 50))\n ((:tag . "JJ") (:stem . "unrealistic") (:form . "unrealistic") (:end . 67)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 78)\n  (:start . 68) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 87) (:start . 82)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 90) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "inward") (:form . "inward") (:end . 97)\n  (:start . 91) (:id . 56))\n ((:tag . "NN") (:stem . "motion") (:form . "motion") (:end . 104)\n  (:start . 98) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 117)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 125)\n  (:start . 118) (:id . 61))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 135)\n  (:start . 126) (:id . 62))\n ((:tag . "NN") (:stem . "depolymerization") (:form . "depolymerization")\n  (:end . 152) (:start . 136) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "couple") (:form . "coupled") (:end . 161)\n  (:start . 154) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 164) (:start . 162)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "decrease") (:form . "decreased") (:end . 174)\n  (:start . 165) (:id . 67))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 182)\n  (:start . 175) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 69))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 190)\n  (:start . 184) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 193) (:start . 191)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n  (:id . 72))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 205)\n  (:start . 198) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 208) (:start . 206)\n  (:id . 74))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 211) (:start . 209)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 222)\n  (:start . 212) (:id . 76))\n ((:tag . "NN") (:stem . "force") (:form . "force") (:end . 228)\n  (:start . 223) (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 231) (:start . 229)\n  (:id . 78))\n ((:tag . "VB") (:stem . "drive") (:form . "drive") (:end . 237)\n  (:start . 232) (:id . 79))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 242) (:start . 238)\n  (:id . 80))\n ((:tag . "NN") (:stem . "movement") (:form . "movement") (:end . 251)\n  (:start . 243) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x4.323.1) (:span 68 78)))\n (:hscopes ((:id . :x4.323.1) (:span 68 251)))\n (:identifiers (:sid . :s4.323) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501376@unknown@formal@none@1@S@Of course, this imperfection would remain undetected if the same mechanism had been described only qualitatively, but it shows that this model requires further refinement to explain the KLP61F concentration versus spindle length data.@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "course") (:form . "course") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "imperfection") (:form . "imperfection") (:end . 28)\n  (:start . 16) (:id . 46))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "VB") (:stem . "remain") (:form . "remain") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "JJ") (:stem . "undetected") (:form . "undetected") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 74)\n  (:start . 65) (:id . 53))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 93)\n  (:start . 84) (:id . 56))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 98) (:start . 94)\n  (:id . 57))\n ((:tag . "RB") (:stem . "qualitatively") (:form . "qualitatively")\n  (:end . 112) (:start . 99) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 117) (:start . 114)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 120) (:start . 118)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 126)\n  (:start . 121) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 131) (:start . 127)\n  (:id . 63))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 136) (:start . 132)\n  (:id . 64))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 142)\n  (:start . 137) (:id . 65))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 151)\n  (:start . 143) (:id . 66))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 159)\n  (:start . 152) (:id . 67))\n ((:tag . "NN") (:stem . "refinement") (:form . "refinement") (:end . 170)\n  (:start . 160) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 173) (:start . 171)\n  (:id . 69))\n ((:tag . "VB") (:stem . "explain") (:form . "explain") (:end . 181)\n  (:start . 174) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 192)\n  (:start . 186) (:id . 72))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 206) (:start . 193) (:id . 73))\n ((:tag . "IN") (:stem . "versus") (:form . "versus") (:end . 213)\n  (:start . 207) (:id . 74))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 221)\n  (:start . 214) (:id . 75))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 228)\n  (:start . 222) (:id . 76))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 233)\n  (:start . 229) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x4.324.1) (:span 29 34)))\n (:hscopes ((:id . :x4.324.1) (:span 29 112)))\n (:identifiers (:sid . :s4.324) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501377@unknown@formal@none@1@S@The latter models were based closely on experimental data, including the dynamics, physical properties, and geometry of embryo spindles as well as the biochemical properties of MTs and mitotic motors.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 52)\n  (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "dynamic") (:form . "dynamics") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "physical") (:form . "physical") (:end . 91)\n  (:start . 83) (:id . 56))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 102)\n  (:start . 92) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "NN") (:stem . "geometry") (:form . "geometry") (:end . 116)\n  (:start . 108) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 126)\n  (:start . 120) (:id . 62))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 135)\n  (:start . 127) (:id . 63))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 138) (:start . 136)\n  (:id . 64))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 143) (:start . 139)\n  (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 146) (:start . 144)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "biochemical") (:form . "biochemical") (:end . 162)\n  (:start . 151) (:id . 68))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 173)\n  (:start . 163) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 180) (:start . 177)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 184) (:start . 181)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 192)\n  (:start . 185) (:id . 73))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 199)\n  (:start . 193) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s4.325) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501378@unknown@formal@none@1@S@The Anaphase B (Brust-Mascher et al., 2004 ) model made several useful predictions, for example, that although KLP61F acts on dynamically unstable ipMTs to drive steady spindle elongation, the actual rate of anaphase B is insensitive to KLP61F concentration, in agreement with the experimental data presented here.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Anaphase") (:form . "Anaphase") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 29) (:start . 16) (:id . 46))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") 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5501379@unknown@formal@none@1@S@It also predicts a spatial gradient of MT catastrophe events at anaphase B onset, which would be difficult to formulate using purely qualitative arguments and which is now being tested (Cheerambathur et al., 2007 ).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "predict") (:form . "predicts") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "spatial") (:form . "spatial") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "MT") (:form . "MT") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "catastrophe") (:form . "catastrophe") (:end . 53)\n  (:start . 42) (:id . 50))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "anaphase") (:form . "anaphase") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "onset") (:form . "onset") (:end . 80) (:start . 75)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 87) (:start . 82)\n  (:id . 57))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 93) (:start . 88)\n  (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 106)\n  (:start . 97) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 109) (:start . 107)\n  (:id . 61))\n ((:tag . "VB") (:stem . "formulate") (:form . "formulate") (:end . 119)\n  (:start . 110) (:id . 62))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 125) (:start . 120)\n  (:id . 63))\n ((:tag . "RB") (:stem . "purely") (:form . "purely") (:end . 132)\n  (:start . 126) (:id . 64))\n ((:tag . "JJ") (:stem . "qualitative") (:form . "qualitative") (:end . 144)\n  (:start . 133) (:id . 65))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 154)\n  (:start . 145) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 158) (:start . 155)\n  (:id . 67))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 164)\n  (:start . 159) (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 167) (:start . 165)\n  (:id . 69))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 171) (:start . 168)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 177) (:start . 172)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 184)\n  (:start . 178) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 186) (:start . 185)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Cheerambathur") (:form . "Cheerambathur")\n  (:end . 199) (:start . 186) (:id . 74))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 202) (:start . 200)\n  (:id . 75))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 206) (:start . 203)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 207) (:start . 206)\n  (:id . 77))\n ((:tag . "CD") (:stem . "2007") (:form . "2007") (:end . 212) (:start . 208)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s4.327) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501380@unknown@formal@none@1@S@In the prometaphase model, the proposed KLP61F and Ncd force balance was subjected to a focused reductionist analysis of individual spindles and purified proteins (Civelekoglu-Scholey, Tao, Brust-Mascher, Wollman, and Scholey, unpublished data).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "prometaphase") (:form . "prometaphase") (:end . 19)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 25) (:start . 20)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "klp61f") (:form . "KLP61F") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "ncd") (:form . "Ncd") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "force") (:form . "force") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "balance") (:form . "balance") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "subject") (:form . "subjected") (:end . 82)\n  (:start . 73) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "focus") (:form . "focused") (:end . 95)\n  (:start . 88) (:id . 58))\n ((:tag . "NN") (:stem . "reductionist") (:form . "reductionist") (:end . 108)\n  (:start . 96) (:id . 59))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 117)\n  (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 131)\n  (:start . 121) (:id . 62))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 140)\n  (:start . 132) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 153)\n  (:start . 145) (:id . 65))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 162)\n  (:start . 154) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Civelekoglu-Scholey")\n  (:form . "Civelekoglu-Scholey") (:end . 183) (:start . 164) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Tao") (:form . "Tao") (:end . 188) (:start . 185)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Brust-Mascher") (:form . "Brust-Mascher")\n  (:end . 203) (:start . 190) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 204) (:start . 203)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Wollman") (:form . "Wollman") (:end . 212)\n  (:start . 205) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 213) (:start . 212)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 217) (:start . 214)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Scholey") (:form . "Scholey") (:end . 225)\n  (:start . 218) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 226) (:start . 225)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "unpublished") (:form . "unpublished") (:end . 238)\n  (:start . 227) (:id . 79))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 243)\n  (:start . 239) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 244) (:start . 243)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 245) (:start . 244)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s4.328) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501381@unknown@formal@none@1@S@This work supports the idea that the KLP61F/Ncd force balance engages immediately after NEB as dynamic ipMT bundles start to form, whereas the subsequent elongation phase requires additional outward acting force-generators, for example, KLP3A on chromosome arms and cortical dynein (Sharp et al., 2000a ; Kwon et al., 2004 ).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "support") (:form . "supports") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . 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5501382@unknown@formal@none@1@S@Although all modeling approaches are useful and merit further refinement and exploration, reductionist models that pay close attention to both experimental evidence and physical chemical principles provide the most useful and realistic descriptions of mitosis.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 32)\n  (:start . 22) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 43)\n  (:start . 37) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "NN") (:stem . "merit") (:form . "merit") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "refinement") (:form . "refinement") (:end . 72)\n  (:start . 62) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "exploration") (:form . "exploration") (:end . 88)\n  (:start . 77) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 54))\n ((:tag . "NN") (:stem . "reductionist") (:form . "reductionist") (:end . 102)\n  (:start . 90) (:id . 55))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 109)\n  (:start . 103) (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 114) (:start . 110)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "pay") (:form . "pay") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "close") (:form . "close") (:end . 124)\n  (:start . 119) (:id . 59))\n ((:tag . "NN") (:stem . "attention") (:form . "attention") (:end . 134)\n  (:start . 125) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 137) (:start . 135)\n  (:id . 61))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 142) (:start . 138)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 155)\n  (:start . 143) (:id . 63))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 164)\n  (:start . 156) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "physical") (:form . "physical") (:end . 177)\n  (:start . 169) (:id . 66))\n ((:tag . "NN") (:stem . "chemical") (:form . "chemical") (:end . 186)\n  (:start . 178) (:id . 67))\n ((:tag . "NNS") (:stem . "principle") (:form . "principles") (:end . 197)\n  (:start . 187) (:id . 68))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 205)\n  (:start . 198) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n  (:id . 70))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 214) (:start . 210)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 221)\n  (:start . 215) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 225) (:start . 222)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "realistic") (:form . "realistic") (:end . 235)\n  (:start . 226) (:id . 74))\n ((:tag . "NNS") (:stem . "description") (:form . "descriptions") (:end . 248)\n  (:start . 236) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 251) (:start . 249)\n  (:id . 76))\n ((:tag . "NN") (:stem . "mitosis") (:form . "mitosis") (:end . 259)\n  (:start . 252) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 260) (:start . 259)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s4.330) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501383@unknown@formal@none@1@S@Our own force-balance models for spindle assembly and function are based on the premise that antagonistic motors mediate the relative sliding (e.g., kinesin-5 and -14) or depolymerization (e.g., kinesin-13) of ipMTs, but other scenarios are also possible.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "force-balance") (:form . "force-balance")\n  (:end . 21) (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 49)\n  (:start . 41) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "NN") (:stem . "premise") (:form . "premise") (:end . 87)\n  (:start . 80) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "antagonistic") (:form . "antagonistic") (:end . 105)\n  (:start . 93) (:id . 57))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 112)\n  (:start . 106) (:id . 58))\n ((:tag . "VBP") (:stem . "mediate") (:form . "mediate") (:end . 120)\n  (:start . 113) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 133)\n  (:start . 125) (:id . 61))\n ((:tag . "NN") (:stem . "sliding") (:form . "sliding") (:end . 141)\n  (:start . 134) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 63))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 147) (:start . 143)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 65))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 158)\n  (:start . 149) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 67))\n ((:tag . "CD") (:stem . "-14") (:form . "-14") (:end . 166) (:start . 163)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 170) (:start . 168)\n  (:id . 70))\n ((:tag . "NN") (:stem . "depolymerization") (:form . "depolymerization")\n  (:end . 187) (:start . 171) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n  (:id . 72))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 193) (:start . 189)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 194) (:start . 193)\n  (:id . 74))\n ((:tag . "NN") (:stem . "kinesin-13") (:form . "kinesin-13") (:end . 205)\n  (:start . 195) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 209) (:start . 207)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "ipmt") (:form . "ipMTs") (:end . 215)\n  (:start . 210) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 216) (:start . 215)\n  (:id . 79))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 220) (:start . 217)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 226)\n  (:start . 221) (:id . 81))\n ((:tag . "NNS") (:stem . "scenario") (:form . "scenarios") (:end . 236)\n  (:start . 227) (:id . 82))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 240) (:start . 237)\n  (:id . 83))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 245) (:start . 241)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 254)\n  (:start . 246) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 255) (:start . 254)\n  (:id . 86)))@@@1@45@((:hcues ((:id . :x4.331.1) (:span 246 254)))\n (:hscopes ((:id . :x4.331.1) (:span 221 254)))\n (:identifiers (:sid . :s4.331) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501384@unknown@formal@none@1@S@For example, a new “slide-and-cluster” model for anastral spindle assembly proposes that kinesin-5 transports MTs that assemble around chromosomes to the spindle poles where they are focused by minus-end–directed motors (Burbank et al., 2007 ).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "slide-and-cluster") (:form . "slide-and-cluster")\n  (:end . 37) (:start . 20) (:id . 48))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 44) (:start . 39)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "anastral") (:form . "anastral") (:end . 57)\n  (:start . 49) (:id . 52))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 65)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 74)\n  (:start . 66) (:id . 54))\n ((:tag . "VBZ") (:stem . "propose") (:form . "proposes") (:end . 83)\n  (:start . 75) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 98)\n  (:start . 89) (:id . 57))\n ((:tag . "NNS") (:stem . "transport") (:form . "transports") (:end . 109)\n  (:start . 99) (:id . 58))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 113) (:start . 110)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 118) (:start . 114)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "assemble") (:form . "assemble") (:end . 127)\n  (:start . 119) (:id . 61))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 134)\n  (:start . 128) (:id . 62))\n ((:tag . "NNS") (:stem . "chromosome") (:form . "chromosomes") (:end . 146)\n  (:start . 135) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 65))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 161)\n  (:start . 154) (:id . 66))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 167)\n  (:start . 162) (:id . 67))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 173)\n  (:start . 168) (:id . 68))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 178) (:start . 174)\n  (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 182) (:start . 179)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "focus") (:form . "focused") (:end . 190)\n  (:start . 183) (:id . 71))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 193) (:start . 191)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "minus-end–directed") (:form . "minus-end–directed")\n  (:end . 212) (:start . 194) (:id . 73))\n ((:tag . "NNS") (:stem . "motor") (:form . "motors") (:end . 219)\n  (:start . 213) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 221) (:start . 220)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Burbank") (:form . "Burbank") (:end . 228)\n  (:start . 221) (:id . 76))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 231) (:start . 229)\n  (:id . 77))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 235) (:start . 232)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 236) (:start . 235)\n  (:id . 79))\n ((:tag . "CD") (:stem . "2007") (:form . "2007") (:end . 241) (:start . 237)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 243) (:start . 242)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x4.332.1) (:span 75 83)))\n (:hscopes ((:id . :x4.332.1) (:span 75 219)))\n (:identifiers (:sid . :s4.332) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501385@unknown@formal@none@1@S@This model apparently generates a force-balance capable of maintaining a robust steady-state spindle length, and it provides a plausible description of chromosome-directed, anastral spindle assembly in Xenopus extracts and elsewhere, possibly including Drosophila late embryos/larvae and S2 cells.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "apparently") (:form . "apparently") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "VBZ") (:stem . "generate") (:form . "generates") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 46))\n ((:tag . "NN") (:stem . "force-balance") (:form . "force-balance")\n  (:end . 47) (:start . 34) (:id . 47))\n ((:tag . "JJ") (:stem . "capable") (:form . "capable") (:end . 55)\n  (:start . 48) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "maintain") (:form . "maintaining") (:end . 70)\n  (:start . 59) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "robust") (:form . "robust") (:end . 79)\n  (:start . 73) (:id . 52))\n ((:tag . "JJ") (:stem . "steady-state") (:form . "steady-state") (:end . 92)\n  (:start . 80) (:id . 53))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 100)\n  (:start . 93) (:id . 54))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 107)\n  (:start . 101) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 115) (:start . 113)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 124)\n  (:start . 116) (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 126) (:start . 125)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "plausible") (:form . "plausible") (:end . 136)\n  (:start . 127) (:id . 61))\n ((:tag . "NN") (:stem . "description") (:form . "description") (:end . 148)\n  (:start . 137) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "chromosome-directed")\n  (:form . "chromosome-directed") (:end . 171) (:start . 152) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "anastral") (:form . "anastral") (:end . 181)\n  (:start . 173) (:id . 66))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 189)\n  (:start . 182) (:id . 67))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 198)\n  (:start . 190) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 201) (:start . 199)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Xenopus") (:form . "Xenopus") (:end . 209)\n  (:start . 202) (:id . 70))\n ((:tag . "NNS") (:stem . "extract") (:form . "extracts") (:end . 218)\n  (:start . 210) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 222) (:start . 219)\n  (:id . 72))\n ((:tag . "RB") (:stem . "elsewhere") (:form . "elsewhere") (:end . 232)\n  (:start . 223) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 233) (:start . 232)\n  (:id . 74))\n ((:tag . "RB") (:stem . "possibly") (:form . "possibly") (:end . 242)\n  (:start . 234) (:id . 75))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 252)\n  (:start . 243) (:id . 76))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 263)\n  (:start . 253) (:id . 77))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 268) (:start . 264)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "embryos/larvae") (:form . "embryos/larvae")\n  (:end . 283) (:start . 269) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 287) (:start . 284)\n  (:id . 80))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 290) (:start . 288)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 296)\n  (:start . 291) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 297) (:start . 296)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x4.333.1) (:span 234 242)) ((:id . :x4.333.2) (:span 11 21)))\n (:hscopes ((:id . :x4.333.1) (:span 234 296))\n  ((:id . :x4.333.2) (:span 11 296)))\n (:identifiers (:sid . :s4.333) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501386@unknown@formal@none@1@S@However, in Drosophila syncytial embryo spindles, where MT assembly is nucleated predominantly at centrosomes, MTs turn over very quickly (half-time, 5 s), and it seems unlikely that kinesin-5 would have sufficient time to transport MTs to the spindle poles for focusing there (Cheerambathur et al., 2007 ).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 22)\n  (:start . 12) (:id . 45))\n ((:tag . "JJ") (:stem . "syncytial") (:form . "syncytial") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "spindle") (:form . "spindles") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "MT") (:form . "MT") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 67)\n  (:start . 59) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "nucleate") (:form . "nucleated") (:end . 80)\n  (:start . 71) (:id . 54))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 94) (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 97) (:start . 95)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "centrosome") (:form . "centrosomes") (:end . 109)\n  (:start . 98) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . 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")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 71))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 162) (:start . 160)\n  (:id . 72))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 168)\n  (:start . 163) (:id . 73))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 177)\n  (:start . 169) (:id . 74))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 182) (:start . 178)\n  (:id . 75))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 192)\n  (:start . 183) (:id . 76))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 198)\n  (:start . 193) (:id . 77))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 203) (:start . 199)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 214)\n  (:start . 204) (:id . 79))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 219) (:start . 215)\n  (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 222) (:start . 220)\n  (:id . 81))\n ((:tag . "VB") (:stem . "transport") (:form . "transport") (:end . 232)\n  (:start . 223) (:id . 82))\n ((:tag . "NNS") (:stem . "mt") (:form . "MTs") (:end . 236) (:start . 233)\n  (:id . 83))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 239) (:start . 237)\n  (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 243) (:start . 240)\n  (:id . 85))\n ((:tag . "NN") (:stem . "spindle") (:form . "spindle") (:end . 251)\n  (:start . 244) (:id . 86))\n ((:tag . "NNS") (:stem . "pole") (:form . "poles") (:end . 257)\n  (:start . 252) (:id . 87))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 261) (:start . 258)\n  (:id . 88))\n ((:tag . "VBG") (:stem . "focus") (:form . "focusing") (:end . 270)\n  (:start . 262) (:id . 89))\n ((:tag . "RB") (:stem . "there") (:form . "there") (:end . 276)\n  (:start . 271) (:id . 90))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 278) (:start . 277)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "Cheerambathur") (:form . "Cheerambathur")\n  (:end . 291) (:start . 278) (:id . 92))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 294) (:start . 292)\n  (:id . 93))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 298) (:start . 295)\n  (:id . 94))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 299) (:start . 298)\n  (:id . 95))\n ((:tag . "CD") (:stem . "2007") (:form . "2007") (:end . 304) (:start . 300)\n  (:id . 96))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 306) (:start . 305)\n  (:id . 97))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 307) (:start . 306)\n  (:id . 98)))@@@1@57@((:hcues ((:id . :x4.334.1) (:span 169 177))\n  ((:id . :x4.334.2) (:span 163 168)))\n (:hscopes ((:id . :x4.334.1) (:span 169 276))\n  ((:id . :x4.334.2) (:span 163 276)))\n (:identifiers (:sid . :s4.334) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501387@unknown@formal@none@1@S@This suggestion again implies that kinesin-5 is deployed in different ways in different systems.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "suggestion") (:form . "suggestion") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "RB") (:stem . "again") (:form . "again") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "imply") (:form . "implies") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 44)\n  (:start . 35) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "deploy") (:form . "deployed") (:end . 56)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 69)\n  (:start . 60) (:id . 51))\n ((:tag . "NNS") (:stem . "way") (:form . "ways") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 87)\n  (:start . 78) (:id . 54))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 95)\n  (:start . 88) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x4.335.1) (:span 22 29)))\n (:hscopes ((:id . :x4.335.1) (:span 22 95)))\n (:identifiers (:sid . :s4.335) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501388@unknown@formal@none@1@S@Summary@(((:tag . "NNP") (:stem . "Summary") (:form . "Summary") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s4.336) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501389@unknown@formal@none@1@S@This comprehensive study has revealed the spectrum of mitotic functions of the kinesin-5 motor, KLP61F, in a single system, the Drosophila embryo.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "comprehensive") (:form . "comprehensive")\n  (:end . 18) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 24) (:start . 19)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "reveal") (:form . "revealed") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "spectrum") (:form . "spectrum") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 71)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "NN") (:stem . "kinesin-5") (:form . "kinesin-5") (:end . 88)\n  (:start . 79) (:id . 54))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 94) (:start . 89)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 102)\n  (:start . 96) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 115)\n  (:start . 109) (:id . 61))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 122)\n  (:start . 116) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 138)\n  (:start . 128) (:id . 65))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 145)\n  (:start . 139) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s4.337) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501390@unknown@formal@none@1@S@We conclude that KLP61F has multiple mitotic functions, all of which are consistent with its MT–MT cross-linking and antiparallel MT sliding activity.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "KLP61F") (:form . "KLP61F") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "JJ") (:stem . "mitotic") (:form . "mitotic") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 54)\n  (:start . 45) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 83)\n  (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 92) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "mt–mt") (:form . "MT–MT") (:end . 98) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "cross-linking") (:form . "cross-linking")\n  (:end . 112) (:start . 99) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "antiparallel") (:form . "antiparallel") (:end . 129)\n  (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "mt") (:form . "MT") (:end . 132) (:start . 130)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "slide") (:form . "sliding") (:end . 140)\n  (:start . 133) (:id . 63))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 149)\n  (:start . 141) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s4.338) (:did . :pmc2655252) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501391@unknown@formal@none@1@S@Distinct Roles for FOXP3+ and FOXP3- CD4+ T Cells in Regulating Cellular Immunity to Uncomplicated and Severe Plasmodium falciparum Malaria@(((:tag . "JJ") (:stem . "distinct") (:form . "Distinct") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "role") (:form . "Roles") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "foxp3+") (:form . "FOXP3+") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "foxp3-") (:form . "FOXP3-") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "regulate") (:form . "Regulating") (:end . 63)\n  (:start . 53) (:id . 52))\n ((:tag . "JJ") (:stem . "cellular") (:form . "Cellular") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . "NNP") (:stem . "Immunity") (:form . "Immunity") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Uncomplicated") (:form . "Uncomplicated")\n  (:end . 98) (:start . 85) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Severe") (:form . "Severe") (:end . 109)\n  (:start . 103) (:id . 58))\n ((:tag . "NNP") (:stem . "Plasmodium") (:form . "Plasmodium") (:end . 120)\n  (:start . 110) (:id . 59))\n ((:tag . "NNP") (:stem . "falciparum") (:form . "falciparum") (:end . 131)\n  (:start . 121) (:id . 60))\n ((:tag . "NNP") (:stem . "Malaria") (:form . "Malaria") (:end . 139)\n  (:start . 132) (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.1) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5501392@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s5.2) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501393@unknown@formal@none@1@S@Failure to establish an appropriate balance between pro- and anti-inflammatory immune responses is believed to contribute to pathogenesis of severe malaria.@(((:tag . "NN") (:stem . "failure") (:form . "Failure") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "VB") (:stem . "establish") (:form . "establish") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 35)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "balance") (:form . "balance") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "JJ") (:stem . "pro-") (:form . "pro-") (:end . 56) (:start . 52)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "anti-inflammatory") (:form . "anti-inflammatory")\n  (:end . 78) (:start . 61) (:id . 51))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 85)\n  (:start . 79) (:id . 52))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 95)\n  (:start . 86) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 98) (:start . 96)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "believe") (:form . "believed") (:end . 107)\n  (:start . 99) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 56))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 121)\n  (:start . 111) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 124) (:start . 122)\n  (:id . 58))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 137)\n  (:start . 125) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 147)\n  (:start . 141) (:id . 61))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 155)\n  (:start . 148) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x5.3.1) (:span 99 107)))\n (:hscopes ((:id . :x5.3.1) (:span 0 155)))\n (:identifiers (:sid . :s5.3) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501394@unknown@formal@none@1@S@To determine whether this balance is maintained by classical regulatory T cells (CD4+ FOXP3+ CD127-/low; Tregs) we compared cellular responses between Gambian children (n=124) with severe Plasmodium falciparum malaria or uncomplicated malaria infections.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "balance") (:form . "balance") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "maintain") (:form . "maintained") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "classical") (:form . "classical") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 73) (:start . 72)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 79) (:start . 74)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "foxp3+") (:form . "FOXP3+") (:end . 92)\n  (:start . 86) (:id . 56))\n ((:tag . "NNP") (:stem . "CD127-/low") (:form . "CD127-/low") (:end . 103)\n  (:start . 93) (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 104) (:start . 103)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 110)\n  (:start . 105) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "compare") (:form . "compared") (:end . 123)\n  (:start . 115) (:id . 62))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 132)\n  (:start . 124) (:id . 63))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 142)\n  (:start . 133) (:id . 64))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 150)\n  (:start . 143) (:id . 65))\n ((:tag . "JJ") (:stem . "gambian") (:form . "Gambian") (:end . 158)\n  (:start . 151) (:id . 66))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 167)\n  (:start . 159) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n  (:id . 68))\n ((:tag . "NN") (:stem . "n=124") (:form . "n=124") (:end . 174)\n  (:start . 169) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 175) (:start . 174)\n  (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 180) (:start . 176)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 187)\n  (:start . 181) (:id . 72))\n ((:tag . "NNP") (:stem . "Plasmodium") (:form . "Plasmodium") (:end . 198)\n  (:start . 188) (:id . 73))\n ((:tag . "NN") (:stem . "falciparum") (:form . "falciparum") (:end . 209)\n  (:start . 199) (:id . 74))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 217)\n  (:start . 210) (:id . 75))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 220) (:start . 218)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 234) (:start . 221) (:id . 77))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 242)\n  (:start . 235) (:id . 78))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 253)\n  (:start . 243) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 254) (:start . 253)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x5.4.1) (:span 13 20)))\n (:hscopes ((:id . :x5.4.1) (:span 13 111)))\n (:identifiers (:sid . :s5.4) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501395@unknown@formal@none@1@S@Although no significant differences in Treg numbers or function were observed between the groups, Treg activity during acute disease was inversely correlated with malaria-specific memory responses detectable 28 days later.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 35)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 46))\n ((:tag . "NN") (:stem . "treg") (:form . "Treg") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 63)\n  (:start . 55) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 77)\n  (:start . 69) (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 85)\n  (:start . 78) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 96)\n  (:start . 90) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 56))\n ((:tag . "NN") (:stem . "treg") (:form . "Treg") (:end . 102) (:start . 98)\n  (:id . 57))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 111)\n  (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 118)\n  (:start . 112) (:id . 59))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 124)\n  (:start . 119) (:id . 60))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 132)\n  (:start . 125) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 136) (:start . 133)\n  (:id . 62))\n ((:tag . "RB") (:stem . "inversely") (:form . "inversely") (:end . 146)\n  (:start . 137) (:id . 63))\n ((:tag . "VBN") (:stem . "correlate") (:form . "correlated") (:end . 157)\n  (:start . 147) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 162) (:start . 158)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "malaria-specific") (:form . "malaria-specific")\n  (:end . 179) (:start . 163) (:id . 66))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 186)\n  (:start . 180) (:id . 67))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 196)\n  (:start . 187) (:id . 68))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 207)\n  (:start . 197) (:id . 69))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 210) (:start . 208)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 215) (:start . 211)\n  (:id . 71))\n ((:tag . "RB") (:stem . "later") (:form . "later") (:end . 221)\n  (:start . 216) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s5.5) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501396@unknown@formal@none@1@S@Thus, while Tregs may not regulate acute malarial inflammation, they may limit memory responses to levels that subsequently facilitate parasite clearance without causing immunopathology.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "VB") (:stem . "regulate") (:form . "regulate") (:end . 34)\n  (:start . 26) (:id . 48))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "malarial") (:form . "malarial") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 62)\n  (:start . 50) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "VB") (:stem . "limit") (:form . "limit") (:end . 78) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 85)\n  (:start . 79) (:id . 56))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 95)\n  (:start . 86) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 105)\n  (:start . 99) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 110) (:start . 106)\n  (:id . 60))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 123)\n  (:start . 111) (:id . 61))\n ((:tag . "VBP") (:stem . "facilitate") (:form . "facilitate") (:end . 134)\n  (:start . 124) (:id . 62))\n ((:tag . "NN") (:stem . "parasite") (:form . "parasite") (:end . 143)\n  (:start . 135) (:id . 63))\n ((:tag . "NN") (:stem . "clearance") (:form . "clearance") (:end . 153)\n  (:start . 144) (:id . 64))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 161)\n  (:start . 154) (:id . 65))\n ((:tag . "VBG") (:stem . "cause") (:form . "causing") (:end . 169)\n  (:start . 162) (:id . 66))\n ((:tag . "NN") (:stem . "immunopathology") (:form . "immunopathology")\n  (:end . 185) (:start . 170) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x5.6.1) (:span 69 72)) ((:id . :x5.6.2) (:span 18 21)))\n (:hscopes ((:id . :x5.6.1) (:span 69 185)) ((:id . :x5.6.2) (:span 18 62)))\n (:identifiers (:sid . :s5.6) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501397@unknown@formal@none@1@S@Importantly, we identified a population of FOXP3-, CD45RO+ CD4+ T cells which coproduce IL-10 and IFN-γ.@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 39)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "FOXP3-") (:form . "FOXP3-") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "cd45ro+") (:form . "CD45RO+") (:end . 58)\n  (:start . 51) (:id . 51))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "coproduce") (:form . "coproduce") (:end . 87)\n  (:start . 78) (:id . 56))\n ((:tag . "NN") (:stem . "il-10") (:form . "IL-10") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 103)\n  (:start . 98) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s5.7) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501398@unknown@formal@none@1@S@These cells are more prevalent in children with uncomplicated malaria than in those with severe disease, suggesting that they may be the regulators of acute malarial inflammation.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "prevalent") (:form . "prevalent") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 61) (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 69)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 83) (:start . 78)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 95)\n  (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 103)\n  (:start . 96) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 115)\n  (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 120) (:start . 116)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 125) (:start . 121)\n  (:id . 61))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "regulator") (:form . "regulators") (:end . 147)\n  (:start . 137) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 156)\n  (:start . 151) (:id . 67))\n ((:tag . "JJ") (:stem . "malarial") (:form . "malarial") (:end . 165)\n  (:start . 157) (:id . 68))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 178)\n  (:start . 166) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x5.8.1) (:span 126 129)) ((:id . :x5.8.2) (:span 105 115)))\n (:hscopes ((:id . :x5.8.1) (:span 126 178)) ((:id . :x5.8.2) (:span 105 178)))\n (:identifiers (:sid . :s5.8) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501399@unknown@formal@none@1@S@Author Summary@(((:tag . "NNP") (:stem . "Author") (:form . "Author") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Summary") (:form . "Summary") (:end . 14)\n  (:start . 7) (:id . 43)))@@@1@2@((:identifiers (:sid . :s5.9) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501400@unknown@formal@none@1@S@While Tregs have been implicated in regulation of the immune response to chronic infections, their potential in determining disease outcome in acute infections is unclear.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 46)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 69)\n  (:start . 61) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "chronic") (:form . "chronic") (:end . 80)\n  (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 91)\n  (:start . 81) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 98)\n  (:start . 93) (:id . 57))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 108)\n  (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "determine") (:form . "determining") (:end . 123)\n  (:start . 112) (:id . 60))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 131)\n  (:start . 124) (:id . 61))\n ((:tag . "NN") (:stem . "outcome") (:form . "outcome") (:end . 139)\n  (:start . 132) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 142) (:start . 140)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 148)\n  (:start . 143) (:id . 64))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 159)\n  (:start . 149) (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 162) (:start . 160)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 170)\n  (:start . 163) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x5.10.1) (:span 163 170)))\n (:hscopes ((:id . :x5.10.1) (:span 93 170)))\n (:identifiers (:sid . :s5.10) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501401@unknown@formal@none@1@S@In this study we have found that Tregs are unable to control the florid inflammation during acute, severe P. falciparum malaria infections, suggesting that this component of the immunoregulatory arsenal may be rapidly overwhelmed by virulent infections.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 38) (:start . 33)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "unable") (:form . "unable") (:end . 49)\n  (:start . 43) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 52))\n ((:tag . "VB") (:stem . "control") (:form . "control") (:end . 60)\n  (:start . 53) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "florid") (:form . "florid") (:end . 71)\n  (:start . 65) (:id . 55))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 84)\n  (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 91)\n  (:start . 85) (:id . 57))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 97) (:start . 92)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 105)\n  (:start . 99) (:id . 60))\n ((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 108) (:start . 106)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "falciparum") (:form . "falciparum") (:end . 119)\n  (:start . 109) (:id . 62))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 127)\n  (:start . 120) (:id . 63))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 138)\n  (:start . 128) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 150)\n  (:start . 140) (:id . 66))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 155) (:start . 151)\n  (:id . 67))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 160) (:start . 156)\n  (:id . 68))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 170)\n  (:start . 161) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "immunoregulatory") (:form . "immunoregulatory")\n  (:end . 194) (:start . 178) (:id . 72))\n ((:tag . "NN") (:stem . "arsenal") (:form . "arsenal") (:end . 202)\n  (:start . 195) (:id . 73))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 206) (:start . 203)\n  (:id . 74))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 209) (:start . 207)\n  (:id . 75))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 217)\n  (:start . 210) (:id . 76))\n ((:tag . "JJ") (:stem . "overwhelmed") (:form . "overwhelmed") (:end . 229)\n  (:start . 218) (:id . 77))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 232) (:start . 230)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "virulent") (:form . "virulent") (:end . 241)\n  (:start . 233) (:id . 79))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 252)\n  (:start . 242) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 253) (:start . 252)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x5.11.1) (:span 203 206)) ((:id . :x5.11.2) (:span 140 150)))\n (:hscopes ((:id . :x5.11.1) (:span 156 252))\n  ((:id . :x5.11.2) (:span 140 252)))\n (:identifiers (:sid . :s5.11) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501402@unknown@formal@none@1@S@Further, we identified, for the first time in an acute human infection, a population of IL-10-producing Th-1 effector cells and found that IL-10-producing Th-1 cells were associated with development of uncomplicated as opposed to severe malaria, leading us to suggest that such “self-regulating” Th-1 cells may contribute to clearing malaria infections without inducing immune-mediated pathology.@(((:tag . "RB") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 22)\n  (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 48) (:start . 46)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 54) (:start . 49)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 60) (:start . 55)\n  (:id . 54))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 70)\n  (:start . 61) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 84)\n  (:start . 74) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "il-10-producing") (:form . "IL-10-producing")\n  (:end . 103) (:start . 88) (:id . 60))\n ((:tag . "NN") (:stem . "th-1") (:form . "Th-1") (:end . 108) (:start . 104)\n  (:id . 61))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 117)\n  (:start . 109) (:id . 62))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 123)\n  (:start . 118) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 133)\n  (:start . 128) (:id . 65))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 138) (:start . 134)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "il-10-producing") (:form . "IL-10-producing")\n  (:end . 154) (:start . 139) (:id . 67))\n ((:tag . "NN") (:stem . "th-1") (:form . 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"VBG") (:stem . "self-regulating") (:form . "self-regulating")\n  (:end . 294) (:start . 279) (:id . 89))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 295) (:start . 294)\n  (:id . 90))\n ((:tag . "NN") (:stem . "th-1") (:form . "Th-1") (:end . 300) (:start . 296)\n  (:id . 91))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 306)\n  (:start . 301) (:id . 92))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 310) (:start . 307)\n  (:id . 93))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 321)\n  (:start . 311) (:id . 94))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 324) (:start . 322)\n  (:id . 95))\n ((:tag . "VBG") (:stem . "clear") (:form . "clearing") (:end . 333)\n  (:start . 325) (:id . 96))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 341)\n  (:start . 334) (:id . 97))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 352)\n  (:start . 342) (:id . 98))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 360)\n  (:start . 353) (:id . 99))\n ((:tag . "VBG") (:stem . "induce") (:form . "inducing") (:end . 369)\n  (:start . 361) (:id . 100))\n ((:tag . "JJ") (:stem . "immune-mediated") (:form . "immune-mediated")\n  (:end . 385) (:start . 370) (:id . 101))\n ((:tag . "NN") (:stem . "pathology") (:form . "pathology") (:end . 395)\n  (:start . 386) (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 396) (:start . 395)\n  (:id . 103)))@@@1@62@((:hcues ((:id . :x5.12.1) (:span 307 310)) ((:id . :x5.12.2) (:span 260 267)))\n (:hscopes ((:id . :x5.12.1) (:span 307 395))\n  ((:id . :x5.12.2) (:span 260 395)))\n (:identifiers (:sid . :s5.12) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501403@unknown@formal@none@1@S@In addition, we found evidence that malaria-induced Tregs may limit the magnitude of malaria-specific memory responses detectable 28 days later, which may reduce the risk of immune-mediated pathology upon reinfection and may explain how immunity to severe disease can be gained after as little as one or two infections.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 21) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . 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"as") (:end . 296) (:start . 294)\n  (:id . 88))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 300) (:start . 297)\n  (:id . 89))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 303) (:start . 301)\n  (:id . 90))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 307) (:start . 304)\n  (:id . 91))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 318)\n  (:start . 308) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 319) (:start . 318)\n  (:id . 93)))@@@1@52@((:hcues ((:id . :x5.13.1) (:span 221 224)) ((:id . :x5.13.2) (:span 151 154))\n  ((:id . :x5.13.3) (:span 58 61)))\n (:hscopes ((:id . :x5.13.1) (:span 221 318))\n  ((:id . :x5.13.2) (:span 151 216)) ((:id . :x5.13.3) (:span 58 143)))\n (:identifiers (:sid . :s5.13) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501404@unknown@formal@none@1@S@We conclude that vaccines designed to induce cell-mediated responses should be assessed for their ability to induce IL-10 producing Th-1 cells and Tregs.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "vaccine") (:form . "vaccines") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "JJ") (:stem . "cell-mediated") (:form . "cell-mediated")\n  (:end . 58) (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 68)\n  (:start . 59) (:id . 50))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 75)\n  (:start . 69) (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 78) (:start . 76)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 87)\n  (:start . 79) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 91) (:start . 88)\n  (:id . 54))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 97)\n  (:start . 92) (:id . 55))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 105)\n  (:start . 98) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 57))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 115)\n  (:start . 109) (:id . 58))\n ((:tag . "NN") (:stem . "il-10") (:form . "IL-10") (:end . 121)\n  (:start . 116) (:id . 59))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 131)\n  (:start . 122) (:id . 60))\n ((:tag . "NN") (:stem . "th-1") (:form . "Th-1") (:end . 136) (:start . 132)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 142)\n  (:start . 137) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 146) (:start . 143)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 152)\n  (:start . 147) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s5.14) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501405@unknown@formal@none@1@S@Introduction@(((:tag . "NN") (:stem . "introduction") (:form . "Introduction") (:end . 12)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s5.15) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501406@unknown@formal@none@1@S@The clinical spectrum of P. falciparum infection ranges from asymptomatic parasite carriage to a febrile disease that may develop into a severe, life-threatening illness.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "spectrum") (:form . "spectrum") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "falciparum") (:form . "falciparum") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . "NNS") (:stem . "range") (:form . "ranges") (:end . 55)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "asymptomatic") (:form . "asymptomatic") (:end . 73)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "parasite") (:form . "parasite") (:end . 82)\n  (:start . 74) (:id . 52))\n ((:tag . "NN") (:stem . "carriage") (:form . "carriage") (:end . 91)\n  (:start . 83) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 96) (:start . 95)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "febrile") (:form . "febrile") (:end . 104)\n  (:start . 97) (:id . 56))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 112)\n  (:start . 105) (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 117) (:start . 113)\n  (:id . 58))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 121) (:start . 118)\n  (:id . 59))\n ((:tag . "VB") (:stem . "develop") (:form . "develop") (:end . 129)\n  (:start . 122) (:id . 60))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 134) (:start . 130)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 136) (:start . 135)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 143)\n  (:start . 137) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "life-threatening") (:form . "life-threatening")\n  (:end . 161) (:start . 145) (:id . 65))\n ((:tag . "NN") (:stem . "illness") (:form . "illness") (:end . 169)\n  (:start . 162) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x5.16.1) (:span 118 121)))\n (:hscopes ((:id . :x5.16.1) (:span 118 169)))\n (:identifiers (:sid . :s5.16) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501407@unknown@formal@none@1@S@The factors that determine disease severity are not completely understood but are likely to include both parasite and host components [1]–[3].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "determine") (:form . "determine") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "severity") (:form . "severity") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 51) (:start . 48)\n  (:id . 49))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 62)\n  (:start . 52) (:id . 50))\n ((:tag . "VBN") (:stem . "understand") (:form . "understood") (:end . 73)\n  (:start . 63) (:id . 51))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 77) (:start . 74)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 81) (:start . 78)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 88)\n  (:start . 82) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "VB") (:stem . "include") (:form . "include") (:end . 99)\n  (:start . 92) (:id . 56))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 104) (:start . 100)\n  (:id . 57))\n ((:tag . "NN") (:stem . "parasite") (:form . "parasite") (:end . 113)\n  (:start . 105) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 59))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 122) (:start . 118)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 133)\n  (:start . 123) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . "CD") (:stem . "1]–[3") (:form . "1]–[3") (:end . 140)\n  (:start . 135) (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 141) (:start . 140)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x5.17.1) (:span 82 88)) ((:id . :x5.17.2) (:span 48 73)))\n (:hscopes ((:id . :x5.17.1) (:span 82 133)) ((:id . :x5.17.2) (:span 0 73)))\n (:identifiers (:sid . :s5.17) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501408@unknown@formal@none@1@S@Ultimately, the interplay between the parasite and the immune response likely determines the outcome of the infection [4].@(((:tag . "RB") (:stem . "ultimately") (:form . "Ultimately") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "interplay") (:form . "interplay") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "parasite") (:form . "parasite") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 61)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "RB") (:stem . "likely") (:form . "likely") (:end . 77)\n  (:start . 71) (:id . 53))\n ((:tag . "VBZ") (:stem . "determine") (:form . "determines") (:end . 88)\n  (:start . 78) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "outcome") (:form . "outcome") (:end . 100)\n  (:start . 93) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 117)\n  (:start . 108) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 121) (:start . 120)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x5.18.1) (:span 71 77)))\n (:hscopes ((:id . :x5.18.1) (:span 71 117)))\n (:identifiers (:sid . :s5.18) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501409@unknown@formal@none@1@S@Although sterile immunity - completely preventing re-infection - is hardly ever seen and protection against clinical symptoms of uncomplicated disease is only acquired after repeated infections [5], immunity to severe disease and death may be acquired after as few as one or two infections [6] suggesting that different immune mechanisms underlie these different levels of immunity.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "sterile") (:form . "sterile") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "immunity") (:form . "immunity") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "VBG") (:stem . "prevent") (:form . 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5501410@unknown@formal@none@1@S@While there is a growing consensus that killing of malaria parasites or malaria-infected red blood cells requires the synergistic action of antibodies and cell-mediated immune responses [5],[7], the mechanisms conferring protection against severe disease are less clear.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "grow") (:form . "growing") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "killing") (:form . "killing") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 58)\n  (:start . 51) (:id . 51))\n ((:tag . "NNS") (:stem . "parasite") (:form . "parasites") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "malaria-infected") (:form . "malaria-infected")\n  (:end . 88) (:start . 72) (:id . 54))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "blood") (:form . "blood") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 104) (:start . 99)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 113)\n  (:start . 105) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "synergistic") (:form . "synergistic") (:end . 129)\n  (:start . 118) (:id . 60))\n ((:tag . "NN") (:stem . "action") (:form . "action") (:end . 136)\n  (:start . 130) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 139) (:start . 137)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 150)\n  (:start . 140) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "cell-mediated") (:form . "cell-mediated")\n  (:end . 168) (:start . 155) (:id . 65))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 175)\n  (:start . 169) (:id . 66))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 185)\n  (:start . 176) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 187) (:start . 186)\n  (:id . 68))\n ((:tag . "CD") (:stem . "5],[7") (:form . "5],[7") (:end . 192)\n  (:start . 187) (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 193) (:start . 192)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 194) (:start . 193)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 198) (:start . 195)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 209)\n  (:start . 199) (:id . 73))\n ((:tag . "VBG") (:stem . "confer") (:form . "conferring") (:end . 220)\n  (:start . 210) (:id . 74))\n ((:tag . "NN") (:stem . "protection") (:form . "protection") (:end . 231)\n  (:start . 221) (:id . 75))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 239)\n  (:start . 232) (:id . 76))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 246)\n  (:start . 240) (:id . 77))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 254)\n  (:start . 247) (:id . 78))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 258) (:start . 255)\n  (:id . 79))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 263) (:start . 259)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 269)\n  (:start . 264) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x5.20.1) (:span 259 269)))\n (:hscopes ((:id . :x5.20.1) (:span 195 269)))\n (:identifiers (:sid . :s5.20) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501411@unknown@formal@none@1@S@Given that pathology of severe disease has repeatedly been linked to sustained and/or excessive inflammatory responses [4], acquiring the ability to regulate these responses adequately may be a key determinant of immunity that protects against severe disease [8].@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "pathology") (:form . "pathology") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "RB") (:stem . "repeatedly") (:form . "repeatedly") (:end . 53)\n  (:start . 43) (:id . 49))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "link") (:form . "linked") (:end . 65) (:start . 59)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "sustained") (:form . "sustained") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 85)\n  (:start . 79) (:id . 54))\n ((:tag . "JJ") (:stem . "excessive") (:form . "excessive") (:end . 95)\n  (:start . 86) (:id . 55))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 108)\n  (:start . 96) (:id . 56))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 118)\n  (:start . 109) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 120) (:start . 119)\n  (:id . 58))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 121) (:start . 120)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 122) (:start . 121)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "acquire") (:form . "acquiring") (:end . 133)\n  (:start . 124) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 63))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 145)\n  (:start . 138) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 65))\n ((:tag . "VB") (:stem . "regulate") (:form . "regulate") (:end . 157)\n  (:start . 149) (:id . 66))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 163)\n  (:start . 158) (:id . 67))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 173)\n  (:start . 164) (:id . 68))\n ((:tag . "RB") (:stem . "adequately") (:form . "adequately") (:end . 184)\n  (:start . 174) (:id . 69))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 188) (:start . 185)\n  (:id . 70))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 191) (:start . 189)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 193) (:start . 192)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 197) (:start . 194)\n  (:id . 73))\n ((:tag . "NN") (:stem . "determinant") (:form . "determinant") (:end . 209)\n  (:start . 198) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 212) (:start . 210)\n  (:id . 75))\n ((:tag . "NN") (:stem . "immunity") (:form . "immunity") (:end . 221)\n  (:start . 213) (:id . 76))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 226) (:start . 222)\n  (:id . 77))\n ((:tag . "VBZ") (:stem . "protect") (:form . "protects") (:end . 235)\n  (:start . 227) (:id . 78))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 243)\n  (:start . 236) (:id . 79))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 250)\n  (:start . 244) (:id . 80))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 258)\n  (:start . 251) (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 260) (:start . 259)\n  (:id . 82))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 261) (:start . 260)\n  (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 262) (:start . 261)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 263) (:start . 262)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x5.21.1) (:span 185 188)))\n (:hscopes ((:id . :x5.21.1) (:span 185 258)))\n (:identifiers (:sid . :s5.21) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501412@unknown@formal@none@1@S@Thus, while an early inflammatory response is needed to control parasite replication in human P. falciparum malaria [9]–[11], excessive levels of pro-inflammatory cytokines such as TNF-α [12]–[15], IFN-γ, [16],[17], IL-1ß and IL-6 [14],[18],[19] are associated with severe pathology.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 20) (:start . 15)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 33)\n  (:start . 21) (:id . 47))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "VBZ") (:stem . 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5501413@unknown@formal@none@1@S@Conversely, low levels of regulatory cytokines such as TGF-ß have been associated with acute [20] and severe malaria [21],[22], a relative deficiency in IL-10 was seen in those who succumbed to severe malaria [23], significantly lower ratios of IL-10 to TNF-α were found in patients with severe malarial anaemia [24],[25], and high ratios of IFN-γ, TNF-α and IL-12 to TGF-ß or IL-10 were associated with decreased risk of malaria but increased risk of clinical disease in those who became infected [26].@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . 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5501414@unknown@formal@none@1@S@In summary, therefore, immunity against severe malaria may depend upon the host's ability to regulate the magnitude and timing of the cellular immune response, allowing the sequential induction of appropriate levels of inflammatory- and anti-inflammatory cytokines at key stages of the infection.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "summary") (:form . "summary") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "immunity") (:form . "immunity") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . 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5501415@unknown@formal@none@1@S@Given these associations between severe disease and exacerbated immune pathology, a number of studies have explored the role of CD4+CD25hiFOXP3+CD127-/lo regulatory T cells (Tregs) in determining the outcome of malaria infection.@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "association") (:form . "associations") (:end . 24)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 39)\n  (:start . 33) (:id . 46))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 47)\n  (:start . 40) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "exacerbated") (:form . "exacerbated") (:end . 63)\n  (:start . 52) (:id . 49))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 70)\n  (:start . 64) (:id . 50))\n ((:tag . "NN") (:stem . "pathology") (:form . "pathology") (:end . 80)\n  (:start . 71) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 83) (:start . 82)\n  (:id . 53))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 90)\n  (:start . 84) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 101)\n  (:start . 94) (:id . 56))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 106) (:start . 102)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "explore") (:form . "explored") (:end . 115)\n  (:start . 107) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 59))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 124) (:start . 120)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "cd4+cd25hifoxp3+cd127-/lo")\n  (:form . "CD4+CD25hiFOXP3+CD127-/lo") (:end . 153) (:start . 128)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 164)\n  (:start . 154) (:id . 63))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 166) (:start . 165)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 172)\n  (:start . 167) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 179)\n  (:start . 174) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 183) (:start . 181)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "determine") (:form . "determining") (:end . 195)\n  (:start . 184) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 199) (:start . 196)\n  (:id . 71))\n ((:tag . "NN") (:stem . "outcome") (:form . "outcome") (:end . 207)\n  (:start . 200) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 210) (:start . 208)\n  (:id . 73))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 218)\n  (:start . 211) (:id . 74))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 228)\n  (:start . 219) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s5.25) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501416@unknown@formal@none@1@S@Induced and/or activated in response to malaria infection [27], Tregs may be beneficial to the host in the later part of the infection - when parasitaemia is being cleared - by down-regulating the inflammatory response and thereby preventing immune-mediated pathology.@(((:tag . "VBN") (:stem . "induce") (:form . "Induced") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 36)\n  (:start . 28) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 47)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 59) (:start . 58)\n  (:id . 50))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "beneficial") (:form . "beneficial") (:end . 87)\n  (:start . 77) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 99) (:start . 95)\n  (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "later") (:form . "later") (:end . 112)\n  (:start . 107) (:id . 63))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 117) (:start . 113)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n  (:id . 66))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 134)\n  (:start . 125) (:id . 67))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 136) (:start . 135)\n  (:id . 68))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 141) (:start . 137)\n  (:id . 69))\n ((:tag . "NN") (:stem . "parasitaemia") (:form . "parasitaemia") (:end . 154)\n  (:start . 142) (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 157) (:start . 155)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 163) (:start . 158)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "clear") (:form . "cleared") (:end . 171)\n  (:start . 164) (:id . 73))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 173) (:start . 172)\n  (:id . 74))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 176) (:start . 174)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "down-regulate") (:form . "down-regulating")\n  (:end . 192) (:start . 177) (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 209)\n  (:start . 197) (:id . 78))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 218)\n  (:start . 210) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 222) (:start . 219)\n  (:id . 80))\n ((:tag . "RB") (:stem . "thereby") (:form . "thereby") (:end . 230)\n  (:start . 223) (:id . 81))\n ((:tag . "VBG") (:stem . "prevent") (:form . "preventing") (:end . 241)\n  (:start . 231) (:id . 82))\n ((:tag . "JJ") (:stem . "immune-mediated") (:form . "immune-mediated")\n  (:end . 257) (:start . 242) (:id . 83))\n ((:tag . "NN") (:stem . "pathology") (:form . "pathology") (:end . 267)\n  (:start . 258) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 268) (:start . 267)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x5.26.1) (:span 70 73)))\n (:hscopes ((:id . :x5.26.1) (:span 70 267)))\n (:identifiers (:sid . :s5.26) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501417@unknown@formal@none@1@S@On the other hand, if Tregs mediate their suppressive effects too early, this could hamper the responses required for initial control of parasitaemia, permitting unbridled parasite growth which may also lead to severe disease.@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "hand") (:form . "hand") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 21) (:start . 19)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 27) (:start . 22)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "mediate") (:form . "mediate") (:end . 35)\n  (:start . 28) (:id . 49))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 41)\n  (:start . 36) (:id . 50))\n ((:tag . "JJ") (:stem . "suppressive") (:form . "suppressive") (:end . 53)\n  (:start . 42) (:id . 51))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "RB") (:stem . "early") (:form . "early") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 77) (:start . 73)\n  (:id . 56))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 83) (:start . 78)\n  (:id . 57))\n ((:tag . "VB") (:stem . "hamper") (:form . "hamper") (:end . 90)\n  (:start . 84) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 104)\n  (:start . 95) (:id . 60))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 113)\n  (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 125)\n  (:start . 118) (:id . 63))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 133)\n  (:start . 126) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 65))\n ((:tag . "NN") (:stem . "parasitaemia") (:form . "parasitaemia") (:end . 149)\n  (:start . 137) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "permit") (:form . "permitting") (:end . 161)\n  (:start . 151) (:id . 68))\n ((:tag . "JJ") (:stem . "unbridled") (:form . "unbridled") (:end . 171)\n  (:start . 162) (:id . 69))\n ((:tag . "NN") (:stem . "parasite") (:form . "parasite") (:end . 180)\n  (:start . 172) (:id . 70))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 187)\n  (:start . 181) (:id . 71))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 193)\n  (:start . 188) (:id . 72))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 197) (:start . 194)\n  (:id . 73))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 202) (:start . 198)\n  (:id . 74))\n ((:tag . "VB") (:stem . "lead") (:form . "lead") (:end . 207) (:start . 203)\n  (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 210) (:start . 208)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 217)\n  (:start . 211) (:id . 77))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 225)\n  (:start . 218) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x5.27.1) (:span 194 197)))\n (:hscopes ((:id . :x5.27.1) (:span 194 225)))\n (:identifiers (:sid . :s5.27) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501418@unknown@formal@none@1@S@Malaria-specific induction of Tregs has been observed in a variety of experimental malaria infections in mice [28]–[31], but their role in preventing severe malarial pathology is unclear.@(((:tag . "JJ") (:stem . "malaria-specific") (:form . "Malaria-specific")\n  (:end . 16) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "induction") (:form . "induction") (:end . 26)\n  (:start . 17) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 35) (:start . 30)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 39) (:start . 36)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 44) (:start . 40)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 53)\n  (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "variety") (:form . "variety") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 82)\n  (:start . 70) (:id . 53))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 90)\n  (:start . 83) (:id . 54))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 101)\n  (:start . 91) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 109)\n  (:start . 105) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 111) (:start . 110)\n  (:id . 58))\n ((:tag . "CD") (:stem . "28]–[31") (:form . "28]–[31") (:end . 118)\n  (:start . 111) (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 124) (:start . 121)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 130)\n  (:start . 125) (:id . 63))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 135) (:start . 131)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 138) (:start . 136)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "prevent") (:form . "preventing") (:end . 149)\n  (:start . 139) (:id . 66))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 156)\n  (:start . 150) (:id . 67))\n ((:tag . "JJ") (:stem . "malarial") (:form . "malarial") (:end . 165)\n  (:start . 157) (:id . 68))\n ((:tag . "NN") (:stem . "pathology") (:form . "pathology") (:end . 175)\n  (:start . 166) (:id . 69))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 178) (:start . 176)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 186)\n  (:start . 179) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x5.28.1) (:span 179 186)))\n (:hscopes ((:id . :x5.28.1) (:span 125 186)))\n (:identifiers (:sid . :s5.28) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501419@unknown@formal@none@1@S@Thus, in BALB/c mice infected with a lethal strain of P. yoelii, ablation of Treg activity by depletion of CD25+ cells either allowed mice to control parasitaemia and survive [32] or had no impact on the course of disease [33].@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "balb/c") (:form . "BALB/c") (:end . 15) (:start . 9)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "infect") (:form . "infected") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "lethal") (:form . "lethal") (:end . 43)\n  (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "strain") (:form . "strain") (:end . 50)\n  (:start . 44) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "yoelii") (:form . "yoelii") (:end . 63)\n  (:start . 57) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "ablation") (:form . "ablation") (:end . 73)\n  (:start . 65) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 57))\n ((:tag . "NN") (:stem . "treg") (:form . "Treg") (:end . 81) (:start . 77)\n  (:id . 58))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 90)\n  (:start . 82) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . "NN") (:stem . "depletion") (:form . "depletion") (:end . 103)\n  (:start . 94) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "cd25+") (:form . "CD25+") (:end . 112)\n  (:start . 107) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 118)\n  (:start . 113) (:id . 64))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 125)\n  (:start . 119) (:id . 65))\n ((:tag . "VBN") (:stem . "allow") (:form . "allowed") (:end . 133)\n  (:start . 126) (:id . 66))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 138)\n  (:start . 134) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 141) (:start . 139)\n  (:id . 68))\n ((:tag . "VB") (:stem . "control") (:form . "control") (:end . 149)\n  (:start . 142) (:id . 69))\n ((:tag . "NN") (:stem . "parasitaemia") (:form . "parasitaemia") (:end . 162)\n  (:start . 150) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n  (:id . 71))\n ((:tag . "NN") (:stem . "survive") (:form . "survive") (:end . 174)\n  (:start . 167) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 176) (:start . 175)\n  (:id . 73))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 178) (:start . 176)\n  (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 179) (:start . 178)\n  (:id . 75))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 182) (:start . 180)\n  (:id . 76))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 186) (:start . 183)\n  (:id . 77))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 189) (:start . 187)\n  (:id . 78))\n ((:tag . "NN") (:stem . "impact") (:form . "impact") (:end . 196)\n  (:start . 190) (:id . 79))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 199) (:start . 197)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n  (:id . 81))\n ((:tag . "NN") (:stem . "course") (:form . "course") (:end . 210)\n  (:start . 204) (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 213) (:start . 211)\n  (:id . 83))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 221)\n  (:start . 214) (:id . 84))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 223) (:start . 222)\n  (:id . 85))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 225) (:start . 223)\n  (:id . 86))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 226) (:start . 225)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s5.29) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501420@unknown@formal@none@1@S@Depleting CD25+ cells of BALB/c mice infected with either P. berghei NK65 [34] or P berghei ANKA [35] reduced neither parasitaemia nor mortality, but increased the severity of symptoms in the diseased mice, suggesting at least some benefit from Tregs in this model.@(((:tag . "VBG") (:stem . "deplete") (:form . "Depleting") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "cd25+") (:form . "CD25+") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "balb/c") (:form . "BALB/c") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "infect") (:form . "infected") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . 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5501421@unknown@formal@none@1@S@Rather oddly, infection of CD25+ T cell-depleted BALB/c mice with P. chabaudi adami DS led to increased parasitaemia and more severe anaemia [30].@(((:tag . "RB") (:stem . "rather") (:form . "Rather") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "oddly") (:form . "oddly") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "cd25+") (:form . "CD25+") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "cell-depleted") (:form . "cell-depleted")\n  (:end . 48) (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "balb/c") (:form . "BALB/c") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "chabaudi") (:form . "chabaudi") (:end . 77)\n  (:start . 69) (:id . 54))\n ((:tag . "NN") (:stem . "adami") (:form . "adami") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . "NN") (:stem . "ds") (:form . "DS") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "lead") (:form . "led") (:end . 90) (:start . 87)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 103)\n  (:start . 94) (:id . 59))\n ((:tag . "NN") (:stem . "parasitaemia") (:form . "parasitaemia") (:end . 116)\n  (:start . 104) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 125) (:start . 121)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 132)\n  (:start . 126) (:id . 63))\n ((:tag . "NN") (:stem . "anaemia") (:form . "anaemia") (:end . 140)\n  (:start . 133) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 142) (:start . 141)\n  (:id . 65))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 144) (:start . 142)\n  (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 145) (:start . 144)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s5.31) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501422@unknown@formal@none@1@S@Finally, CD25+ T cell depletion around the time of parasite inoculation reduced the incidence of experimental cerebral malaria in C57BL/6 mice infected with P. berghei ANKA in two independent studies [29],[31], but not when CD25+ T cells were depleted 30 days prior to infection [31].@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "cd25+") (:form . "CD25+") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "depletion") (:form . "depletion") (:end . 31)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "DT") (:stem . 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5501423@unknown@formal@none@1@S@Whilst various explanations have been offered for these discrepant results, including differences in the various strains of mice and parasites employed, the microbial microenvironment in which the mice are kept, and the precise CD25 depletion protocols employed, these studies are currently not very helpful when trying to understand the role of Tregs in human malaria infections.@(((:tag . "IN") (:stem . "whilst") (:form . "Whilst") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "explanation") (:form . "explanations") (:end . 27)\n  (:start . 15) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 32) (:start . 28)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "offer") (:form . 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5501424@unknown@formal@none@1@S@Malaria naive individuals undergoing experimental P. falciparum sporozoite infection showed an increase in FOXP3 mRNA expression and expansion of Tregs 10 days after infection; Treg induction correlated with high circulating levels of TGF-ß, low levels of pro-inflammatory cytokines and rapid parasite growth [27] suggesting - but not proving - that Treg activation early in infection may inhibit the development of effective cellular immunity.@(((:tag . "NNP") (:stem . "Malaria") (:form . "Malaria") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "naive") (:form . "naive") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "individual") (:form . "individuals") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "VBG") (:stem . "undergo") (:form . "undergoing") (:end . 36)\n  (:start . 26) (:id . 45))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 49)\n  (:start . 37) (:id . 46))\n ((:tag . 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"cellular") (:end . 434)\n  (:start . 426) (:id . 107))\n ((:tag . "NN") (:stem . "immunity") (:form . "immunity") (:end . 443)\n  (:start . 435) (:id . 108))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 444) (:start . 443)\n  (:id . 109)))@@@1@68@((:hcues ((:id . :x5.34.1) (:span 385 388)) ((:id . :x5.34.2) (:span 314 324)))\n (:hscopes ((:id . :x5.34.1) (:span 385 443))\n  ((:id . :x5.34.2) (:span 314 443)))\n (:identifiers (:sid . :s5.34) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501425@unknown@formal@none@1@S@More recently, we have observed that Treg populations appear to be transiently expanded and activated during the malaria transmission season in individuals from a malaria endemic community [36], again suggesting that naturally acquired malaria infection can drive the expansion and activation of Tregs.@(((:tag . "RBR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . 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"malaria") (:end . 243)\n  (:start . 236) (:id . 79))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 253)\n  (:start . 244) (:id . 80))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 257) (:start . 254)\n  (:id . 81))\n ((:tag . "VB") (:stem . "drive") (:form . "drive") (:end . 263)\n  (:start . 258) (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 267) (:start . 264)\n  (:id . 83))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 277)\n  (:start . 268) (:id . 84))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 281) (:start . 278)\n  (:id . 85))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 292)\n  (:start . 282) (:id . 86))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 295) (:start . 293)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 301)\n  (:start . 296) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 302) (:start . 301)\n  (:id . 89)))@@@1@48@((:hcues ((:id . :x5.35.1) (:span 254 257)) ((:id . :x5.35.2) (:span 201 211))\n  ((:id . :x5.35.3) (:span 54 60)))\n (:hscopes ((:id . :x5.35.1) (:span 254 301))\n  ((:id . :x5.35.2) (:span 201 301)) ((:id . :x5.35.3) (:span 37 188)))\n (:identifiers (:sid . :s5.35) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501426@unknown@formal@none@1@S@However, although Tregs have been implicated in IL-10-mediated down-regulation of Th1-like responses in the placenta of malaria-infected women [37] and reduced Treg frequencies and function have been linked to enhanced anti-parasite immunity in certain ethnic groups in West Africa [38] the potential for Tregs to influence the clinical outcome of malaria infections is still unclear.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "VBN") (:stem . 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"infections") (:end . 366)\n  (:start . 356) (:id . 98))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 369) (:start . 367)\n  (:id . 99))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 375)\n  (:start . 370) (:id . 100))\n ((:tag . "JJ") (:stem . "unclear") (:form . "unclear") (:end . 383)\n  (:start . 376) (:id . 101))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 384) (:start . 383)\n  (:id . 102)))@@@1@61@((:hcues ((:id . :x5.36.1) (:span 376 383)))\n (:hscopes ((:id . :x5.36.1) (:span 287 383)))\n (:identifiers (:sid . :s5.36) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501427@unknown@formal@none@1@S@To investigate the role of Tregs during clinical malaria infection, we have compared cellular immune responses of children with either severe or uncomplicated malaria.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 66)\n  (:start . 57) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 84)\n  (:start . 76) (:id . 55))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 93)\n  (:start . 85) (:id . 56))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 100)\n  (:start . 94) (:id . 57))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 110)\n  (:start . 101) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 122)\n  (:start . 114) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 127) (:start . 123)\n  (:id . 61))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 134)\n  (:start . 128) (:id . 62))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 141)\n  (:start . 135) (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 158) (:start . 145) (:id . 65))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 166)\n  (:start . 159) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s5.37) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501428@unknown@formal@none@1@S@Interestingly, although we did not observe any significant differences in Treg numbers or function between severe and uncomplicated malaria cases, our data do indicate that malaria-induced Tregs may limit the magnitude of malaria-specific Th1 memory responses and thus moderate pro-inflammatory responses to subsequent infections, providing a possible explanation for the very rapid acquisition of immunity to severe malaria.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . 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"Th1") (:end . 242) (:start . 239)\n  (:id . 77))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 249)\n  (:start . 243) (:id . 78))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 259)\n  (:start . 250) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 263) (:start . 260)\n  (:id . 80))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 268) (:start . 264)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "moderate") (:form . "moderate") (:end . 277)\n  (:start . 269) (:id . 82))\n ((:tag . "JJ") (:stem . "pro-inflammatory") (:form . "pro-inflammatory")\n  (:end . 294) (:start . 278) (:id . 83))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 304)\n  (:start . 295) (:id . 84))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 307) (:start . 305)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 318)\n  (:start . 308) (:id . 86))\n ((:tag . "NNS") (:stem . 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"acquisition") (:end . 394)\n  (:start . 383) (:id . 97))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 397) (:start . 395)\n  (:id . 98))\n ((:tag . "NN") (:stem . "immunity") (:form . "immunity") (:end . 406)\n  (:start . 398) (:id . 99))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 409) (:start . 407)\n  (:id . 100))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 416)\n  (:start . 410) (:id . 101))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 424)\n  (:start . 417) (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 425) (:start . 424)\n  (:id . 103)))@@@1@62@((:hcues ((:id . :x5.38.1) (:span 343 351)) ((:id . :x5.38.2) (:span 195 198))\n  ((:id . :x5.38.3) (:span 159 172)))\n (:hscopes ((:id . :x5.38.1) (:span 343 424))\n  ((:id . :x5.38.2) (:span 195 329)) ((:id . :x5.38.3) (:span 159 329)))\n (:identifiers (:sid . :s5.38) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501429@unknown@formal@none@1@S@Moreover, we have identified a population of FOXP3-, CD45RO+, CD4+ T cells which co-produce IL-10 and IFN-γ and which are more prevalent in children with uncomplicated malaria than in those with severe disease.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 41)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "FOXP3-") (:form . "FOXP3-") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "cd45ro+") (:form . "CD45RO+") (:end . 60)\n  (:start . 53) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 74) (:start . 69)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 80) (:start . 75)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "co-produce") (:form . "co-produce") (:end . 91)\n  (:start . 81) (:id . 58))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 97) (:start . 92)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 107)\n  (:start . 102) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 62))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 117)\n  (:start . 112) (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 121) (:start . 118)\n  (:id . 64))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 126) (:start . 122)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "prevalent") (:form . "prevalent") (:end . 136)\n  (:start . 127) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 139) (:start . 137)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 148)\n  (:start . 140) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 153) (:start . 149)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 167) (:start . 154) (:id . 70))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 175)\n  (:start . 168) (:id . 71))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 180) (:start . 176)\n  (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 183) (:start . 181)\n  (:id . 73))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 189)\n  (:start . 184) (:id . 74))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 194) (:start . 190)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 201)\n  (:start . 195) (:id . 76))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 209)\n  (:start . 202) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s5.39) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501430@unknown@formal@none@1@S@We suggest that these IL-10 producing effector T cells may contribute to clearing malaria infection without-inducing immune-mediated pathology.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "il-10") (:form . "IL-10") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 37)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 69)\n  (:start . 59) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "clear") (:form . "clearing") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 89)\n  (:start . 82) (:id . 55))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 99)\n  (:start . 90) (:id . 56))\n ((:tag . "VBG") (:stem . "without-induce") (:form . "without-inducing")\n  (:end . 116) (:start . 100) (:id . 57))\n ((:tag . "JJ") (:stem . "immune-mediated") (:form . "immune-mediated")\n  (:end . 132) (:start . 117) (:id . 58))\n ((:tag . "NN") (:stem . "pathology") (:form . "pathology") (:end . 142)\n  (:start . 133) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x5.40.1) (:span 55 58)) ((:id . :x5.40.2) (:span 3 10)))\n (:hscopes ((:id . :x5.40.1) (:span 55 142)) ((:id . :x5.40.2) (:span 3 142)))\n (:identifiers (:sid . :s5.40) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501431@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s5.41) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501432@unknown@formal@none@1@S@Immune responses of 59 Gambian children with severe P. falciparum malaria were compared with those of 65 children with uncomplicated clinical malaria and with 20 healthy (control) children of similar age and recruited from the same study area at the same time (Table 1).@(((:tag . "JJ") (:stem . "immune") (:form . "Immune") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 16)\n  (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "CD") (:stem . "59") (:form . "59") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "gambian") (:form . "Gambian") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . 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"same") (:end . 231) (:start . 227)\n  (:id . 79))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 237)\n  (:start . 232) (:id . 80))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 242) (:start . 238)\n  (:id . 81))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 245) (:start . 243)\n  (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 249) (:start . 246)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 254) (:start . 250)\n  (:id . 84))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 259) (:start . 255)\n  (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 261) (:start . 260)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 266)\n  (:start . 261) (:id . 87))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 268) (:start . 267)\n  (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 269) (:start . 268)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s5.42) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501433@unknown@formal@none@1@S@On admission, only 12 (9.4%) patients had a white blood cell count (WBC) above the age-specific norm and there was no significant difference in median WBC count between uncomplicated and severe cases, suggesting that few if any children had a concomitant systemic bacterial infection.@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "admission") (:form . "admission") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "CD") (:stem . "9.4") (:form . "9.4") (:end . 26) (:start . 23)\n  (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . 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5501434@unknown@formal@none@1@S@No difference was observed in the differential WBC between the two groups.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "differential") (:form . "differential") (:end . 46)\n  (:start . 34) (:id . 48))\n ((:tag . "NNP") (:stem . "WBC") (:form . "WBC") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 58)\n  (:start . 51) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s5.44) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501435@unknown@formal@none@1@S@As expected, [39]–[41] numbers of lymphocytes, CD3+ and CD4+ T cells were significantly lower during the acute disease than during convalescence in both the severe and the uncomplicated groups (Table 1A).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "CD") (:stem . "39]–[41") (:form . "39]–[41") (:end . 21)\n  (:start . 14) (:id . 46))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 30)\n  (:start . 23) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 45)\n  (:start . 34) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "cd3+") (:form . "CD3+") (:end . 51) (:start . 47)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 60) (:start . 56)\n  (:id . 54))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 68) (:start . 63)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 73) (:start . 69)\n  (:id . 57))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 87) (:start . 74) (:id . 58))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 93) (:start . 88)\n  (:id . 59))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 100)\n  (:start . 94) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 110)\n  (:start . 105) (:id . 62))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 118)\n  (:start . 111) (:id . 63))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 123) (:start . 119)\n  (:id . 64))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 130)\n  (:start . 124) (:id . 65))\n ((:tag . "NN") (:stem . "convalescence") (:form . "convalescence")\n  (:end . 144) (:start . 131) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 147) (:start . 145)\n  (:id . 67))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 152) (:start . 148)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 163)\n  (:start . 157) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 171) (:start . 168)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 185) (:start . 172) (:id . 73))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 192)\n  (:start . 186) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 194) (:start . 193)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 199)\n  (:start . 194) (:id . 76))\n ((:tag . "NN") (:stem . "1a") (:form . "1A") (:end . 202) (:start . 200)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 203) (:start . 202)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s5.45) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501436@unknown@formal@none@1@S@Parasite density on admission was two-fold higher in patients with severe malaria than in those with uncomplicated malaria; severely ill children also had significantly lower hemoglobin levels and were on average 2.4 years younger than children with uncomplicated disease.@(((:tag . "NNP") (:stem . "Parasite") (:form . "Parasite") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "density") (:form . "density") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "NN") (:stem . "admission") (:form . "admission") (:end . 29)\n  (:start . 20) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "RB") (:stem . "two-fold") (:form . "two-fold") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 49) (:start . 43)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 73)\n  (:start . 67) (:id . 52))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 81)\n  (:start . 74) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 95) (:start . 90)\n  (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 100) (:start . 96)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 114) (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 122)\n  (:start . 115) (:id . 59))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 123) (:start . 122)\n  (:id . 60))\n ((:tag . "RB") (:stem . "severely") (:form . "severely") (:end . 132)\n  (:start . 124) (:id . 61))\n ((:tag . "JJ") (:stem . "ill") (:form . "ill") (:end . 136) (:start . 133)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 145)\n  (:start . 137) (:id . 63))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 150) (:start . 146)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 154) (:start . 151)\n  (:id . 65))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 168) (:start . 155) (:id . 66))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 174) (:start . 169)\n  (:id . 67))\n ((:tag . "NN") (:stem . "hemoglobin") (:form . "hemoglobin") (:end . 185)\n  (:start . 175) (:id . 68))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 192)\n  (:start . 186) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 196) (:start . 193)\n  (:id . 70))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 201) (:start . 197)\n  (:id . 71))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 204) (:start . 202)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 212)\n  (:start . 205) (:id . 73))\n ((:tag . "CD") (:stem . "2.4") (:form . "2.4") (:end . 216) (:start . 213)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 222)\n  (:start . 217) (:id . 75))\n ((:tag . "JJR") (:stem . "young") (:form . "younger") (:end . 230)\n  (:start . 223) (:id . 76))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 235) (:start . 231)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 244)\n  (:start . 236) (:id . 78))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 249) (:start . 245)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 263) (:start . 250) (:id . 80))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 271)\n  (:start . 264) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 272) (:start . 271)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s5.46) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501437@unknown@formal@none@1@S@The number of P. falciparum clones per clinical isolate ranged from 1 to 4 (with an overall mean of 2 (CI95%: 1.8–2.1)), and – as has been observed previously [42] - did not differ significantly between the three groups (p=0.3, Table 1B).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "falciparum") (:form . "falciparum") (:end . 27)\n  (:start . 17) (:id . 46))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "clinical") (:form . 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5501438@unknown@formal@none@1@S@Other factors potentially confounding immune responses, such as the degree of malnutrition or intestinal helminth infections were of similarly low prevalence in both severe and uncomplicated malaria cases and were not associated with severity of disease (Table 1B).@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "RB") (:stem . "potentially") (:form . "potentially") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "VBG") (:stem . "confound") (:form . "confounding") (:end . 37)\n  (:start . 26) (:id . 45))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 44)\n  (:start . 38) (:id . 46))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 54)\n  (:start . 45) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 60) (:start . 56)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 51))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 74)\n  (:start . 68) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "NN") (:stem . "malnutrition") (:form . "malnutrition") (:end . 90)\n  (:start . 78) (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 93) (:start . 91)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "intestinal") (:form . "intestinal") (:end . 104)\n  (:start . 94) (:id . 56))\n ((:tag . "JJ") (:stem . "helminth") (:form . "helminth") (:end . 113)\n  (:start . 105) (:id . 57))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 124)\n  (:start . 114) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 129) (:start . 125)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 60))\n ((:tag . "RB") (:stem . "similarly") (:form . "similarly") (:end . 142)\n  (:start . 133) (:id . 61))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 146) (:start . 143)\n  (:id . 62))\n ((:tag . "NN") (:stem . "prevalence") (:form . "prevalence") (:end . 157)\n  (:start . 147) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 160) (:start . 158)\n  (:id . 64))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 165) (:start . 161)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 172)\n  (:start . 166) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 190) (:start . 177) (:id . 68))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 198)\n  (:start . 191) (:id . 69))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 204)\n  (:start . 199) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 208) (:start . 205)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 213) (:start . 209)\n  (:id . 72))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 217) (:start . 214)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 228)\n  (:start . 218) (:id . 74))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 233) (:start . 229)\n  (:id . 75))\n ((:tag . "NN") (:stem . "severity") (:form . "severity") (:end . 242)\n  (:start . 234) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 245) (:start . 243)\n  (:id . 77))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 253)\n  (:start . 246) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 255) (:start . 254)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 260)\n  (:start . 255) (:id . 80))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 263) (:start . 261)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 264) (:start . 263)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x5.48.1) (:span 14 25)))\n (:hscopes ((:id . :x5.48.1) (:span 14 54)))\n (:identifiers (:sid . :s5.48) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501439@unknown@formal@none@1@S@Characteristics of study participants (A) and distribution of potential confounding factors (B).@(((:tag . "NNS") (:stem . "characteristic") (:form . "Characteristics")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 24) (:start . 19)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "participant") (:form . "participants") (:end . 37)\n  (:start . 25) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 40) (:start . 39)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 58)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 71)\n  (:start . 62) (:id . 52))\n ((:tag . "VBG") (:stem . "confound") (:form . "confounding") (:end . 83)\n  (:start . 72) (:id . 53))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 91)\n  (:start . 84) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 94) (:start . 93)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s5.49) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5501440@unknown@formal@none@1@S@For statistical analysis, patients were classified as uncomplicated or severe cases, with the latter being further subdivided into those patients suffering from cerebral malaria (CM), severe anaemia (SA) or severe respiratory distress (SRD) (grouped together as SA) and those suffering only from severe prostration (grouped as SB).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "classify") (:form . 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5501441@unknown@formal@none@1@S@Data were analysed using linear regression, with a random effect to allow for the within subject measurements over time, adjusting for age, sex, duration of prior symptoms and numbers of clones causing the infection.@(((:tag . "NNP") (:stem . "Datum") (:form . "Data") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "analyse") (:form . "analysed") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "linear") (:form . "linear") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "regression") (:form . "regression") (:end . 42)\n  (:start . 32) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 57)\n  (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 64)\n  (:start . 58) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 56))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 88)\n  (:start . 82) (:id . 57))\n ((:tag . "JJ") (:stem . "subject") (:form . "subject") (:end . 96)\n  (:start . 89) (:id . 58))\n ((:tag . "NNS") (:stem . "measurement") (:form . "measurements") (:end . 109)\n  (:start . 97) (:id . 59))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 114) (:start . 110)\n  (:id . 60))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 119) (:start . 115)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "adjust") (:form . "adjusting") (:end . 130)\n  (:start . 121) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 134) (:start . 131)\n  (:id . 64))\n ((:tag . "NN") (:stem . "age") (:form . "age") (:end . 138) (:start . 135)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 66))\n ((:tag . "NN") (:stem . "sex") (:form . "sex") (:end . 143) (:start . 140)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 68))\n ((:tag . "NN") (:stem . "duration") (:form . "duration") (:end . 153)\n  (:start . 145) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 156) (:start . 154)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 162)\n  (:start . 157) (:id . 71))\n ((:tag . "NNS") (:stem . "symptom") (:form . "symptoms") (:end . 171)\n  (:start . 163) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 183)\n  (:start . 176) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 186) (:start . 184)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 193)\n  (:start . 187) (:id . 76))\n ((:tag . "VBG") (:stem . "cause") (:form . "causing") (:end . 201)\n  (:start . 194) (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 205) (:start . 202)\n  (:id . 78))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 215)\n  (:start . 206) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s5.51) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501442@unknown@formal@none@1@S@Due to the multiplicity of comparisons that were made within the model, resulting from multiple responses and multiple comparisons within response, hypotheses rejected with a probability of less than 0.012 have a false discovery rate of 5% [43].@(((:tag . "JJ") (:stem . "due") (:form . "Due") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "multiplicity") (:form . "multiplicity") (:end . 23)\n  (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 38)\n  (:start . 27) (:id . 47))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 81)\n  (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 95)\n  (:start . 87) (:id . 57))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 105)\n  (:start . 96) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 118)\n  (:start . 110) (:id . 60))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 130)\n  (:start . 119) (:id . 61))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 137)\n  (:start . 131) (:id . 62))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 146)\n  (:start . 138) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "hypothesis") (:form . "hypotheses") (:end . 158)\n  (:start . 148) (:id . 65))\n ((:tag . "VBD") (:stem . "reject") (:form . "rejected") (:end . 167)\n  (:start . 159) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 172) (:start . 168)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 174) (:start . 173)\n  (:id . 68))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 186)\n  (:start . 175) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 189) (:start . 187)\n  (:id . 70))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 194) (:start . 190)\n  (:id . 71))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 199) (:start . 195)\n  (:id . 72))\n ((:tag . "CD") (:stem . "0.012") (:form . "0.012") (:end . 205)\n  (:start . 200) (:id . 73))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 210) (:start . 206)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 212) (:start . 211)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 218)\n  (:start . 213) (:id . 76))\n ((:tag . "NN") (:stem . "discovery") (:form . "discovery") (:end . 228)\n  (:start . 219) (:id . 77))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 233) (:start . 229)\n  (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 236) (:start . 234)\n  (:id . 79))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 238) (:start . 237)\n  (:id . 80))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 239) (:start . 238)\n  (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 241) (:start . 240)\n  (:id . 82))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 243) (:start . 241)\n  (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 244) (:start . 243)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 245) (:start . 244)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s5.52) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501443@unknown@formal@none@1@S@Similar numbers and proportions of Tregs among uncomplicated and severe malaria cases, increasing during convalescence@(((:tag . "JJ") (:stem . "similar") (:form . "Similar") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "proportion") (:form . "proportions") (:end . 31)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 40) (:start . 35)\n  (:id . 47))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 46) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 60) (:start . 47) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 71)\n  (:start . 65) (:id . 51))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 79)\n  (:start . 72) (:id . 52))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 85) (:start . 80)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 97)\n  (:start . 87) (:id . 55))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 104)\n  (:start . 98) (:id . 56))\n ((:tag . "NN") (:stem . "convalescence") (:form . "convalescence")\n  (:end . 118) (:start . 105) (:id . 57)))@@@1@16@((:identifiers (:sid . :s5.53) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501444@unknown@formal@none@1@S@We hypothesized that children with severe malaria would have fewer circulating Tregs than children with uncomplicated malaria, or that Tregs of severely ill children would be less active than those of children with uncomplicated disease.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "hypothesize") (:form . "hypothesized") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 41)\n  (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 66) (:start . 61)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "circulate") (:form . "circulating") (:end . 78)\n  (:start . 67) (:id . 52))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 84) (:start . 79)\n  (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 89) (:start . 85)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 98)\n  (:start . 90) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 103) (:start . 99)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 117) (:start . 104) (:id . 57))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 125)\n  (:start . 118) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 59))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 129) (:start . 127)\n  (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 134) (:start . 130)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 140)\n  (:start . 135) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 63))\n ((:tag . "RB") (:stem . "severely") (:form . "severely") (:end . 152)\n  (:start . 144) (:id . 64))\n ((:tag . "JJ") (:stem . "ill") (:form . "ill") (:end . 156) (:start . 153)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 165)\n  (:start . 157) (:id . 66))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 171)\n  (:start . 166) (:id . 67))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 174) (:start . 172)\n  (:id . 68))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 179) (:start . 175)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 186)\n  (:start . 180) (:id . 70))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 191) (:start . 187)\n  (:id . 71))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 197)\n  (:start . 192) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 200) (:start . 198)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 209)\n  (:start . 201) (:id . 74))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 214) (:start . 210)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 228) (:start . 215) (:id . 76))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 236)\n  (:start . 229) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 237) (:start . 236)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x5.54.1) (:span 166 171)) ((:id . :x5.54.3) (:span 127 129))\n  ((:id . :x5.54.2) (:span 50 55)) ((:id . :x5.54.4) (:span 3 15)))\n (:hscopes ((:id . :x5.54.1) (:span 166 236)) ((:id . :x5.54.2) (:span 50 125))\n  ((:id . :x5.54.3) (:span 16 236)) ((:id . :x5.54.4) (:span 3 236)))\n (:identifiers (:sid . :s5.54) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501445@unknown@formal@none@1@S@However, the proportion of cells expressing a Treg phenotype (defined by flow cytometry as CD3+CD4+ lymphocytes being FOXP3+and CD127-/low; Figure 1A, 1B, and 1C) was similar in the acute (D0) and the convalescent phase (D28) for both uncomplicated and severe cases (SA+SB) and in healthy control children; on average, 2–3% of CD4+ T cells expressed the regulatory phenotype (Figure 1D).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Treg") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 60)\n  (:start . 51) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 69)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cytometry") (:form . "cytometry") (:end . 87)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "cd3+cd4+") (:form . 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5501446@unknown@formal@none@1@S@However, when the number of cells expressing a Treg phenotype was calculated using lymphocyte and monocyte counts from the differential WBC, we found that the absolute numbers of Tregs (per litre of blood) were significantly and similarly elevated in both severe and uncomplicated malaria cases during convalescence when compared to the acute phase (p<0.001) or when compared to the control group of healthy children (p=0.037) (Figure 1E).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . 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5501447@unknown@formal@none@1@S@A similar kinetic was observed for FOXP3 mRNA levels (Figure 1F).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "kinetic") (:form . "kinetic") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "foxp3") (:form . "FOXP3") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 60)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "1f") (:form . "1F") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s5.57) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501448@unknown@formal@none@1@S@Similar number and proportion of Tregs in uncomplicated and severe disease, increasing during convalescence.@(((:tag . "JJ") (:stem . "similar") (:form . "Similar") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 55) (:start . 42) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 66)\n  (:start . 60) (:id . 51))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 74)\n  (:start . 67) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 86)\n  (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 93)\n  (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "convalescence") (:form . "convalescence")\n  (:end . 107) (:start . 94) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s5.58) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501449@unknown@formal@none@1@S@Although not supportive of our original hypothesis, these observations are consistent with the notion that acute malaria infection drives expansion of Treg populations which then persist for some weeks to maintain immune homeostasis during the contraction phase of the effector response [36].@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "supportive") (:form . "supportive") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 50)\n  (:start . 40) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 70)\n  (:start . 58) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 74) (:start . 71)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 85)\n  (:start . 75) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 55))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 101)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 106) (:start . 102)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 112)\n  (:start . 107) (:id . 58))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 120)\n  (:start . 113) (:id . 59))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 130)\n  (:start . 121) (:id . 60))\n ((:tag . "VBZ") (:stem . "drive") (:form . "drives") (:end . 137)\n  (:start . 131) (:id . 61))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 147)\n  (:start . 138) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 63))\n ((:tag . "NN") (:stem . "treg") (:form . "Treg") (:end . 155) (:start . 151)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "population") (:form . "populations") (:end . 167)\n  (:start . 156) (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 173)\n  (:start . 168) (:id . 66))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 178) (:start . 174)\n  (:id . 67))\n ((:tag . "VBP") (:stem . "persist") (:form . "persist") (:end . 186)\n  (:start . 179) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 190) (:start . 187)\n  (:id . 69))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 195) (:start . 191)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "week") (:form . "weeks") (:end . 201)\n  (:start . 196) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 204) (:start . 202)\n  (:id . 72))\n ((:tag . "VB") (:stem . "maintain") (:form . "maintain") (:end . 213)\n  (:start . 205) (:id . 73))\n ((:tag . "JJ") (:stem . "immune") (:form . "immune") (:end . 220)\n  (:start . 214) (:id . 74))\n ((:tag . "NN") (:stem . "homeostasis") (:form . "homeostasis") (:end . 232)\n  (:start . 221) (:id . 75))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 239)\n  (:start . 233) (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 243) (:start . 240)\n  (:id . 77))\n ((:tag . "NN") (:stem . "contraction") (:form . "contraction") (:end . 255)\n  (:start . 244) (:id . 78))\n ((:tag . "NN") (:stem . "phase") (:form . "phase") (:end . 261)\n  (:start . 256) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 264) (:start . 262)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 268) (:start . 265)\n  (:id . 81))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 277)\n  (:start . 269) (:id . 82))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 286)\n  (:start . 278) (:id . 83))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 288) (:start . 287)\n  (:id . 84))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 290) (:start . 288)\n  (:id . 85))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 291) (:start . 290)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 292) (:start . 291)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s5.59) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501450@unknown@formal@none@1@S@In accordance with this notion, and in agreement with our previous observation that increased levels of Tregs were associated with faster parasite growth during the early stages of blood stage infection [27], we observe here in - children with either severe or uncomplicated malaria infections - a significant positive correlation between parasite density and the frequency of Tregs within the CD4+ T cell population (p=0.002, Figure 2).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "accordance") (:form . "accordance") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . 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"density") (:form . "density") (:end . 355)\n  (:start . 348) (:id . 98))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 359) (:start . 356)\n  (:id . 99))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 363) (:start . 360)\n  (:id . 100))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 373)\n  (:start . 364) (:id . 101))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 376) (:start . 374)\n  (:id . 102))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 382)\n  (:start . 377) (:id . 103))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 389)\n  (:start . 383) (:id . 104))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 393) (:start . 390)\n  (:id . 105))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 398) (:start . 394)\n  (:id . 106))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 400) (:start . 399)\n  (:id . 107))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 405) (:start . 401)\n  (:id . 108))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 416)\n  (:start . 406) (:id . 109))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 418) (:start . 417)\n  (:id . 110))\n ((:tag . "NN") (:stem . "p=0.002") (:form . "p=0.002") (:end . 425)\n  (:start . 418) (:id . 111))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 426) (:start . 425)\n  (:id . 112))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 433)\n  (:start . 427) (:id . 113))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 435) (:start . 434)\n  (:id . 114))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 436) (:start . 435)\n  (:id . 115))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 437) (:start . 436)\n  (:id . 116)))@@@1@75@((:identifiers (:sid . :s5.60) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501451@unknown@formal@none@1@S@Proportion of T cells expressing a Treg phenotype correlates with parasitaemia.@(((:tag . "NN") (:stem . "proportion") (:form . "Proportion") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Treg") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "VBZ") (:stem . "correlate") (:form . "correlates") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "parasitaemia") (:form . "parasitaemia") (:end . 78)\n  (:start . 66) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s5.61) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501452@unknown@formal@none@1@S@Tregs display an activated memory phenotype during acute disease@(((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 50)\n  (:start . 44) (:id . 48))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 56) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 64)\n  (:start . 57) (:id . 50)))@@@1@9@((:identifiers (:sid . :s5.62) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501453@unknown@formal@none@1@S@Since fully differentiated Tregs predominantly express an activated/memory phenotype [44] T cells from children with severe and uncomplicated malaria were analysed for expression of CD45RO (Figure 3A and 3B).@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "fully") (:form . "fully") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "differentiate") (:form . "differentiated")\n  (:end . 26) (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 32) (:start . 27)\n  (:id . 45))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 46) (:start . 33) (:id . 46))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 54)\n  (:start . 47) (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 57) (:start . 55)\n  (:id . 48))\n ((:tag . "NN") (:stem . "activated/memory") (:form . "activated/memory")\n  (:end . 74) (:start . 58) (:id . 49))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 84)\n  (:start . 75) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 86) (:start . 85)\n  (:id . 51))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 88) (:start . 86)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 89) (:start . 88)\n  (:id . 53))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 91) (:start . 90)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 97) (:start . 92)\n  (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 102) (:start . 98)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 111)\n  (:start . 103) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 116) (:start . 112)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 123)\n  (:start . 117) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 141) (:start . 128) (:id . 61))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 149)\n  (:start . 142) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 154) (:start . 150)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "analyse") (:form . "analysed") (:end . 163)\n  (:start . 155) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 167) (:start . 164)\n  (:id . 65))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 178)\n  (:start . 168) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 181) (:start . 179)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "CD45RO") (:form . "CD45RO") (:end . 188)\n  (:start . 182) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 190) (:start . 189)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 196)\n  (:start . 190) (:id . 70))\n ((:tag . "NN") (:stem . "3a") (:form . "3A") (:end . 199) (:start . 197)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 203) (:start . 200)\n  (:id . 72))\n ((:tag . "NN") (:stem . "3b") (:form . "3B") (:end . 206) (:start . 204)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 207) (:start . 206)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s5.63) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501454@unknown@formal@none@1@S@In both uncomplicated and severe cases, the proportion of all T cells expressing CD45RO was significantly higher (p<0.001) during acute infection than during convalescence (data not shown).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 21) (:start . 8) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 80)\n  (:start . 70) (:id . 55))\n ((:tag . "NN") (:stem . "cd45ro") (:form . "CD45RO") (:end . 87)\n  (:start . 81) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 91) (:start . 88)\n  (:id . 57))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 105) (:start . 92) (:id . 58))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 112)\n  (:start . 106) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 60))\n ((:tag . "CD") (:stem . "p<0.001") (:form . "p<0.001") (:end . 121)\n  (:start . 114) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 129)\n  (:start . 123) (:id . 63))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 135)\n  (:start . 130) (:id . 64))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 145)\n  (:start . 136) (:id . 65))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 150) (:start . 146)\n  (:id . 66))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 157)\n  (:start . 151) (:id . 67))\n ((:tag . "NN") (:stem . "convalescence") (:form . "convalescence")\n  (:end . 171) (:start . 158) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 173) (:start . 172)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 177)\n  (:start . 173) (:id . 70))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 181) (:start . 178)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 187)\n  (:start . 182) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s5.64) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501455@unknown@formal@none@1@S@Irrespective of disease severity, more than 90% of Tregs expressed CD45RO during the acute phase of infection but expression of this marker decreased significantly (to approx 70%) during convalescence (Figure 3C).@(((:tag . "JJ") (:stem . "irrespective") (:form . "Irrespective") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "severity") (:form . "severity") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 46))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "express") (:form . "expressed") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "cd45ro") (:form . "CD45RO") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 80)\n  (:start . 74) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "NN") (:stem . "phase") (:form . "phase") (:end . 96) (:start . 91)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 59))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 109)\n  (:start . 100) (:id . 60))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 113) (:start . 110)\n  (:id . 61))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 124)\n  (:start . 114) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 132) (:start . 128)\n  (:id . 64))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 139)\n  (:start . 133) (:id . 65))\n ((:tag . "VBD") (:stem . "decrease") (:form . "decreased") (:end . 149)\n  (:start . 140) (:id . 66))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 163) (:start . 150) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 165) (:start . 164)\n  (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 167) (:start . 165)\n  (:id . 69))\n ((:tag . "VB") (:stem . "approx") (:form . "approx") (:end . 174)\n  (:start . 168) (:id . 70))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 177) (:start . 175)\n  (:id . 71))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 178) (:start . 177)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 73))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 186)\n  (:start . 180) (:id . 74))\n ((:tag . "NN") (:stem . "convalescence") (:form . "convalescence")\n  (:end . 200) (:start . 187) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 202) (:start . 201)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 208)\n  (:start . 202) (:id . 77))\n ((:tag . "NN") (:stem . "3c") (:form . "3C") (:end . 211) (:start . 209)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 212) (:start . 211)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s5.65) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501456@unknown@formal@none@1@S@Likewise, the median fluorescence intensity (MFI) of CD45RO staining was 1.5 fold higher (p=0.0025) during acute disease than during convalescence (Figure 3D).@(((:tag . "RB") (:stem . "likewise") (:form . "Likewise") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "median") (:form . "median") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 33)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "MFI") (:form . "MFI") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "CD45RO") (:form . "CD45RO") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "CD") (:stem . "1.5") (:form . "1.5") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "RB") (:stem . "fold") (:form . "fold") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 88) (:start . 82)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "p=0.0025") (:form . "p=0.0025") (:end . 98)\n  (:start . 90) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 60))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 106)\n  (:start . 100) (:id . 61))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 112)\n  (:start . 107) (:id . 62))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 120)\n  (:start . 113) (:id . 63))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 125) (:start . 121)\n  (:id . 64))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 132)\n  (:start . 126) (:id . 65))\n ((:tag . "NN") (:stem . "convalescence") (:form . "convalescence")\n  (:end . 146) (:start . 133) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 154)\n  (:start . 148) (:id . 68))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 157) (:start . 155)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s5.66) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501457@unknown@formal@none@1@S@Taken together, these data indicate that in both uncomplicated and severe cases of malaria Tregs are predominantly of a memory phenotype and are activated during acute malaria infection.@(((:tag . "VBN") (:stem . "take") (:form . "Taken") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 62) (:start . 49) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 90)\n  (:start . 83) (:id . 56))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 114) (:start . 101) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 119) (:start . 118)\n  (:id . 61))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 126)\n  (:start . 120) (:id . 62))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 136)\n  (:start . 127) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 144) (:start . 141)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 154)\n  (:start . 145) (:id . 66))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 161)\n  (:start . 155) (:id . 67))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 167)\n  (:start . 162) (:id . 68))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 175)\n  (:start . 168) (:id . 69))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 185)\n  (:start . 176) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x5.67.1) (:span 27 40)))\n (:hscopes ((:id . :x5.67.1) (:span 27 185)))\n (:identifiers (:sid . :s5.67) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501458@unknown@formal@none@1@S@Tregs display an activated memory phenotype during acute disease.@(((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 50)\n  (:start . 44) (:id . 48))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 56) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 64)\n  (:start . 57) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s5.68) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501459@unknown@formal@none@1@S@Similar Treg function in uncomplicated and severe malaria patients@(((:tag . "JJ") (:stem . "similar") (:form . "Similar") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Treg") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 38) (:start . 25) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 49)\n  (:start . 43) (:id . 48))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 66)\n  (:start . 58) (:id . 50)))@@@1@9@((:identifiers (:sid . :s5.69) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501460@unknown@formal@none@1@S@Three different indicators were used to assess the regulatory potential of Tregs during acute malaria infection.@(((:tag . "CD") (:stem . "three") (:form . "Three") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "indicator") (:form . "indicators") (:end . 26)\n  (:start . 16) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 46)\n  (:start . 40) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 61)\n  (:start . 51) (:id . 50))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 71)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 80) (:start . 75)\n  (:id . 53))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 87)\n  (:start . 81) (:id . 54))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 93) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 101)\n  (:start . 94) (:id . 56))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 111)\n  (:start . 102) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s5.70) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501461@unknown@formal@none@1@S@Firstly, using a classical anti-CD25 depletion assay, we assessed the ability of Tregs to suppress P. falciparum shizont extract (PfSE)-driven lymphocyte proliferation.@(((:tag . "RB") (:stem . "firstly") (:form . "Firstly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "classical") (:form . "classical") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "anti-cd25") (:form . "anti-CD25") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "depletion") (:form . "depletion") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "assess") (:form . "assessed") (:end . 65)\n  (:start . 57) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 77)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 86) (:start . 81)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "VB") (:stem . "suppress") (:form . "suppress") (:end . 98)\n  (:start . 90) (:id . 58))\n ((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "falciparum") (:form . "falciparum") (:end . 112)\n  (:start . 102) (:id . 60))\n ((:tag . "NN") (:stem . "shizont") (:form . "shizont") (:end . 120)\n  (:start . 113) (:id . 61))\n ((:tag . "NN") (:stem . "extract") (:form . "extract") (:end . 128)\n  (:start . 121) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "PfSE)-driven") (:form . "PfSE)-driven")\n  (:end . 142) (:start . 130) (:id . 64))\n ((:tag . "NN") (:stem . "lymphocyte") (:form . "lymphocyte") (:end . 153)\n  (:start . 143) (:id . 65))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 167) (:start . 154) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s5.71) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501462@unknown@formal@none@1@S@Anti CD25 treatment removed approximately half (geometric mean 48.8%; CI95%: 41–58%) of the CD4+ T cells that were FOXP3+CD127-/low and this was associated with a 1.76 fold and 1.57-fold (geometric means) increase in PfSE-induced lymphoproliferation in severe and uncomplicated cases, respectively, with no significant difference between the groups (p=0.343, Figure 4A).@(((:tag . "JJ") (:stem . "anti") (:form . "Anti") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "CD25") (:form . "CD25") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "remove") (:form . "removed") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 41) (:start . 28) (:id . 46))\n ((:tag . "JJ") (:stem . "half") (:form . "half") (:end . 46) (:start . 42)\n  (:id . 47))\n ((:tag . 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5501463@unknown@formal@none@1@S@Tregs from severe and uncomplicated cases have similar functional capacity.@(((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 35) (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 65)\n  (:start . 55) (:id . 50))\n ((:tag . "NN") (:stem . "capacity") (:form . "capacity") (:end . 74)\n  (:start . 66) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s5.73) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501464@unknown@formal@none@1@S@Next, since reduced expression of SOCS-2, a member of the suppressors of cytokine signaling family confined to Tregs [45], has been linked to impaired Treg function in Africans [38] we compared SOCS-2 mRNA levels among severe and uncomplicated cases.@(((:tag . "RB") (:stem . "next") (:form . "Next") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 30)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "socs-2") (:form . "SOCS-2") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "member") (:form . "member") (:end . 50)\n  (:start . 44) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "suppressor") (:form . "suppressors") (:end . 69)\n  (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 81)\n  (:start . 73) (:id . 56))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 91)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 98)\n  (:start . 92) (:id . 58))\n ((:tag . "VBN") (:stem . "confine") (:form . "confined") (:end . 107)\n  (:start . 99) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 116)\n  (:start . 111) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 120) (:start . 118)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 126) (:start . 123)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 131) (:start . 127)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "link") (:form . "linked") (:end . 138)\n  (:start . 132) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 141) (:start . 139)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "impaired") (:form . "impaired") (:end . 150)\n  (:start . 142) (:id . 70))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Treg") (:end . 155) (:start . 151)\n  (:id . 71))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 164)\n  (:start . 156) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 167) (:start . 165)\n  (:id . 73))\n ((:tag . "NNPS") (:stem . "African") (:form . "Africans") (:end . 176)\n  (:start . 168) (:id . 74))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 178) (:start . 177)\n  (:id . 75))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 180) (:start . 178)\n  (:id . 76))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 181) (:start . 180)\n  (:id . 77))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 184) (:start . 182)\n  (:id . 78))\n ((:tag . "VBD") (:stem . "compare") (:form . "compared") (:end . 193)\n  (:start . 185) (:id . 79))\n ((:tag . "NN") (:stem . "socs-2") (:form . "SOCS-2") (:end . 200)\n  (:start . 194) (:id . 80))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 205) (:start . 201)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 212)\n  (:start . 206) (:id . 82))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 218)\n  (:start . 213) (:id . 83))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 225)\n  (:start . 219) (:id . 84))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 229) (:start . 226)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 243) (:start . 230) (:id . 86))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 249)\n  (:start . 244) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 250) (:start . 249)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s5.74) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501465@unknown@formal@none@1@S@While SOCS-2 levels were found to be significantly reduced during acute disease compared to convalescence (p=0.0076), no difference was observed between those with severe and those with uncomplicated malaria (data not shown).@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "socs-2") (:form . "SOCS-2") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 50) (:start . 37) (:id . 49))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 58)\n  (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 65)\n  (:start . 59) (:id . 51))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 71) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 79)\n  (:start . 72) (:id . 53))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 88)\n  (:start . 80) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "convalescence") (:form . "convalescence")\n  (:end . 105) (:start . 92) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 57))\n ((:tag . "NN") (:stem . "p=0.0076") (:form . "p=0.0076") (:end . 115)\n  (:start . 107) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 60))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 120) (:start . 118)\n  (:id . 61))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 131)\n  (:start . 121) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 135) (:start . 132)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 144)\n  (:start . 136) (:id . 64))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 152)\n  (:start . 145) (:id . 65))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 158)\n  (:start . 153) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 163) (:start . 159)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 170)\n  (:start . 164) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 174) (:start . 171)\n  (:id . 69))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 180)\n  (:start . 175) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 185) (:start . 181)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 199) (:start . 186) (:id . 72))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 207)\n  (:start . 200) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 209) (:start . 208)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 213)\n  (:start . 209) (:id . 75))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 217) (:start . 214)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 223)\n  (:start . 218) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 224) (:start . 223)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s5.75) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501466@unknown@formal@none@1@S@Finally, since high concentrations of TNF-α have been reported to impair Treg activity (by upregulating and then signaling via TNFR2, leading to decreased FOXP3 mRNA and protein expression [46]), and the functional impairment of Tregs observed in rheumatoid arthritis patients can be reversed by anti-TNF-α antibodies [47], we considered the hypothesis that the high levels of TNF-α seen in severe malaria patients [13],[15], might upregulate TNFR2 and impair Treg function.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 34) (:start . 20) (:id . 46))\n ((:tag . 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5501467@unknown@formal@none@1@S@TNFR2 expression on Tregs was assessed by flow cytometry (Figure 4B and 4C).@(((:tag . "NN") (:stem . "tnfr2") (:form . "TNFR2") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 25) (:start . 20)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cytometry") (:form . "cytometry") (:end . 56)\n  (:start . 47) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 64)\n  (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "4b") (:form . "4B") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "4c") (:form . "4C") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s5.77) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501468@unknown@formal@none@1@S@However, although a significantly higher proportion of Tregs expressed TNFR2 (Figure 4D) - with higher MFI (data not shown, p=0.028) - during acute disease compared to convalescence, no difference was seen in TNFR2 expression on Tregs between severe and uncomplicated cases (Figure 4D).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 33) (:start . 20) (:id . 46))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 40) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 51)\n  (:start . 41) (:id . 48))\n ((:tag . 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5501469@unknown@formal@none@1@S@Moreover, there was no correlation between plasma levels of TNF-α and TNFR2 expression on Tregs, neither among severe or uncomplicated cases nor among all cases combined; neither did we observe any inverse correlation between TNF-α concentration and FOXP3 expression.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 34)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "plasma") (:form . "plasma") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 65) (:start . 60)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "tnfr2") (:form . "TNFR2") (:end . 75) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 86)\n  (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 95) (:start . 90)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . "CC") (:stem . "neither") (:form . "neither") (:end . 104)\n  (:start . 97) (:id . 59))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 110)\n  (:start . 105) (:id . 60))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 117)\n  (:start . 111) (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 120) (:start . 118)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 134) (:start . 121) (:id . 63))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 140)\n  (:start . 135) (:id . 64))\n ((:tag . "CC") (:stem . "nor") (:form . "nor") (:end . 144) (:start . 141)\n  (:id . 65))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 154) (:start . 151)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 160)\n  (:start . 155) (:id . 68))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 169)\n  (:start . 161) (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 170) (:start . 169)\n  (:id . 70))\n ((:tag . "CC") (:stem . "neither") (:form . "neither") (:end . 178)\n  (:start . 171) (:id . 71))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 182) (:start . 179)\n  (:id . 72))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 185) (:start . 183)\n  (:id . 73))\n ((:tag . "VBP") (:stem . "observe") (:form . "observe") (:end . 193)\n  (:start . 186) (:id . 74))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 197) (:start . 194)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "inverse") (:form . "inverse") (:end . 205)\n  (:start . 198) (:id . 76))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 217)\n  (:start . 206) (:id . 77))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 225)\n  (:start . 218) (:id . 78))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 231)\n  (:start . 226) (:id . 79))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 245) (:start . 232) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 249) (:start . 246)\n  (:id . 81))\n ((:tag . "NN") (:stem . "foxp3") (:form . "FOXP3") (:end . 255)\n  (:start . 250) (:id . 82))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 266)\n  (:start . 256) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 267) (:start . 266)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s5.79) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501470@unknown@formal@none@1@S@Rather, the MFI of TNFR2 on Tregs was positively correlated with the MFI of FOXP3 in Tregs (r: 0.476; p<0.0001).@(((:tag . "RB") (:stem . "rather") (:form . "Rather") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "MFI") (:form . "MFI") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "TNFR2") (:form . "TNFR2") (:end . 24) (:start . 19)\n  (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 33) (:start . 28)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 37) (:start . 34)\n  (:id . 50))\n ((:tag . "RB") (:stem . "positively") (:form . "positively") (:end . 48)\n  (:start . 38) (:id . 51))\n ((:tag . "VBN") (:stem . "correlate") (:form . "correlated") (:end . 59)\n  (:start . 49) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "MFI") (:form . "MFI") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "FOXP3") (:form . "FOXP3") (:end . 81) (:start . 76)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 90) (:start . 85)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 60))\n ((:tag . "NN") (:stem . "r") (:form . "r") (:end . 93) (:start . 92)\n  (:id . 61))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 94) (:start . 93)\n  (:id . 62))\n ((:tag . "CD") (:stem . "0.476") (:form . "0.476") (:end . 100) (:start . 95)\n  (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 101) (:start . 100)\n  (:id . 64))\n ((:tag . "CD") (:stem . "p<0.0001") (:form . "p<0.0001") (:end . 110)\n  (:start . 102) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s5.80) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501471@unknown@formal@none@1@S@Thus, our data seem to be more in line with data from mice suggesting that the interaction of TNF-α with TNFR2 on Tregs promotes their expansion and upregulation of FOXP3 [48] than with the data from studies of human rheumatoid arthritis.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 14) (:start . 10)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "seem") (:form . "seem") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 25) (:start . 23)\n  (:id . 48))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 30) (:start . 26)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 50))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 38) (:start . 34)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 43) (:start . 39)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 48) (:start . 44)\n  (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 53) (:start . 49)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 58) (:start . 54)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 69)\n  (:start . 59) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 74) (:start . 70)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 58))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 90)\n  (:start . 79) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 99) (:start . 94)\n  (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 104) (:start . 100)\n  (:id . 62))\n ((:tag . "NN") (:stem . "tnfr2") (:form . "TNFR2") (:end . 110)\n  (:start . 105) (:id . 63))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 113) (:start . 111)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 119)\n  (:start . 114) (:id . 65))\n ((:tag . "VBZ") (:stem . "promote") (:form . "promotes") (:end . 128)\n  (:start . 120) (:id . 66))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 134)\n  (:start . 129) (:id . 67))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 144)\n  (:start . 135) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n  (:id . 69))\n ((:tag . "NN") (:stem . "upregulation") (:form . "upregulation") (:end . 161)\n  (:start . 149) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 164) (:start . 162)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "FOXP3") (:form . "FOXP3") (:end . 170)\n  (:start . 165) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 172) (:start . 171)\n  (:id . 73))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 174) (:start . 172)\n  (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 175) (:start . 174)\n  (:id . 75))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 180) (:start . 176)\n  (:id . 76))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 185) (:start . 181)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 189) (:start . 186)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 194)\n  (:start . 190) (:id . 79))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 199) (:start . 195)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 207)\n  (:start . 200) (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 210) (:start . 208)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 216)\n  (:start . 211) (:id . 83))\n ((:tag . "JJ") (:stem . "rheumatoid") (:form . "rheumatoid") (:end . 227)\n  (:start . 217) (:id . 84))\n ((:tag . "NN") (:stem . "arthritis") (:form . "arthritis") (:end . 237)\n  (:start . 228) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 86)))@@@1@45@((:hcues ((:id . :x5.81.1) (:span 59 69)) ((:id . :x5.81.2) (:span 15 19)))\n (:hscopes ((:id . :x5.81.1) (:span 59 237)) ((:id . :x5.81.2) (:span 6 237)))\n (:identifiers (:sid . :s5.81) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501472@unknown@formal@none@1@S@Stronger Th-1 responses observed in severe compared to uncomplicated cases are balanced by IL-10@(((:tag . "JJR") (:stem . "strong") (:form . "Stronger") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "th-1") (:form . "Th-1") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 42)\n  (:start . 36) (:id . 47))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 68) (:start . 55) (:id . 50))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 74) (:start . 69)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 78) (:start . 75)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "balance") (:form . "balanced") (:end . 87)\n  (:start . 79) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 96) (:start . 91)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s5.82) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501473@unknown@formal@none@1@S@Since the balance of T-effector to Treg responses is likely to be as important, or more important, than the absolute levels of either [26], we compared the ratio of the levels of mRNA for the Th1 transcription factor T-BET with those for FOXP3, currently considered the best marker for Tregs, and the ratio of T-effector cells (defined as CD3+CD4+CD25+FOXP3-, T-effector) over Tregs among the various groups.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "balance") (:form . "balance") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "T-effector") (:form . "T-effector") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . 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5501474@unknown@formal@none@1@S@As shown in Figure 5A, in all groups the T-BET/FOXP3 ratio was significantly higher during acute disease than during convalescence and a similar, albeit not significant, trend was observed for the ratio of T-effector/Tregs (data not shown).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "5a") (:form . "5A") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n  (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 29) (:start . 26)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 36)\n  (:start . 30) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 51))\n ((:tag . "NN") (:stem . "t-bet/foxp3") (:form . "T-BET/FOXP3") (:end . 52)\n  (:start . 41) (:id . 52))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 58) (:start . 53)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 76) (:start . 63) (:id . 55))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 83) (:start . 77)\n  (:id . 56))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 90)\n  (:start . 84) (:id . 57))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 96) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 104)\n  (:start . 97) (:id . 59))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 116)\n  (:start . 110) (:id . 61))\n ((:tag . "NN") (:stem . "convalescence") (:form . "convalescence")\n  (:end . 130) (:start . 117) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 144)\n  (:start . 137) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . "IN") (:stem . "albeit") (:form . "albeit") (:end . 152)\n  (:start . 146) (:id . 67))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 156) (:start . 153)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 168)\n  (:start . 157) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 70))\n ((:tag . "NN") (:stem . "trend") (:form . "trend") (:end . 175)\n  (:start . 170) (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 179) (:start . 176)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 188)\n  (:start . 180) (:id . 73))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 192) (:start . 189)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 75))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 202)\n  (:start . 197) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "T-effector/Treg") (:form . "T-effector/Tregs")\n  (:end . 222) (:start . 206) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 224) (:start . 223)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 228)\n  (:start . 224) (:id . 80))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 232) (:start . 229)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 238)\n  (:start . 233) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 239) (:start . 238)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 240) (:start . 239)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s5.84) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501475@unknown@formal@none@1@S@Moreover, since the absolute number of circulating T-effector cells was significantly higher in severe cases than in uncomplicated cases (p=0.01, data not shown), the T-effector/Treg ratio tended to be higher among severe cases than uncomplicated cases on day 0 (p=0.039) and a similar trend was seen for the T-BET/FOXP3 ratio (p=0.058).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "absolute") (:form . "absolute") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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5501476@unknown@formal@none@1@S@The ratio of FOXP3 to GATA-3 (Th2 lineage factor) mRNA was similar for both time points in all groups (data not shown) but the Th1/Th2 ratio (T-BET/GATA-3 mRNA) was significantly higher during acute disease in children with CM, SA or SRD compared to those suffering from severe prostration (p=0.0075), indicating that the expansion of the T-effector population is biased towards Th1 responses.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "foxp3") (:form . "FOXP3") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "GATA-3") (:form . "GATA-3") (:end . 28)\n  (:start . 22) (:id . 47))\n ((:tag . "(") (:stem . 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5501477@unknown@formal@none@1@S@Ratios of Th1 over Treg cells and pro-inflammatory over regulatory cytokines.@(((:tag . "NNS") (:stem . "ratio") (:form . "Ratios") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "treg") (:form . "Treg") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "pro-inflammatory") (:form . "pro-inflammatory")\n  (:end . 50) (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 66)\n  (:start . 56) (:id . 51))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 76)\n  (:start . 67) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s5.87) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501478@unknown@formal@none@1@S@These data confirm previous studies indicating a shift towards a more inflammatory response during acute and severe malaria but, significantly, our data extend the previous observations by revealing that this inflammation is not balanced by a commensurate increase in Treg function.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "confirm") (:form . "confirm") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 46)\n  (:start . 36) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 54) (:start . 49)\n  (:id . 49))\n ((:tag . "IN") (:stem . "towards") (:form . "towards") (:end . 62)\n  (:start . 55) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 51))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 69) (:start . 65)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 82)\n  (:start . 70) (:id . 53))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 91)\n  (:start . 83) (:id . 54))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 98)\n  (:start . 92) (:id . 55))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 104) (:start . 99)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 115)\n  (:start . 109) (:id . 58))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 123)\n  (:start . 116) (:id . 59))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 127) (:start . 124)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 61))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 142) (:start . 129) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 63))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 147) (:start . 144)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 152)\n  (:start . 148) (:id . 65))\n ((:tag . "VBP") (:stem . "extend") (:form . "extend") (:end . 159)\n  (:start . 153) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 172)\n  (:start . 164) (:id . 68))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 185)\n  (:start . 173) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 188) (:start . 186)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "reveal") (:form . "revealing") (:end . 198)\n  (:start . 189) (:id . 71))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 203) (:start . 199)\n  (:id . 72))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 208) (:start . 204)\n  (:id . 73))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 221)\n  (:start . 209) (:id . 74))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 224) (:start . 222)\n  (:id . 75))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 228) (:start . 225)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "balance") (:form . "balanced") (:end . 237)\n  (:start . 229) (:id . 77))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 240) (:start . 238)\n  (:id . 78))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 242) (:start . 241)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "commensurate") (:form . "commensurate") (:end . 255)\n  (:start . 243) (:id . 80))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 264)\n  (:start . 256) (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 267) (:start . 265)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Treg") (:end . 272) (:start . 268)\n  (:id . 83))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 281)\n  (:start . 273) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 282) (:start . 281)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x5.88.1) (:span 36 46)))\n (:hscopes ((:id . :x5.88.1) (:span 36 123)))\n (:identifiers (:sid . :s5.88) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501479@unknown@formal@none@1@S@Indeed, our data strongly suggest that the potent inflammation induced during an acute malaria infection overwhelms the normal homeostatic capacity of the immune system and, in particular, that the Treg response in children with severe malaria is insufficient to balance a much stronger Th1 effector response.@(((:tag . "RB") (:stem . "indeed") (:form . "Indeed") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . 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5501480@unknown@formal@none@1@S@To investigate further the dynamics of pro-inflammatory/regulatory responses during clinical malaria, plasma concentrations and mRNA transcripts of inflammatory (IFN-γ, TNF-α) and regulatory cytokines (IL-10) were assayed.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "dynamic") (:form . "dynamics") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "pro-inflammatory/regulatory")\n  (:form . "pro-inflammatory/regulatory") (:end . 66) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 76)\n  (:start . 67) (:id . 49))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 83)\n  (:start . 77) (:id . 50))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 92)\n  (:start . 84) (:id . 51))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 100)\n  (:start . 93) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 53))\n ((:tag . "NN") (:stem . "plasma") (:form . "plasma") (:end . 108)\n  (:start . 102) (:id . 54))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 123) (:start . 109) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 56))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 132) (:start . 128)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "transcript") (:form . "transcripts") (:end . 144)\n  (:start . 133) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 160)\n  (:start . 148) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 167)\n  (:start . 162) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 174)\n  (:start . 169) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 175) (:start . 174)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 190)\n  (:start . 180) (:id . 67))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 200)\n  (:start . 191) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 202) (:start . 201)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 207)\n  (:start . 202) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 208) (:start . 207)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 213) (:start . 209)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "assay") (:form . "assayed") (:end . 221)\n  (:start . 214) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s5.90) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501481@unknown@formal@none@1@S@In accordance with previous observations, plasma concentrations of IFN-γ, TNF-α and IL-10 were all significantly higher during acute disease than during convalescence, with significantly higher levels in severely ill children compared to uncomplicated cases (Figure 5B, 5C, and 5D).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "accordance") (:form . "accordance") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 40)\n  (:start . 28) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 47))\n ((:tag . "NN") (:stem . "plasma") (:form . "plasma") (:end . 48)\n  (:start . 42) (:id . 48))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 63) (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 72) (:start . 67)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 79) (:start . 74)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 89) (:start . 84)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 112) (:start . 99) (:id . 58))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 119)\n  (:start . 113) (:id . 59))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 126)\n  (:start . 120) (:id . 60))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 132)\n  (:start . 127) (:id . 61))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 140)\n  (:start . 133) (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 145) (:start . 141)\n  (:id . 63))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 152)\n  (:start . 146) (:id . 64))\n ((:tag . "NN") (:stem . "convalescence") (:form . "convalescence")\n  (:end . 166) (:start . 153) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 172) (:start . 168)\n  (:id . 67))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 186) (:start . 173) (:id . 68))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 193)\n  (:start . 187) (:id . 69))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 200)\n  (:start . 194) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 203) (:start . 201)\n  (:id . 71))\n ((:tag . "RB") (:stem . "severely") (:form . "severely") (:end . 212)\n  (:start . 204) (:id . 72))\n ((:tag . "JJ") (:stem . "ill") (:form . "ill") (:end . 216) (:start . 213)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 225)\n  (:start . 217) (:id . 74))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 234)\n  (:start . 226) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 237) (:start . 235)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 251) (:start . 238) (:id . 77))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 257)\n  (:start . 252) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 259) (:start . 258)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 265)\n  (:start . 259) (:id . 80))\n ((:tag . "NN") (:stem . "5b") (:form . "5B") (:end . 268) (:start . 266)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 269) (:start . 268)\n  (:id . 82))\n ((:tag . "NN") (:stem . "5c") (:form . "5C") (:end . 272) (:start . 270)\n  (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 273) (:start . 272)\n  (:id . 84))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 277) (:start . 274)\n  (:id . 85))\n ((:tag . "NN") (:stem . "5d") (:form . "5D") (:end . 280) (:start . 278)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 281) (:start . 280)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 282) (:start . 281)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s5.91) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501482@unknown@formal@none@1@S@Levels of mRNA transcripts for IL-10 and IFN-γ were also significantly elevated in all groups during acute disease, but there was no significant difference between severity groups (Figure S1A and S1B).@(((:tag . "NNS") (:stem . "level") (:form . "Levels") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "transcript") (:form . "transcripts") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 70) (:start . 57) (:id . 52))\n ((:tag . "JJ") (:stem . "elevated") (:form . "elevated") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 93)\n  (:start . 87) (:id . 56))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 100)\n  (:start . 94) (:id . 57))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 106)\n  (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 114)\n  (:start . 107) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 60))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 119) (:start . 116)\n  (:id . 61))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 125)\n  (:start . 120) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 129) (:start . 126)\n  (:id . 63))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 132) (:start . 130)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 144)\n  (:start . 133) (:id . 65))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 155)\n  (:start . 145) (:id . 66))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 163)\n  (:start . 156) (:id . 67))\n ((:tag . "NN") (:stem . "severity") (:form . "severity") (:end . 172)\n  (:start . 164) (:id . 68))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 179)\n  (:start . 173) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 181) (:start . 180)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 187)\n  (:start . 181) (:id . 71))\n ((:tag . "NNP") (:stem . "S1A") (:form . "S1A") (:end . 191) (:start . 188)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 195) (:start . 192)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "S1B") (:form . "S1B") (:end . 199) (:start . 196)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 200) (:start . 199)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s5.92) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501483@unknown@formal@none@1@S@For both severe and uncomplicated cases, levels of IFN-γ mRNA were highly correlated with levels of IL-10 mRNA during the acute phase (severe: r=0.833 p<0.001, uncomplicated: r=0.693 p<0.001), suggesting that IFN-γ production is being balanced by IL-10 production.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 33) (:start . 20) (:id . 46))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "VBN") (:stem . "correlate") (:form . "correlated") (:end . 84)\n  (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 96)\n  (:start . 90) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 105)\n  (:start . 100) (:id . 59))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 110) (:start . 106)\n  (:id . 60))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 117)\n  (:start . 111) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 127)\n  (:start . 122) (:id . 63))\n ((:tag . "NN") (:stem . "phase") (:form . "phase") (:end . 133)\n  (:start . 128) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 141)\n  (:start . 135) (:id . 66))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 142) (:start . 141)\n  (:id . 67))\n ((:tag . "NN") (:stem . "r=0.833") (:form . "r=0.833") (:end . 150)\n  (:start . 143) (:id . 68))\n ((:tag . "CD") (:stem . "p<0.001") (:form . "p<0.001") (:end . 158)\n  (:start . 151) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 173) (:start . 160) (:id . 71))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 174) (:start . 173)\n  (:id . 72))\n ((:tag . "NN") (:stem . "r=0.693") (:form . "r=0.693") (:end . 182)\n  (:start . 175) (:id . 73))\n ((:tag . "CD") (:stem . "p<0.001") (:form . "p<0.001") (:end . 190)\n  (:start . 183) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 191) (:start . 190)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 192) (:start . 191)\n  (:id . 76))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 203)\n  (:start . 193) (:id . 77))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 208) (:start . 204)\n  (:id . 78))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 214)\n  (:start . 209) (:id . 79))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 225)\n  (:start . 215) (:id . 80))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 228) (:start . 226)\n  (:id . 81))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 234) (:start . 229)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "balance") (:form . "balanced") (:end . 243)\n  (:start . 235) (:id . 83))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 246) (:start . 244)\n  (:id . 84))\n ((:tag . "NN") (:stem . "il-10") (:form . "IL-10") (:end . 252)\n  (:start . 247) (:id . 85))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 263)\n  (:start . 253) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 264) (:start . 263)\n  (:id . 87)))@@@1@46@((:hcues ((:id . :x5.93.1) (:span 193 203)))\n (:hscopes ((:id . :x5.93.1) (:span 193 263)))\n (:identifiers (:sid . :s5.93) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501484@unknown@formal@none@1@S@Interestingly, IFN-γ mRNA levels on day 0 correlated with FOXP3 mRNA on day 0 for both severe (r: 0.39 p=0.003) and uncomplicated cases (r: 0.44 p=0.0001), suggesting that IFN-γ may also be driving FOXP3 expression.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "correlate") (:form . "correlated") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "FOXP3") (:form . "FOXP3") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 81) (:start . 78)\n  (:id . 57))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 86) (:start . 82)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 93)\n  (:start . 87) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "r") (:form . "r") (:end . 96) (:start . 95)\n  (:id . 61))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 97) (:start . 96)\n  (:id . 62))\n ((:tag . "CD") (:stem . "0.39") (:form . "0.39") (:end . 102) (:start . 98)\n  (:id . 63))\n ((:tag . "NN") (:stem . "p=0.003") (:form . "p=0.003") (:end . 110)\n  (:start . 103) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 129) (:start . 116) (:id . 67))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 135)\n  (:start . 130) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 69))\n ((:tag . "NN") (:stem . "r") (:form . "r") (:end . 138) (:start . 137)\n  (:id . 70))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 139) (:start . 138)\n  (:id . 71))\n ((:tag . "CD") (:stem . "0.44") (:form . "0.44") (:end . 144) (:start . 140)\n  (:id . 72))\n ((:tag . "NN") (:stem . "p=0.0001") (:form . "p=0.0001") (:end . 153)\n  (:start . 145) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 166)\n  (:start . 156) (:id . 76))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 171) (:start . 167)\n  (:id . 77))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 177)\n  (:start . 172) (:id . 78))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 181) (:start . 178)\n  (:id . 79))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 186) (:start . 182)\n  (:id . 80))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 189) (:start . 187)\n  (:id . 81))\n ((:tag . "VBG") (:stem . "drive") (:form . "driving") (:end . 197)\n  (:start . 190) (:id . 82))\n ((:tag . "NN") (:stem . "foxp3") (:form . "FOXP3") (:end . 203)\n  (:start . 198) (:id . 83))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 214)\n  (:start . 204) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x5.94.1) (:span 178 181)) ((:id . :x5.94.2) (:span 156 166)))\n (:hscopes ((:id . :x5.94.1) (:span 178 214))\n  ((:id . :x5.94.2) (:span 156 214)))\n (:identifiers (:sid . :s5.94) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501485@unknown@formal@none@1@S@The balance of pro-and anti inflammatory cytokine responses clearly changed with time, but somewhat surprisingly, there were no marked differences in cytokines ratios between children with differing levels of disease severity.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "balance") (:form . "balance") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "pro-and") (:form . "pro-and") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "JJ") (:stem . "anti") (:form . "anti") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 40)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 49)\n  (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 59)\n  (:start . 50) (:id . 49))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 67)\n  (:start . 60) (:id . 50))\n ((:tag . "VBD") (:stem . "change") (:form . "changed") (:end . 75)\n  (:start . 68) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 80) (:start . 76)\n  (:id . 52))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 85) (:start . 81)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 54))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 90) (:start . 87)\n  (:id . 55))\n ((:tag . "RB") (:stem . "somewhat") (:form . "somewhat") (:end . 99)\n  (:start . 91) (:id . 56))\n ((:tag . "RB") (:stem . "surprisingly") (:form . "surprisingly") (:end . 112)\n  (:start . 100) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 58))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 119)\n  (:start . 114) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 124) (:start . 120)\n  (:id . 60))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 127) (:start . 125)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "marked") (:form . "marked") (:end . 134)\n  (:start . 128) (:id . 62))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 146)\n  (:start . 135) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 159)\n  (:start . 150) (:id . 65))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 166)\n  (:start . 160) (:id . 66))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 174)\n  (:start . 167) (:id . 67))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 183)\n  (:start . 175) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 188) (:start . 184)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "differ") (:form . "differing") (:end . 198)\n  (:start . 189) (:id . 70))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 205)\n  (:start . 199) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 208) (:start . 206)\n  (:id . 72))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 216)\n  (:start . 209) (:id . 73))\n ((:tag . "NN") (:stem . "severity") (:form . "severity") (:end . 225)\n  (:start . 217) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s5.95) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501486@unknown@formal@none@1@S@Thus, the ratios of TNF-α or IFN-γ to IL-10 on day 0 were similar in all disease severity groups (Figure 5E and 5F) and ratios of IFN-γ to IL-10 mRNA were similar in all disease severity groups both on day 0 and day 28 (Figure S1F).@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 16)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 25) (:start . 20)\n  (:id . 47))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 34) (:start . 29)\n  (:id . 49))\n ((:tag . 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5501487@unknown@formal@none@1@S@However, IFN-γ mRNA levels were on average only 3.2-fold higher on day 0 than day 28 but IL-10 mRNA levels were 29-fold higher on day 0, resulting in a significantly lower IFN-γ/IL-10 mRNA ratio on day 0 than day 28 (Figure S1F).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "RB") (:stem . "3.2-fold") (:form . "3.2-fold") (:end . 56)\n  (:start . 48) (:id . 51))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 63) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 77) (:start . 73)\n  (:id . 56))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 81) (:start . 78)\n  (:id . 57))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 88) (:start . 85)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 94) (:start . 89)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 99) (:start . 95)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 106)\n  (:start . 100) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 111) (:start . 107)\n  (:id . 63))\n ((:tag . "RB") (:stem . "29-fold") (:form . "29-fold") (:end . 119)\n  (:start . 112) (:id . 64))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 126)\n  (:start . 120) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 129) (:start . 127)\n  (:id . 66))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 133) (:start . 130)\n  (:id . 67))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 135) (:start . 134)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 146)\n  (:start . 137) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 151) (:start . 150)\n  (:id . 72))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 165) (:start . 152) (:id . 73))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 171) (:start . 166)\n  (:id . 74))\n ((:tag . "NN") (:stem . "ifn-γ/il-10") (:form . "IFN-γ/IL-10") (:end . 183)\n  (:start . 172) (:id . 75))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 188) (:start . 184)\n  (:id . 76))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 194)\n  (:start . 189) (:id . 77))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 197) (:start . 195)\n  (:id . 78))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 201) (:start . 198)\n  (:id . 79))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 203) (:start . 202)\n  (:id . 80))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 208) (:start . 204)\n  (:id . 81))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 212) (:start . 209)\n  (:id . 82))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 215) (:start . 213)\n  (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 217) (:start . 216)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 223)\n  (:start . 217) (:id . 85))\n ((:tag . "NNP") (:stem . "S1F") (:form . "S1F") (:end . 227) (:start . 224)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 228) (:start . 227)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s5.97) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501488@unknown@formal@none@1@S@CD25-FOXP3- CD45RO+ T cells but not Tregs are the major source of IL-10 during acute malaria@(((:tag . "JJ") (:stem . "cd25-foxp3-") (:form . "CD25-FOXP3-") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "cd45ro+") (:form . "CD45RO+") (:end . 19)\n  (:start . 12) (:id . 43))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 21) (:start . 20)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NNPS") (:stem . "Treg") (:form . "Tregs") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 55) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "il-10") (:form . "IL-10") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 78)\n  (:start . 72) (:id . 55))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 84) (:start . 79)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "malaria") (:form . "malaria") (:end . 92)\n  (:start . 85) (:id . 57)))@@@1@16@((:identifiers (:sid . :s5.98) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501489@unknown@formal@none@1@S@IL-10 is a crucial immunoregulatory cytokine in both human [23] and murine [33],[49] malaria; we have recently identified CD4+ T effector cells as a major source of IL-10 [33], but the source of IL-10 in human malaria infection is unknown.@(((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 18)\n  (:start . 11) (:id . 45))\n ((:tag . "JJ") (:stem . "immunoregulatory") (:form . "immunoregulatory")\n  (:end . 35) (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "CC") (:stem . "both") (:form . 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(:end . 239) (:start . 238)\n  (:id . 90)))@@@1@49@((:hcues ((:id . :x5.99.1) (:span 231 238)))\n (:hscopes ((:id . :x5.99.1) (:span 181 238)))\n (:identifiers (:sid . :s5.99) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501490@unknown@formal@none@1@S@In other protozoal infections of mice CD4+ effector T cells that co-produce IFN-γ and IL-10 have been identified [50]–[52].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "protozoal") (:form . "protozoal") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "co-produce") (:form . "co-produce") (:end . 75)\n  (:start . 65) (:id . 53))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 91) (:start . 86)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 112)\n  (:start . 102) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 114) (:start . 113)\n  (:id . 60))\n ((:tag . "CD") (:stem . "50]–[52") (:form . "50]–[52") (:end . 121)\n  (:start . 114) (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s5.100) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501491@unknown@formal@none@1@S@We therefore cultured freshly isolated PBMCs from 30 children with acute malaria (17 severe, 13 uncomplicated) and 20 healthy control children, with or without PMA and Ionomycin (PI), for 5 hours and analyzed them for the presence of intracellular IL-10 and IFN-γ by flow cytometry (Figure 6A).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "culture") (:form . "cultured") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "RB") (:stem . "freshly") (:form . "freshly") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "NNS") (:stem . "pbmc") (:form . "PBMCs") (:end . 44) (:start . 39)\n  (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . 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5501492@unknown@formal@none@1@S@No cytokine production was observed in unstimulated cells (data not shown), and PBMC from healthy children failed to produce any IL-10 in response to PI (data not shown), indicating that stimulation with PI predominantly induces cytokine production from recently activated cells.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "unstimulated") (:form . "unstimulated") (:end . 51)\n  (:start . 39) (:id . 48))\n ((:tag . 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5501493@unknown@formal@none@1@S@Phenotypic characterization of cytokine-producing cells.@(((:tag . "JJ") (:stem . "phenotypic") (:form . "Phenotypic") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "characterization") (:form . "characterization")\n  (:end . 27) (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "cytokine-producing") (:form . "cytokine-producing")\n  (:end . 49) (:start . 31) (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 55) (:start . 50)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s5.103) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501494@unknown@formal@none@1@S@By contrast, distinct populations of IL-10+ and IFN-γ+ cells were seen among the PI-stimulated cells from children with acute severe or uncomplicated malaria, with a small but easily distinguishable population of cells (approx 1% of all PBMC) producing both cytokines simultaneously (Figure 6A, right plot).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "population") (:form . "populations") (:end . 33)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "il-10+") (:form . 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5501495@unknown@formal@none@1@S@In both severe and uncomplicated cases, IL-10 producing cells were predominantly CD45RO+ CD4+ T cells (Figure 6B and 6C) and were almost exclusively FOXP3- and CD25- (Figure 6D).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 32) (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "producing") (:form . "producing") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 80) (:start . 67) (:id . 53))\n ((:tag . "JJ") (:stem . "cd45ro+") (:form . "CD45RO+") (:end . 88)\n  (:start . 81) (:id . 54))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 93) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 101) (:start . 96)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 109)\n  (:start . 103) (:id . 59))\n ((:tag . "NN") (:stem . "6b") (:form . "6B") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "NN") (:stem . "6c") (:form . "6C") (:end . 119) (:start . 117)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 129) (:start . 125)\n  (:id . 65))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 136)\n  (:start . 130) (:id . 66))\n ((:tag . "RB") (:stem . "exclusively") (:form . "exclusively") (:end . 148)\n  (:start . 137) (:id . 67))\n ((:tag . "NN") (:stem . "foxp3-") (:form . "FOXP3-") (:end . 155)\n  (:start . 149) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "CD25-") (:form . "CD25-") (:end . 165)\n  (:start . 160) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 173)\n  (:start . 167) (:id . 72))\n ((:tag . "NN") (:stem . "6d") (:form . "6D") (:end . 176) (:start . 174)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 177) (:start . 176)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s5.105) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501496@unknown@formal@none@1@S@Moreover, although a transient increase of FOXP3 in activated human T-effector cells has been reported [53], in our hands less than 1% (median 0.97%, CI95%: 0.67–1.27%) of IFN-γ producing cells were FOXP3+ (Figure 6E).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "transient") (:form . "transient") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "foxp3") (:form . "FOXP3") (:end . 48) (:start . 43)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "t-effector") (:form . "T-effector") (:end . 78)\n  (:start . 68) (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 84) (:start . 79)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 88) (:start . 85)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 102)\n  (:start . 94) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 104) (:start . 103)\n  (:id . 58))\n ((:tag . "CD") (:stem . "53") (:form . "53") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 115) (:start . 112)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "hand") (:form . "hands") (:end . 121)\n  (:start . 116) (:id . 64))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 126) (:start . 122)\n  (:id . 65))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 131) (:start . 127)\n  (:id . 66))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 133) (:start . 132)\n  (:id . 67))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 134) (:start . 133)\n  (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 136) (:start . 135)\n  (:id . 69))\n ((:tag . "NN") (:stem . "median") (:form . "median") (:end . 142)\n  (:start . 136) (:id . 70))\n ((:tag . "CD") (:stem . "0.97") (:form . "0.97") (:end . 147) (:start . 143)\n  (:id . 71))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 148) (:start . 147)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "CI95") (:form . "CI95") (:end . 154) (:start . 150)\n  (:id . 74))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 155) (:start . 154)\n  (:id . 75))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 156) (:start . 155)\n  (:id . 76))\n ((:tag . "CD") (:stem . "0.67–1.27") (:form . "0.67–1.27") (:end . 166)\n  (:start . 157) (:id . 77))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 167) (:start . 166)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 168) (:start . 167)\n  (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 80))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 177)\n  (:start . 172) (:id . 81))\n ((:tag . "NN") (:stem . "producing") (:form . "producing") (:end . 187)\n  (:start . 178) (:id . 82))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 193)\n  (:start . 188) (:id . 83))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 198) (:start . 194)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "foxp3+") (:form . "FOXP3+") (:end . 205)\n  (:start . 199) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 207) (:start . 206)\n  (:id . 86))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 213)\n  (:start . 207) (:id . 87))\n ((:tag . "NN") (:stem . "6e") (:form . "6E") (:end . 216) (:start . 214)\n  (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 217) (:start . 216)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s5.106) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501497@unknown@formal@none@1@S@Overall, among children with acute malaria, approx 4% of PI-stimulated CD4+ T cells produced IL-10 and approx 8% produced IFN-γ and neither the proportions of cells producing one or the other cytokine (Figure 6F) nor the ratio of IFN-γ/IL-10 producing cells (data not shown) differed significantly between severe and uncomplicated cases.@(((:tag . "RB") (:stem . "overall") (:form . "Overall") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "malaria") (:form . 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5501498@unknown@formal@none@1@S@However, intriguingly, the proportion of CD4+ T cells simultaneously producing IL-10 and IFN-γ was three fold higher in uncomplicated cases than severe cases (geometric mean 5.2% vs 1.6%, p=0.041, Figure 6F).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "RB") (:stem . "intriguingly") (:form . "intriguingly") (:end . 21)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n  (:end . 68) (:start . 54) (:id . 52))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 84) (:start . 79)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 94) (:start . 89)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 104) (:start . 99)\n  (:id . 58))\n ((:tag . "RB") (:stem . "fold") (:form . "fold") (:end . 109) (:start . 105)\n  (:id . 59))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 116)\n  (:start . 110) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 133) (:start . 120) (:id . 62))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 139)\n  (:start . 134) (:id . 63))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 144) (:start . 140)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 151)\n  (:start . 145) (:id . 65))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 157)\n  (:start . 152) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "geometric") (:form . "geometric") (:end . 168)\n  (:start . 159) (:id . 68))\n ((:tag . "NN") (:stem . "mean") (:form . "mean") (:end . 173) (:start . 169)\n  (:id . 69))\n ((:tag . "CD") (:stem . "5.2") (:form . "5.2") (:end . 177) (:start . 174)\n  (:id . 70))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 178) (:start . 177)\n  (:id . 71))\n ((:tag . "IN") (:stem . "vs") (:form . "vs") (:end . 181) (:start . 179)\n  (:id . 72))\n ((:tag . "CD") (:stem . "1.6") (:form . "1.6") (:end . 185) (:start . 182)\n  (:id . 73))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 186) (:start . 185)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 187) (:start . 186)\n  (:id . 75))\n ((:tag . "NN") (:stem . "p=0.041") (:form . "p=0.041") (:end . 195)\n  (:start . 188) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 203)\n  (:start . 197) (:id . 78))\n ((:tag . "NN") (:stem . "6f") (:form . "6F") (:end . 206) (:start . 204)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 207) (:start . 206)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s5.108) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501499@unknown@formal@none@1@S@Moreover, the proportion of IFN-γ+ CD4+ T cells that also produce IL-10 was almost twice as high among uncomplicated cases as among severe cases (p=0.045, Figure 6G).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "ifn-γ+") (:form . "IFN-γ+") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "produce") (:form . "produce") (:end . 65)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "il-10") (:form . "IL-10") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 82)\n  (:start . 76) (:id . 56))\n ((:tag . "RB") (:stem . "twice") (:form . "twice") (:end . 88) (:start . 83)\n  (:id . 57))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 96) (:start . 92)\n  (:id . 59))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 102) (:start . 97)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 116) (:start . 103) (:id . 61))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 122)\n  (:start . 117) (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 125) (:start . 123)\n  (:id . 63))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 131)\n  (:start . 126) (:id . 64))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 138)\n  (:start . 132) (:id . 65))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 144)\n  (:start . 139) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n  (:id . 67))\n ((:tag . "NN") (:stem . "p=0.045") (:form . "p=0.045") (:end . 153)\n  (:start . 146) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 161)\n  (:start . 155) (:id . 70))\n ((:tag . "NN") (:stem . "6g") (:form . "6G") (:end . 164) (:start . 162)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s5.109) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501500@unknown@formal@none@1@S@Taken together, these data indicate that during acute, uncomplicated or severe, malaria infections IL-10 producing cells are overwhelmingly T effector cells and that Th1 effector cells that also produce IL-10 are more prevalent in children with uncomplicated malaria than in children with severe malaria.@(((:tag . "VBN") (:stem . "take") (:form . "Taken") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . 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"malaria") (:end . 303)\n  (:start . 296) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 304) (:start . 303)\n  (:id . 89)))@@@1@48@((:hcues ((:id . :x5.110.1) (:span 27 40)))\n (:hscopes ((:id . :x5.110.1) (:span 27 303)))\n (:identifiers (:sid . :s5.110) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501501@unknown@formal@none@1@S@The frequency of Tregs during acute disease is negatively associated with the magnitude of subsequent malaria-specific IFN-γ memory responses@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "RB") (:stem . "negatively") (:form . "negatively") (:end . 57)\n  (:start . 47) (:id . 50))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 68)\n  (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "NN") (:stem . "magnitude") (:form . "magnitude") (:end . 87)\n  (:start . 78) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 101)\n  (:start . 91) (:id . 56))\n ((:tag . "JJ") (:stem . "malaria-specific") (:form . "malaria-specific")\n  (:end . 118) (:start . 102) (:id . 57))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 124)\n  (:start . 119) (:id . 58))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 131)\n  (:start . 125) (:id . 59))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 141)\n  (:start . 132) (:id . 60)))@@@1@19@((:identifiers (:sid . :s5.111) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501502@unknown@formal@none@1@S@It has been reported that Tregs present at the time of infection [54] or vaccination [55] may restrict the development of subsequent Th1 memory responses.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 64)\n  (:start . 55) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "CD") (:stem . "54") (:form . "54") (:end . 68) (:start . 66)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 69) (:start . 68)\n  (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 72) (:start . 70)\n  (:id . 57))\n ((:tag . "NN") (:stem . "vaccination") (:form . "vaccination") (:end . 84)\n  (:start . 73) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 86) (:start . 85)\n  (:id . 59))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 88) (:start . 86)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 89) (:start . 88)\n  (:id . 61))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 93) (:start . 90)\n  (:id . 62))\n ((:tag . "VB") (:stem . "restrict") (:form . "restrict") (:end . 102)\n  (:start . 94) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 64))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 118)\n  (:start . 107) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 132)\n  (:start . 122) (:id . 67))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 136) (:start . 133)\n  (:id . 68))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 143)\n  (:start . 137) (:id . 69))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 153)\n  (:start . 144) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x5.112.1) (:span 90 93)))\n (:hscopes ((:id . :x5.112.1) (:span 90 153)))\n (:identifiers (:sid . :s5.112) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501503@unknown@formal@none@1@S@To determine whether Tregs present during acute malaria infection might similarly affect the induction of immunological memory, we compared FOXP3 mRNA levels on day 0 with malaria specific IFN-γ memory responses (as assessed by PfSE-specific cultured ELISPOT) among PBMC collected from 34 of our convalescent malaria patients (19 severe and 15 uncomplicated) on Day 28.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 41)\n  (:start . 35) (:id . 47))\n ((:tag . "JJ") (:stem . 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5501504@unknown@formal@none@1@S@As shown in Figure 7A, cells from uncomplicated and severe cases mounted similarly strong IFN-γ memory responses following culture with PfSE.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "NNP") (:stem . "7A") (:form . "7A") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 28) (:start . 23)\n  (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 33) (:start . 29)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 47) (:start . 34) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 58)\n  (:start . 52) (:id . 52))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 64) (:start . 59)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "mount") (:form . "mounted") (:end . 72)\n  (:start . 65) (:id . 54))\n ((:tag . "RB") (:stem . "similarly") (:form . "similarly") (:end . 82)\n  (:start . 73) (:id . 55))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 89)\n  (:start . 83) (:id . 56))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 95) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 102)\n  (:start . 96) (:id . 58))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 112)\n  (:start . 103) (:id . 59))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 122)\n  (:start . 113) (:id . 60))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 130)\n  (:start . 123) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 135) (:start . 131)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "PfSE") (:form . "PfSE") (:end . 140) (:start . 136)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s5.114) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501505@unknown@formal@none@1@S@When plotted against FOXP3 mRNA levels measured on day 0, a linear by linear hyperbolic fit revealed that higher levels of FOXP3 mRNA on day 0 were highly significantly (p=0.009) associated with lower malaria-specific IFN-γ memory responses on Day 28, suggesting that Tregs induced during the acute infection may limit the magnitude of subsequent Th1 responses (Figure 7B).@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "plot") (:form . "plotted") (:end . 12) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "foxp3") (:form . "FOXP3") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "VBN") (:stem . 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(:end . 373) (:start . 372)\n  (:id . 106)))@@@1@65@((:hcues ((:id . :x5.115.1) (:span 309 312))\n  ((:id . :x5.115.2) (:span 252 262)))\n (:hscopes ((:id . :x5.115.1) (:span 309 360))\n  ((:id . :x5.115.2) (:span 252 360)))\n (:identifiers (:sid . :s5.115) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501506@unknown@formal@none@1@S@For neither group could a significant effect of parasitaemia on the memory response be observed (r=-0.12 p=0.962 for severe and r=0.015, p=0.957 for uncomplicated cases).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "neither") (:form . "neither") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "parasitaemia") (:form . "parasitaemia") (:end . 60)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 74)\n  (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 83)\n  (:start . 75) (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 95)\n  (:start . 87) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "r=-0.12") (:form . "r=-0.12") (:end . 104)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "p=0.962") (:form . "p=0.962") (:end . 112)\n  (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 123)\n  (:start . 117) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 62))\n ((:tag . "NN") (:stem . "r=0.015") (:form . "r=0.015") (:end . 135)\n  (:start . 128) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . "NN") (:stem . "p=0.957") (:form . "p=0.957") (:end . 144)\n  (:start . 137) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 148) (:start . 145)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 162) (:start . 149) (:id . 67))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 168)\n  (:start . 163) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s5.116) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501507@unknown@formal@none@1@S@Tregs induced during the clinical episode under study limit the magnitude of subsequent malaria-specific IFN-γ memory responses.@(((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "episode") (:form . "episode") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 47) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "limit") (:form . "limit") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "magnitude") (:form . "magnitude") (:end . 73)\n  (:start . 64) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 87)\n  (:start . 77) (:id . 54))\n ((:tag . "JJ") (:stem . "malaria-specific") (:form . "malaria-specific")\n  (:end . 104) (:start . 88) (:id . 55))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 110)\n  (:start . 105) (:id . 56))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 117)\n  (:start . 111) (:id . 57))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 127)\n  (:start . 118) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s5.117) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501508@unknown@formal@none@1@S@Discussion@(((:tag . "NN") (:stem . "discussion") (:form . "Discussion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s5.118) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501509@unknown@formal@none@1@S@We hypothesized that the balance of inflammatory to regulatory immune responses would be biased towards a more inflammatory response in children with severe malaria than in children with uncomplicated malaria, that this balance would be restored during convalescence and – crucially – that this would be associated with differences in the proportion, absolute number or function of circulating classical (CD4+ CD127-/lo FOXP3+) regulatory T cells.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "hypothesize") (:form . "hypothesized") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "balance") (:form . "balance") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . 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")") (:end . 427) (:start . 426)\n  (:id . 107))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 438)\n  (:start . 428) (:id . 108))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 440) (:start . 439)\n  (:id . 109))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 446)\n  (:start . 441) (:id . 110))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 447) (:start . 446)\n  (:id . 111)))@@@1@70@((:hcues ((:id . :x5.119.1) (:span 295 300))\n  ((:id . :x5.119.2) (:span 228 233)) ((:id . :x5.119.3) (:span 80 85))\n  ((:id . :x5.119.4) (:span 3 15)))\n (:hscopes ((:id . :x5.119.1) (:span 290 446))\n  ((:id . :x5.119.2) (:span 215 266)) ((:id . :x5.119.3) (:span 21 208))\n  ((:id . :x5.119.4) (:span 3 446)))\n (:identifiers (:sid . :s5.119) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501510@unknown@formal@none@1@S@In partial support of these hypotheses, the number of cells expressing a Treg phenotype and FOXP3-mRNA levels were both significantly higher during convalescence than during the acute clinical episode and the ratio of the Th1 transcription factor T-BET to the Treg transcription factor FOXP3 was significantly higher during acute disease than during convalescence in both severe and uncomplicated cases, compatible with the notion that Tregs fail to sufficiently regulate pro-inflammatory responses which might contribute to the onset of symptomatic malaria infection.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . 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5501511@unknown@formal@none@1@S@Given our previous observation of Treg expansion during the pre-patent phase of malaria infection [27], we suggest that Tregs are induced/activated shortly after parasite emergence from the liver, that their numbers in peripheral blood then decline as a result of sequestration of CD4+ T cells during acute disease [40],[41],[56] and then, as has been described for other T cell subsets [39],[57], Tregs regain access to the circulation after malaria is cured.@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 30)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . 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5501512@unknown@formal@none@1@S@The significant positive correlation of Treg numbers with parasitaemia, as well as the correlation between FOXP3 mRNA and IFN-γ mRNA levels in acute samples, further supports the notion that the initial infection induces a proportional increase in Tregs, attempting to balance the effector T cell response, and is in line with the recently proposed concept that antigenic challenge will give rise to an antigen specific Treg response, proportional in size to the inflammatory response [58].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 36)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . 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5501513@unknown@formal@none@1@S@Moreover, the Tregs circulating during acute malaria infections almost exclusively expressed an activated memory phenotype suggesting that they have expanded from a pre-existing pool of memory T-cells.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "circulate") (:form . "circulating") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 63)\n  (:start . 53) (:id . 50))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 70)\n  (:start . 64) (:id . 51))\n ((:tag . "RB") (:stem . "exclusively") (:form . "exclusively") (:end . 82)\n  (:start . 71) (:id . 52))\n ((:tag . "VBD") (:stem . "express") (:form . "expressed") (:end . 92)\n  (:start . 83) (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 95) (:start . 93)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 105)\n  (:start . 96) (:id . 55))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 112)\n  (:start . 106) (:id . 56))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 122)\n  (:start . 113) (:id . 57))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 133)\n  (:start . 123) (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 138) (:start . 134)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 143) (:start . 139)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 148) (:start . 144)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "expand") (:form . "expanded") (:end . 157)\n  (:start . 149) (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 162) (:start . 158)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 164) (:start . 163)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "pre-existing") (:form . "pre-existing") (:end . 177)\n  (:start . 165) (:id . 65))\n ((:tag . "NN") (:stem . "pool") (:form . "pool") (:end . 182) (:start . 178)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 185) (:start . 183)\n  (:id . 67))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 192)\n  (:start . 186) (:id . 68))\n ((:tag . "NNS") (:stem . "t-cell") (:form . "T-cells") (:end . 200)\n  (:start . 193) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x5.123.1) (:span 123 133)))\n (:hscopes ((:id . :x5.123.1) (:span 123 200)))\n (:identifiers (:sid . :s5.123) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501514@unknown@formal@none@1@S@This interpretation would be in line with recent elegant work in humans demonstrating that Tregs are derived by rapid turnover of memory populations in vivo [59], and with data from murine studies where, after CD25-depletion, malaria infection very rapidly drives differentiation of Tregs from circulating mature CD4+ T cells [60].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "interpretation") (:form . "interpretation")\n  (:end . 19) (:start . 5) (:id . 43))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 25) (:start . 20)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . 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5501515@unknown@formal@none@1@S@Obviously, it would be of interest to study the relationship between Tregs and effector T cell kinetics and parasite biomass, which is not readily measurable.@(((:tag . "RB") (:stem . "obviously") (:form . "Obviously") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 34)\n  (:start . 26) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "VB") (:stem . "study") (:form . "study") (:end . 43) (:start . 38)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 60)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 87)\n  (:start . 79) (:id . 56))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 94) (:start . 90)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "kinetic") (:form . "kinetics") (:end . 103)\n  (:start . 95) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 60))\n ((:tag . "NN") (:stem . "parasite") (:form . "parasite") (:end . 116)\n  (:start . 108) (:id . 61))\n ((:tag . "NN") (:stem . "biomass") (:form . "biomass") (:end . 124)\n  (:start . 117) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 63))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 131)\n  (:start . 126) (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 134) (:start . 132)\n  (:id . 65))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 138) (:start . 135)\n  (:id . 66))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 146)\n  (:start . 139) (:id . 67))\n ((:tag . "JJ") (:stem . "measurable") (:form . "measurable") (:end . 157)\n  (:start . 147) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x5.125.1) (:span 14 19)))\n (:hscopes ((:id . :x5.125.1) (:span 14 157)))\n (:identifiers (:sid . :s5.125) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501516@unknown@formal@none@1@S@Future studies may explore the usefulness of P. falciparum Histidine Rich Protein 2 in this context, which has recently been suggested as a surrogate marker for parasite biomass [61].@(((:tag . "JJ") (:stem . "future") (:form . "Future") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "VB") (:stem . "explore") (:form . "explore") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "usefulness") (:form . "usefulness") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "falciparum") (:form . "falciparum") (:end . 58)\n  (:start . 48) (:id . 50))\n ((:tag . "NNP") (:stem . "Histidine") (:form . "Histidine") (:end . 68)\n  (:start . 59) (:id . 51))\n ((:tag . "NNP") (:stem . "Rich") (:form . "Rich") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 81)\n  (:start . 74) (:id . 53))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 99)\n  (:start . 92) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 106)\n  (:start . 101) (:id . 59))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 119)\n  (:start . 111) (:id . 61))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 124) (:start . 120)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "suggest") (:form . "suggested") (:end . 134)\n  (:start . 125) (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 139) (:start . 138)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "surrogate") (:form . "surrogate") (:end . 149)\n  (:start . 140) (:id . 66))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 156)\n  (:start . 150) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 160) (:start . 157)\n  (:id . 68))\n ((:tag . "NN") (:stem . "parasite") (:form . "parasite") (:end . 169)\n  (:start . 161) (:id . 69))\n ((:tag . "NN") (:stem . "biomass") (:form . "biomass") (:end . 177)\n  (:start . 170) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 179) (:start . 178)\n  (:id . 71))\n ((:tag . "CD") (:stem . "61") (:form . "61") (:end . 181) (:start . 179)\n  (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 182) (:start . 181)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x5.126.1) (:span 125 134)) ((:id . :x5.126.2) (:span 15 18)))\n (:hscopes ((:id . :x5.126.1) (:span 101 177))\n  ((:id . :x5.126.2) (:span 15 177)))\n (:identifiers (:sid . :s5.126) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501517@unknown@formal@none@1@S@However, despite clear evidence of Treg induction and reallocation during acute malaria infection, we could not find any robust differences in Treg parameters between children with severe and uncomplicated disease.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "despite") (:form . "despite") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "treg") (:form . "Treg") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "induction") (:form . "induction") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "reallocation") (:form . "reallocation") (:end . 66)\n  (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 73)\n  (:start . 67) (:id . 52))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 79) (:start . 74)\n  (:id . 53))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 87)\n  (:start . 80) (:id . 54))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 97)\n  (:start . 88) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 101) (:start . 99)\n  (:id . 57))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 107)\n  (:start . 102) (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "VB") (:stem . "find") (:form . "find") (:end . 116) (:start . 112)\n  (:id . 60))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "robust") (:form . "robust") (:end . 127)\n  (:start . 121) (:id . 62))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 139)\n  (:start . 128) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Treg") (:end . 147) (:start . 143)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 158)\n  (:start . 148) (:id . 66))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 166)\n  (:start . 159) (:id . 67))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 175)\n  (:start . 167) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 180) (:start . 176)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 187)\n  (:start . 181) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 191) (:start . 188)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 205) (:start . 192) (:id . 72))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 213)\n  (:start . 206) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s5.127) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501518@unknown@formal@none@1@S@Thus, neither Treg numbers nor FOXP3 mRNA levels differed significantly between children with uncomplicated malaria and those with severe malaria, and three different indicators of Treg function - their capacity to suppress lymphoproliferation, their expression of SOCS-2 [45] and TNFR2 [46],[48] were all similar in severely ill children and children with uncomplicated disease.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "neither") (:form . "neither") (:end . 13)\n  (:start . 6) (:id . 44))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Treg") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "CC") (:stem . "nor") (:form . "nor") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . 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5501519@unknown@formal@none@1@S@Furthermore, the similar distortion in the T-BET/FOXP3 mRNA ratio during acute disease and the lack of any marked differences between the two groups in ratios of inflammatory to anti-inflammatory cytokines, as well as the close correlation between IFN-γ and IL-10 in both groups which is in line with previous observations in experimental human malaria infections [62], suggests that the systemic shift towards a pro-inflammatory immune response is similar in children with either severe or uncomplicated disease.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "distortion") (:form . 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5501520@unknown@formal@none@1@S@At first glance, these data do not appear to support the hypothesis that deficiencies in Treg function underlie the tendency of some children to develop severe, life threatening malaria.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "glance") (:form . "glance") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 34) (:start . 31)\n  (:id . 49))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 41)\n  (:start . 35) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "VB") (:stem . "support") (:form . "support") (:end . 52)\n  (:start . 45) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 67)\n  (:start . 57) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "deficiency") (:form . "deficiencies") (:end . 85)\n  (:start . 73) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Treg") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . "VBP") (:stem . "underlie") (:form . "underlie") (:end . 111)\n  (:start . 103) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 61))\n ((:tag . "NN") (:stem . "tendency") (:form . "tendency") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 132) (:start . 128)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 141)\n  (:start . 133) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 144) (:start . 142)\n  (:id . 66))\n ((:tag . "VB") (:stem . "develop") (:form . "develop") (:end . 152)\n  (:start . 145) (:id . 67))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 159)\n  (:start . 153) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 69))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 165) (:start . 161)\n  (:id . 70))\n ((:tag . "NN") (:stem . "threatening") (:form . "threatening") (:end . 177)\n  (:start . 166) (:id . 71))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 185)\n  (:start . 178) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x5.130.1) (:span 57 67)) ((:id . :x5.130.2) (:span 35 41)))\n (:hscopes ((:id . :x5.130.1) (:span 57 185))\n  ((:id . :x5.130.2) (:span 17 185)))\n (:identifiers (:sid . :s5.130) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501521@unknown@formal@none@1@S@However, we did observe significantly higher Th1 effector responses (more T-effector cells, higher concentrations of IFN-γ and TNF-α) in severely ill children than in children with uncomplicated disease, suggesting that the classical FOXP3+ Treg response that develops during acute malaria infection may be insufficient to balance the florid effector T cell response that develops particularly in children with severe disease.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "VB") (:stem . "observe") (:form . "observe") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "RB") (:stem . "significantly") (:form . 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5501522@unknown@formal@none@1@S@This would be in line with evidence showing that as the strength of the inflammatory stimulus increases, the suppressive capacity of human Tregs declines and the resistance of T-effector cells to regulation increases [63].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 35)\n  (:start . 27) (:id . 48))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "strength") (:form . "strength") (:end . 64)\n  (:start . 56) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "inflammatory") (:form . "inflammatory") (:end . 84)\n  (:start . 72) (:id . 56))\n ((:tag . "NN") (:stem . "stimulus") (:form . "stimulus") (:end . 93)\n  (:start . 85) (:id . 57))\n ((:tag . "NNS") (:stem . "increase") (:form . "increases") (:end . 103)\n  (:start . 94) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "suppressive") (:form . "suppressive") (:end . 120)\n  (:start . 109) (:id . 61))\n ((:tag . "NN") (:stem . "capacity") (:form . "capacity") (:end . 129)\n  (:start . 121) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 138)\n  (:start . 133) (:id . 64))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 144)\n  (:start . 139) (:id . 65))\n ((:tag . "NNS") (:stem . "decline") (:form . "declines") (:end . 153)\n  (:start . 145) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 68))\n ((:tag . "NN") (:stem . "resistance") (:form . "resistance") (:end . 172)\n  (:start . 162) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 175) (:start . 173)\n  (:id . 70))\n ((:tag . "NN") (:stem . "t-effector") (:form . "T-effector") (:end . 186)\n  (:start . 176) (:id . 71))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 192)\n  (:start . 187) (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 195) (:start . 193)\n  (:id . 73))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 206)\n  (:start . 196) (:id . 74))\n ((:tag . "NNS") (:stem . "increase") (:form . "increases") (:end . 216)\n  (:start . 207) (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 218) (:start . 217)\n  (:id . 76))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 220) (:start . 218)\n  (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 221) (:start . 220)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x5.132.1) (:span 5 10)))\n (:hscopes ((:id . :x5.132.1) (:span 5 216)))\n (:identifiers (:sid . :s5.132) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501523@unknown@formal@none@1@S@The situation observed during an acute, clinical malaria infection is thus in clear contrast to the situation in healthy, malaria-exposed individuals where Treg numbers closely track numbers of T-effectors, precisely maintaining an apparently optimal T-effectorTreg ratio [36].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "situation") (:form . "situation") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 29)\n  (:start . 23) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 66)\n  (:start . 57) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 74) (:start . 70)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "situation") (:form . "situation") (:end . 109)\n  (:start . 100) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "healthy") (:form . "healthy") (:end . 120)\n  (:start . 113) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "malaria-exposed") (:form . "malaria-exposed")\n  (:end . 137) (:start . 122) (:id . 63))\n ((:tag . "NNS") (:stem . "individual") (:form . "individuals") (:end . 149)\n  (:start . 138) (:id . 64))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 155)\n  (:start . 150) (:id . 65))\n ((:tag . "NN") (:stem . "treg") (:form . "Treg") (:end . 160) (:start . 156)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 168)\n  (:start . 161) (:id . 67))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 176)\n  (:start . 169) (:id . 68))\n ((:tag . "VBP") (:stem . "track") (:form . "track") (:end . 182)\n  (:start . 177) (:id . 69))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 190)\n  (:start . 183) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 193) (:start . 191)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "t-effector") (:form . "T-effectors") (:end . 205)\n  (:start . 194) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 206) (:start . 205)\n  (:id . 73))\n ((:tag . "RB") (:stem . "precisely") (:form . "precisely") (:end . 216)\n  (:start . 207) (:id . 74))\n ((:tag . "VBG") (:stem . "maintain") (:form . "maintaining") (:end . 228)\n  (:start . 217) (:id . 75))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 231) (:start . 229)\n  (:id . 76))\n ((:tag . "RB") (:stem . "apparently") (:form . "apparently") (:end . 242)\n  (:start . 232) (:id . 77))\n ((:tag . "JJ") (:stem . "optimal") (:form . "optimal") (:end . 250)\n  (:start . 243) (:id . 78))\n ((:tag . "NNP") (:stem . "T-effectorTreg") (:form . "T-effectorTreg")\n  (:end . 265) (:start . 251) (:id . 79))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 271)\n  (:start . 266) (:id . 80))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 273) (:start . 272)\n  (:id . 81))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 275) (:start . 273)\n  (:id . 82))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 276) (:start . 275)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 277) (:start . 276)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s5.133) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501524@unknown@formal@none@1@S@IL-10 is well-established as a vital homeostatic regulator of malaria-induced inflammation that prevents immune-pathology in mice [49],[64], promotes the necessary switch from early Th1 to subsequent Th2 responses [65],[66], and has been linked to protection from severe malaria anaemia [24],[25], and death [23] in humans.@(((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "well-established") (:form . "well-established")\n  (:end . 25) (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "vital") (:form . "vital") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "homeostatic") (:form . 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5501525@unknown@formal@none@1@S@However, the cellular source of IL-10 in human malaria cases was, until now, ill defined.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "il-10") (:form . "IL-10") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 71) (:start . 66)\n  (:id . 55))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 57))\n ((:tag . "VB") (:stem . "ill") (:form . "ill") (:end . 80) (:start . 77)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 88)\n  (:start . 81) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s5.135) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501526@unknown@formal@none@1@S@Contrary to our expectations, but in striking agreement with observations in P. yoelii-infected mice [33], CD45RO+ CD4+ T cells (that are CD25- and FOXP3-) and not classical Tregs are the only substantial source of IL-10 during acute malaria infection.@(((:tag . "JJ") (:stem . "contrary") (:form . "Contrary") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "expectation") (:form . "expectations") (:end . 28)\n  (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "striking") (:form . "striking") (:end . 45)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 73)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "yoelii-infected") (:form . "yoelii-infected")\n  (:end . 95) (:start . 80) (:id . 55))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 100) (:start . 96)\n  (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 102) (:start . 101)\n  (:id . 57))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 105) (:start . 104)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "cd45ro+") (:form . "CD45RO+") (:end . 114)\n  (:start . 107) (:id . 61))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 119) (:start . 115)\n  (:id . 62))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 121) (:start . 120)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 127)\n  (:start . 122) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 133) (:start . 129)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 137) (:start . 134)\n  (:id . 67))\n ((:tag . "NN") (:stem . "cd25-") (:form . "CD25-") (:end . 143)\n  (:start . 138) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n  (:id . 69))\n ((:tag . "NN") (:stem . "foxp3-") (:form . "FOXP3-") (:end . 154)\n  (:start . 148) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 72))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 163) (:start . 160)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "classical") (:form . "classical") (:end . 173)\n  (:start . 164) (:id . 74))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 179)\n  (:start . 174) (:id . 75))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 183) (:start . 180)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 187) (:start . 184)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 192) (:start . 188)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "substantial") (:form . "substantial") (:end . 204)\n  (:start . 193) (:id . 79))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 211)\n  (:start . 205) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 214) (:start . 212)\n  (:id . 81))\n ((:tag . "NN") (:stem . "il-10") (:form . "IL-10") (:end . 220)\n  (:start . 215) (:id . 82))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 227)\n  (:start . 221) (:id . 83))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 233)\n  (:start . 228) (:id . 84))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 241)\n  (:start . 234) (:id . 85))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 251)\n  (:start . 242) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s5.136) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501527@unknown@formal@none@1@S@This observation is reminiscent of that made by Nylen [67] in patients with acute visceral leishmaniasis.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "reminiscent") (:form . "reminiscent") (:end . 31)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Nylen") (:form . "Nylen") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "CD") (:stem . "67") (:form . "67") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 70)\n  (:start . 62) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 81) (:start . 76)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "visceral") (:form . "visceral") (:end . 90)\n  (:start . 82) (:id . 58))\n ((:tag . "NN") (:stem . "leishmaniasis") (:form . "leishmaniasis")\n  (:end . 104) (:start . 91) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s5.137) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501528@unknown@formal@none@1@S@Moreover, in our patients, a significant proportion of IL-10 producing CD4+ T cells were simultaneously producing IFN-γ, identifying them as Th1 cells.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 40)\n  (:start . 29) (:id . 49))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 51)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 70)\n  (:start . 61) (:id . 53))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 77) (:start . 76)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 83) (:start . 78)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n  (:end . 103) (:start . 89) (:id . 58))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 113)\n  (:start . 104) (:id . 59))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 119)\n  (:start . 114) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 132)\n  (:start . 121) (:id . 62))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 137) (:start . 133)\n  (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 140) (:start . 138)\n  (:id . 64))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 144) (:start . 141)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s5.138) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501529@unknown@formal@none@1@S@Although IL-10 secreting Th1 cells have been described recently in two murine models of toxoplasmosis [50], and cutaneous leishmaniasis [51], as far as we are aware, this is the first demonstration of IL-10 producing Th1 cells during human infections.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "secrete") (:form . "secreting") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 54)\n  (:start . 45) (:id . 49))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 63)\n  (:start . 55) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "murine") (:form . "murine") (:end . 77)\n  (:start . 71) (:id . 53))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 84)\n  (:start . 78) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "toxoplasmosis") (:form . "toxoplasmosis")\n  (:end . 101) (:start . 88) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 103) (:start . 102)\n  (:id . 57))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "cutaneous") (:form . "cutaneous") (:end . 121)\n  (:start . 112) (:id . 62))\n ((:tag . "NN") (:stem . "leishmaniasis") (:form . "leishmaniasis")\n  (:end . 135) (:start . 122) (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 137) (:start . 136)\n  (:id . 64))\n ((:tag . "CD") (:stem . "51") (:form . "51") (:end . 139) (:start . 137)\n  (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 140) (:start . 139)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 67))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 144) (:start . 142)\n  (:id . 68))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 148) (:start . 145)\n  (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 151) (:start . 149)\n  (:id . 70))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 154) (:start . 152)\n  (:id . 71))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 158) (:start . 155)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "aware") (:form . "aware") (:end . 164)\n  (:start . 159) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 74))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 170) (:start . 166)\n  (:id . 75))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 173) (:start . 171)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 183)\n  (:start . 178) (:id . 78))\n ((:tag . "NN") (:stem . "demonstration") (:form . "demonstration")\n  (:end . 197) (:start . 184) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 200) (:start . 198)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 206)\n  (:start . 201) (:id . 81))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 216)\n  (:start . 207) (:id . 82))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 220) (:start . 217)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 226)\n  (:start . 221) (:id . 84))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 233)\n  (:start . 227) (:id . 85))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 239)\n  (:start . 234) (:id . 86))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 250)\n  (:start . 240) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 251) (:start . 250)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s5.139) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501530@unknown@formal@none@1@S@Intriguingly, the proportion of these cells within the total CD4+ T cell population was significantly higher in children with uncomplicated malaria than in children with severe malaria suggesting that in human P. falciparum infection, as in murine T.gondii infections [50], IL-10 producing Th1 cells, activated by a strong inflammatory stimulus, may act as anti-parasitic effector cells with a “built in” control mechanism to prevent the onset of immune pathology.@(((:tag . "RB") (:stem . "intriguingly") (:form . "Intriguingly") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . 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5501531@unknown@formal@none@1@S@If so, then the ability of these self-regulating effector cells to localize to sites of parasite sequestration in tissues, where they mediate parasite killing whilst simultaneously blocking tissue damage, may be key to clinical immunity to malaria.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 11) (:start . 7)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 46))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 23)\n  (:start . 16) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 32) (:start . 27)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "self-regulating") (:form . "self-regulating")\n  (:end . 48) (:start . 33) (:id . 50))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "VB") (:stem . "localize") (:form . "localize") (:end . 75)\n  (:start . 67) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 84) (:start . 79)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "NN") (:stem . "parasite") (:form . "parasite") (:end . 96)\n  (:start . 88) (:id . 58))\n ((:tag . "NN") (:stem . "sequestration") (:form . "sequestration")\n  (:end . 110) (:start . 97) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 121)\n  (:start . 114) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 128)\n  (:start . 123) (:id . 63))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 133) (:start . 129)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "mediate") (:form . "mediate") (:end . 141)\n  (:start . 134) (:id . 65))\n ((:tag . "JJ") (:stem . "parasite") (:form . "parasite") (:end . 150)\n  (:start . 142) (:id . 66))\n ((:tag . "NN") (:stem . "killing") (:form . "killing") (:end . 158)\n  (:start . 151) (:id . 67))\n ((:tag . "IN") (:stem . "whilst") (:form . "whilst") (:end . 165)\n  (:start . 159) (:id . 68))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n  (:end . 180) (:start . 166) (:id . 69))\n ((:tag . "VBG") (:stem . "block") (:form . "blocking") (:end . 189)\n  (:start . 181) (:id . 70))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 196)\n  (:start . 190) (:id . 71))\n ((:tag . "NN") (:stem . "damage") (:form . "damage") (:end . 203)\n  (:start . 197) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 204) (:start . 203)\n  (:id . 73))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 208) (:start . 205)\n  (:id . 74))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 211) (:start . 209)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 215) (:start . 212)\n  (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 218) (:start . 216)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 227)\n  (:start . 219) (:id . 78))\n ((:tag . "NN") (:stem . "immunity") (:form . "immunity") (:end . 236)\n  (:start . 228) (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 239) (:start . 237)\n  (:id . 80))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 247)\n  (:start . 240) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 248) (:start . 247)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x5.141.1) (:span 205 208)))\n (:hscopes ((:id . :x5.141.1) (:span 205 247)))\n (:identifiers (:sid . :s5.141) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501532@unknown@formal@none@1@S@Thus, our data strongly suggest that the percentage of IL-10-producing Th1 effector cells, rather than the cocktail of circulating cytokines, may be the most relevant biomarker of effective immunity to severe malaria.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 14) (:start . 10)\n  (:id . 45))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 23)\n  (:start . 15) (:id . 46))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 51)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "il-10-producing") (:form . "IL-10-producing")\n  (:end . 70) (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 74) (:start . 71)\n  (:id . 53))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 83)\n  (:start . 75) (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 89) (:start . 84)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 56))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 97)\n  (:start . 91) (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 102) (:start . 98)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cocktail") (:form . "cocktail") (:end . 115)\n  (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "circulate") (:form . "circulating") (:end . 130)\n  (:start . 119) (:id . 62))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 140)\n  (:start . 131) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 64))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 145) (:start . 142)\n  (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 148) (:start . 146)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 67))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 157) (:start . 153)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 166)\n  (:start . 158) (:id . 69))\n ((:tag . "NN") (:stem . "biomarker") (:form . "biomarker") (:end . 176)\n  (:start . 167) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 179) (:start . 177)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 189)\n  (:start . 180) (:id . 72))\n ((:tag . "NN") (:stem . "immunity") (:form . "immunity") (:end . 198)\n  (:start . 190) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 201) (:start . 199)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 208)\n  (:start . 202) (:id . 75))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 216)\n  (:start . 209) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x5.142.1) (:span 142 145)) ((:id . :x5.142.2) (:span 24 31)))\n (:hscopes ((:id . :x5.142.1) (:span 142 216))\n  ((:id . :x5.142.2) (:span 24 216)))\n (:identifiers (:sid . :s5.142) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501533@unknown@formal@none@1@S@Although (Tregs may not seem to determine the outcome of current P. falciparum infections) we did find evidence that they affect the magnitude of the malaria specific memory response induced by the current infection.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "VB") (:stem . "seem") (:form . "seem") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 41)\n  (:start . 32) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "outcome") (:form . "outcome") (:end . 53)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 64)\n  (:start . 57) (:id . 53))\n ((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "falciparum") (:form . "falciparum") (:end . 78)\n  (:start . 68) (:id . 55))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 89)\n  (:start . 79) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "VB") (:stem . "find") (:form . "find") (:end . 102) (:start . 98)\n  (:id . 60))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 111)\n  (:start . 103) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n  (:id . 62))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 121) (:start . 117)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "affect") (:form . "affect") (:end . 128)\n  (:start . 122) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 65))\n ((:tag . "NN") (:stem . "magnitude") (:form . "magnitude") (:end . 142)\n  (:start . 133) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 149) (:start . 146)\n  (:id . 68))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 157)\n  (:start . 150) (:id . 69))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 166)\n  (:start . 158) (:id . 70))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 173)\n  (:start . 167) (:id . 71))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 182)\n  (:start . 174) (:id . 72))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 190)\n  (:start . 183) (:id . 73))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 193) (:start . 191)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 205)\n  (:start . 198) (:id . 76))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 215)\n  (:start . 206) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x5.143.1) (:span 16 19 24 28)))\n (:hscopes ((:id . :x5.143.1) (:span 9 89)))\n (:identifiers (:sid . :s5.143) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501534@unknown@formal@none@1@S@A similar observation has been made in P. berghei ANKA-infected mice; animals that were depleted of CD25+ cells prior to infection and drug-cured on day 5 developed significantly stronger IFN-γ memory responses on day 14 than did intact infected/cured mice, and these mice also developed much more severe, and frequently fatal, clinical symptoms upon reinfection, despite more efficient parasite clearance [35].@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "make") (:form . 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"clinical") (:end . 336)\n  (:start . 328) (:id . 97))\n ((:tag . "NNS") (:stem . "symptom") (:form . "symptoms") (:end . 345)\n  (:start . 337) (:id . 98))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 350) (:start . 346)\n  (:id . 99))\n ((:tag . "NN") (:stem . "reinfection") (:form . "reinfection") (:end . 362)\n  (:start . 351) (:id . 100))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 363) (:start . 362)\n  (:id . 101))\n ((:tag . "IN") (:stem . "despite") (:form . "despite") (:end . 371)\n  (:start . 364) (:id . 102))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 376) (:start . 372)\n  (:id . 103))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 386)\n  (:start . 377) (:id . 104))\n ((:tag . "NN") (:stem . "parasite") (:form . "parasite") (:end . 395)\n  (:start . 387) (:id . 105))\n ((:tag . "NN") (:stem . "clearance") (:form . "clearance") (:end . 405)\n  (:start . 396) (:id . 106))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 407) (:start . 406)\n  (:id . 107))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 409) (:start . 407)\n  (:id . 108))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 410) (:start . 409)\n  (:id . 109))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 411) (:start . 410)\n  (:id . 110)))@@@1@69@((:identifiers (:sid . :s5.144) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501535@unknown@formal@none@1@S@Thus, malaria specific Tregs acquired during a primary infection may limit the magnitude of Th1 effector responses to subsequent infections to a level that allows parasite clearance without causing immunopathology.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 13)\n  (:start . 6) (:id . 44))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "acquire") (:form . "acquired") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "VB") (:stem . "limit") (:form . "limit") (:end . 74) (:start . 69)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "magnitude") (:form . "magnitude") (:end . 88)\n  (:start . 79) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "NN") (:stem . "effector") (:form . "effector") (:end . 104)\n  (:start . 96) (:id . 58))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 114)\n  (:start . 105) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 128)\n  (:start . 118) (:id . 61))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 139)\n  (:start . 129) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 144) (:start . 143)\n  (:id . 64))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 150)\n  (:start . 145) (:id . 65))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 155) (:start . 151)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 162)\n  (:start . 156) (:id . 67))\n ((:tag . "NN") (:stem . "parasite") (:form . "parasite") (:end . 171)\n  (:start . 163) (:id . 68))\n ((:tag . "NN") (:stem . "clearance") (:form . "clearance") (:end . 181)\n  (:start . 172) (:id . 69))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 189)\n  (:start . 182) (:id . 70))\n ((:tag . "VBG") (:stem . "cause") (:form . "causing") (:end . 197)\n  (:start . 190) (:id . 71))\n ((:tag . "NN") (:stem . "immunopathology") (:form . "immunopathology")\n  (:end . 213) (:start . 198) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x5.145.1) (:span 65 68)))\n (:hscopes ((:id . :x5.145.1) (:span 65 213)))\n (:identifiers (:sid . :s5.145) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501536@unknown@formal@none@1@S@Future studies should be designed to test the hypothesis that Tregs may contribute to the very rapid development of resistance to severe malaria.@(((:tag . "JJ") (:stem . "future") (:form . "Future") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 82)\n  (:start . 72) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 94) (:start . 90)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 100) (:start . 95)\n  (:id . 58))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 112)\n  (:start . 101) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . "NN") (:stem . "resistance") (:form . "resistance") (:end . 126)\n  (:start . 116) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 129) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 136)\n  (:start . 130) (:id . 63))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 144)\n  (:start . 137) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x5.146.1) (:span 68 71)) ((:id . :x5.146.2) (:span 46 56)))\n (:hscopes ((:id . :x5.146.1) (:span 68 144))\n  ((:id . :x5.146.2) (:span 46 144)))\n (:identifiers (:sid . :s5.146) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501537@unknown@formal@none@1@S@In summary, our data indicate that classical FOXP3+ Tregs are unable to control the florid inflammation that accompanies acute malaria infections and this component of the immunoregulatory arsenal is rapidly overwhelmed in children with either mild or severe malaria.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "summary") (:form . "summary") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "classical") (:form . "classical") (:end . 44)\n  (:start . 35) (:id . 49))\n ((:tag . "JJ") (:stem . "foxp3+") (:form . "FOXP3+") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "NNS") (:stem . "treg") (:form . "Tregs") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "unable") (:form . "unable") (:end . 68)\n  (:start . 62) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "VB") (:stem . "control") (:form . "control") (:end . 79)\n  (:start . 72) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "NN") (:stem . "florid") (:form . "florid") (:end . 90)\n  (:start . 84) (:id . 57))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 103)\n  (:start . 91) (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "accompany") (:form . "accompanies") (:end . 120)\n  (:start . 109) (:id . 60))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 126)\n  (:start . 121) (:id . 61))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 134)\n  (:start . 127) (:id . 62))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 145)\n  (:start . 135) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 149) (:start . 146)\n  (:id . 64))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 154) (:start . 150)\n  (:id . 65))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 164)\n  (:start . 155) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 167) (:start . 165)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 171) (:start . 168)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "immunoregulatory") (:form . "immunoregulatory")\n  (:end . 188) (:start . 172) (:id . 69))\n ((:tag . "NN") (:stem . "arsenal") (:form . "arsenal") (:end . 196)\n  (:start . 189) (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 199) (:start . 197)\n  (:id . 71))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 207)\n  (:start . 200) (:id . 72))\n ((:tag . "VBN") (:stem . "overwhelm") (:form . "overwhelmed") (:end . 219)\n  (:start . 208) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 222) (:start . 220)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 231)\n  (:start . 223) (:id . 75))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 236) (:start . 232)\n  (:id . 76))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 243)\n  (:start . 237) (:id . 77))\n ((:tag . "JJ") (:stem . "mild") (:form . "mild") (:end . 248) (:start . 244)\n  (:id . 78))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 251) (:start . 249)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 258)\n  (:start . 252) (:id . 80))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 266)\n  (:start . 259) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 267) (:start . 266)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x5.147.1) (:span 21 34)))\n (:hscopes ((:id . :x5.147.1) (:span 21 266)))\n (:identifiers (:sid . :s5.147) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501538@unknown@formal@none@1@S@Importantly however we have identified, for the first time in an acute human infection, a population of IL-10 producing Th1 effector cells which appear to be a major source of this key anti-inflammatory cytokine during acute malaria infection, and which are associated with development of uncomplicated as opposed to severe malaria.@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 19)\n  (:start . 12) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . 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"of") (:end . 288) (:start . 286)\n  (:id . 89))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 302) (:start . 289) (:id . 90))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 305) (:start . 303)\n  (:id . 91))\n ((:tag . "VBN") (:stem . "oppose") (:form . "opposed") (:end . 313)\n  (:start . 306) (:id . 92))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 316) (:start . 314)\n  (:id . 93))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 323)\n  (:start . 317) (:id . 94))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 331)\n  (:start . 324) (:id . 95))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 332) (:start . 331)\n  (:id . 96)))@@@1@55@((:hcues ((:id . :x5.148.1) (:span 145 151)))\n (:hscopes ((:id . :x5.148.1) (:span 139 242)))\n (:identifiers (:sid . :s5.148) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501539@unknown@formal@none@1@S@We propose that IL-10-producing Th1 cells may be the essential regulators of acute infection-induced inflammation and that such “self-regulating” Th1 cells may be essential for the infection to be cleared without inducing immune-mediated pathology.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "propose") (:form . "propose") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "il-10-producing") (:form . "IL-10-producing")\n  (:end . 31) (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 62)\n  (:start . 53) (:id . 51))\n ((:tag . "NNS") (:stem . "regulator") (:form . "regulators") (:end . 73)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 82) (:start . 77)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "infection-induced") (:form . "infection-induced")\n  (:end . 100) (:start . 83) (:id . 55))\n ((:tag . "NN") (:stem . "inflammation") (:form . "inflammation") (:end . 113)\n  (:start . 101) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 122) (:start . 118)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 127) (:start . 123)\n  (:id . 59))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 129) (:start . 128)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "self-regulating") (:form . "self-regulating")\n  (:end . 144) (:start . 129) (:id . 61))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 145) (:start . 144)\n  (:id . 62))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 149) (:start . 146)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 155)\n  (:start . 150) (:id . 64))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 159) (:start . 156)\n  (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 162) (:start . 160)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 172)\n  (:start . 163) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 176) (:start . 173)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 180) (:start . 177)\n  (:id . 69))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 190)\n  (:start . 181) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 193) (:start . 191)\n  (:id . 71))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 196) (:start . 194)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "clear") (:form . "cleared") (:end . 204)\n  (:start . 197) (:id . 73))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 212)\n  (:start . 205) (:id . 74))\n ((:tag . "VBG") (:stem . "induce") (:form . "inducing") (:end . 221)\n  (:start . 213) (:id . 75))\n ((:tag . "JJ") (:stem . "immune-mediated") (:form . "immune-mediated")\n  (:end . 237) (:start . 222) (:id . 76))\n ((:tag . "NN") (:stem . "pathology") (:form . "pathology") (:end . 247)\n  (:start . 238) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 248) (:start . 247)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x5.149.1) (:span 156 159)) ((:id . :x5.149.2) (:span 42 45))\n  ((:id . :x5.149.3) (:span 3 10)))\n (:hscopes ((:id . :x5.149.1) (:span 156 247))\n  ((:id . :x5.149.2) (:span 42 113)) ((:id . :x5.149.3) (:span 3 247)))\n (:identifiers (:sid . :s5.149) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501540@unknown@formal@none@1@S@Moreover, we have found evidence in support of the hypothesis that Tregs limit the magnitude of the Th1 memory response raising the intriguing possibility that they may play an important role in the rapid evolution of clinical immunity to severe malaria.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 61)\n  (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Treg") (:form . "Tregs") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "limit") (:form . "limit") (:end . 78) (:start . 73)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "NN") (:stem . "magnitude") (:form . "magnitude") (:end . 92)\n  (:start . 83) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "th1") (:form . "Th1") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 110)\n  (:start . 104) (:id . 61))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 119)\n  (:start . 111) (:id . 62))\n ((:tag . "VBG") (:stem . "raise") (:form . "raising") (:end . 127)\n  (:start . 120) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "intriguing") (:form . "intriguing") (:end . 142)\n  (:start . 132) (:id . 65))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 154)\n  (:start . 143) (:id . 66))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 159) (:start . 155)\n  (:id . 67))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 164) (:start . 160)\n  (:id . 68))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 168) (:start . 165)\n  (:id . 69))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 173) (:start . 169)\n  (:id . 70))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 176) (:start . 174)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 186)\n  (:start . 177) (:id . 72))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 191) (:start . 187)\n  (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 194) (:start . 192)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 198) (:start . 195)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 204)\n  (:start . 199) (:id . 76))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 214)\n  (:start . 205) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 217) (:start . 215)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 226)\n  (:start . 218) (:id . 79))\n ((:tag . "NN") (:stem . "immunity") (:form . "immunity") (:end . 235)\n  (:start . 227) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 238) (:start . 236)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 245)\n  (:start . 239) (:id . 82))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 253)\n  (:start . 246) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 254) (:start . 253)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x5.150.1) (:span 165 168))\n  ((:id . :x5.150.2) (:span 143 154)) ((:id . :x5.150.3) (:span 51 61)))\n (:hscopes ((:id . :x5.150.1) (:span 165 253))\n  ((:id . :x5.150.2) (:span 143 253)) ((:id . :x5.150.3) (:span 51 253)))\n (:identifiers (:sid . :s5.150) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501541@unknown@formal@none@1@S@Materials and Methods@(((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 21)\n  (:start . 14) (:id . 44)))@@@1@3@((:identifiers (:sid . :s5.151) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501542@unknown@formal@none@1@S@Subject recruitment, study design, and study procedures@(((:tag . "NN") (:stem . "subject") (:form . "Subject") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "recruitment") (:form . "recruitment") (:end . 19)\n  (:start . 8) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "design") (:form . "design") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 55)\n  (:start . 45) (:id . 50)))@@@1@9@((:identifiers (:sid . :s5.152) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501543@unknown@formal@none@1@S@A case-control study was conducted in Gambian children with severe or uncomplicated malaria, resident in a peri-urban area within a 40 km radius south of the capital, Banjul, with low levels of malaria transmission [68],[69].@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "case-control") (:form . "case-control") (:end . 14)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "conduct") (:form . "conducted") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "gambian") (:form . "Gambian") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 66)\n  (:start . 60) (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 83) (:start . 70) (:id . 53))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 91)\n  (:start . 84) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "resident") (:form . "resident") (:end . 101)\n  (:start . 93) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 106) (:start . 105)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "peri-urban") (:form . "peri-urban") (:end . 117)\n  (:start . 107) (:id . 59))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 122) (:start . 118)\n  (:id . 60))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 129)\n  (:start . 123) (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 131) (:start . 130)\n  (:id . 62))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 134) (:start . 132)\n  (:id . 63))\n ((:tag . "NN") (:stem . "km") (:form . "km") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . "NN") (:stem . "radius") (:form . "radius") (:end . 144)\n  (:start . 138) (:id . 65))\n ((:tag . "RB") (:stem . "south") (:form . "south") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 153) (:start . 151)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n  (:id . 68))\n ((:tag . "NN") (:stem . "capital") (:form . "capital") (:end . 165)\n  (:start . 158) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Banjul") (:form . "Banjul") (:end . 173)\n  (:start . 167) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 72))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 179) (:start . 175)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 183) (:start . 180)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 190)\n  (:start . 184) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 193) (:start . 191)\n  (:id . 76))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 201)\n  (:start . 194) (:id . 77))\n ((:tag . "NN") (:stem . "transmission") (:form . "transmission") (:end . 214)\n  (:start . 202) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 216) (:start . 215)\n  (:id . 79))\n ((:tag . "CD") (:stem . "68],[69") (:form . "68],[69") (:end . 223)\n  (:start . 216) (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 224) (:start . 223)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s5.153) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501544@unknown@formal@none@1@S@Patients were enrolled at Brikama Health Centre, the MRC Fajara Gate Clinic or the Jammeh Foundation for Peace Hospital in Serekunda between September 2007 and January 2008, after written informed consent was obtained from the parents or guardians.@(((:tag . "NNPS") (:stem . "Patient") (:form . "Patients") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "enrol") (:form . "enrolled") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Brikama") (:form . "Brikama") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "NNP") (:stem . "Health") (:form . "Health") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "NNP") (:stem . "Centre") (:form . "Centre") (:end . 47)\n  (:start . 41) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "MRC") (:form . "MRC") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Fajara") (:form . "Fajara") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "NNP") (:stem . "Gate") (:form . "Gate") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Clinic") (:form . "Clinic") (:end . 75)\n  (:start . 69) (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Jammeh") (:form . "Jammeh") (:end . 89)\n  (:start . 83) (:id . 57))\n ((:tag . "NNP") (:stem . "Foundation") (:form . "Foundation") (:end . 100)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Peace") (:form . "Peace") (:end . 110)\n  (:start . 105) (:id . 60))\n ((:tag . "NNP") (:stem . "Hospital") (:form . "Hospital") (:end . 119)\n  (:start . 111) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Serekunda") (:form . "Serekunda") (:end . 132)\n  (:start . 123) (:id . 63))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 140)\n  (:start . 133) (:id . 64))\n ((:tag . "NNP") (:stem . "September") (:form . "September") (:end . 150)\n  (:start . 141) (:id . 65))\n ((:tag . "CD") (:stem . "2007") (:form . "2007") (:end . 155) (:start . 151)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "January") (:form . "January") (:end . 167)\n  (:start . 160) (:id . 68))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 172) (:start . 168)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 70))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 179)\n  (:start . 174) (:id . 71))\n ((:tag . "VBN") (:stem . "write") (:form . "written") (:end . 187)\n  (:start . 180) (:id . 72))\n ((:tag . "VBN") (:stem . "inform") (:form . "informed") (:end . 196)\n  (:start . 188) (:id . 73))\n ((:tag . "NN") (:stem . "consent") (:form . "consent") (:end . 204)\n  (:start . 197) (:id . 74))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 208) (:start . 205)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 217)\n  (:start . 209) (:id . 76))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 222) (:start . 218)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 226) (:start . 223)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "parent") (:form . "parents") (:end . 234)\n  (:start . 227) (:id . 79))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 237) (:start . 235)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "guardian") (:form . "guardians") (:end . 247)\n  (:start . 238) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 248) (:start . 247)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s5.154) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501545@unknown@formal@none@1@S@Uncomplicated disease was defined as an episode of fever (temperature >37.5°C) within the last 48 hours with more than 5000 parasites/µl detected by slide microscopy.@(((:tag . "JJ") (:stem . "uncomplicated") (:form . "Uncomplicated")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 21)\n  (:start . 14) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 33)\n  (:start . 26) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "episode") (:form . "episode") (:end . 47)\n  (:start . 40) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "fever") (:form . "fever") (:end . 56) (:start . 51)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 69)\n  (:start . 58) (:id . 52))\n ((:tag . "NNP") (:stem . ">37.5°C") (:form . ">37.5°C") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 85)\n  (:start . 79) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 94) (:start . 90)\n  (:id . 57))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 103) (:start . 98)\n  (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 108) (:start . 104)\n  (:id . 60))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 118) (:start . 114)\n  (:id . 62))\n ((:tag . "CD") (:stem . "5000") (:form . "5000") (:end . 123) (:start . 119)\n  (:id . 63))\n ((:tag . "NN") (:stem . "parasites/µl") (:form . "parasites/µl") (:end . 136)\n  (:start . 124) (:id . 64))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 145)\n  (:start . 137) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 148) (:start . 146)\n  (:id . 66))\n ((:tag . "NN") (:stem . "slide") (:form . "slide") (:end . 154)\n  (:start . 149) (:id . 67))\n ((:tag . "NN") (:stem . "microscopy") (:form . "microscopy") (:end . 165)\n  (:start . 155) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s5.155) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501546@unknown@formal@none@1@S@Severe disease was defined using modified WHO criteria [70]: SA, defined as Hb<6 g/dl; SRD defined as serum lactate >7 mmol/L; CM defined as a Blantyre coma score ≤2 in the absence of hypoglycaemia, with the coma lasting at least for 2 hours.@(((:tag . "JJ") (:stem . "severe") (:form . "Severe") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "modify") (:form . "modified") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "who") (:form . "WHO") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "criterion") (:form . 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5501547@unknown@formal@none@1@S@To avoid the confounding effects of other pathogens in children with concomitant systemic bacterial infections [71], children with clinical and/or laboratory evidence of infections other than malaria were not enrolled into the study.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "avoid") (:form . "avoid") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "confounding") (:form . "confounding") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "pathogen") (:form . "pathogens") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "concomitant") (:form . "concomitant") (:end . 80)\n  (:start . 69) (:id . 53))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . "JJ") (:stem . "bacterial") (:form . "bacterial") (:end . 99)\n  (:start . 90) (:id . 55))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 110)\n  (:start . 100) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 112) (:start . 111)\n  (:id . 57))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 114) (:start . 112)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 115) (:start . 114)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 125)\n  (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 130) (:start . 126)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 139)\n  (:start . 131) (:id . 63))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 146)\n  (:start . 140) (:id . 64))\n ((:tag . "JJ") (:stem . "laboratory") (:form . "laboratory") (:end . 157)\n  (:start . 147) (:id . 65))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 166)\n  (:start . 158) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 169) (:start . 167)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 180)\n  (:start . 170) (:id . 68))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 186)\n  (:start . 181) (:id . 69))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 191) (:start . 187)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "malaria") (:form . "malaria") (:end . 199)\n  (:start . 192) (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 204) (:start . 200)\n  (:id . 72))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 208) (:start . 205)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "enrol") (:form . "enrolled") (:end . 217)\n  (:start . 209) (:id . 74))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 222) (:start . 218)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 226) (:start . 223)\n  (:id . 76))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 232)\n  (:start . 227) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 233) (:start . 232)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s5.157) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501548@unknown@formal@none@1@S@For some experiments, healthy children of the same age and recruited from the same area at the same time of the year were enrolled as controls.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "healthy") (:form . "healthy") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "age") (:form . "age") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "recruit") (:form . "recruited") (:end . 68)\n  (:start . 59) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 82) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 87) (:start . 83)\n  (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 99) (:start . 95)\n  (:id . 60))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 104) (:start . 100)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 63))\n ((:tag . "NN") (:stem . "year") (:form . "year") (:end . 116) (:start . 112)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 121) (:start . 117)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "enrol") (:form . "enrolled") (:end . 130)\n  (:start . 122) (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 133) (:start . 131)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 142)\n  (:start . 134) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s5.158) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501549@unknown@formal@none@1@S@In total, 59 severe, 65 uncomplicated and 20 control cases were enrolled.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "CD") (:stem . "59") (:form . "59") (:end . 12) (:start . 10)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 19)\n  (:start . 13) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . "CD") (:stem . "65") (:form . "65") (:end . 23) (:start . 21)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 37) (:start . 24) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 52)\n  (:start . 45) (:id . 52))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 58) (:start . 53)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 63) (:start . 59)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "enrol") (:form . "enrolled") (:end . 72)\n  (:start . 64) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s5.159) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501550@unknown@formal@none@1@S@On admission (D0) and after 4 weeks (D28±3 days) one ml of blood was collected in RNA stabilizing agent (PAXgene™ Blood RNA system, Pre-AnalytiX) and a maximum of 4 mls of blood (mean: 3.2 mls CI 95%: 3.1–3.3 mls) were collected into heparinized vacutainers® (BD).@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "admission") (:form . "admission") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "D0") (:form . "D0") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 27) (:start . 22)\n  (:id . 48))\n ((:tag . "CD") (:stem . "4") (:form . 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5501551@unknown@formal@none@1@S@All patients received standard care according to the Gambian Government Treatment Guidelines, provided by the health centre staff.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "receive") (:form . "received") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "care") (:form . "care") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 45)\n  (:start . 36) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "gambian") (:form . "Gambian") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . "NNP") (:stem . "Government") (:form . "Government") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "NNP") (:stem . "Treatment") (:form . "Treatment") (:end . 81)\n  (:start . 72) (:id . 52))\n ((:tag . "NNP") (:stem . "Guidelines") (:form . "Guidelines") (:end . 92)\n  (:start . 82) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 102)\n  (:start . 94) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 105) (:start . 103)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 57))\n ((:tag . "NN") (:stem . "health") (:form . "health") (:end . 116)\n  (:start . 110) (:id . 58))\n ((:tag . "NN") (:stem . "centre") (:form . "centre") (:end . 123)\n  (:start . 117) (:id . 59))\n ((:tag . "NN") (:stem . "staff") (:form . "staff") (:end . 129)\n  (:start . 124) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.161) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501552@unknown@formal@none@1@S@The children's health was reviewed 7 days after admission.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "health") (:form . "health") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "review") (:form . "reviewed") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "admission") (:form . "admission") (:end . 57)\n  (:start . 48) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s5.162) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501553@unknown@formal@none@1@S@The study was reviewed and approved by the Joint Gambian Government/MRC Ethics Committee and the Ethics Committee of the London School of Hygiene & Tropical Medicine (London, UK).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "review") (:form . "reviewed") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "approve") (:form . "approved") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Joint") (:form . "Joint") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Gambian") (:form . "Gambian") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "NNP") (:stem . "Government/MRC") (:form . "Government/MRC")\n  (:end . 71) (:start . 57) (:id . 52))\n ((:tag . "NNP") (:stem . "Ethics") (:form . "Ethics") (:end . 78)\n  (:start . 72) (:id . 53))\n ((:tag . "NNP") (:stem . "Committee") (:form . "Committee") (:end . 88)\n  (:start . 79) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Ethics") (:form . "Ethics") (:end . 103)\n  (:start . 97) (:id . 57))\n ((:tag . "NNP") (:stem . "Committee") (:form . "Committee") (:end . 113)\n  (:start . 104) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "London") (:form . "London") (:end . 127)\n  (:start . 121) (:id . 61))\n ((:tag . "NNP") (:stem . "School") (:form . "School") (:end . 134)\n  (:start . 128) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Hygiene") (:form . "Hygiene") (:end . 145)\n  (:start . 138) (:id . 64))\n ((:tag . "CC") (:stem . "&") (:form . "&") (:end . 147) (:start . 146)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Tropical") (:form . "Tropical") (:end . 156)\n  (:start . 148) (:id . 66))\n ((:tag . "NNP") (:stem . "Medicine") (:form . "Medicine") (:end . 165)\n  (:start . 157) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "London") (:form . "London") (:end . 173)\n  (:start . 167) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "UK") (:form . "UK") (:end . 177) (:start . 175)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 178) (:start . 177)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s5.163) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501554@unknown@formal@none@1@S@P. falciparum parasites were identified by slide microscopy of 50 high power fields of a thick film.@(((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "falciparum") (:form . "falciparum") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "parasite") (:form . "parasites") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 39)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "NN") (:stem . "slide") (:form . "slide") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "microscopy") (:form . "microscopy") (:end . 59)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 70) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 76) (:start . 71)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "field") (:form . "fields") (:end . 83)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "thick") (:form . "thick") (:end . 94) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "film") (:form . "film") (:end . 99) (:start . 95)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s5.164) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501555@unknown@formal@none@1@S@Full differential blood counts were obtained on days 0 and 28 using a Medonic™ instrument (Clinical Diagnostics Solutions, Inc); the presence of intestinal helminths was assessed by microscopy from stool samples collected into BioSepar ParasiTrap® diagnosis system, following the manufacturers' instructions.@(((:tag . "JJ") (:stem . "full") (:form . "Full") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "differential") (:form . "differential") (:end . 17)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "blood") (:form . "blood") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "count") (:form . "counts") (:end . 30)\n  (:start . 24) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . 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5501556@unknown@formal@none@1@S@Sickle cell status was determined by metabisulfite test and confirmed on cellulose acetate electrophoresis [72].@(((:tag . "NNP") (:stem . "Sickle") (:form . "Sickle") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "status") (:form . "status") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 33)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "metabisulfite") (:form . "metabisulfite")\n  (:end . 50) (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 55) (:start . 51)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 69)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cellulose") (:form . "cellulose") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "acetate") (:form . "acetate") (:end . 90)\n  (:start . 83) (:id . 54))\n ((:tag . "NN") (:stem . "electrophoresis") (:form . "electrophoresis")\n  (:end . 106) (:start . 91) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 108) (:start . 107)\n  (:id . 56))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 110) (:start . 108)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 111) (:start . 110)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s5.166) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501557@unknown@formal@none@1@S@Cell preparation@(((:tag . "NN") (:stem . "cell") (:form . "Cell") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "preparation") (:form . "preparation") (:end . 16)\n  (:start . 5) (:id . 43)))@@@1@2@((:identifiers (:sid . :s5.167) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501558@unknown@formal@none@1@S@Blood samples were processed within 2 hours of collection.@(((:tag . "NNP") (:stem . "Blood") (:form . "Blood") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "process") (:form . "processed") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 35)\n  (:start . 29) (:id . 46))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "collection") (:form . "collection") (:end . 57)\n  (:start . 47) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s5.168) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501559@unknown@formal@none@1@S@Plasma was removed, stored at -80°C and replaced by an equal volume of RPMI 1640 (Sigma-Aldrich).@(((:tag . "NN") (:stem . "plasma") (:form . "Plasma") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "remove") (:form . "removed") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "store") (:form . "stored") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "-80°c") (:form . "-80°C") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "replace") (:form . "replaced") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 60) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "volume") (:form . "volume") (:end . 67)\n  (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "RPMI") (:form . "RPMI") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1640") (:form . "1640") (:end . 80) (:start . 76)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "sigma-aldrich") (:form . "Sigma-Aldrich")\n  (:end . 95) (:start . 82) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.169) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501560@unknown@formal@none@1@S@PBMC were isolated after density centrifugation over a 1.077 Nycoprep (Nycomed, Sweden) gradient (800 g, 30 min) and washed twice in RPM 1640.@(((:tag . "NNP") (:stem . "PBMC") (:form . "PBMC") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "density") (:form . "density") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "centrifugation") (:form . "centrifugation")\n  (:end . 47) (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 52) (:start . 48)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "CD") (:stem . "1.077") (:form . "1.077") (:end . 60) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "nycoprep") (:form . "Nycoprep") (:end . 69)\n  (:start . 61) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Nycomed") (:form . "Nycomed") (:end . 78)\n  (:start . 71) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sweden") (:form . "Sweden") (:end . 86)\n  (:start . 80) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 96)\n  (:start . 88) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "CD") (:stem . "800") (:form . "800") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "g") (:form . "g") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 61))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 107) (:start . 105)\n  (:id . 62))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 111) (:start . 108)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "wash") (:form . "washed") (:end . 123)\n  (:start . 117) (:id . 66))\n ((:tag . "RB") (:stem . "twice") (:form . "twice") (:end . 129)\n  (:start . 124) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "RPM") (:form . "RPM") (:end . 136) (:start . 133)\n  (:id . 69))\n ((:tag . "CD") (:stem . "1640") (:form . "1640") (:end . 141) (:start . 137)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s5.170) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501561@unknown@formal@none@1@S@Cells were either stained for flow cytometry directly ex-vivo, or cultured in RPMI 1640 containing 10% human AB+ serum, 100 µg/ml streptomycin, 100 U/ml penicillin (all Sigma-Aldrich), and 2 mM L-glutamine (Invitrogen Life Technologies), referred to as complete growth medium (GM).@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "either") (:form . "either") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cytometry") (:form . "cytometry") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . "RB") (:stem . 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5501562@unknown@formal@none@1@S@Flow cytometry@(((:tag . "NNP") (:stem . "Flow") (:form . "Flow") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cytometry") (:form . "cytometry") (:end . 14)\n  (:start . 5) (:id . 43)))@@@1@2@((:identifiers (:sid . :s5.172) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501563@unknown@formal@none@1@S@Fresh PBMC were stained using the following fluorochrome labeled mouse or rat anti-human antibodies: FITC anti-TNF-receptor II (R&D), PE anti-FOXP3 (clone PCH101), Pacific Blue anti CD3, APC-Alexa Fluor 750 anti-CD127 (all Ebioscience), APC anti-CD25, PerCP anti CD4 (BD systems), ECD anti-CD45R0 (Beckman-Coulter), and appropriate isotype controls.@(((:tag . "JJ") (:stem . "fresh") (:form . "Fresh") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "PBMC") (:form . "PBMC") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "follow") (:form . 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5501564@unknown@formal@none@1@S@IL-10 and IFN-γ production by PBMC from 30 children with acute P. falciparum (D0) was assessed after 5 hours stimulation in GM containing PMA (50 ng/ml) and Ionomycin (1000 ng/ml) or GM alone.@(((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "PBMC") (:form . "PBMC") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "child") (:form . "children") (:end . 51)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "falciparum") (:form . "falciparum") (:end . 76)\n  (:start . 66) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "D0") (:form . "D0") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 85) (:start . 82)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 94)\n  (:start . 86) (:id . 59))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 100) (:start . 95)\n  (:id . 60))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 108)\n  (:start . 103) (:id . 62))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 120)\n  (:start . 109) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "GM") (:form . "GM") (:end . 126) (:start . 124)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 137)\n  (:start . 127) (:id . 66))\n ((:tag . "NNP") (:stem . "PMA") (:form . "PMA") (:end . 141) (:start . 138)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 68))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 145) (:start . 143)\n  (:id . 69))\n ((:tag . "NN") (:stem . "ng/ml") (:form . "ng/ml") (:end . 151)\n  (:start . 146) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Ionomycin") (:form . "Ionomycin") (:end . 166)\n  (:start . 157) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 168) (:start . 167)\n  (:id . 74))\n ((:tag . "CD") (:stem . "1000") (:form . "1000") (:end . 172) (:start . 168)\n  (:id . 75))\n ((:tag . "NN") (:stem . "ng/ml") (:form . "ng/ml") (:end . 178)\n  (:start . 173) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 77))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 182) (:start . 180)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "GM") (:form . "GM") (:end . 185) (:start . 183)\n  (:id . 79))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 191)\n  (:start . 186) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s5.174) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501565@unknown@formal@none@1@S@Cells were stained with FITC anti-IFN-γ, PE anti-FOXP3, PE-Cy7 anti-CD25, APC-AF750 anti-CD8, Pacific Blue anti-CD3 (all Ebioscience), PerCP anti-CD4, APC anti-IL-10 (both BD), and ECD anti-CD45R0 (Beckman-Coulter).@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "FITC") (:form . "FITC") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "anti-IFN-γ") (:form . "anti-IFN-γ") (:end . 39)\n  (:start . 29) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PE") (:form . "PE") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "anti-foxp3") (:form . "anti-FOXP3") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "pe-cy7") (:form . "PE-Cy7") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "NN") (:stem . "anti-cd25") (:form . "anti-CD25") (:end . 72)\n  (:start . 63) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "APC-AF750") (:form . "APC-AF750") (:end . 83)\n  (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "anti-cd8") (:form . "anti-CD8") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Pacific") (:form . "Pacific") (:end . 101)\n  (:start . 94) (:id . 58))\n ((:tag . "NNP") (:stem . "Blue") (:form . "Blue") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "NN") (:stem . "anti-cd3") (:form . "anti-CD3") (:end . 115)\n  (:start . 107) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 120) (:start . 117)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Ebioscience") (:form . "Ebioscience") (:end . 132)\n  (:start . 121) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "PerCP") (:form . "PerCP") (:end . 140)\n  (:start . 135) (:id . 66))\n ((:tag . "NN") (:stem . "anti-cd4") (:form . "anti-CD4") (:end . 149)\n  (:start . 141) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "APC") (:form . "APC") (:end . 154) (:start . 151)\n  (:id . 69))\n ((:tag . "NN") (:stem . "anti-il-10") (:form . "anti-IL-10") (:end . 165)\n  (:start . 155) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 171) (:start . 167)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "BD") (:form . "BD") (:end . 174) (:start . 172)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 175) (:start . 174)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 176) (:start . 175)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 180) (:start . 177)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "ECD") (:form . "ECD") (:end . 184) (:start . 181)\n  (:id . 77))\n ((:tag . "NN") (:stem . "anti-cd45r0") (:form . "anti-CD45R0") (:end . 196)\n  (:start . 185) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 198) (:start . 197)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Beckman-Coulter") (:form . "Beckman-Coulter")\n  (:end . 213) (:start . 198) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s5.175) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501566@unknown@formal@none@1@S@To ascertain specificity of the intracellular cytokine staining, aliquots of some samples were incubated with saturating amounts of purified non-labelled antibody of the same clone prior to staining with the fluorochrome labeled ICS antibody.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "ascertain") (:form . "ascertain") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "intracellular") (:form . "intracellular")\n  (:end . 45) (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 54)\n  (:start . 46) (:id . 48))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 63)\n  (:start . 55) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "aliquot") (:form . "aliquots") (:end . 73)\n  (:start . 65) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 52))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 81) (:start . 77)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 89)\n  (:start . 82) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 104)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 109) (:start . 105)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "saturate") (:form . "saturating") (:end . 120)\n  (:start . 110) (:id . 58))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 128)\n  (:start . 121) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 140)\n  (:start . 132) (:id . 61))\n ((:tag . "JJ") (:stem . "non-labelled") (:form . "non-labelled") (:end . 153)\n  (:start . 141) (:id . 62))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 162)\n  (:start . 154) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 165) (:start . 163)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 174) (:start . 170)\n  (:id . 66))\n ((:tag . "NN") (:stem . "clone") (:form . "clone") (:end . 180)\n  (:start . 175) (:id . 67))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 186)\n  (:start . 181) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 189) (:start . 187)\n  (:id . 69))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 198)\n  (:start . 190) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 203) (:start . 199)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 207) (:start . 204)\n  (:id . 72))\n ((:tag . "NN") (:stem . "fluorochrome") (:form . "fluorochrome") (:end . 220)\n  (:start . 208) (:id . 73))\n ((:tag . "JJ") (:stem . "labeled") (:form . "labeled") (:end . 228)\n  (:start . 221) (:id . 74))\n ((:tag . "NN") (:stem . "ics") (:form . "ICS") (:end . 232) (:start . 229)\n  (:id . 75))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 241)\n  (:start . 233) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 242) (:start . 241)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s5.176) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501567@unknown@formal@none@1@S@The FOXP3 staining buffer set (Ebioscience) was used following the manufacturer's protocol.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "foxp3") (:form . "FOXP3") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Ebioscience") (:form . "Ebioscience") (:end . 42)\n  (:start . 31) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 79)\n  (:start . 67) (:id . 54))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 90)\n  (:start . 82) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s5.177) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501568@unknown@formal@none@1@S@Samples were acquired on a 3 laser/9 channel CyAn™ ADP flowcytometer using Summit 4.3 software (Dako).@(((:tag . "NNS") (:stem . "sample") (:form . "Samples") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "acquire") (:form . "acquired") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "laser/9") (:form . "laser/9") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "NN") (:stem . "channel") (:form . "channel") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "NNP") (:stem . "CyAn™") (:form . "CyAn™") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "ADP") (:form . "ADP") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "flowcytometer") (:form . "flowcytometer")\n  (:end . 68) (:start . 55) (:id . 52))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 74) (:start . 69)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Summit") (:form . "Summit") (:end . 81)\n  (:start . 75) (:id . 54))\n ((:tag . "CD") (:stem . "4.3") (:form . "4.3") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 94)\n  (:start . 86) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Dako") (:form . "Dako") (:end . 100) (:start . 96)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s5.178) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501569@unknown@formal@none@1@S@Analysis was performed using FlowJo (Tree Star Inc.).@(((:tag . "NNP") (:stem . "Analysis") (:form . "Analysis") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "FlowJo") (:form . "FlowJo") (:end . 35)\n  (:start . 29) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Tree") (:form . "Tree") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Star") (:form . "Star") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Inc.") (:form . "Inc.") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s5.179) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501570@unknown@formal@none@1@S@All flowcytometric analysis was performed at the MRC laboratories, The Gambia on freshly isolated cells.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "flowcytometric") (:form . "flowcytometric")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 27)\n  (:start . 19) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 31) (:start . 28)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 41)\n  (:start . 32) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "MRC") (:form . "MRC") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "laboratory") (:form . "laboratories") (:end . 65)\n  (:start . 53) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Gambia") (:form . "Gambia") (:end . 77)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "RB") (:stem . "freshly") (:form . "freshly") (:end . 88)\n  (:start . 81) (:id . 55))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 97)\n  (:start . 89) (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 103) (:start . 98)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s5.180) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501571@unknown@formal@none@1@S@Multiplex analysis of plasma cytokine concentration@(((:tag . "JJ") (:stem . "multiplex") (:form . "Multiplex") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 18)\n  (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "plasma") (:form . "plasma") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "cytokine") (:form . "cytokine") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 51) (:start . 38) (:id . 47)))@@@1@6@((:identifiers (:sid . :s5.181) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501572@unknown@formal@none@1@S@Plasma concentrations of IFN-γ, TNF-α and IL-10 were determined for each subject and time point on the Bio-Plex® 200 system, using X-Plex™ assays (both Bio-Rad Laboratories), according to the manufacturer's instructions.@(((:tag . "NN") (:stem . "plasma") (:form . "Plasma") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 21) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 30) (:start . 25)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "TNF-α") (:form . "TNF-α") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 63)\n  (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "NN") (:stem . "subject") (:form . "subject") (:end . 80)\n  (:start . 73) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 95) (:start . 90)\n  (:id . 57))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 98) (:start . 96)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Bio-Plex®") (:form . "Bio-Plex®") (:end . 112)\n  (:start . 103) (:id . 60))\n ((:tag . "CD") (:stem . "200") (:form . "200") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 123)\n  (:start . 117) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 130) (:start . 125)\n  (:id . 64))\n ((:tag . "NN") (:stem . "x-plex™") (:form . "X-Plex™") (:end . 138)\n  (:start . 131) (:id . 65))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 145)\n  (:start . 139) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 67))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 151) (:start . 147)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Bio-Rad") (:form . "Bio-Rad") (:end . 159)\n  (:start . 152) (:id . 69))\n ((:tag . "NNPS") (:stem . "Laboratories") (:form . "Laboratories")\n  (:end . 172) (:start . 160) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 173) (:start . 172)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 184)\n  (:start . 175) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 187) (:start . 185)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n  (:id . 75))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 204)\n  (:start . 192) (:id . 76))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 206) (:start . 204)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 219)\n  (:start . 207) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s5.182) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501573@unknown@formal@none@1@S@Data were analysed using the Bio-Plex® Manager software.@(((:tag . "NNP") (:stem . "Datum") (:form . "Data") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "analyse") (:form . "analysed") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Bio-Plex®") (:form . "Bio-Plex®") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "NNP") (:stem . "Manager") (:form . "Manager") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s5.183) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501574@unknown@formal@none@1@S@The detection limit was defined as the concentration corresponding to a fluorescence value above the mean background fluorescence in control wells plus 3 SD, being 8.76 pg/ml for IFN-γ, 5 pg/ml for TNF-α and 0.57 pg/ml for IL-10.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "detection") (:form . "detection") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "limit") (:form . "limit") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 52) (:start . 39) (:id . 49))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 66)\n  (:start . 53) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 84)\n  (:start . 72) (:id . 53))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 90) (:start . 85)\n  (:id . 54))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 96) (:start . 91)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "mean") (:form . "mean") (:end . 105) (:start . 101)\n  (:id . 57))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 116)\n  (:start . 106) (:id . 58))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 129)\n  (:start . 117) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 60))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 140)\n  (:start . 133) (:id . 61))\n ((:tag . "NNS") (:stem . "well") (:form . "wells") (:end . 146)\n  (:start . 141) (:id . 62))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 151) (:start . 147)\n  (:id . 63))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 153) (:start . 152)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "SD") (:form . "SD") (:end . 156) (:start . 154)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 163) (:start . 158)\n  (:id . 67))\n ((:tag . "CD") (:stem . "8.76") (:form . "8.76") (:end . 168) (:start . 164)\n  (:id . 68))\n ((:tag . "NN") (:stem . "pg/ml") (:form . "pg/ml") (:end . 174)\n  (:start . 169) (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 178) (:start . 175)\n  (:id . 70))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 184)\n  (:start . 179) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 72))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 187) (:start . 186)\n  (:id . 73))\n ((:tag . "NN") (:stem . "pg/ml") (:form . "pg/ml") (:end . 193)\n  (:start . 188) (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 197) (:start . 194)\n  (:id . 75))\n ((:tag . "NN") (:stem . "tnf-α") (:form . "TNF-α") (:end . 203)\n  (:start . 198) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 207) (:start . 204)\n  (:id . 77))\n ((:tag . "CD") (:stem . "0.57") (:form . "0.57") (:end . 212) (:start . 208)\n  (:id . 78))\n ((:tag . "NN") (:stem . "pg/ml") (:form . "pg/ml") (:end . 218)\n  (:start . 213) (:id . 79))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 222) (:start . 219)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 228)\n  (:start . 223) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s5.184) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501575@unknown@formal@none@1@S@Values below this threshold were set to these levels.@(((:tag . "NNS") (:stem . "value") (:form . "Values") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s5.185) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501576@unknown@formal@none@1@S@Plasmodium falciparum culture and schizont antigens@(((:tag . "NNP") (:stem . "Plasmodium") (:form . "Plasmodium") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "falciparum") (:form . "falciparum") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 29)\n  (:start . 22) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 45))\n ((:tag . "NN") (:stem . "schizont") (:form . "schizont") (:end . 42)\n  (:start . 34) (:id . 46))\n ((:tag . "NNS") (:stem . "antigen") (:form . "antigens") (:end . 51)\n  (:start . 43) (:id . 47)))@@@1@6@((:identifiers (:sid . :s5.186) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501577@unknown@formal@none@1@S@P. falciparum parasites (3D7 strain) were cultured in vitro as described [73] and were routinely shown to be mycoplasma free by PCR (Bio Whittaker).@(((:tag . "NNP") (:stem . "P.") (:form . "P.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "falciparum") (:form . "falciparum") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "parasite") (:form . "parasites") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "3d7") (:form . "3D7") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "strain") (:form . "strain") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 50)\n  (:start . 42) (:id . 50))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 72)\n  (:start . 63) (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "CD") (:stem . "73") (:form . "73") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 77) (:start . 76)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 86) (:start . 82)\n  (:id . 59))\n ((:tag . "RB") (:stem . "routinely") (:form . "routinely") (:end . 96)\n  (:start . 87) (:id . 60))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 102) (:start . 97)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n  (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 108) (:start . 106)\n  (:id . 63))\n ((:tag . "NN") (:stem . "mycoplasma") (:form . "mycoplasma") (:end . 119)\n  (:start . 109) (:id . 64))\n ((:tag . "JJ") (:stem . "free") (:form . "free") (:end . 124) (:start . 120)\n  (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 127) (:start . 125)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 131) (:start . 128)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Bio") (:form . "Bio") (:end . 136) (:start . 133)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Whittaker") (:form . "Whittaker") (:end . 146)\n  (:start . 137) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s5.187) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501578@unknown@formal@none@1@S@Schizont-infected erythrocytes were harvested from synchronized cultures by centrifugation through a Percoll gradient (Sigma-Aldrich).@(((:tag . "JJ") (:stem . "schizont-infected") (:form . "Schizont-infected")\n  (:end . 17) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "erythrocyte") (:form . "erythrocytes") (:end . 30)\n  (:start . 18) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "harvest") (:form . "harvested") (:end . 45)\n  (:start . 36) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 50) (:start . 46)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "synchronize") (:form . "synchronized") (:end . 63)\n  (:start . 51) (:id . 47))\n ((:tag . "NNS") (:stem . "culture") (:form . "cultures") (:end . 72)\n  (:start . 64) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n  (:id . 49))\n ((:tag . "NN") (:stem . "centrifugation") (:form . "centrifugation")\n  (:end . 90) (:start . 76) (:id . 50))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 98)\n  (:start . 91) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Percoll") (:form . "Percoll") (:end . 108)\n  (:start . 101) (:id . 53))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 117)\n  (:start . 109) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 119) (:start . 118)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "sigma-aldrich") (:form . "Sigma-Aldrich")\n  (:end . 132) (:start . 119) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s5.188) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501579@unknown@formal@none@1@S@PfSE was prepared by two rapid freeze-thaw cycles in liquid nitrogen and a 37°C water bath.@(((:tag . "NNP") (:stem . "PfSE") (:form . "PfSE") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "freeze-thaw") (:form . "freeze-thaw") (:end . 42)\n  (:start . 31) (:id . 48))\n ((:tag . "NNS") (:stem . "cycle") (:form . "cycles") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "liquid") (:form . "liquid") (:end . 59)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "nitrogen") (:form . "nitrogen") (:end . 68)\n  (:start . 60) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "water") (:form . "water") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "NN") (:stem . "bath") (:form . "bath") (:end . 90) (:start . 86)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s5.189) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501580@unknown@formal@none@1@S@Extracts of uninfected erythrocytes (uRBC) were prepared in the same way.@(((:tag . "NNS") (:stem . "extract") (:form . "Extracts") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "uninfected") (:form . "uninfected") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "erythrocyte") (:form . "erythrocytes") (:end . 35)\n  (:start . 23) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 46))\n ((:tag . "NN") (:stem . "urbc") (:form . "uRBC") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s5.190) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501581@unknown@formal@none@1@S@Proliferation assay@(((:tag . "NN") (:stem . "proliferation") (:form . "Proliferation")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 19) (:start . 14)\n  (:id . 43)))@@@1@2@((:identifiers (:sid . :s5.191) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501582@unknown@formal@none@1@S@PBMC from 10 severe and 10 uncomplicated malaria cases collected on day 0 were depleted of CD25hi cells or mock depleted using magnetic beads (Dynal Biotech, UK), at a bead to PBMC ratio of 71, and cell proliferation was determined by [3H]-thymidine (Amersham, UK) incorporation after 6 days in culture with PfSE, uRBC (RBCPBMC ratio equivalent to 21), GM, or 2 days culture with PMA (10 ng/ml)+ Ionomycin (100 ng/ml), as described [27].@(((:tag . "NNP") (:stem . "PBMC") (:form . "PBMC") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "CD") (:stem . "10") (:form . 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"with") (:form . "with") (:end . 379) (:start . 375)\n  (:id . 119))\n ((:tag . "NNP") (:stem . "PMA") (:form . "PMA") (:end . 383) (:start . 380)\n  (:id . 120))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 385) (:start . 384)\n  (:id . 121))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 387) (:start . 385)\n  (:id . 122))\n ((:tag . "NNP") (:stem . "ng/ml)+") (:form . "ng/ml)+") (:end . 395)\n  (:start . 388) (:id . 123))\n ((:tag . "NNP") (:stem . "Ionomycin") (:form . "Ionomycin") (:end . 405)\n  (:start . 396) (:id . 124))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 407) (:start . 406)\n  (:id . 125))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 410) (:start . 407)\n  (:id . 126))\n ((:tag . "NN") (:stem . "ng/ml") (:form . "ng/ml") (:end . 416)\n  (:start . 411) (:id . 127))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 417) (:start . 416)\n  (:id . 128))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 418) (:start . 417)\n  (:id . 129))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 421) (:start . 419)\n  (:id . 130))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 431)\n  (:start . 422) (:id . 131))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 433) (:start . 432)\n  (:id . 132))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 435) (:start . 433)\n  (:id . 133))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 436) (:start . 435)\n  (:id . 134))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 437) (:start . 436)\n  (:id . 135)))@@@1@94@((:identifiers (:sid . :s5.192) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501583@unknown@formal@none@1@S@Cultured ELISpot@(((:tag . "NNP") (:stem . "Cultured") (:form . "Cultured") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "ELISpot") (:form . "ELISpot") (:end . 16)\n  (:start . 9) (:id . 43)))@@@1@2@((:identifiers (:sid . :s5.193) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501584@unknown@formal@none@1@S@Cultured ELISPOTs were performed to assess malaria specific IFN-γ memory responses, adapting an established method [74].@(((:tag . "VBN") (:stem . "culture") (:form . "Cultured") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "ELISPOT") (:form . "ELISPOTs") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 42)\n  (:start . 36) (:id . 47))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 59)\n  (:start . 51) (:id . 49))\n ((:tag . "NN") (:stem . "ifn-γ") (:form . "IFN-γ") (:end . 65) (:start . 60)\n  (:id . 50))\n ((:tag . "NN") (:stem . "memory") (:form . "memory") (:end . 72)\n  (:start . 66) (:id . 51))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 82)\n  (:start . 73) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "adapt") (:form . "adapting") (:end . 92)\n  (:start . 84) (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 95) (:start . 93)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "establish") (:form . "established") (:end . 107)\n  (:start . 96) (:id . 56))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 114)\n  (:start . 108) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 116) (:start . 115)\n  (:id . 58))\n ((:tag . "CD") (:stem . "74") (:form . "74") (:end . 118) (:start . 116)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.194) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501585@unknown@formal@none@1@S@Up to 1 million PBMCs collected on day 28 were cultured in 24 well plates for 6 days in 1 ml GM and stimulated with either PfSE, uRBC (RBCPBMC ratio equivalent to 21), or GM respectively.@(((:tag . "IN") (:stem . "up") (:form . "Up") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "CD") (:stem . "million") (:form . "million") (:end . 15)\n  (:start . 8) (:id . 45))\n ((:tag . "NNS") (:stem . "pbmc") (:form . "PBMCs") (:end . 21) (:start . 16)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 31)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 46) (:start . 42)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 55)\n  (:start . 47) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 61) (:start . 59)\n  (:id . 54))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 66) (:start . 62)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "plat") (:form . "plates") (:end . 73) (:start . 67)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 79) (:start . 78)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 84) (:start . 80)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 89) (:start . 88)\n  (:id . 61))\n ((:tag . "NN") (:stem . "ml") (:form . "ml") (:end . 92) (:start . 90)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "GM") (:form . "GM") (:end . 95) (:start . 93)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 110)\n  (:start . 100) (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 115) (:start . 111)\n  (:id . 66))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 122)\n  (:start . 116) (:id . 67))\n ((:tag . "NNP") (:stem . "PfSE") (:form . "PfSE") (:end . 127) (:start . 123)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 69))\n ((:tag . "NN") (:stem . "urbc") (:form . "uRBC") (:end . 133) (:start . 129)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "RBCPBMC") (:form . "RBCPBMC") (:end . 142)\n  (:start . 135) (:id . 72))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 148)\n  (:start . 143) (:id . 73))\n ((:tag . "JJ") (:stem . "equivalent") (:form . "equivalent") (:end . 159)\n  (:start . 149) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 162) (:start . 160)\n  (:id . 75))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 165) (:start . 163)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 78))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 170) (:start . 168)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "GM") (:form . "GM") (:end . 173) (:start . 171)\n  (:id . 80))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 186)\n  (:start . 174) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s5.195) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501586@unknown@formal@none@1@S@At day 3, half the medium was exchanged and rIL-2 (final concentration 20 IU/well) was added.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 8) (:start . 7)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 45))\n ((:tag . "PDT") (:stem . "half") (:form . "half") (:end . 14) (:start . 10)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 47))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 25)\n  (:start . 19) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "exchange") (:form . "exchanged") (:end . 39)\n  (:start . 30) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "NN") (:stem . "ril-2") (:form . "rIL-2") (:end . 49) (:start . 44)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 56) (:start . 51)\n  (:id . 54))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 70) (:start . 57) (:id . 55))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "IU/well") (:form . "IU/well") (:end . 81)\n  (:start . 74) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 86) (:start . 83)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 92) (:start . 87)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s5.196) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501587@unknown@formal@none@1@S@On day 6 cells were harvested, washed three times, and 1.5×105 cells seeded into duplicate wells onto Millipore MAIP S45 plates and restimulated overnight with PfSE, uRBC (concentrations as above), GM or PHA-L (5 µg/ml).@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 8) (:start . 7)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 14) (:start . 9)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "harvest") (:form . "harvested") (:end . 29)\n  (:start . 20) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "wash") (:form . "washed") (:end . 37) (:start . 31)\n  (:id . 49))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 43) (:start . 38)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 49) (:start . 44)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1.5×105") (:form . "1.5×105") (:end . 62)\n  (:start . 55) (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 68) (:start . 63)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "seed") (:form . "seeded") (:end . 75) (:start . 69)\n  (:id . 56))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 80) (:start . 76)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "duplicate") (:form . "duplicate") (:end . 90)\n  (:start . 81) (:id . 58))\n ((:tag . "NNS") (:stem . "well") (:form . "wells") (:end . 96) (:start . 91)\n  (:id . 59))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 101) (:start . 97)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Millipore") (:form . "Millipore") (:end . 111)\n  (:start . 102) (:id . 61))\n ((:tag . "NNP") (:stem . "MAIP") (:form . "MAIP") (:end . 116) (:start . 112)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "S45") (:form . "S45") (:end . 120) (:start . 117)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "plat") (:form . "plates") (:end . 127)\n  (:start . 121) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "restimulate") (:form . "restimulated") (:end . 144)\n  (:start . 132) (:id . 66))\n ((:tag . "RB") (:stem . "overnight") (:form . "overnight") (:end . 154)\n  (:start . 145) (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 159) (:start . 155)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "PfSE") (:form . "PfSE") (:end . 164) (:start . 160)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 70))\n ((:tag . "NN") (:stem . "urbc") (:form . "uRBC") (:end . 170) (:start . 166)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 186) (:start . 172) (:id . 73))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 189) (:start . 187)\n  (:id . 74))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 195)\n  (:start . 190) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 196) (:start . 195)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "GM") (:form . "GM") (:end . 200) (:start . 198)\n  (:id . 78))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 203) (:start . 201)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "PHA-L") (:form . "PHA-L") (:end . 209)\n  (:start . 204) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 211) (:start . 210)\n  (:id . 81))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 212) (:start . 211)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "µg/ml") (:form . "µg/ml") (:end . 218)\n  (:start . 213) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 219) (:start . 218)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s5.197) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501588@unknown@formal@none@1@S@IFN-γ ELISpot was performed using MabTech antibodies according to the manufacturer's instructions.@(((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "ELISpot") (:form . "ELISpot") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "MabTech") (:form . "MabTech") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 52)\n  (:start . 42) (:id . 48))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 62)\n  (:start . 53) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 82)\n  (:start . 70) (:id . 52))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 84) (:start . 82)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 97)\n  (:start . 85) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s5.198) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501589@unknown@formal@none@1@S@Spot forming cell numbers were counted using an ELISPOT plate reader (AutoImmuneDiagnostica, Vers. 3.2).@(((:tag . "NN") (:stem . "spot") (:form . "Spot") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 12) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "count") (:form . "counted") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "elispot") (:form . "ELISPOT") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "plate") (:form . "plate") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "reader") (:form . "reader") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "AutoImmuneDiagnostica")\n  (:form . "AutoImmuneDiagnostica") (:end . 91) (:start . 70) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Vers.") (:form . "Vers.") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "CD") (:stem . "3.2") (:form . "3.2") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s5.199) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501590@unknown@formal@none@1@S@Results are expressed as spot forming units (SFU) per million PBMC after subtraction of individual background values (GM for PHA-L, uRBC for PfSE) being deducted.@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "spot") (:form . "spot") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "unit") (:form . "units") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "SFU") (:form . "SFU") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "CD") (:stem . "million") (:form . "million") (:end . 61)\n  (:start . 54) (:id . 53))\n ((:tag . "NNP") (:stem . "PBMC") (:form . "PBMC") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 72) (:start . 67)\n  (:id . 55))\n ((:tag . "NN") (:stem . "subtraction") (:form . "subtraction") (:end . 84)\n  (:start . 73) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 98)\n  (:start . 88) (:id . 58))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 109)\n  (:start . 99) (:id . 59))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 116)\n  (:start . 110) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "GM") (:form . "GM") (:end . 120) (:start . 118)\n  (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 124) (:start . 121)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "PHA-L") (:form . "PHA-L") (:end . 130)\n  (:start . 125) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 65))\n ((:tag . "NN") (:stem . "urbc") (:form . "uRBC") (:end . 136) (:start . 132)\n  (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 140) (:start . 137)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "PfSE") (:form . "PfSE") (:end . 145) (:start . 141)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 152) (:start . 147)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "deduct") (:form . "deducted") (:end . 161)\n  (:start . 153) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s5.200) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501591@unknown@formal@none@1@S@Assays were discounted if the positive control (PHA-L) was <50 SFU, or the negative control was >30 SFU.@(((:tag . "NNS") (:stem . "assay") (:form . "Assays") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "discount") (:form . "discounted") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "PHA-L") (:form . "PHA-L") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "CD") (:stem . "<50") (:form . "<50") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sfu") (:form . "SFU") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 70) (:start . 68)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 83)\n  (:start . 75) (:id . 58))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 91)\n  (:start . 84) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 95) (:start . 92)\n  (:id . 60))\n ((:tag . "CD") (:stem . ">30") (:form . ">30") (:end . 99) (:start . 96)\n  (:id . 61))\n ((:tag . "NN") (:stem . "sfu") (:form . "SFU") (:end . 103) (:start . 100)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s5.201) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501592@unknown@formal@none@1@S@RT-PCR@(((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 6) (:start . 0)\n  (:id . 42)))@@@1@1@((:identifiers (:sid . :s5.202) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501593@unknown@formal@none@1@S@For quantitative reverse transcription-polymerase chain reaction (RT-PCR), total RNA was extracted from PAX tubes following the manufacturer's instructions and reverse transcribed into cDNA using TaqMan® reagents for reverse transcription (Applied Biosystems), following the manufacturer's protocol.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "NN") (:stem . "transcription-polymerase")\n  (:form . "transcription-polymerase") (:end . 49) (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "chain") (:form . "chain") (:end . 55) (:start . 50)\n  (:id . 46))\n ((:tag . "NN") (:stem . "reaction") (:form . "reaction") (:end . 64)\n  (:start . 56) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 72)\n  (:start . 66) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 80) (:start . 75)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 84) (:start . 81)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 88) (:start . 85)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 98)\n  (:start . 89) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 103) (:start . 99)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "PAX") (:form . "PAX") (:end . 107) (:start . 104)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "tube") (:form . "tubes") (:end . 113)\n  (:start . 108) (:id . 58))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 123)\n  (:start . 114) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 60))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 140)\n  (:start . 128) (:id . 61))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 142) (:start . 140)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 155)\n  (:start . 143) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 64))\n ((:tag . "VB") (:stem . "reverse") (:form . "reverse") (:end . 167)\n  (:start . 160) (:id . 65))\n ((:tag . "VBN") (:stem . "transcribe") (:form . "transcribed") (:end . 179)\n  (:start . 168) (:id . 66))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 184) (:start . 180)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "cDNA") (:form . "cDNA") (:end . 189) (:start . 185)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 195) (:start . 190)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "TaqMan®") (:form . "TaqMan®") (:end . 203)\n  (:start . 196) (:id . 70))\n ((:tag . "NNS") (:stem . "reagent") (:form . "reagents") (:end . 212)\n  (:start . 204) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 216) (:start . 213)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 224)\n  (:start . 217) (:id . 73))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 238) (:start . 225) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 240) (:start . 239)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Applied") (:form . "Applied") (:end . 247)\n  (:start . 240) (:id . 76))\n ((:tag . "NNP") (:stem . "Biosystems") (:form . "Biosystems") (:end . 258)\n  (:start . 248) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 259) (:start . 258)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 260) (:start . 259)\n  (:id . 79))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 270)\n  (:start . 261) (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 274) (:start . 271)\n  (:id . 81))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 287)\n  (:start . 275) (:id . 82))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 289) (:start . 287)\n  (:id . 83))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 298)\n  (:start . 290) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 299) (:start . 298)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s5.203) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501594@unknown@formal@none@1@S@Gene expression profiles for FOXP3, IL-10, SOCS-2 and IFN-γ were measured by RT-PCR on a DNA Engine Opticon® (MJ Research) with QuantiTect SYBR Green PCR kits (Qiagen Ltd) using primers (all Sigma Genosys) previously described: IFN-γ, IL-10; FOXP3 designed by [75], and SOCS-2 designed by [76].@(((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "FOXP3") (:form . "FOXP3") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "socs-2") (:form . "SOCS-2") (:end . 49)\n  (:start . 43) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 73)\n  (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 83)\n  (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 88) (:start . 87)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 92) (:start . 89)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Engine") (:form . "Engine") (:end . 99)\n  (:start . 93) (:id . 60))\n ((:tag . "NNP") (:stem . "Opticon®") (:form . "Opticon®") (:end . 108)\n  (:start . 100) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "MJ") (:form . "MJ") (:end . 112) (:start . 110)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Research") (:form . "Research") (:end . 121)\n  (:start . 113) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 127) (:start . 123)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "QuantiTect") (:form . "QuantiTect") (:end . 138)\n  (:start . 128) (:id . 67))\n ((:tag . "NNP") (:stem . "SYBR") (:form . "SYBR") (:end . 143) (:start . 139)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "green") (:form . "Green") (:end . 149)\n  (:start . 144) (:id . 69))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 153) (:start . 150)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "kit") (:form . "kits") (:end . 158) (:start . 154)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Qiagen") (:form . "Qiagen") (:end . 166)\n  (:start . 160) (:id . 73))\n ((:tag . "NNP") (:stem . "Ltd") (:form . "Ltd") (:end . 170) (:start . 167)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 171) (:start . 170)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 177) (:start . 172)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 185)\n  (:start . 178) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 187) (:start . 186)\n  (:id . 78))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 190) (:start . 187)\n  (:id . 79))\n ((:tag . 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5501595@unknown@formal@none@1@S@T-BET and GATA-3 gene expression was determined using the TaqMan® Probe kit using the primers (all Metabion) designed by [77]. 18S rRNA, amplified using a commercially available kit (rRNA primers and VIC labeled probe, Applied Biosystems), was used as an internal control.@(((:tag . "NNP") (:stem . "T-BET") (:form . "T-BET") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "GATA-3") (:form . "GATA-3") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "VBG") (:stem . 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5501596@unknown@formal@none@1@S@Data were analysed using Opticon Monitor 3™ analysis software (BioRad) and are expressed as the ratio of the transcript number of the gene of interest over the endogenous control, 18S rRNA.@(((:tag . "NNP") (:stem . "Datum") (:form . "Data") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "analyse") (:form . "analysed") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Opticon") (:form . "Opticon") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NNP") (:stem . "Monitor") (:form . "Monitor") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "3™") (:form . "3™") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "BioRad") (:form . "BioRad") (:end . 69)\n  (:start . 63) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 88)\n  (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "NN") (:stem . "transcript") (:form . "transcript") (:end . 119)\n  (:start . 109) (:id . 62))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 126)\n  (:start . 120) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 65))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 138) (:start . 134)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 141) (:start . 139)\n  (:id . 67))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 150)\n  (:start . 142) (:id . 68))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 155) (:start . 151)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 170)\n  (:start . 160) (:id . 71))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 178)\n  (:start . 171) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 179) (:start . 178)\n  (:id . 73))\n ((:tag . "NN") (:stem . "18s") (:form . "18S") (:end . 183) (:start . 180)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "rRNA") (:form . "rRNA") (:end . 188) (:start . 184)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s5.206) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501597@unknown@formal@none@1@S@Parasite genotyping@(((:tag . "NNP") (:stem . "Parasite") (:form . "Parasite") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "genotyping") (:form . "genotyping") (:end . 19)\n  (:start . 9) (:id . 43)))@@@1@2@((:identifiers (:sid . :s5.207) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501598@unknown@formal@none@1@S@Genomic DNA from each parasite isolate was genotyped by sequencing the highly polymorphic block 2 region of the msp1 gene to assess the number of clones infecting each patient [78].@(((:tag . "JJ") (:stem . "genomic") (:form . "Genomic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "parasite") (:form . "parasite") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "isolate") (:form . "isolate") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "genotype") (:form . "genotyped") (:end . 52)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "sequence") (:form . "sequencing") (:end . 66)\n  (:start . 56) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 77)\n  (:start . 71) (:id . 53))\n ((:tag . "JJ") (:stem . "polymorphic") (:form . "polymorphic") (:end . 89)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "block") (:form . "block") (:end . 95) (:start . 90)\n  (:id . 55))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 97) (:start . 96)\n  (:id . 56))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 104)\n  (:start . 98) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "NN") (:stem . "msp1") (:form . "msp1") (:end . 116) (:start . 112)\n  (:id . 60))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 121) (:start . 117)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 124) (:start . 122)\n  (:id . 62))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 131)\n  (:start . 125) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 135) (:start . 132)\n  (:id . 64))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 142)\n  (:start . 136) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 152)\n  (:start . 146) (:id . 67))\n ((:tag . "VBG") (:stem . "infect") (:form . "infecting") (:end . 162)\n  (:start . 153) (:id . 68))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 167) (:start . 163)\n  (:id . 69))\n ((:tag . "NN") (:stem . "patient") (:form . "patient") (:end . 175)\n  (:start . 168) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 177) (:start . 176)\n  (:id . 71))\n ((:tag . "CD") (:stem . "78") (:form . "78") (:end . 179) (:start . 177)\n  (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 180) (:start . 179)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s5.208) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501599@unknown@formal@none@1@S@Statistical analysis@(((:tag . "JJ") (:stem . "statistical") (:form . "Statistical") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 20)\n  (:start . 12) (:id . 43)))@@@1@2@((:identifiers (:sid . :s5.209) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501600@unknown@formal@none@1@S@Analysis was performed using linear regression, with a random effect to allow for the within subject measurements over time, where the response variables were log transformed to improve the normality and constant variance assumptions.@(((:tag . "NNP") (:stem . "Analysis") (:form . "Analysis") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "linear") (:form . "linear") (:end . 35)\n  (:start . 29) (:id . 46))\n ((:tag . "NN") (:stem . "regression") (:form . "regression") (:end . 46)\n  (:start . 36) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 61)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 77) (:start . 72)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 92)\n  (:start . 86) (:id . 57))\n ((:tag . "JJ") (:stem . "subject") (:form . "subject") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "measurement") (:form . "measurements") (:end . 113)\n  (:start . 101) (:id . 59))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 118) (:start . 114)\n  (:id . 60))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 62))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 130)\n  (:start . 125) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n  (:id . 64))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 143)\n  (:start . 135) (:id . 65))\n ((:tag . "NNS") (:stem . "variable") (:form . "variables") (:end . 153)\n  (:start . 144) (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 158) (:start . 154)\n  (:id . 67))\n ((:tag . "NN") (:stem . "log") (:form . "log") (:end . 162) (:start . 159)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "transform") (:form . "transformed") (:end . 174)\n  (:start . 163) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 177) (:start . 175)\n  (:id . 70))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 185)\n  (:start . 178) (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 189) (:start . 186)\n  (:id . 72))\n ((:tag . "NN") (:stem . "normality") (:form . "normality") (:end . 199)\n  (:start . 190) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 203) (:start . 200)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "constant") (:form . "constant") (:end . 212)\n  (:start . 204) (:id . 75))\n ((:tag . "NN") (:stem . "variance") (:form . "variance") (:end . 221)\n  (:start . 213) (:id . 76))\n ((:tag . "NNS") (:stem . "assumption") (:form . "assumptions") (:end . 233)\n  (:start . 222) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s5.210) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501601@unknown@formal@none@1@S@Significance (measured at the 5% level) tests for the effects of malaria group (uncomplicated, SA or SB), time (day 0 and day 28) and their interaction were adjusted for the possible confounding effects of age, sex, duration of prior symptoms and numbers of clones causing the infection.@(((:tag . "NN") (:stem . "significance") (:form . "Significance") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . 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(:end . 287) (:start . 286)\n  (:id . 100)))@@@1@59@((:hcues ((:id . :x5.211.1) (:span 174 182)))\n (:hscopes ((:id . :x5.211.1) (:span 174 286)))\n (:identifiers (:sid . :s5.211) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501602@unknown@formal@none@1@S@Where there was no significant malaria group and time interaction, p-values for the overall comparison of day 0 vs. day 28 are given.@(((:tag . "WRB") (:stem . "where") (:form . "Where") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 30)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 65)\n  (:start . 54) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "p-value") (:form . "p-values") (:end . 75)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 91)\n  (:start . 84) (:id . 56))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 102)\n  (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . "IN") (:stem . "vs.") (:form . "vs.") (:end . 115) (:start . 112)\n  (:id . 61))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 119) (:start . 116)\n  (:id . 62))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 126) (:start . 123)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 132)\n  (:start . 127) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s5.212) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501603@unknown@formal@none@1@S@Within day 0, comparisons of severe vs. uncomplicated and the two groups of severely ill patients (SA vs SB) were adjusted for any malaria group and time interactions.@(((:tag . "IN") (:stem . "within") (:form . "Within") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 25)\n  (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 35)\n  (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "vs.") (:form . "vs.") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "uncomplicated") (:form . "uncomplicated")\n  (:end . 53) (:start . 40) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 72)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "RB") (:stem . "severely") (:form . "severely") (:end . 84)\n  (:start . 76) (:id . 56))\n ((:tag . "JJ") (:stem . "ill") (:form . "ill") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "patient") (:form . "patients") (:end . 97)\n  (:start . 89) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "SA") (:form . "SA") (:end . 101) (:start . 99)\n  (:id . 60))\n ((:tag . "IN") (:stem . "vs") (:form . "vs") (:end . 104) (:start . 102)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "SB") (:form . "SB") (:end . 107) (:start . 105)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 113) (:start . 109)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "adjust") (:form . "adjusted") (:end . 122)\n  (:start . 114) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 126) (:start . 123)\n  (:id . 66))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 130) (:start . 127)\n  (:id . 67))\n ((:tag . "NN") (:stem . "malaria") (:form . "malaria") (:end . 138)\n  (:start . 131) (:id . 68))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 144)\n  (:start . 139) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n  (:id . 70))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 153) (:start . 149)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 166)\n  (:start . 154) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s5.213) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501604@unknown@formal@none@1@S@To allow for the multiplicity of tests resulting from multiple responses and multiple comparisons within a response performed in the model, a false discovery rate (FDR) of 5% was assumed.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "multiplicity") (:form . "multiplicity") (:end . 29)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 48)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 85)\n  (:start . 77) (:id . 54))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 97)\n  (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 104)\n  (:start . 98) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 106) (:start . 105)\n  (:id . 57))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 115)\n  (:start . 107) (:id . 58))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 125)\n  (:start . 116) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 61))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 138)\n  (:start . 133) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 141) (:start . 140)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 147)\n  (:start . 142) (:id . 65))\n ((:tag . "NN") (:stem . "discovery") (:form . "discovery") (:end . 157)\n  (:start . 148) (:id . 66))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 162) (:start . 158)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "FDR") (:form . "FDR") (:end . 167) (:start . 164)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 168) (:start . 167)\n  (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 71))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 173) (:start . 172)\n  (:id . 72))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 174) (:start . 173)\n  (:id . 73))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 178) (:start . 175)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "assume") (:form . "assumed") (:end . 186)\n  (:start . 179) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s5.214) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501605@unknown@formal@none@1@S@Using the Benjamini and Hochberg approach [43] only tests with a p-value below 0.012 have an FDR of ≤5%.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Benjamini") (:form . "Benjamini") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Hochberg") (:form . "Hochberg") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "test") (:form . "tests") (:end . 57) (:start . 52)\n  (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 72)\n  (:start . 65) (:id . 55))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 78) (:start . 73)\n  (:id . 56))\n ((:tag . "CD") (:stem . "0.012") (:form . "0.012") (:end . 84) (:start . 79)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 89) (:start . 85)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . "NN") (:stem . "fdr") (:form . "FDR") (:end . 96) (:start . 93)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 61))\n ((:tag . "CD") (:stem . "≤5") (:form . "≤5") (:end . 102) (:start . 100)\n  (:id . 62))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 103) (:start . 102)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s5.215) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501606@unknown@formal@none@1@S@Due to the large number of tests family-wise error rate correction methods were too conservative.@(((:tag . "JJ") (:stem . "due") (:form . "Due") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "family-wise") (:form . "family-wise") (:end . 44)\n  (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "correction") (:form . "correction") (:end . 66)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 74)\n  (:start . 67) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "conservative") (:form . "conservative") (:end . 96)\n  (:start . 84) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s5.216) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501607@unknown@formal@none@1@S@Analyses were performed using Stata version 9 and Matlab version R2008a.@(((:tag . "NNS") (:stem . "analysis") (:form . "Analyses") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 29) (:start . 24)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Stata") (:form . "Stata") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Matlab") (:form . "Matlab") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 64)\n  (:start . 57) (:id . 51))\n ((:tag . "NNP") (:stem . "R2008a") (:form . "R2008a") (:end . 71)\n  (:start . 65) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s5.217) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501608@unknown@formal@none@1@S@Supporting Information@(((:tag . "VBG") (:stem . "support") (:form . "Supporting") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Information") (:form . "Information") (:end . 22)\n  (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s5.218) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501609@unknown@formal@none@1@S@Figure S1 mRNA levels for IFN-γ, IL-10 and Th-1 as well as Th-2 lineage transcription factors in severe and mild disease. (1.99 MB TIF)@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "IFN-γ") (:form . "IFN-γ") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "IL-10") (:form . "IL-10") (:end . 38) (:start . 33)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Th-1") (:form . "Th-1") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 58) (:start . 56)\n  (:id . 54))\n ((:tag . "NN") (:stem . "th-2") (:form . "Th-2") (:end . 63) (:start . 59)\n  (:id . 55))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 71)\n  (:start . 64) (:id . 56))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 85) (:start . 72) (:id . 57))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 93)\n  (:start . 86) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 103)\n  (:start . 97) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "mild") (:form . "mild") (:end . 112) (:start . 108)\n  (:id . 62))\n ((:tag . "NN") (:stem . "disease.") (:form . "disease.") (:end . 121)\n  (:start . 113) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 64))\n ((:tag . "CD") (:stem . "1.99") (:form . "1.99") (:end . 127) (:start . 123)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 130) (:start . 128)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 134) (:start . 131)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 135) (:start . 134)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s5.219) (:did . :pmc2658808) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501610@unknown@formal@none@1@S@Myeloid Neoplasia: CBFß is critical for AML1-ETO and TEL-AML1 activity@(((:tag . "NNP") (:stem . "Myeloid") (:form . "Myeloid") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Neoplasia") (:form . "Neoplasia") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "tel-aml1") (:form . "TEL-AML1") (:end . 61)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 70)\n  (:start . 62) (:id . 52)))@@@1@11@((:identifiers (:sid . :s6.1) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5501611@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s6.2) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501612@unknown@formal@none@1@S@AML1-ETO and TEL-AML1 are chimeric proteins resulting from the t(8;21)(q22;q22) in acute myeloid leukemia, and the t(12;21)(p13;q22) in pre-B-cell leukemia, respectively.@(((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "chimeric") (:form . "chimeric") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 53)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 58) (:start . 54)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "t(8;21)(q22;q22)") (:form . "t(8;21)(q22;q22)")\n  (:end . 79) (:start . 63) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 88) (:start . 83)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "myeloid") (:form . "myeloid") (:end . 96)\n  (:start . 89) (:id . 54))\n ((:tag . "NN") (:stem . "leukemia") (:form . "leukemia") (:end . 105)\n  (:start . 97) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 58))\n ((:tag . "NN") (:stem . "t(12;21)(p13;q22)") (:form . "t(12;21)(p13;q22)")\n  (:end . 132) (:start . 115) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "pre-b-cell") (:form . "pre-B-cell") (:end . 146)\n  (:start . 136) (:id . 61))\n ((:tag . "NN") (:stem . "leukemia") (:form . "leukemia") (:end . 155)\n  (:start . 147) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 63))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 169)\n  (:start . 157) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s6.3) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501613@unknown@formal@none@1@S@The Runt domain of AML1 in both proteins mediates DNA binding and heterodimerization with the core binding factor ß (CBFß) subunit.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "aml1") (:form . "AML1") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 40)\n  (:start . 32) (:id . 49))\n ((:tag . "VBZ") (:stem . "mediate") (:form . "mediates") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "heterodimerization") (:form . "heterodimerization")\n  (:end . 84) (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 89) (:start . 85)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 56))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 98) (:start . 94)\n  (:id . 57))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 106)\n  (:start . 99) (:id . 58))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 113)\n  (:start . 107) (:id . 59))\n ((:tag . "NN") (:stem . "ß") (:form . "ß") (:end . 115) (:start . 114)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 121) (:start . 117)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . "NN") (:stem . "subunit") (:form . "subunit") (:end . 130)\n  (:start . 123) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s6.4) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501614@unknown@formal@none@1@S@To determine whether CBFß is required for AML1-ETO and TEL-AML1 activity, we introduced amino acid substitutions into the Runt domain that disrupt heterodimerization with CBFß but not DNA binding.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 50)\n  (:start . 42) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "tel-aml1") (:form . "TEL-AML1") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 72)\n  (:start . 64) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "introduce") (:form . "introduced") (:end . 87)\n  (:start . 77) (:id . 55))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 93) (:start . 88)\n  (:id . 56))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 98) (:start . 94)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "substitution") (:form . "substitutions")\n  (:end . 112) (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 117) (:start . 113)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 60))\n ((:tag . "NN") (:stem . "runt") (:form . "Runt") (:end . 126) (:start . 122)\n  (:id . 61))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 133)\n  (:start . 127) (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 138) (:start . 134)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "disrupt") (:form . "disrupt") (:end . 146)\n  (:start . 139) (:id . 64))\n ((:tag . "NN") (:stem . "heterodimerization") (:form . "heterodimerization")\n  (:end . 165) (:start . 147) (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 170) (:start . 166)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 175) (:start . 171)\n  (:id . 67))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 179) (:start . 176)\n  (:id . 68))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 183) (:start . 180)\n  (:id . 69))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 187) (:start . 184)\n  (:id . 70))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 195)\n  (:start . 188) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x6.5.1) (:span 13 20)))\n (:hscopes ((:id . :x6.5.1) (:span 13 72)))\n (:identifiers (:sid . :s6.5) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501615@unknown@formal@none@1@S@We show that CBFß contributes to AML1-ETO's inhibition of granulocyte differentiation, is essential for its ability to enhance the clonogenic potential of primary mouse bone marrow cells, and is indispensable for its cooperativity with the activated receptor tyrosine kinase TEL-PDGFßR in generating acute myeloid leukemia in mice.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "contribute") (:form . "contributes") (:end . 29)\n  (:start . 18) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "granulocyte") (:form . "granulocyte") (:end . 69)\n  (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 85) (:start . 70) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 99)\n  (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 103) (:start . 100)\n  (:id . 57))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 107) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 115)\n  (:start . 108) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 118) (:start . 116)\n  (:id . 60))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 126)\n  (:start . 119) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "clonogenic") (:form . "clonogenic") (:end . 141)\n  (:start . 131) (:id . 63))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 151)\n  (:start . 142) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 162)\n  (:start . 155) (:id . 66))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 168)\n  (:start . 163) (:id . 67))\n ((:tag . "NN") (:stem . "bone") (:form . "bone") (:end . 173) (:start . 169)\n  (:id . 68))\n ((:tag . "NN") (:stem . "marrow") (:form . "marrow") (:end . 180)\n  (:start . 174) (:id . 69))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 186)\n  (:start . 181) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 187) (:start . 186)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 191) (:start . 188)\n  (:id . 72))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 194) (:start . 192)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "indispensable") (:form . "indispensable")\n  (:end . 208) (:start . 195) (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 212) (:start . 209)\n  (:id . 75))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 216) (:start . 213)\n  (:id . 76))\n ((:tag . "NN") (:stem . "cooperativity") (:form . "cooperativity")\n  (:end . 230) (:start . 217) (:id . 77))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 235) (:start . 231)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 239) (:start . 236)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 249)\n  (:start . 240) (:id . 80))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 258)\n  (:start . 250) (:id . 81))\n ((:tag . "NN") (:stem . "tyrosine") (:form . "tyrosine") (:end . 267)\n  (:start . 259) (:id . 82))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 274)\n  (:start . 268) (:id . 83))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 285)\n  (:start . 275) (:id . 84))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 288) (:start . 286)\n  (:id . 85))\n ((:tag . "VBG") (:stem . "generate") (:form . "generating") (:end . 299)\n  (:start . 289) (:id . 86))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 305)\n  (:start . 300) (:id . 87))\n ((:tag . "JJ") (:stem . "myeloid") (:form . "myeloid") (:end . 313)\n  (:start . 306) (:id . 88))\n ((:tag . "NN") (:stem . "leukemia") (:form . "leukemia") (:end . 322)\n  (:start . 314) (:id . 89))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 325) (:start . 323)\n  (:id . 90))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 330)\n  (:start . 326) (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 331) (:start . 330)\n  (:id . 92)))@@@1@51@((:identifiers (:sid . :s6.6) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501616@unknown@formal@none@1@S@Similarly, CBFß is essential for TEL-AML1's ability to promote self-renewal of B cell precursors in vitro.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 51)\n  (:start . 44) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "self-renewal") (:form . "self-renewal") (:end . 75)\n  (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 96)\n  (:start . 86) (:id . 57))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 105)\n  (:start . 100) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.7) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501617@unknown@formal@none@1@S@These studies validate the Runt domain/CBFß interaction as a therapeutic target in core binding factor leukemias.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "validate") (:form . "validate") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "domain/cbfß") (:form . "domain/CBFß") (:end . 43)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 55)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 58) (:start . 56)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 60) (:start . 59)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "therapeutic") (:form . "therapeutic") (:end . 72)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 79)\n  (:start . 73) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 53))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 87) (:start . 83)\n  (:id . 54))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 95)\n  (:start . 88) (:id . 55))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 102)\n  (:start . 96) (:id . 56))\n ((:tag . "NNS") (:stem . "leukemia") (:form . "leukemias") (:end . 112)\n  (:start . 103) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.8) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501618@unknown@formal@none@1@S@Introduction@(((:tag . "NN") (:stem . "introduction") (:form . "Introduction") (:end . 12)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s6.9) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501619@unknown@formal@none@1@S@RUNX1 and CBFB are very frequent targets of mutations and gene rearrangements in leukemia.1,2@(((:tag . "NNP") (:stem . "RUNX1") (:form . "RUNX1") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "CBFB") (:form . "CBFB") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "rearrangement") (:form . "rearrangements")\n  (:end . 77) (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "CD") (:stem . "leukemia.1,2") (:form . "leukemia.1,2") (:end . 93)\n  (:start . 81) (:id . 55)))@@@1@14@((:identifiers (:sid . :s6.10) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501620@unknown@formal@none@1@S@Among the most commonly identified rearrangements are the t(8;21)(q22;q22) in 12% of adult acute myeloid leukemia (AML) and the t(12;21)(p13;q22) in 25% of pediatric acute lymphocytic leukemia (ALL), both of which involve the RUNX1 gene.3@(((:tag . "IN") (:stem . "among") (:form . "Among") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "rearrangement") (:form . "rearrangements")\n  (:end . 49) (:start . 35) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 53) (:start . 50)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 49))\n ((:tag . "NN") (:stem . "t(8;21)(q22;q22)") (:form . "t(8;21)(q22;q22)")\n  (:end . 74) (:start . 58) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 51))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 80) (:start . 78)\n  (:id . 52))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 81) (:start . 80)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 90) (:start . 85)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "myeloid") (:form . "myeloid") (:end . 104)\n  (:start . 97) (:id . 57))\n ((:tag . "NN") (:stem . "leukemia") (:form . "leukemia") (:end . 113)\n  (:start . 105) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "AML") (:form . "AML") (:end . 118) (:start . 115)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . "NN") (:stem . "t(12;21)(p13;q22)") (:form . "t(12;21)(p13;q22)")\n  (:end . 145) (:start . 128) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n  (:id . 65))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 151) (:start . 149)\n  (:id . 66))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 152) (:start . 151)\n  (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "pediatric") (:form . "pediatric") (:end . 165)\n  (:start . 156) (:id . 69))\n ((:tag . "JJ") (:stem . "acute") (:form . "acute") (:end . 171)\n  (:start . 166) (:id . 70))\n ((:tag . "JJ") (:stem . "lymphocytic") (:form . "lymphocytic") (:end . 183)\n  (:start . 172) (:id . 71))\n ((:tag . "NN") (:stem . "leukemia") (:form . "leukemia") (:end . 192)\n  (:start . 184) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 194) (:start . 193)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "ALL") (:form . "ALL") (:end . 197) (:start . 194)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 198) (:start . 197)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 199) (:start . 198)\n  (:id . 76))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 204) (:start . 200)\n  (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 207) (:start . 205)\n  (:id . 78))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 213)\n  (:start . 208) (:id . 79))\n ((:tag . "VBP") (:stem . "involve") (:form . "involve") (:end . 221)\n  (:start . 214) (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 225) (:start . 222)\n  (:id . 81))\n ((:tag . "NN") (:stem . "runx1") (:form . "RUNX1") (:end . 231)\n  (:start . 226) (:id . 82))\n ((:tag . "NN") (:stem . "gene.3") (:form . "gene.3") (:end . 238)\n  (:start . 232) (:id . 83)))@@@1@42@((:identifiers (:sid . :s6.11) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501621@unknown@formal@none@1@S@The molecular consequence of these translocations is the generation of fusion proteins, AML1-ETO and TEL-AML1, respectively.4–7@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "consequence") (:form . "consequence") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "translocation") (:form . "translocations")\n  (:end . 49) (:start . 35) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 67)\n  (:start . 57) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 51))\n ((:tag . "NN") (:stem . "fusion") (:form . "fusion") (:end . 77)\n  (:start . 71) (:id . 52))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 86)\n  (:start . 78) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 96)\n  (:start . 88) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 109)\n  (:start . 101) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 58))\n ((:tag . "NN") (:stem . "respectively.4–7") (:form . "respectively.4–7")\n  (:end . 127) (:start . 111) (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.12) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501622@unknown@formal@none@1@S@AML1-ETO contains the N-terminal 177 amino acids of the Runx1 DNA-binding subunit fused in frame with nearly all of ETO (821; encoded by RUNX1T1).4,5@(((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 32)\n  (:start . 22) (:id . 45))\n ((:tag . "CD") (:stem . "177") (:form . "177") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 42) (:start . 37)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "runx1") (:form . "Runx1") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "dna-binding") (:form . "DNA-binding") (:end . 73)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "subunit") (:form . "subunit") (:end . 81)\n  (:start . 74) (:id . 53))\n ((:tag . "VBN") (:stem . "fuse") (:form . "fused") (:end . 87) (:start . 82)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 101) (:start . 97)\n  (:id . 57))\n ((:tag . "RB") (:stem . "nearly") (:form . "nearly") (:end . 108)\n  (:start . 102) (:id . 58))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "ETO") (:form . "ETO") (:end . 119) (:start . 116)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 62))\n ((:tag . "CD") (:stem . "821") (:form . "821") (:end . 124) (:start . 121)\n  (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 133)\n  (:start . 126) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 136) (:start . 134)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "RUNX1T1).4,5") (:form . "RUNX1T1).4,5")\n  (:end . 149) (:start . 137) (:id . 67)))@@@1@26@((:identifiers (:sid . :s6.13) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501623@unknown@formal@none@1@S@Runx1 is required for normal hematopoiesis.8@(((:tag . "NNP") (:stem . "Runx1") (:form . "Runx1") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "hematopoiesis.8") (:form . "hematopoiesis.8")\n  (:end . 44) (:start . 29) (:id . 47)))@@@1@6@((:identifiers (:sid . :s6.14) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501624@unknown@formal@none@1@S@The function of ETO itself is not particularly well understood.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "ETO") (:form . "ETO") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 46)\n  (:start . 34) (:id . 49))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "understand") (:form . "understood") (:end . 62)\n  (:start . 52) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s6.15) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501625@unknown@formal@none@1@S@Its Drosophila homolog, Nervy, interacts directly with the transcription factor daughterless, and represses the activity of enhancers normally activated by the achaete-scute complex in the sensory organ precursor cell.9@(((:tag . "PRP$") (:stem . "its") (:form . "Its") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Nervy") (:form . "Nervy") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "interact") (:form . "interacts") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 72) (:start . 59) (:id . 52))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 79)\n  (:start . 73) (:id . 53))\n ((:tag . "JJ") (:stem . "daughterless") (:form . "daughterless") (:end . 92)\n  (:start . 80) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "repress") (:form . "represses") (:end . 107)\n  (:start . 98) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 58))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 120)\n  (:start . 112) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "enhancer") (:form . "enhancers") (:end . 133)\n  (:start . 124) (:id . 61))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 142)\n  (:start . 134) (:id . 62))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 152)\n  (:start . 143) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 155) (:start . 153)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "achaete-scute") (:form . "achaete-scute")\n  (:end . 173) (:start . 160) (:id . 66))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 181)\n  (:start . 174) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 184) (:start . 182)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 196)\n  (:start . 189) (:id . 70))\n ((:tag . "NN") (:stem . "organ") (:form . "organ") (:end . 202)\n  (:start . 197) (:id . 71))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 212)\n  (:start . 203) (:id . 72))\n ((:tag . "NN") (:stem . "cell.9") (:form . "cell.9") (:end . 219)\n  (:start . 213) (:id . 73)))@@@1@32@((:identifiers (:sid . :s6.16) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501626@unknown@formal@none@1@S@Homozygous disruption of Runx1t1 in mice resulted in gastrointestinal defects, but no hematopoietic deficiencies.10@(((:tag . "JJ") (:stem . "homozygous") (:form . "Homozygous") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "disruption") (:form . "disruption") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 44))\n ((:tag . "NN") (:stem . "runx1t1") (:form . "Runx1t1") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 49)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "gastrointestinal") (:form . "gastrointestinal")\n  (:end . 69) (:start . 53) (:id . 50))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 77)\n  (:start . 70) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 82) (:start . 79)\n  (:id . 53))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 85) (:start . 83)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "hematopoietic") (:form . "hematopoietic")\n  (:end . 99) (:start . 86) (:id . 55))\n ((:tag . "NN") (:stem . "deficiencies.10") (:form . "deficiencies.10")\n  (:end . 115) (:start . 100) (:id . 56)))@@@1@15@((:identifiers (:sid . :s6.17) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501627@unknown@formal@none@1@S@AML1-ETO has 5 conserved domains, one from Runx1 (the Runt domain) and 4 from ETO.11,12@(((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Runx1") (:form . "Runx1") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 58) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 65)\n  (:start . 59) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 56))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 72) (:start . 71)\n  (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 77) (:start . 73)\n  (:id . 58))\n ((:tag . "NN") (:stem . "ETO.11,12") (:form . "ETO.11,12") (:end . 87)\n  (:start . 78) (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.18) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501628@unknown@formal@none@1@S@The eTAFH (or NHR1) domain interacts with the nuclear hormone receptor corepressor (N-CoR),13 and also with the activation domain of E proteins (E2A and HEB).14@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "etafh") (:form . "eTAFH") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "nhr1") (:form . "NHR1") (:end . 18) (:start . 14)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 19) (:start . 18)\n  (:id . 47))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 26)\n  (:start . 20) (:id . 48))\n ((:tag . "VBZ") (:stem . "interact") (:form . "interacts") (:end . 36)\n  (:start . 27) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 53)\n  (:start . 46) (:id . 52))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 61)\n  (:start . 54) (:id . 53))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 70)\n  (:start . 62) (:id . 54))\n ((:tag . "NN") (:stem . "corepressor") (:form . "corepressor") (:end . 82)\n  (:start . 71) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "N-CoR),13") (:form . "N-CoR),13") (:end . 93)\n  (:start . 84) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 107) (:start . 103)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 61))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 122)\n  (:start . 112) (:id . 62))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 129)\n  (:start . 123) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 64))\n ((:tag . "NN") (:stem . "e") (:form . "E") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 143)\n  (:start . 135) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "E2A") (:form . "E2A") (:end . 148) (:start . 145)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 69))\n ((:tag . "NN") (:stem . "HEB).14") (:form . "HEB).14") (:end . 160)\n  (:start . 153) (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.19) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501629@unknown@formal@none@1@S@The HHR (NHR2) domain forms an α-helical tetramer that mediates oligomerization of AML1-ETO with itself and other ETO proteins and interacts with the corepressor Sin3, Gfi1, and histone deacetylases 1 and 3.12,15–20@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "HHR") (:form . "HHR") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "NNP") (:stem . "NHR2") (:form . "NHR2") (:end . 13) (:start . 9)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 21)\n  (:start . 15) (:id . 47))\n ((:tag . "VBZ") (:stem . "form") (:form . "forms") (:end . 27) (:start . 22)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "α-helical") (:form . "α-helical") (:end . 40)\n  (:start . 31) (:id . 50))\n ((:tag . "NN") (:stem . "tetramer") (:form . "tetramer") (:end . 49)\n  (:start . 41) (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 54) (:start . 50)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "mediate") (:form . "mediates") (:end . 63)\n  (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "oligomerization") (:form . "oligomerization")\n  (:end . 79) (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 91)\n  (:start . 83) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 113)\n  (:start . 108) (:id . 60))\n ((:tag . "NN") (:stem . "eto") (:form . "ETO") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 126)\n  (:start . 118) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "interact") (:form . "interacts") (:end . 140)\n  (:start . 131) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 145) (:start . 141)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 149) (:start . 146)\n  (:id . 66))\n ((:tag . "NN") (:stem . "corepressor") (:form . "corepressor") (:end . 161)\n  (:start . 150) (:id . 67))\n ((:tag . "NN") (:stem . "sin3") (:form . "Sin3") (:end . 166) (:start . 162)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Gfi1") (:form . "Gfi1") (:end . 172) (:start . 168)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 177) (:start . 174)\n  (:id . 72))\n ((:tag . "NN") (:stem . "histone") (:form . "histone") (:end . 185)\n  (:start . 178) (:id . 73))\n ((:tag . "NNS") (:stem . "deacetylas") (:form . "deacetylases") (:end . 198)\n  (:start . 186) (:id . 74))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 200) (:start . 199)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 204) (:start . 201)\n  (:id . 76))\n ((:tag . "CD") (:stem . "3.12,15–20") (:form . "3.12,15–20") (:end . 215)\n  (:start . 205) (:id . 77)))@@@1@36@((:identifiers (:sid . :s6.20) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501630@unknown@formal@none@1@S@Nervy (NHR3) is an α-helical domain that interacts with the regulatory subunit of type II cyclic AMP-dependent protein kinase. 21,22@(((:tag . "NN") (:stem . "nervy") (:form . "Nervy") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "nhr3") (:form . "NHR3") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 18) (:start . 16)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "α-helical") (:form . "α-helical") (:end . 28)\n  (:start . 19) (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 35)\n  (:start . 29) (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "interact") (:form . "interacts") (:end . 50)\n  (:start . 41) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 70)\n  (:start . 60) (:id . 54))\n ((:tag . "NN") (:stem . "subunit") (:form . "subunit") (:end . 78)\n  (:start . 71) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "cyclic") (:form . "cyclic") (:end . 96)\n  (:start . 90) (:id . 59))\n ((:tag . "JJ") (:stem . "amp-dependent") (:form . "AMP-dependent")\n  (:end . 110) (:start . 97) (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 118)\n  (:start . 111) (:id . 61))\n ((:tag . "NN") (:stem . "kinase.") (:form . "kinase.") (:end . 126)\n  (:start . 119) (:id . 62))\n ((:tag . "CD") (:stem . "21,22") (:form . "21,22") (:end . 132)\n  (:start . 127) (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.21) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501631@unknown@formal@none@1@S@Myeloid-Nervy-DEAF-1 (MYND or NHR4) is a zinc-chelating domain structurally homologous to the PHD and RING finger domains and mediates interactions with N-CoR, the silencing mediator of retinoid and thyroid hormone receptor (SMRT), and the DNA binding protein SON. 16,23–26@(((:tag . "NNP") (:stem . "Myeloid-Nervy-DEAF-1")\n  (:form . "Myeloid-Nervy-DEAF-1") (:end . 20) (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "MYND") (:form . "MYND") (:end . 26) (:start . 22)\n  (:id . 44))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "NHR4") (:form . "NHR4") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "zinc-chelating") (:form . "zinc-chelating")\n  (:end . 55) (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "RB") (:stem . "structurally") (:form . "structurally") (:end . 75)\n  (:start . 63) (:id . 52))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 86)\n  (:start . 76) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PHD") (:form . "PHD") (:end . 97) (:start . 94)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "RING") (:form . "RING") (:end . 106) (:start . 102)\n  (:id . 58))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 113)\n  (:start . 107) (:id . 59))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 121)\n  (:start . 114) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "mediate") (:form . "mediates") (:end . 134)\n  (:start . 126) (:id . 62))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 147)\n  (:start . 135) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 152) (:start . 148)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "N-CoR") (:form . "N-CoR") (:end . 158)\n  (:start . 153) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "silencing") (:form . "silencing") (:end . 173)\n  (:start . 164) (:id . 68))\n ((:tag . "NN") (:stem . "mediator") (:form . "mediator") (:end . 182)\n  (:start . 174) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 185) (:start . 183)\n  (:id . 70))\n ((:tag . "NN") (:stem . "retinoid") (:form . "retinoid") (:end . 194)\n  (:start . 186) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 198) (:start . 195)\n  (:id . 72))\n ((:tag . "NN") (:stem . "thyroid") (:form . "thyroid") (:end . 206)\n  (:start . 199) (:id . 73))\n ((:tag . "NN") (:stem . "hormone") (:form . "hormone") (:end . 214)\n  (:start . 207) (:id . 74))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 223)\n  (:start . 215) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 225) (:start . 224)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "SMRT") (:form . "SMRT") (:end . 229) (:start . 225)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 230) (:start . 229)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 231) (:start . 230)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 235) (:start . 232)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 239) (:start . 236)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 243) (:start . 240)\n  (:id . 82))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 251)\n  (:start . 244) (:id . 83))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 259)\n  (:start . 252) (:id . 84))\n ((:tag . "NNP") (:stem . "SON.") (:form . "SON.") (:end . 264) (:start . 260)\n  (:id . 85))\n ((:tag . "CD") (:stem . "16,23–26") (:form . "16,23–26") (:end . 273)\n  (:start . 265) (:id . 86)))@@@1@45@((:identifiers (:sid . :s6.22) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501632@unknown@formal@none@1@S@A foreshortened splice variant of AML1-ETO lacking both the Nervy and MYND domains (AML1-ETO9a), or full-length AML1-ETO with a mutation predicted to disrupt the structure of the MYND domain and shown to impair SON binding had increased leukemogenic potential.23,27,28@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "foreshorten") (:form . "foreshortened") (:end . 15)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "splice") (:form . "splice") (:end . 22)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "variant") (:form . "variant") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "VBG") (:stem . "lack") (:form . "lacking") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 55) (:start . 51)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Nervy") (:form . "Nervy") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "MYND") (:form . "MYND") (:end . 74) (:start . 70)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 82)\n  (:start . 75) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AML1-ETO9a") (:form . "AML1-ETO9a") (:end . 94)\n  (:start . 84) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 99) (:start . 97)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 111)\n  (:start . 100) (:id . 60))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 120)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 125) (:start . 121)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 127) (:start . 126)\n  (:id . 63))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 136)\n  (:start . 128) (:id . 64))\n ((:tag . "VBD") (:stem . "predict") (:form . "predicted") (:end . 146)\n  (:start . 137) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n  (:id . 66))\n ((:tag . "VB") (:stem . "disrupt") (:form . "disrupt") (:end . 157)\n  (:start . 150) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 68))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 171)\n  (:start . 162) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 174) (:start . 172)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "MYND") (:form . "MYND") (:end . 183) (:start . 179)\n  (:id . 72))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 190)\n  (:start . 184) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 200)\n  (:start . 195) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 203) (:start . 201)\n  (:id . 76))\n ((:tag . "VB") (:stem . "impair") (:form . "impair") (:end . 210)\n  (:start . 204) (:id . 77))\n ((:tag . "NNP") (:stem . "SON") (:form . "SON") (:end . 214) (:start . 211)\n  (:id . 78))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 222)\n  (:start . 215) (:id . 79))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 226) (:start . 223)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 236)\n  (:start . 227) (:id . 81))\n ((:tag . "JJ") (:stem . "leukemogenic") (:form . "leukemogenic") (:end . 249)\n  (:start . 237) (:id . 82))\n ((:tag . "CD") (:stem . "potential.23,27,28") (:form . "potential.23,27,28")\n  (:end . 268) (:start . 250) (:id . 83)))@@@1@42@((:identifiers (:sid . :s6.23) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501633@unknown@formal@none@1@S@The Runt domain from Runx1 mediates both DNA binding and heterodimerization with CBFß.29@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Runx1") (:form . "Runx1") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "mediate") (:form . "mediates") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "heterodimerization") (:form . "heterodimerization")\n  (:end . 75) (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 80) (:start . 76)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cbfß.29") (:form . "CBFß.29") (:end . 88)\n  (:start . 81) (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.24) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501634@unknown@formal@none@1@S@Both of these properties are essential for normal Runx1 function in vivo.30@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "runx1") (:form . "Runx1") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 64)\n  (:start . 56) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "vivo.30") (:form . "vivo.30") (:end . 75)\n  (:start . 68) (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.25) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501635@unknown@formal@none@1@S@CBFß enhances the affinity of the Runt domain for DNA by 7- to 10-fold through quenching conformational exchange in several dynamic regions 31–36 and may additionally inhibit Runx1 degradation mediated by the ubiquitin proteasome pathway.37@(((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "enhance") (:form . "enhances") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "runt") (:form . "Runt") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "CD") (:stem . "7-") (:form . "7-") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . "RB") (:stem . "10-fold") (:form . "10-fold") (:end . 70)\n  (:start . 63) (:id . 55))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 78)\n  (:start . 71) (:id . 56))\n ((:tag . "VBG") (:stem . "quench") (:form . "quenching") (:end . 88)\n  (:start . 79) (:id . 57))\n ((:tag . "JJ") (:stem . "conformational") (:form . "conformational")\n  (:end . 103) (:start . 89) (:id . 58))\n ((:tag . "NN") (:stem . "exchange") (:form . "exchange") (:end . 112)\n  (:start . 104) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 123)\n  (:start . 116) (:id . 61))\n ((:tag . "JJ") (:stem . "dynamic") (:form . "dynamic") (:end . 131)\n  (:start . 124) (:id . 62))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 139)\n  (:start . 132) (:id . 63))\n ((:tag . "CD") (:stem . "31–36") (:form . "31–36") (:end . 145)\n  (:start . 140) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 149) (:start . 146)\n  (:id . 65))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 153) (:start . 150)\n  (:id . 66))\n ((:tag . "RB") (:stem . "additionally") (:form . "additionally") (:end . 166)\n  (:start . 154) (:id . 67))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 174)\n  (:start . 167) (:id . 68))\n ((:tag . "NN") (:stem . "runx1") (:form . "Runx1") (:end . 180)\n  (:start . 175) (:id . 69))\n ((:tag . "NN") (:stem . "degradation") (:form . "degradation") (:end . 192)\n  (:start . 181) (:id . 70))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 201)\n  (:start . 193) (:id . 71))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 204) (:start . 202)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 208) (:start . 205)\n  (:id . 73))\n ((:tag . "NN") (:stem . "ubiquitin") (:form . "ubiquitin") (:end . 218)\n  (:start . 209) (:id . 74))\n ((:tag . "NN") (:stem . "proteasome") (:form . "proteasome") (:end . 229)\n  (:start . 219) (:id . 75))\n ((:tag . "NN") (:stem . "pathway.37") (:form . "pathway.37") (:end . 240)\n  (:start . 230) (:id . 76)))@@@1@35@((:hcues ((:id . :x6.26.1) (:span 150 153)))\n (:hscopes ((:id . :x6.26.1) (:span 150 237)))\n (:identifiers (:sid . :s6.26) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501636@unknown@formal@none@1@S@An R174Q mutation in Runx1 found in AML of the M0 subtype and in familial platelet disorder with predisposition for AML (FPD/AML) that disrupts only DNA but not CBFß binding generated a weakly dominant negative Runx1 allele.30,38–40@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Runx1") (:form . "Runx1") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AML") (:form . "AML") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "m0") (:form . "M0") (:end . 49) (:start . 47)\n  (:id . 52))\n ((:tag . "NN") (:stem . "subtype") (:form . "subtype") (:end . 57)\n  (:start . 50) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "familial") (:form . "familial") (:end . 73)\n  (:start . 65) (:id . 56))\n ((:tag . "NN") (:stem . "platelet") (:form . "platelet") (:end . 82)\n  (:start . 74) (:id . 57))\n ((:tag . "NN") (:stem . "disorder") (:form . "disorder") (:end . 91)\n  (:start . 83) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 96) (:start . 92)\n  (:id . 59))\n ((:tag . "NN") (:stem . "predisposition") (:form . "predisposition")\n  (:end . 111) (:start . 97) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 115) (:start . 112)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "AML") (:form . "AML") (:end . 119) (:start . 116)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "FPD/AML") (:form . "FPD/AML") (:end . 128)\n  (:start . 121) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 134) (:start . 130)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "disrupt") (:form . "disrupts") (:end . 143)\n  (:start . 135) (:id . 67))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 148) (:start . 144)\n  (:id . 68))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 152) (:start . 149)\n  (:id . 69))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 156) (:start . 153)\n  (:id . 70))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 160) (:start . 157)\n  (:id . 71))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 165) (:start . 161)\n  (:id . 72))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 173)\n  (:start . 166) (:id . 73))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 183)\n  (:start . 174) (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 185) (:start . 184)\n  (:id . 75))\n ((:tag . "RB") (:stem . "weakly") (:form . "weakly") (:end . 192)\n  (:start . 186) (:id . 76))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 201)\n  (:start . 193) (:id . 77))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 210)\n  (:start . 202) (:id . 78))\n ((:tag . "NN") (:stem . "runx1") (:form . "Runx1") (:end . 216)\n  (:start . 211) (:id . 79))\n ((:tag . "CD") (:stem . "allele.30,38–40") (:form . "allele.30,38–40")\n  (:end . 232) (:start . 217) (:id . 80)))@@@1@39@((:identifiers (:sid . :s6.27) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501637@unknown@formal@none@1@S@Single amino acid substitutions in Runx1 that impaired CBFß but not DNA binding resulted in hypomorphic alleles that diminished but did not eliminate Runx1's in vivo activity.30@(((:tag . "JJ") (:stem . "single") (:form . "Single") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "substitution") (:form . "substitutions")\n  (:end . 31) (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "NN") (:stem . "runx1") (:form . "Runx1") (:end . 40) (:start . 35)\n  (:id . 47))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "impair") (:form . "impaired") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 88)\n  (:start . 80) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "hypomorphic") (:form . "hypomorphic") (:end . 103)\n  (:start . 92) (:id . 57))\n ((:tag . "NNS") (:stem . "allele") (:form . "alleles") (:end . 111)\n  (:start . 104) (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "diminish") (:form . "diminished") (:end . 127)\n  (:start . 117) (:id . 60))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 131) (:start . 128)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 135) (:start . 132)\n  (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 139) (:start . 136)\n  (:id . 63))\n ((:tag . "VB") (:stem . "eliminate") (:form . "eliminate") (:end . 149)\n  (:start . 140) (:id . 64))\n ((:tag . "NNP") (:stem . "Runx1") (:form . "Runx1") (:end . 155)\n  (:start . 150) (:id . 65))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 157) (:start . 155)\n  (:id . 66))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 160) (:start . 158)\n  (:id . 67))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 165) (:start . 161)\n  (:id . 68))\n ((:tag . "NN") (:stem . "activity.30") (:form . "activity.30") (:end . 177)\n  (:start . 166) (:id . 69)))@@@1@28@((:identifiers (:sid . :s6.28) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501638@unknown@formal@none@1@S@The most commonly accepted models of AML1-ETO–mediated leukemogenesis posit that it functions either as a dominant inhibitor of CBF function41–43 or as a constitutive repressor of CBF target gene expression.44@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "VBN") (:stem . "accept") (:form . "accepted") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "aml1-eto–mediated") (:form . "AML1-ETO–mediated")\n  (:end . 54) (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "leukemogenesis") (:form . "leukemogenesis")\n  (:end . 69) (:start . 55) (:id . 49))\n ((:tag . "NN") (:stem . "posit") (:form . "posit") (:end . 75) (:start . 70)\n  (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 80) (:start . 76)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 83) (:start . 81)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "function") (:form . "functions") (:end . 93)\n  (:start . 84) (:id . 53))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 100)\n  (:start . 94) (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 103) (:start . 101)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 105) (:start . 104)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 114)\n  (:start . 106) (:id . 57))\n ((:tag . "NN") (:stem . "inhibitor") (:form . "inhibitor") (:end . 124)\n  (:start . 115) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "CBF") (:form . "CBF") (:end . 131) (:start . 128)\n  (:id . 60))\n ((:tag . "NN") (:stem . "function41–43") (:form . "function41–43")\n  (:end . 145) (:start . 132) (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 148) (:start . 146)\n  (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 151) (:start . 149)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 153) (:start . 152)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 166)\n  (:start . 154) (:id . 65))\n ((:tag . "NN") (:stem . "repressor") (:form . "repressor") (:end . 176)\n  (:start . 167) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 179) (:start . 177)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "CBF") (:form . "CBF") (:end . 183) (:start . 180)\n  (:id . 68))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 190)\n  (:start . 184) (:id . 69))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 195) (:start . 191)\n  (:id . 70))\n ((:tag . "NN") (:stem . "expression.44") (:form . "expression.44")\n  (:end . 209) (:start . 196) (:id . 71)))@@@1@30@((:identifiers (:sid . :s6.29) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501639@unknown@formal@none@1@S@Inhibition or repression is presumably mediated by the recruitment of corepressor complexes interacting with ETO domains to genomic targets recognized by the Runt domain.11,12@(((:tag . "NNP") (:stem . "Inhibition") (:form . "Inhibition") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "repression") (:form . "repression") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "RB") (:stem . "presumably") (:form . "presumably") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 47)\n  (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "recruitment") (:form . "recruitment") (:end . 66)\n  (:start . 55) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "NN") (:stem . "corepressor") (:form . "corepressor") (:end . 81)\n  (:start . 70) (:id . 52))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 91)\n  (:start . 82) (:id . 53))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 103)\n  (:start . 92) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 108) (:start . 104)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "ETO") (:form . "ETO") (:end . 112) (:start . 109)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 120)\n  (:start . 113) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 123) (:start . 121)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 131)\n  (:start . 124) (:id . 59))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 139)\n  (:start . 132) (:id . 60))\n ((:tag . "VBN") (:stem . "recognize") (:form . "recognized") (:end . 150)\n  (:start . 140) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 153) (:start . 151)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 162) (:start . 158)\n  (:id . 64))\n ((:tag . "CD") (:stem . "domain.11,12") (:form . "domain.11,12") (:end . 175)\n  (:start . 163) (:id . 65)))@@@1@24@((:hcues ((:id . :x6.30.1) (:span 28 38)))\n (:hscopes ((:id . :x6.30.1) (:span 0 169)))\n (:identifiers (:sid . :s6.30) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501640@unknown@formal@none@1@S@However, increasing evidence in cell line models suggests that the real situation may be substantially more complex.14,45–48@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 48)\n  (:start . 42) (:id . 49))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 57)\n  (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "real") (:form . "real") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "situation") (:form . "situation") (:end . 81)\n  (:start . 72) (:id . 54))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "RB") (:stem . "substantially") (:form . "substantially")\n  (:end . 102) (:start . 89) (:id . 57))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 107) (:start . 103)\n  (:id . 58))\n ((:tag . "CD") (:stem . "complex.14,45–48") (:form . "complex.14,45–48")\n  (:end . 124) (:start . 108) (:id . 59)))@@@1@18@((:hcues ((:id . :x6.31.1) (:span 82 85)) ((:id . :x6.31.2) (:span 49 57)))\n (:hscopes ((:id . :x6.31.1) (:span 82 115)) ((:id . :x6.31.2) (:span 49 115)))\n (:identifiers (:sid . :s6.31) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501641@unknown@formal@none@1@S@For example, it was proposed that AML1-ETO may function by sequestering transcription factors (such as E-box proteins), SON, or other regulatory proteins into subnuclear compartments13,23 and that its DNA binding function may not be necessary.13@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 42)\n  (:start . 34) (:id . 49))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "sequester") (:form . "sequestering") (:end . 71)\n  (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 85) (:start . 72) (:id . 54))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 99) (:start . 95)\n  (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 102) (:start . 100)\n  (:id . 58))\n ((:tag . "NN") (:stem . "e-box") (:form . "E-box") (:end . 108)\n  (:start . 103) (:id . 59))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 117)\n  (:start . 109) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "SON") (:form . "SON") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 127) (:start . 125)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 133)\n  (:start . 128) (:id . 66))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 144)\n  (:start . 134) (:id . 67))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 153)\n  (:start . 145) (:id . 68))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 158) (:start . 154)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "subnuclear") (:form . "subnuclear") (:end . 169)\n  (:start . 159) (:id . 70))\n ((:tag . "CD") (:stem . "compartments13,23") (:form . "compartments13,23")\n  (:end . 187) (:start . 170) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 191) (:start . 188)\n  (:id . 72))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 196) (:start . 192)\n  (:id . 73))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 200) (:start . 197)\n  (:id . 74))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 204) (:start . 201)\n  (:id . 75))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 212)\n  (:start . 205) (:id . 76))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 221)\n  (:start . 213) (:id . 77))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 225) (:start . 222)\n  (:id . 78))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 229) (:start . 226)\n  (:id . 79))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 232) (:start . 230)\n  (:id . 80))\n ((:tag . "NN") (:stem . "necessary.13") (:form . "necessary.13") (:end . 245)\n  (:start . 233) (:id . 81)))@@@1@40@((:hcues ((:id . :x6.32.1) (:span 222 225)) ((:id . :x6.32.2) (:span 43 46))\n  ((:id . :x6.32.3) (:span 20 28)))\n (:hscopes ((:id . :x6.32.1) (:span 222 242)) ((:id . :x6.32.2) (:span 43 182))\n  ((:id . :x6.32.3) (:span 13 242)))\n (:identifiers (:sid . :s6.32) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501642@unknown@formal@none@1@S@It has also been proposed that AML1-ETO functions by dysregulating the expression of E-box protein targets.14@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "dysregulate") (:form . "dysregulating") (:end . 66)\n  (:start . 53) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 81)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "NN") (:stem . "e-box") (:form . "E-box") (:end . 90) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 98)\n  (:start . 91) (:id . 56))\n ((:tag . "NN") (:stem . "targets.14") (:form . "targets.14") (:end . 109)\n  (:start . 99) (:id . 57)))@@@1@16@((:hcues ((:id . :x6.33.1) (:span 17 25)))\n (:hscopes ((:id . :x6.33.1) (:span 0 106)))\n (:identifiers (:sid . :s6.33) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501643@unknown@formal@none@1@S@The essential contribution of DNA binding by the Runt domain to overt leukemia was, however, recently and unequivocally established by demonstrating that an R174Q mutation that disrupts DNA but not CBFß binding abolished AML1-ETO's activity.30,49@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "contribution") (:form . "contribution") (:end . 26)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "overt") (:form . "overt") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "leukemia") (:form . "leukemia") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 91)\n  (:start . 84) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 101)\n  (:start . 93) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "RB") (:stem . "unequivocally") (:form . "unequivocally")\n  (:end . 119) (:start . 106) (:id . 61))\n ((:tag . "VBN") (:stem . "establish") (:form . "established") (:end . 131)\n  (:start . 120) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 134) (:start . 132)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating")\n  (:end . 148) (:start . 135) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 153) (:start . 149)\n  (:id . 65))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 156) (:start . 154)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 162)\n  (:start . 157) (:id . 67))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 171)\n  (:start . 163) (:id . 68))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 176) (:start . 172)\n  (:id . 69))\n ((:tag . "VBZ") (:stem . "disrupt") (:form . "disrupts") (:end . 185)\n  (:start . 177) (:id . 70))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 189) (:start . 186)\n  (:id . 71))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 193) (:start . 190)\n  (:id . 72))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 197) (:start . 194)\n  (:id . 73))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 202) (:start . 198)\n  (:id . 74))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 210)\n  (:start . 203) (:id . 75))\n ((:tag . "VBD") (:stem . "abolish") (:form . "abolished") (:end . 220)\n  (:start . 211) (:id . 76))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 229)\n  (:start . 221) (:id . 77))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 231) (:start . 229)\n  (:id . 78))\n ((:tag . "CD") (:stem . "activity.30,49") (:form . "activity.30,49")\n  (:end . 246) (:start . 232) (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.34) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501644@unknown@formal@none@1@S@On the other hand, the role of CBFß binding for AML1-ETO's leukemogenic activity has not been accessed.@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "hand") (:form . "hand") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 27) (:start . 23)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 35) (:start . 31)\n  (:id . 50))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 43)\n  (:start . 36) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 56)\n  (:start . 48) (:id . 53))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 58) (:start . 56)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "leukemogenic") (:form . "leukemogenic") (:end . 71)\n  (:start . 59) (:id . 55))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 80)\n  (:start . 72) (:id . 56))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 88) (:start . 85)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 93) (:start . 89)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "access") (:form . "accessed") (:end . 102)\n  (:start . 94) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.35) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501645@unknown@formal@none@1@S@TEL-AML1 contains the N-terminal, non-DNA binding region of TEL (translocation-ETS-leukemia; encoded by ETV6) fused to nearly all of Runx1.7,50@(((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 32)\n  (:start . 22) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "non-dna") (:form . "non-DNA") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 56)\n  (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "TEL") (:form . "TEL") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "translocation-ets-leukemia")\n  (:form . "translocation-ETS-leukemia") (:end . 91) (:start . 65) (:id . 53))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 92) (:start . 91)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 100)\n  (:start . 93) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 103) (:start . 101)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "ETV6") (:form . "ETV6") (:end . 108) (:start . 104)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 109) (:start . 108)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "fuse") (:form . "fused") (:end . 115)\n  (:start . 110) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 118) (:start . 116)\n  (:id . 60))\n ((:tag . "RB") (:stem . "nearly") (:form . "nearly") (:end . 125)\n  (:start . 119) (:id . 61))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Runx1.7,50") (:form . "Runx1.7,50") (:end . 143)\n  (:start . 133) (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.36) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501646@unknown@formal@none@1@S@The components of TEL retained in the fusion protein include the Pointed domain, which forms a head-to-tail polymeric structure, as well as a corepressor binding domain, which together mediate interaction with N-CoR, SMRT, and mSin3a.6,51–55@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "TEL") (:form . "TEL") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "retain") (:form . "retained") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "fusion") (:form . "fusion") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Pointed") (:form . "Pointed") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 79)\n  (:start . 73) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 86) (:start . 81)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "form") (:form . "forms") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "head-to-tail") (:form . "head-to-tail") (:end . 107)\n  (:start . 95) (:id . 59))\n ((:tag . "JJ") (:stem . "polymeric") (:form . "polymeric") (:end . 117)\n  (:start . 108) (:id . 60))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 127)\n  (:start . 118) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 62))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 131) (:start . 129)\n  (:id . 63))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 136) (:start . 132)\n  (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 139) (:start . 137)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 141) (:start . 140)\n  (:id . 66))\n ((:tag . "NN") (:stem . "corepressor") (:form . "corepressor") (:end . 153)\n  (:start . 142) (:id . 67))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 161)\n  (:start . 154) (:id . 68))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 168)\n  (:start . 162) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 70))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 175)\n  (:start . 170) (:id . 71))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 184)\n  (:start . 176) (:id . 72))\n ((:tag . "VBP") (:stem . "mediate") (:form . "mediate") (:end . 192)\n  (:start . 185) (:id . 73))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 204)\n  (:start . 193) (:id . 74))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 209) (:start . 205)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "N-CoR") (:form . "N-CoR") (:end . 215)\n  (:start . 210) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 216) (:start . 215)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "SMRT") (:form . "SMRT") (:end . 221) (:start . 217)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 222) (:start . 221)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 226) (:start . 223)\n  (:id . 80))\n ((:tag . "CD") (:stem . "mSin3a.6,51–55") (:form . "mSin3a.6,51–55")\n  (:end . 241) (:start . 227) (:id . 81)))@@@1@40@((:identifiers (:sid . :s6.37) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501647@unknown@formal@none@1@S@The predominant model of TEL-AML1 function posits that it recruits corepressor complexes to CBF target genes in a Runt domain-dependent manner, resulting in inappropriate gene regulation.52,56,57@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "predominant") (:form . "predominant") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "tel-aml1") (:form . "TEL-AML1") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "VBZ") (:stem . "posit") (:form . "posits") (:end . 49)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "recruit") (:form . "recruits") (:end . 66)\n  (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "corepressor") (:form . "corepressor") (:end . 78)\n  (:start . 67) (:id . 52))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 88)\n  (:start . 79) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "CBF") (:form . "CBF") (:end . 95) (:start . 92)\n  (:id . 55))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 102)\n  (:start . 96) (:id . 56))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 108)\n  (:start . 103) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 118) (:start . 114)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "domain-dependent") (:form . "domain-dependent")\n  (:end . 135) (:start . 119) (:id . 61))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 142)\n  (:start . 136) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 153)\n  (:start . 144) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 156) (:start . 154)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "inappropriate") (:form . "inappropriate")\n  (:end . 170) (:start . 157) (:id . 66))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 175) (:start . 171)\n  (:id . 67))\n ((:tag . "CD") (:stem . "regulation.52,56,57")\n  (:form . "regulation.52,56,57") (:end . 195) (:start . 176) (:id . 68)))@@@1@27@((:identifiers (:sid . :s6.38) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501648@unknown@formal@none@1@S@Mechanisms invoking off-DNA activities including sequestration of transcriptional complexes and disruption of wild-type TEL function have also been proposed.58–60@(((:tag . "NNPS") (:stem . "Mechanism") (:form . "Mechanisms") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBG") (:stem . "invoke") (:form . "invoking") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "JJ") (:stem . "off-dna") (:form . "off-DNA") (:end . 27)\n  (:start . 20) (:id . 44))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 38)\n  (:start . 28) (:id . 45))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 48)\n  (:start . 39) (:id . 46))\n ((:tag . "NN") (:stem . "sequestration") (:form . "sequestration")\n  (:end . 62) (:start . 49) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 81) (:start . 66) (:id . 49))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 91)\n  (:start . 82) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 51))\n ((:tag . "NN") (:stem . "disruption") (:form . "disruption") (:end . 106)\n  (:start . 96) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 119)\n  (:start . 110) (:id . 54))\n ((:tag . "NNP") (:stem . "TEL") (:form . "TEL") (:end . 123) (:start . 120)\n  (:id . 55))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 132)\n  (:start . 124) (:id . 56))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 137) (:start . 133)\n  (:id . 57))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 142) (:start . 138)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 147) (:start . 143)\n  (:id . 59))\n ((:tag . "NN") (:stem . "proposed.58–60") (:form . "proposed.58–60")\n  (:end . 162) (:start . 148) (:id . 60)))@@@1@19@((:hcues ((:id . :x6.39.1) (:span 148 156)))\n (:hscopes ((:id . :x6.39.1) (:span 0 156)))\n (:identifiers (:sid . :s6.39) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501649@unknown@formal@none@1@S@However, recent work using the equivalent of an AML1-ETO R174Q substitution in the Runt domain that specifically disrupted DNA binding resulted in a loss of TEL-AML1 activity in B-cell precursors, demonstrating the centrality of this function.61@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "equivalent") (:form . "equivalent") (:end . 41)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 56)\n  (:start . 48) (:id . 51))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 75)\n  (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "runt") (:form . "Runt") (:end . 87) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 94)\n  (:start . 88) (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 99) (:start . 95)\n  (:id . 58))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 112)\n  (:start . 100) (:id . 59))\n ((:tag . "VBD") (:stem . "disrupt") (:form . "disrupted") (:end . 122)\n  (:start . 113) (:id . 60))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 134)\n  (:start . 127) (:id . 62))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 143)\n  (:start . 135) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 148) (:start . 147)\n  (:id . 65))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 153) (:start . 149)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 156) (:start . 154)\n  (:id . 67))\n ((:tag . "NN") (:stem . "tel-aml1") (:form . "TEL-AML1") (:end . 165)\n  (:start . 157) (:id . 68))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 174)\n  (:start . 166) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 177) (:start . 175)\n  (:id . 70))\n ((:tag . "NN") (:stem . "b-cell") (:form . "B-cell") (:end . 184)\n  (:start . 178) (:id . 71))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 195)\n  (:start . 185) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating")\n  (:end . 210) (:start . 197) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 214) (:start . 211)\n  (:id . 75))\n ((:tag . "NN") (:stem . "centrality") (:form . "centrality") (:end . 225)\n  (:start . 215) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 228) (:start . 226)\n  (:id . 77))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 233) (:start . 229)\n  (:id . 78))\n ((:tag . "NN") (:stem . "function.61") (:form . "function.61") (:end . 245)\n  (:start . 234) (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.40) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501650@unknown@formal@none@1@S@These mechanistic uncertainties underscore the importance of characterizing the specific contributions of each domain in AML1-ETO and TEL-AML1 to their in vivo activities.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "mechanistic") (:form . "mechanistic") (:end . 17)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "uncertainty") (:form . "uncertainties") (:end . 31)\n  (:start . 18) (:id . 44))\n ((:tag . "VBP") (:stem . "underscore") (:form . "underscore") (:end . 42)\n  (:start . 32) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 46))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 57)\n  (:start . 47) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "characterize") (:form . "characterizing")\n  (:end . 75) (:start . 61) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 88)\n  (:start . 80) (:id . 51))\n ((:tag . "NNS") (:stem . "contribution") (:form . "contributions")\n  (:end . 102) (:start . 89) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 53))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 110) (:start . 106)\n  (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 117)\n  (:start . 111) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 129)\n  (:start . 121) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 142)\n  (:start . 134) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 145) (:start . 143)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 151)\n  (:start . 146) (:id . 61))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n  (:id . 62))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 159) (:start . 155)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 170)\n  (:start . 160) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s6.41) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501651@unknown@formal@none@1@S@Herein we analyzed the importance of CBFß binding by the Runt domain for both AML1-ETO and TEL-AML1 function.@(((:tag . "RB") (:stem . "herein") (:form . "Herein") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "analyze") (:form . "analyzed") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 33)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "runt") (:form . "Runt") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 68)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 57))\n ((:tag . "NN") (:stem . "tel-aml1") (:form . "TEL-AML1") (:end . 99)\n  (:start . 91) (:id . 58))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 108)\n  (:start . 100) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.42) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501652@unknown@formal@none@1@S@The residues involved in DNA binding and heterodimerization are on distinct surfaces of the Runt domain, and extensive mutational analysis has been performed on both interfaces.30,34,36,62–65@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "heterodimerization") (:form . "heterodimerization")\n  (:end . 59) (:start . 41) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 75)\n  (:start . 67) (:id . 52))\n ((:tag . "NNS") (:stem . "surface") (:form . "surfaces") (:end . 84)\n  (:start . 76) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 96) (:start . 92)\n  (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 103)\n  (:start . 97) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 118)\n  (:start . 109) (:id . 60))\n ((:tag . "JJ") (:stem . "mutational") (:form . "mutational") (:end . 129)\n  (:start . 119) (:id . 61))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 138)\n  (:start . 130) (:id . 62))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 142) (:start . 139)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 147) (:start . 143)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 157)\n  (:start . 148) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 160) (:start . 158)\n  (:id . 66))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 165) (:start . 161)\n  (:id . 67))\n ((:tag . "CD") (:stem . "interfaces.30,34,36,62–65")\n  (:form . "interfaces.30,34,36,62–65") (:end . 191) (:start . 166)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s6.43) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501653@unknown@formal@none@1@S@Importantly, the majority of mutations in the Runt domain destabilize its structure, and negatively impact both DNA and CBFß binding.30,63,65@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 57)\n  (:start . 51) (:id . 51))\n ((:tag . "VBP") (:stem . "destabilize") (:form . "destabilize") (:end . 69)\n  (:start . 58) (:id . 52))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 83)\n  (:start . 74) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "RB") (:stem . "negatively") (:form . "negatively") (:end . 99)\n  (:start . 89) (:id . 57))\n ((:tag . "NN") (:stem . "impact") (:form . "impact") (:end . 106)\n  (:start . 100) (:id . 58))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 111) (:start . 107)\n  (:id . 59))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 115) (:start . 112)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n  (:id . 61))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 124) (:start . 120)\n  (:id . 62))\n ((:tag . "CD") (:stem . "binding.30,63,65") (:form . "binding.30,63,65")\n  (:end . 141) (:start . 125) (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.44) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501654@unknown@formal@none@1@S@We used the available biophysical information to introduce and carefully characterize amino acid substitutions that selectively target CBFß binding.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "JJ") (:stem . "biophysical") (:form . "biophysical") (:end . 33)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 45)\n  (:start . 34) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "VB") (:stem . "introduce") (:form . "introduce") (:end . 58)\n  (:start . 49) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "RB") (:stem . "carefully") (:form . "carefully") (:end . 72)\n  (:start . 63) (:id . 51))\n ((:tag . "VBP") (:stem . "characterize") (:form . "characterize") (:end . 85)\n  (:start . 73) (:id . 52))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 91) (:start . 86)\n  (:id . 53))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 96) (:start . 92)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "substitution") (:form . "substitutions")\n  (:end . 110) (:start . 97) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 115) (:start . 111)\n  (:id . 56))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 127)\n  (:start . 116) (:id . 57))\n ((:tag . "VBP") (:stem . "target") (:form . "target") (:end . 134)\n  (:start . 128) (:id . 58))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 139) (:start . 135)\n  (:id . 59))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 147)\n  (:start . 140) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.45) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501655@unknown@formal@none@1@S@We incorporated these mutations into AML1-ETO and TEL-AML1 and obtained evidence that CBFß binding is critical for their respective activities.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "incorporate") (:form . "incorporated") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 58)\n  (:start . 50) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 71)\n  (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 80)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 85) (:start . 81)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 90) (:start . 86)\n  (:id . 54))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 98)\n  (:start . 91) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 101) (:start . 99)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 110)\n  (:start . 102) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 114) (:start . 111)\n  (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 120)\n  (:start . 115) (:id . 59))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 131)\n  (:start . 121) (:id . 60))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 142)\n  (:start . 132) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.46) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501656@unknown@formal@none@1@S@Methods@(((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s6.47) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501657@unknown@formal@none@1@S@Cloning, expression, and protein purification@(((:tag . "NNP") (:stem . "Cloning") (:form . "Cloning") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "purification") (:form . "purification") (:end . 45)\n  (:start . 33) (:id . 48)))@@@1@7@((:identifiers (:sid . :s6.48) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501658@unknown@formal@none@1@S@A retroviral vector expressing TEL-PDGFßR plus human CD4 (hCD4) was made by cloning a blunted EcoRI fragment from the TEL-PDGFßR cDNA into the HpaI site of the MSV2.2-IRES-hCD4 vector.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "retroviral") (:form . "retroviral") (:end . 12)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "tel-pdgfßr") (:form . "TEL-PDGFßR") (:end . 41)\n  (:start . 31) (:id . 46))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 46) (:start . 42)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 52) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cd4") (:form . "CD4") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "hcd4") (:form . "hCD4") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "clone") (:form . "cloning") (:end . 83)\n  (:start . 76) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 85) (:start . 84)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "blunt") (:form . "blunted") (:end . 93)\n  (:start . 86) (:id . 58))\n ((:tag . "NNP") (:stem . "EcoRI") (:form . "EcoRI") (:end . 99) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 108)\n  (:start . 100) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 128)\n  (:start . 118) (:id . 63))\n ((:tag . "NNP") (:stem . "cDNA") (:form . "cDNA") (:end . 133) (:start . 129)\n  (:id . 64))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 138) (:start . 134)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "HpaI") (:form . "HpaI") (:end . 147) (:start . 143)\n  (:id . 67))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 152) (:start . 148)\n  (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 70))\n ((:tag . "NN") (:stem . "msv2.2-ires-hcd4") (:form . "MSV2.2-IRES-hCD4")\n  (:end . 176) (:start . 160) (:id . 71))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 183)\n  (:start . 177) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s6.49) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501659@unknown@formal@none@1@S@The MigR1-AML1-ETO-IRES-EGFP, pMSCV-IRES-EGFP (MSCV-EGFP), and pMSCV-TEL-AML1-IRES-EGFP (MSCV-T/A) vectors were described previously.15,66@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "MigR1-AML1-ETO-IRES-EGFP")\n  (:form . "MigR1-AML1-ETO-IRES-EGFP") (:end . 28) (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "pMSCV-IRES-EGFP") (:form . "pMSCV-IRES-EGFP")\n  (:end . 45) (:start . 30) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 47) (:start . 46)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "MSCV-EGFP") (:form . "MSCV-EGFP") (:end . 56)\n  (:start . 47) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "pMSCV-TEL-AML1-IRES-EGFP")\n  (:form . "pMSCV-TEL-AML1-IRES-EGFP") (:end . 87) (:start . 63) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "MSCV-T/A") (:form . "MSCV-T/A") (:end . 97)\n  (:start . 89) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "vector") (:form . "vectors") (:end . 106)\n  (:start . 99) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 111) (:start . 107)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 121)\n  (:start . 112) (:id . 57))\n ((:tag . "CD") (:stem . "previously.15,66") (:form . "previously.15,66")\n  (:end . 138) (:start . 122) (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.50) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501660@unknown@formal@none@1@S@CBFß (amino acids 1-141) and the wild-type Runt domain (residues 41-190) were cloned between the BamHI and EcoRI sites and the NcoI and XhoI sites of the pHis parallel vector,67 respectively.@(((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "CD") (:stem . "1-141") (:form . "1-141") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 24) (:start . 23)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 42)\n  (:start . 33) (:id . 50))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 64)\n  (:start . 56) (:id . 54))\n ((:tag . "CD") (:stem . "41-190") (:form . "41-190") (:end . 71)\n  (:start . 65) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 77) (:start . 73)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "clone") (:form . "cloned") (:end . 84)\n  (:start . 78) (:id . 58))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 92)\n  (:start . 85) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "BamHI") (:form . "BamHI") (:end . 102)\n  (:start . 97) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "EcoRI") (:form . "EcoRI") (:end . 112)\n  (:start . 107) (:id . 63))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 118)\n  (:start . 113) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "NcoI") (:form . "NcoI") (:end . 131) (:start . 127)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "XhoI") (:form . "XhoI") (:end . 140) (:start . 136)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 146)\n  (:start . 141) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 72))\n ((:tag . "NN") (:stem . "phis") (:form . "pHis") (:end . 158) (:start . 154)\n  (:id . 73))\n ((:tag . "NN") (:stem . "parallel") (:form . "parallel") (:end . 167)\n  (:start . 159) (:id . 74))\n ((:tag . "CD") (:stem . "vector,67") (:form . "vector,67") (:end . 177)\n  (:start . 168) (:id . 75))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 190)\n  (:start . 178) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s6.51) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501661@unknown@formal@none@1@S@The proteins were expressed in Rosetta(DE3) cells (Novagen, San Diego, CA) by inducing with 0.8 mM isopropyl-ß-D-thiogalactopyranoside (IPTG) at 25°C (for CBFß) or 20°C (for Runt domain) when optical density (OD)600 nm reached 0.5 to approximately 0.7, and purified on a Ni-NTA column (QIAGEN, Valencia CA).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "CD") (:stem . "Rosetta(DE3)") (:form . "Rosetta(DE3)") (:end . 43)\n  (:start . 31) (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . 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"optical") (:form . "optical") (:end . 199)\n  (:start . 192) (:id . 80))\n ((:tag . "NN") (:stem . "density") (:form . "density") (:end . 207)\n  (:start . 200) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 209) (:start . 208)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "OD)600") (:form . "OD)600") (:end . 215)\n  (:start . 209) (:id . 83))\n ((:tag . "NN") (:stem . "nm") (:form . "nm") (:end . 218) (:start . 216)\n  (:id . 84))\n ((:tag . "VBD") (:stem . "reach") (:form . "reached") (:end . 226)\n  (:start . 219) (:id . 85))\n ((:tag . "CD") (:stem . "0.5") (:form . "0.5") (:end . 230) (:start . 227)\n  (:id . 86))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 233) (:start . 231)\n  (:id . 87))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 247) (:start . 234) (:id . 88))\n ((:tag . "CD") (:stem . "0.7") (:form . "0.7") (:end . 251) (:start . 248)\n  (:id . 89))\n ((:tag . ",") (:stem . ",") (:form . 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5501662@unknown@formal@none@1@S@The 6 × His tag was cleaved by AcTEV (Invitrogen, Carlsbad, CA), and proteins were further purified on an S-100 column (CBFß) or SP-Sepharose column (Runt domain; GE Healthcare, Piscataway, NJ).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "PDT") (:stem . "×") (:form . "×") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "PRP$") (:stem . "his") (:form . "His") (:end . 11) (:start . 8)\n  (:id . 45))\n ((:tag . "NN") (:stem . "tag") (:form . "tag") (:end . 15) (:start . 12)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 19) (:start . 16)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "cleave") (:form . "cleaved") (:end . 27)\n  (:start . 20) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "AcTEV") (:form . "AcTEV") (:end . 36) (:start . 31)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 48)\n  (:start . 38) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Carlsbad") (:form . "Carlsbad") (:end . 58)\n  (:start . 50) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "CA") (:form . "CA") (:end . 62) (:start . 60)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 77)\n  (:start . 69) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 82) (:start . 78)\n  (:id . 61))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 90)\n  (:start . 83) (:id . 62))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 99)\n  (:start . 91) (:id . 63))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 102) (:start . 100)\n  (:id . 64))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 105) (:start . 103)\n  (:id . 65))\n ((:tag . "NN") (:stem . "s-100") (:form . "S-100") (:end . 111)\n  (:start . 106) (:id . 66))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 118)\n  (:start . 112) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 120) (:start . 119)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 124) (:start . 120)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 70))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 128) (:start . 126)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "SP-Sepharose") (:form . "SP-Sepharose")\n  (:end . 141) (:start . 129) (:id . 72))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 148)\n  (:start . 142) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 154) (:start . 150)\n  (:id . 75))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 161)\n  (:start . 155) (:id . 76))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 162) (:start . 161)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "GE") (:form . "GE") (:end . 165) (:start . 163)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Healthcare") (:form . "Healthcare") (:end . 176)\n  (:start . 166) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Piscataway") (:form . "Piscataway") (:end . 188)\n  (:start . 178) (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "NJ") (:form . "NJ") (:end . 192) (:start . 190)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 193) (:start . 192)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s6.53) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501663@unknown@formal@none@1@S@All mutations were generated using the QuikChange XLII Site-Directed Mutagenesis kit (Stratagene, La Jolla, CA).@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "QuikChange") (:form . "QuikChange") (:end . 49)\n  (:start . 39) (:id . 48))\n ((:tag . "NNP") (:stem . "XLII") (:form . "XLII") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "site-directed") (:form . "Site-Directed")\n  (:end . 68) (:start . 55) (:id . 50))\n ((:tag . "NNP") (:stem . "Mutagenesis") (:form . "Mutagenesis") (:end . 80)\n  (:start . 69) (:id . 51))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 84) (:start . 81)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Stratagene") (:form . "Stratagene") (:end . 96)\n  (:start . 86) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "La") (:form . "La") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Jolla") (:form . "Jolla") (:end . 106)\n  (:start . 101) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "CA") (:form . "CA") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.54) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501664@unknown@formal@none@1@S@Urea denaturation, electrophoretic mobility shift assays, and isothermal titration calorimetry measurements@(((:tag . "NNP") (:stem . "Urea") (:form . "Urea") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "denaturation") (:form . "denaturation") (:end . 17)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "electrophoretic") (:form . "electrophoretic")\n  (:end . 34) (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 43)\n  (:start . 35) (:id . 46))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 49) (:start . 44)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 56)\n  (:start . 50) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "isothermal") (:form . "isothermal") (:end . 72)\n  (:start . 62) (:id . 51))\n ((:tag . "NN") (:stem . "titration") (:form . "titration") (:end . 82)\n  (:start . 73) (:id . 52))\n ((:tag . "NN") (:stem . "calorimetry") (:form . "calorimetry") (:end . 94)\n  (:start . 83) (:id . 53))\n ((:tag . "NNS") (:stem . "measurement") (:form . "measurements") (:end . 107)\n  (:start . 95) (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.55) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501665@unknown@formal@none@1@S@All assays were performed as previously described.65,68@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 39)\n  (:start . 29) (:id . 47))\n ((:tag . "CD") (:stem . "described.65,68") (:form . "described.65,68")\n  (:end . 55) (:start . 40) (:id . 48)))@@@1@7@((:identifiers (:sid . :s6.56) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501666@unknown@formal@none@1@S@Retroviral transduction@(((:tag . "JJ") (:stem . "retroviral") (:form . "Retroviral") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 23)\n  (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s6.57) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501667@unknown@formal@none@1@S@Bone marrow (BM) harvested from C57BL/6J mice treated 7 days previously with 150 mg/kg 5-fluorouracil (5-FU; Sigma-Aldrich, St Louis, MO) was suspended in 1 mL transplant media per mouse hind-leg [RPMI, 20% fetal calf serum (FCS), 100 IU/mL penicillin, 100 µg/mL streptomycin (Mediatech, Herndon, VA), 10 ng/mL interleukin-3 (IL-3), 20 ng/mL IL-6, 20 ng/mL stem cell factor (SCF; R&D Systems, Minneapolis, MN)] and incubated overnight at 37°C in ultra-low attachment plates (Costar, Corning, NY).@(((:tag . "NN") (:stem . "bone") (:form . "Bone") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "marrow") (:form . "marrow") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . "VBN") (:stem . 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5501669@unknown@formal@none@1@S@Cells were then resuspended in fresh transplant media with cytokines at 6 × 106 cells/3 mL and centrifuged (1000g for 90 minutes) onto the virally preloaded plates with an additional 0.5 mL each virus.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "resuspend") (:form . "resuspended") (:end . 27)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "fresh") (:form . "fresh") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "transplant") (:form . "transplant") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "medium") (:form . "media") (:end . 53)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cytokine") (:form . "cytokines") (:end . 68)\n  (:start . 59) (:id . 51))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "SYM") (:stem . "×") (:form . "×") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "CD") (:stem . "106") (:form . "106") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cells/3") (:form . "cells/3") (:end . 87)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "ml") (:form . "mL") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "centrifuge") (:form . "centrifuged") (:end . 106)\n  (:start . 95) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1000g") (:form . "1000g") (:end . 113)\n  (:start . 108) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 120) (:start . 118)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "minute") (:form . "minutes") (:end . 128)\n  (:start . 121) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 134) (:start . 130)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 67))\n ((:tag . "RB") (:stem . "virally") (:form . "virally") (:end . 146)\n  (:start . 139) (:id . 68))\n ((:tag . "VBN") (:stem . "preloade") (:form . "preloaded") (:end . 156)\n  (:start . 147) (:id . 69))\n ((:tag . "NNS") (:stem . "plate") (:form . "plates") (:end . 163)\n  (:start . 157) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 168) (:start . 164)\n  (:id . 71))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 171) (:start . 169)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 182)\n  (:start . 172) (:id . 73))\n ((:tag . "CD") (:stem . "0.5") (:form . "0.5") (:end . 186) (:start . 183)\n  (:id . 74))\n ((:tag . "NN") (:stem . "ml") (:form . "mL") (:end . 189) (:start . 187)\n  (:id . 75))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 194) (:start . 190)\n  (:id . 76))\n ((:tag . "NN") (:stem . "virus") (:form . "virus") (:end . 200)\n  (:start . 195) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s6.60) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501670@unknown@formal@none@1@S@A second spinfection (150g for 10 minutes) was performed 12 hours later onto new virally precoated plates, and cells were incubated at 37°C for 3.5 hours.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "spinfection") (:form . "spinfection") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "CD") (:stem . "150g") (:form . "150g") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "minute") (:form . "minutes") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 56)\n  (:start . 47) (:id . 52))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . "RBR") (:stem . "later") (:form . "later") (:end . 71) (:start . 66)\n  (:id . 55))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 76) (:start . 72)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "RB") (:stem . "virally") (:form . "virally") (:end . 88)\n  (:start . 81) (:id . 58))\n ((:tag . "JJ") (:stem . "precoated") (:form . "precoated") (:end . 98)\n  (:start . 89) (:id . 59))\n ((:tag . "NNS") (:stem . "plate") (:form . "plates") (:end . 105)\n  (:start . 99) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 116)\n  (:start . 111) (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 121) (:start . 117)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 131)\n  (:start . 122) (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 134) (:start . 132)\n  (:id . 66))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 139) (:start . 135)\n  (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 143) (:start . 140)\n  (:id . 68))\n ((:tag . "CD") (:stem . "3.5") (:form . "3.5") (:end . 147) (:start . 144)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 153)\n  (:start . 148) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s6.61) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501671@unknown@formal@none@1@S@Hematopoietic assays and flow cytometry@(((:tag . "JJ") (:stem . "hematopoietic") (:form . "Hematopoietic")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 20)\n  (:start . 14) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 44))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cytometry") (:form . "cytometry") (:end . 39)\n  (:start . 30) (:id . 46)))@@@1@5@((:identifiers (:sid . :s6.62) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501672@unknown@formal@none@1@S@Granulocyte differentiation, BrDU staining, serial replating, and c-Kit+ B-cell progenitor colony forming assays were performed as described previously.15,25,61,66@(((:tag . "NNP") (:stem . "Granulocyte") (:form . "Granulocyte") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 27) (:start . 12) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "BrDU") (:form . "BrDU") (:end . 33) (:start . 29)\n  (:id . 45))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 42)\n  (:start . 34) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "serial") (:form . "serial") (:end . 50)\n  (:start . 44) (:id . 48))\n ((:tag . "VBG") (:stem . "replate") (:form . "replating") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "c-kit+") (:form . "c-Kit+") (:end . 72)\n  (:start . 66) (:id . 52))\n ((:tag . "NN") (:stem . "b-cell") (:form . "B-cell") (:end . 79)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "progenitor") (:form . "progenitor") (:end . 90)\n  (:start . 80) (:id . 54))\n ((:tag . "NN") (:stem . "colony") (:form . "colony") (:end . 97)\n  (:start . 91) (:id . 55))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 105)\n  (:start . 98) (:id . 56))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 112)\n  (:start . 106) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 117) (:start . 113)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 127)\n  (:start . 118) (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 130) (:start . 128)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 140)\n  (:start . 131) (:id . 61))\n ((:tag . "CD") (:stem . "previously.15,25,61,66")\n  (:form . "previously.15,25,61,66") (:end . 163) (:start . 141) (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.63) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501673@unknown@formal@none@1@S@Antibodies used were: allophycocyanin (APC), phycoerythrin (PE), or PerCPcy5.5 conjugated anti–Mac-1 (clone M1/70), APC or PerCP-Cy5.5 conjugated anti–Gr-1 (clone RB6-8C5), APC-conjugated anti-Sca1 (clone D7), PE-Cy5.5 conjugated anti-CD117 (clone 2B8), and PE-conjugated anti–human CD4 (clone L3T4; eBioscience, San Diego, CA).@(((:tag . "NNS") (:stem . "antibody") (:form . "Antibodies") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "allophycocyanin") (:form . "allophycocyanin")\n  (:end . 37) (:start . 22) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "APC") (:form . 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5501674@unknown@formal@none@1@S@Transplantation assays@(((:tag . "NNP") (:stem . "Transplantation") (:form . "Transplantation")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 22)\n  (:start . 16) (:id . 43)))@@@1@2@((:identifiers (:sid . :s6.65) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501675@unknown@formal@none@1@S@Retrovirally transduced cells were washed and resuspended in phosphate-buffered saline (PBS).@(((:tag . "RB") (:stem . "retrovirally") (:form . "Retrovirally") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "VBN") (:stem . "transduce") (:form . "transduced") (:end . 23)\n  (:start . 13) (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 29) (:start . 24)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "wash") (:form . "washed") (:end . 41) (:start . 35)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "resuspend") (:form . "resuspended") (:end . 57)\n  (:start . 46) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "phosphate-buffered") (:form . "phosphate-buffered")\n  (:end . 79) (:start . 61) (:id . 50))\n ((:tag . "NN") (:stem . "saline") (:form . "saline") (:end . 86)\n  (:start . 80) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "PBS") (:form . "PBS") (:end . 91) (:start . 88)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s6.66) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501676@unknown@formal@none@1@S@C57BL/6J males (5 to 6 weeks old) were lethally irradiated with a split dose of 5.5 Gy 3 to 4 hours apart and injected intravenously with 106 infected BM cells and 2 × 105 splenocytes from a C57BL6/J donor.@(((:tag . "NNP") (:stem . "C57BL/6J") (:form . "C57BL/6J") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "male") (:form . "males") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "week") (:form . "weeks") (:end . 28) (:start . 23)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "old") (:form . "old") (:end . 32) (:start . 29)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 33) (:start . 32)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 38) (:start . 34)\n  (:id . 51))\n ((:tag . "RB") (:stem . "lethally") (:form . "lethally") (:end . 47)\n  (:start . 39) (:id . 52))\n ((:tag . "VBN") (:stem . "irradiate") (:form . "irradiated") (:end . 58)\n  (:start . 48) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 63) (:start . 59)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "split") (:form . "split") (:end . 71) (:start . 66)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dose") (:form . "dose") (:end . 76) (:start . 72)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 58))\n ((:tag . "CD") (:stem . "5.5") (:form . "5.5") (:end . 83) (:start . 80)\n  (:id . 59))\n ((:tag . "NN") (:stem . "gy") (:form . "Gy") (:end . 86) (:start . 84)\n  (:id . 60))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 88) (:start . 87)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 62))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 93) (:start . 92)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 99) (:start . 94)\n  (:id . 64))\n ((:tag . "RB") (:stem . "apart") (:form . "apart") (:end . 105)\n  (:start . 100) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 118)\n  (:start . 110) (:id . 67))\n ((:tag . "RB") (:stem . "intravenously") (:form . "intravenously")\n  (:end . 132) (:start . 119) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 137) (:start . 133)\n  (:id . 69))\n ((:tag . "CD") (:stem . "106") (:form . "106") (:end . 141) (:start . 138)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "infected") (:form . "infected") (:end . 150)\n  (:start . 142) (:id . 71))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 153) (:start . 151)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 159)\n  (:start . 154) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 163) (:start . 160)\n  (:id . 74))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 165) (:start . 164)\n  (:id . 75))\n ((:tag . "CC") (:stem . "×") (:form . "×") (:end . 167) (:start . 166)\n  (:id . 76))\n ((:tag . "CD") (:stem . "105") (:form . "105") (:end . 171) (:start . 168)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "splenocyte") (:form . "splenocytes") (:end . 183)\n  (:start . 172) (:id . 78))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 188) (:start . 184)\n  (:id . 79))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 190) (:start . 189)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "C57BL6/J") (:form . "C57BL6/J") (:end . 199)\n  (:start . 191) (:id . 81))\n ((:tag . "NN") (:stem . "donor") (:form . "donor") (:end . 205)\n  (:start . 200) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s6.67) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501677@unknown@formal@none@1@S@Mice were monitored for development of leukemia through peripheral blood analysis for infected cells by fluorescence-activated cell sorting (FACS) and by observation of physical symptoms characterized by lethargy, anemia, and splenomegaly.@(((:tag . "NNS") (:stem . "mouse") (:form . "Mice") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "monitor") (:form . "monitored") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 35)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "leukemia") (:form . "leukemia") (:end . 47)\n  (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "JJ") (:stem . "peripheral") (:form . "peripheral") (:end . 66)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "blood") (:form . "blood") (:end . 72) (:start . 67)\n  (:id . 51))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 81)\n  (:start . 73) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 85) (:start . 82)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "infected") (:form . "infected") (:end . 94)\n  (:start . 86) (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 100) (:start . 95)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 103) (:start . 101)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "fluorescence-activated")\n  (:form . "fluorescence-activated") (:end . 126) (:start . 104) (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 131) (:start . 127)\n  (:id . 58))\n ((:tag . "NN") (:stem . "sorting") (:form . "sorting") (:end . 139)\n  (:start . 132) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 60))\n ((:tag . "NN") (:stem . "facs") (:form . "FACS") (:end . 145) (:start . 141)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 153) (:start . 151)\n  (:id . 64))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 165)\n  (:start . 154) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "physical") (:form . "physical") (:end . 177)\n  (:start . 169) (:id . 67))\n ((:tag . "NNS") (:stem . "symptom") (:form . "symptoms") (:end . 186)\n  (:start . 178) (:id . 68))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n  (:end . 200) (:start . 187) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 203) (:start . 201)\n  (:id . 70))\n ((:tag . "NN") (:stem . "lethargy") (:form . "lethargy") (:end . 212)\n  (:start . 204) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 213) (:start . 212)\n  (:id . 72))\n ((:tag . "NN") (:stem . "anemia") (:form . "anemia") (:end . 220)\n  (:start . 214) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 221) (:start . 220)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 225) (:start . 222)\n  (:id . 75))\n ((:tag . "NN") (:stem . "splenomegaly") (:form . "splenomegaly") (:end . 238)\n  (:start . 226) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s6.68) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501678@unknown@formal@none@1@S@Sick mice were euthanized, and all remaining mice were killed at 63 days.@(((:tag . "NN") (:stem . "sick") (:form . "Sick") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "euthanize") (:form . "euthanized") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 44)\n  (:start . 35) (:id . 49))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "kill") (:form . "killed") (:end . 61) (:start . 55)\n  (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s6.69) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501679@unknown@formal@none@1@S@All animal procedures were approved by the Institutional Animal Care and Use Committee at Dartmouth College.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "animal") (:form . "animal") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "approve") (:form . "approved") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Institutional") (:form . "Institutional")\n  (:end . 56) (:start . 43) (:id . 49))\n ((:tag . "NNP") (:stem . "Animal") (:form . "Animal") (:end . 63)\n  (:start . 57) (:id . 50))\n ((:tag . "NNP") (:stem . "Care") (:form . "Care") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Use") (:form . "Use") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Committee") (:form . "Committee") (:end . 86)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Dartmouth") (:form . "Dartmouth") (:end . 99)\n  (:start . 90) (:id . 56))\n ((:tag . "NNP") (:stem . "College") (:form . "College") (:end . 107)\n  (:start . 100) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.70) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501680@unknown@formal@none@1@S@Western blot analysis@(((:tag . "NN") (:stem . "western") (:form . "Western") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 21)\n  (:start . 13) (:id . 44)))@@@1@3@((:identifiers (:sid . :s6.71) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501681@unknown@formal@none@1@S@AML1-ETO and TEL-AML1 proteins were detected in retrovirally transduced NIH3T3 cells as described previously.15,25,61,66@(((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "tel-aml1") (:form . "TEL-AML1") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "RB") (:stem . "retrovirally") (:form . "retrovirally") (:end . 60)\n  (:start . 48) (:id . 49))\n ((:tag . "VBN") (:stem . "transduce") (:form . "transduced") (:end . 71)\n  (:start . 61) (:id . 50))\n ((:tag . "NN") (:stem . "nih3t3") (:form . "NIH3T3") (:end . 78)\n  (:start . 72) (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 84) (:start . 79)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 87) (:start . 85)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 97)\n  (:start . 88) (:id . 54))\n ((:tag . "CD") (:stem . "previously.15,25,61,66")\n  (:form . "previously.15,25,61,66") (:end . 120) (:start . 98) (:id . 55)))@@@1@14@((:identifiers (:sid . :s6.72) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501682@unknown@formal@none@1@S@Splenocyte extracts were prepared by lysing approximately 5 × 105 cells in 3× sodium dodecyl sulfate (SDS) sample buffer (New England Biolabs, Ipswich, MA) with 0.1 M dithiothreitol for 10 minutes on ice, boiling 5 minutes at 95°C, and the proteins were resolved through NuPAGE Novex 4%-12% Bis-Tris mini gels (Invitrogen) and transferred onto a polyvinylidene fluoride, (PVDF) membrane.@(((:tag . "NNP") (:stem . "Splenocyte") (:form . "Splenocyte") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "extract") (:form . "extracts") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "lyse") (:form . 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5501687@unknown@formal@none@1@S@We compared the contribution of DNA versus CBFß binding to AML1-ETO–mediated leukemogenesis by introducing amino acid substitutions at both interfaces.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "compare") (:form . "compared") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "contribution") (:form . "contribution") (:end . 28)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "CC") (:stem . "versus") (:form . "versus") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "aml1-eto–mediated") (:form . "AML1-ETO–mediated")\n  (:end . 76) (:start . 59) (:id . 52))\n ((:tag . "NN") (:stem . "leukemogenesis") (:form . "leukemogenesis")\n  (:end . 91) (:start . 77) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 94) (:start . 92)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "introduce") (:form . "introducing") (:end . 106)\n  (:start . 95) (:id . 55))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 112)\n  (:start . 107) (:id . 56))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 117) (:start . 113)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "substitution") (:form . "substitutions")\n  (:end . 131) (:start . 118) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 134) (:start . 132)\n  (:id . 59))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 139) (:start . 135)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "interface") (:form . "interfaces") (:end . 150)\n  (:start . 140) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.78) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501688@unknown@formal@none@1@S@An R174Q substitution caused a greater than 40000-fold reduction in DNA binding by the isolated Runt domain without perturbing heterodimerization with CBFß, its structure, or its thermodynamic stability.30@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 21)\n  (:start . 9) (:id . 44))\n ((:tag . "VBD") (:stem . "cause") (:form . "caused") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "40000-fold") (:form . "40000-fold") (:end . 54)\n  (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 64)\n  (:start . 55) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 79)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 95)\n  (:start . 87) (:id . 56))\n ((:tag . "NN") (:stem . "runt") (:form . "Runt") (:end . 100) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 107)\n  (:start . 101) (:id . 58))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 115)\n  (:start . 108) (:id . 59))\n ((:tag . "VBG") (:stem . "perturb") (:form . "perturbing") (:end . 126)\n  (:start . 116) (:id . 60))\n ((:tag . "NN") (:stem . "heterodimerization") (:form . "heterodimerization")\n  (:end . 145) (:start . 127) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 150) (:start . 146)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 155) (:start . 151)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 64))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 160) (:start . 157)\n  (:id . 65))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 170)\n  (:start . 161) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 174) (:start . 172)\n  (:id . 68))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 178) (:start . 175)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "thermodynamic") (:form . "thermodynamic")\n  (:end . 192) (:start . 179) (:id . 70))\n ((:tag . "NN") (:stem . "stability.30") (:form . "stability.30") (:end . 205)\n  (:start . 193) (:id . 71)))@@@1@30@((:identifiers (:sid . :s6.79) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501689@unknown@formal@none@1@S@A T161A mutation, on the other hand, caused a 40-fold reduction in CBFß binding while having no effect on DNA binding.65@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 30) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . "hand") (:form . "hand") (:end . 35) (:start . 31)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "cause") (:form . "caused") (:end . 43)\n  (:start . 37) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "40-fold") (:form . "40-fold") (:end . 53)\n  (:start . 46) (:id . 53))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 63)\n  (:start . 54) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 71) (:start . 67)\n  (:id . 56))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 79)\n  (:start . 72) (:id . 57))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 85) (:start . 80)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "have") (:form . "having") (:end . 92) (:start . 86)\n  (:id . 59))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 95) (:start . 93)\n  (:id . 60))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 102)\n  (:start . 96) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 105) (:start . 103)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 109) (:start . 106)\n  (:id . 63))\n ((:tag . "NN") (:stem . "binding.65") (:form . "binding.65") (:end . 120)\n  (:start . 110) (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.80) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501690@unknown@formal@none@1@S@The T161A mutation did not perturb the Runt domain's structure as assessed in 15N-1H HSQC spectra,65 although it did moderately decrease its thermodynamic stability.30@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "VB") (:stem . "perturb") (:form . "perturb") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 74)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "15N-1H") (:form . "15N-1H") (:end . 84)\n  (:start . 78) (:id . 56))\n ((:tag . "NNP") (:stem . "HSQC") (:form . "HSQC") (:end . 89) (:start . 85)\n  (:id . 57))\n ((:tag . "CD") (:stem . "spectra,65") (:form . "spectra,65") (:end . 100)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 109)\n  (:start . 101) (:id . 59))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "RB") (:stem . "moderately") (:form . "moderately") (:end . 127)\n  (:start . 117) (:id . 62))\n ((:tag . "VB") (:stem . "decrease") (:form . "decrease") (:end . 136)\n  (:start . 128) (:id . 63))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 140) (:start . 137)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "thermodynamic") (:form . "thermodynamic")\n  (:end . 154) (:start . 141) (:id . 65))\n ((:tag . "NN") (:stem . "stability.30") (:form . "stability.30") (:end . 167)\n  (:start . 155) (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.81) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501691@unknown@formal@none@1@S@Since the T161A mutation, when introduced into the Runx1 locus in mice, did not completely eliminate Runx1's in vivo function,30 we sought to disrupt CBFß binding further by combining it with a second mutation.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "introduce") (:form . "introduced") (:end . 41)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "runx1") (:form . "Runx1") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 79) (:start . 76)\n  (:id . 57))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 90)\n  (:start . 80) (:id . 58))\n ((:tag . "VB") (:stem . "eliminate") (:form . "eliminate") (:end . 100)\n  (:start . 91) (:id . 59))\n ((:tag . "NNP") (:stem . "Runx1") (:form . "Runx1") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 108) (:start . 106)\n  (:id . 61))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 62))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 116) (:start . 112)\n  (:id . 63))\n ((:tag . "CD") (:stem . "function,30") (:form . "function,30") (:end . 128)\n  (:start . 117) (:id . 64))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 131) (:start . 129)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "seek") (:form . "sought") (:end . 138)\n  (:start . 132) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 141) (:start . 139)\n  (:id . 67))\n ((:tag . "VB") (:stem . "disrupt") (:form . "disrupt") (:end . 149)\n  (:start . 142) (:id . 68))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 154) (:start . 150)\n  (:id . 69))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 162)\n  (:start . 155) (:id . 70))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 170)\n  (:start . 163) (:id . 71))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 173) (:start . 171)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "combine") (:form . "combining") (:end . 183)\n  (:start . 174) (:id . 73))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 186) (:start . 184)\n  (:id . 74))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 191) (:start . 187)\n  (:id . 75))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 193) (:start . 192)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 200)\n  (:start . 194) (:id . 77))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 209)\n  (:start . 201) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.82) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501692@unknown@formal@none@1@S@The majority (approximately two-thirds) of alanine substitutions in the Runt domain perturb its fold, particularly those within the ß-barrel, one surface of which comprises the CBFß interface.30,63,65@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 27) (:start . 14) (:id . 45))\n ((:tag . "NNS") (:stem . "two-third") (:form . "two-thirds") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 39) (:start . 38)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "alanine") (:form . "alanine") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "substitution") (:form . "substitutions")\n  (:end . 64) (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 83)\n  (:start . 77) (:id . 54))\n ((:tag . "VB") (:stem . "perturb") (:form . "perturb") (:end . 91)\n  (:start . 84) (:id . 55))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 95) (:start . 92)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 100) (:start . 96)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 114)\n  (:start . 102) (:id . 59))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 120)\n  (:start . 115) (:id . 60))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 127)\n  (:start . 121) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "ß-barrel") (:form . "ß-barrel") (:end . 140)\n  (:start . 132) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 64))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 145) (:start . 142)\n  (:id . 65))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 153)\n  (:start . 146) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 156) (:start . 154)\n  (:id . 67))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 162)\n  (:start . 157) (:id . 68))\n ((:tag . "VBZ") (:stem . "comprise") (:form . "comprises") (:end . 172)\n  (:start . 163) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 176) (:start . 173)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 181) (:start . 177)\n  (:id . 71))\n ((:tag . "CD") (:stem . "interface.30,63,65") (:form . "interface.30,63,65")\n  (:end . 200) (:start . 182) (:id . 72)))@@@1@31@((:identifiers (:sid . :s6.83) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501693@unknown@formal@none@1@S@A Y113A mutation was one of only a few that decreased the affinity for CBFß (by approximately 5-fold), while causing only minimal, local effects on the Runt domain fold as assessed in 15N-1H HSQC spectra.65@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Y113A") (:form . "Y113A") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 38) (:start . 35)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 43) (:start . 39)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "decrease") (:form . "decreased") (:end . 53)\n  (:start . 44) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 66)\n  (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 79) (:start . 77)\n  (:id . 58))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 93) (:start . 80) (:id . 59))\n ((:tag . "RB") (:stem . "5-fold") (:form . "5-fold") (:end . 100)\n  (:start . 94) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 108)\n  (:start . 103) (:id . 63))\n ((:tag . "VBG") (:stem . "cause") (:form . "causing") (:end . 116)\n  (:start . 109) (:id . 64))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 121) (:start . 117)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "minimal") (:form . "minimal") (:end . 129)\n  (:start . 122) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 136)\n  (:start . 131) (:id . 68))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 144)\n  (:start . 137) (:id . 69))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 147) (:start . 145)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 156) (:start . 152)\n  (:id . 72))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 163)\n  (:start . 157) (:id . 73))\n ((:tag . "RB") (:stem . "fold") (:form . "fold") (:end . 168) (:start . 164)\n  (:id . 74))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 171) (:start . 169)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 180)\n  (:start . 172) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 183) (:start . 181)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "15N-1H") (:form . "15N-1H") (:end . 190)\n  (:start . 184) (:id . 78))\n ((:tag . "NNP") (:stem . "HSQC") (:form . "HSQC") (:end . 195) (:start . 191)\n  (:id . 79))\n ((:tag . "NN") (:stem . "spectra.65") (:form . "spectra.65") (:end . 206)\n  (:start . 196) (:id . 80)))@@@1@39@((:identifiers (:sid . :s6.84) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501694@unknown@formal@none@1@S@We showed that the Y113A/T161A dual mutations did not further decrease the Runt domain's thermodynamic stability compared with the T161A mutation alone (Figure 1B).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 30)\n  (:start . 19) (:id . 46))\n ((:tag . "JJ") (:stem . "dual") (:form . "dual") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 45)\n  (:start . 36) (:id . 48))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "VB") (:stem . "decrease") (:form . "decrease") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 86)\n  (:start . 80) (:id . 55))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "thermodynamic") (:form . "thermodynamic")\n  (:end . 102) (:start . 89) (:id . 57))\n ((:tag . "NN") (:stem . "stability") (:form . "stability") (:end . 112)\n  (:start . 103) (:id . 58))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 121)\n  (:start . 113) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 126) (:start . 122)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 136)\n  (:start . 131) (:id . 62))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 145)\n  (:start . 137) (:id . 63))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 151)\n  (:start . 146) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 159)\n  (:start . 153) (:id . 66))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 162) (:start . 160)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 163) (:start . 162)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s6.85) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501695@unknown@formal@none@1@S@The dissociation constant (K2; Figure 1C) of the Y113A/T161A mutant Runt domain for DNA was unaltered (Figure 1D).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "dissociation") (:form . "dissociation") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "constant") (:form . "constant") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "K2") (:form . "K2") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "1c") (:form . "1C") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 60)\n  (:start . 49) (:id . 53))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 67)\n  (:start . 61) (:id . 54))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 79)\n  (:start . 73) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "unaltered") (:form . "unaltered") (:end . 101)\n  (:start . 92) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 109)\n  (:start . 103) (:id . 62))\n ((:tag . "NN") (:stem . "1d") (:form . "1D") (:end . 112) (:start . 110)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s6.86) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501696@unknown@formal@none@1@S@Since DNA binding is highly sensitive to mutations in the Runt domain that perturb its structure,30,63 we reasoned that the Y113A/T161A mutant Runt domain's fold is intact despite its modestly decreased thermodynamic stability.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "JJ") (:stem . "sensitive") (:form . "sensitive") (:end . 37)\n  (:start . 28) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "runt") (:form . "Runt") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "perturb") (:form . "perturb") (:end . 82)\n  (:start . 75) (:id . 55))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 86) (:start . 83)\n  (:id . 56))\n ((:tag . "CD") (:stem . "structure,30,63") (:form . "structure,30,63")\n  (:end . 102) (:start . 87) (:id . 57))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "reason") (:form . "reasoned") (:end . 114)\n  (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 119) (:start . 115)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 135)\n  (:start . 124) (:id . 62))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 142)\n  (:start . 136) (:id . 63))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 147) (:start . 143)\n  (:id . 64))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 154)\n  (:start . 148) (:id . 65))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 156) (:start . 154)\n  (:id . 66))\n ((:tag . "NN") (:stem . "fold") (:form . "fold") (:end . 161) (:start . 157)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 164) (:start . 162)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "intact") (:form . "intact") (:end . 171)\n  (:start . 165) (:id . 69))\n ((:tag . "IN") (:stem . "despite") (:form . "despite") (:end . 179)\n  (:start . 172) (:id . 70))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 183) (:start . 180)\n  (:id . 71))\n ((:tag . "RB") (:stem . "modestly") (:form . "modestly") (:end . 192)\n  (:start . 184) (:id . 72))\n ((:tag . "VBD") (:stem . "decrease") (:form . "decreased") (:end . 202)\n  (:start . 193) (:id . 73))\n ((:tag . "JJ") (:stem . "thermodynamic") (:form . "thermodynamic")\n  (:end . 216) (:start . 203) (:id . 74))\n ((:tag . "NN") (:stem . "stability") (:form . "stability") (:end . 226)\n  (:start . 217) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.87) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501697@unknown@formal@none@1@S@Amino acid substitutions in the Runx1 Runt domain that specifically disrupt DNA and CBFß binding.@(((:tag . "NN") (:stem . "amino") (:form . "Amino") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "substitution") (:form . "substitutions")\n  (:end . 24) (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "runx1") (:form . "Runx1") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 67)\n  (:start . 55) (:id . 51))\n ((:tag . "VBP") (:stem . "disrupt") (:form . "disrupt") (:end . 75)\n  (:start . 68) (:id . 52))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 79) (:start . 76)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 96)\n  (:start . 89) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s6.88) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501698@unknown@formal@none@1@S@(A) Structures of the Runt domain and CBFß are shown in gray and blue, respectively, and the DNA is purple.36@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Structure") (:form . "Structures") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 26) (:start . 22)\n  (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 33)\n  (:start . 27) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 42) (:start . 38)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 46) (:start . 43)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 52) (:start . 47)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "gray") (:form . "gray") (:end . 60) (:start . 56)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 69) (:start . 65)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 58))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 83)\n  (:start . 71) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 62))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 96) (:start . 93)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 99) (:start . 97)\n  (:id . 64))\n ((:tag . "NN") (:stem . "purple.36") (:form . "purple.36") (:end . 109)\n  (:start . 100) (:id . 65)))@@@1@24@((:identifiers (:sid . :s6.89) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501699@unknown@formal@none@1@S@The R174 side chain in the Runt domain is green, and the T161 and Y113 side chains are orange.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "r174") (:form . "R174") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "chain") (:form . "chain") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 38)\n  (:start . 32) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 47) (:start . 42)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 54))\n ((:tag . "NN") (:stem . "t161") (:form . "T161") (:end . 61) (:start . 57)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 56))\n ((:tag . "NN") (:stem . "y113") (:form . "Y113") (:end . 70) (:start . 66)\n  (:id . 57))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 75) (:start . 71)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "chain") (:form . "chains") (:end . 82)\n  (:start . 76) (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 86) (:start . 83)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "orange") (:form . "orange") (:end . 93)\n  (:start . 87) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.90) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501700@unknown@formal@none@1@S@(B) Urea denaturation monitored by tryptophan fluorescence for the wild-type Runt domain and point mutants thereof.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "urea") (:form . "Urea") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "denaturation") (:form . "denaturation") (:end . 21)\n  (:start . 9) (:id . 46))\n ((:tag . "VBN") (:stem . "monitor") (:form . "monitored") (:end . 31)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "tryptophan") (:form . "tryptophan") (:end . 45)\n  (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 58)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 76)\n  (:start . 67) (:id . 53))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 81) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 88)\n  (:start . 82) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 98) (:start . 93)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 106)\n  (:start . 99) (:id . 58))\n ((:tag . "RB") (:stem . "thereof") (:form . "thereof") (:end . 114)\n  (:start . 107) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.91) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501701@unknown@formal@none@1@S@Plotted is the fraction of unfolded Runt domain in the presence of increasing concentrations of urea.@(((:tag . "VBN") (:stem . "plot") (:form . "Plotted") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "unfolded") (:form . "unfolded") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "runt") (:form . "Runt") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 77)\n  (:start . 67) (:id . 54))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 92) (:start . 78) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "urea") (:form . "urea") (:end . 100) (:start . 96)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.92) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501702@unknown@formal@none@1@S@Data from the wild-type Runt domain, R174Q, and T161A are from Matheny et al.30@(((:tag . "NNP") (:stem . "Datum") (:form . "Data") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 53) (:start . 48)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 62) (:start . 58)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Matheny") (:form . "Matheny") (:end . 70)\n  (:start . 63) (:id . 55))\n ((:tag . "NNP") (:stem . "et") (:form . "et") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . ".") (:stem . "al.30") (:form . "al.30") (:end . 79) (:start . 74)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s6.93) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501703@unknown@formal@none@1@S@(C) Diagram of the potential interactions between the Runt Domain, CBFß, and DNA.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Diagram") (:form . "Diagram") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 28)\n  (:start . 19) (:id . 48))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 41)\n  (:start . 29) (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 49)\n  (:start . 42) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Domain") (:form . "Domain") (:end . 65)\n  (:start . 59) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 71) (:start . 67)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 80) (:start . 77)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x6.94.1) (:span 19 28)))\n (:hscopes ((:id . :x6.94.1) (:span 19 80)))\n (:identifiers (:sid . :s6.94) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501704@unknown@formal@none@1@S@(D) EMSA measuring the affinity of the Y113A/T161A Runt domain for DNA (K2).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "EMSA") (:form . "EMSA") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "measure") (:form . "measuring") (:end . 18)\n  (:start . 9) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 31)\n  (:start . 23) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 50)\n  (:start . 39) (:id . 51))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 62)\n  (:start . 56) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "K2") (:form . "K2") (:end . 74) (:start . 72)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.95) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501705@unknown@formal@none@1@S@Shown is a representative example of 3 experiments.@(((:tag . "NNP") (:stem . "Shown") (:form . "Shown") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 25) (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 50)\n  (:start . 39) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 51) (:start . 50)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s6.96) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501706@unknown@formal@none@1@S@Triangles indicate decreasing concentrations of the Runt domain (2 × 10-6 to 4 × 10-15 M).@(((:tag . "NNS") (:stem . "triangle") (:form . "Triangles") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 18)\n  (:start . 10) (:id . 43))\n ((:tag . "VBG") (:stem . "decrease") (:form . "decreasing") (:end . 29)\n  (:start . 19) (:id . 44))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 44) (:start . 30) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 56) (:start . 52)\n  (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 63)\n  (:start . 57) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 50))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 66) (:start . 65)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "×") (:form . "×") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "CD") (:stem . "10-6") (:form . "10-6") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 80) (:start . 79)\n  (:id . 56))\n ((:tag . "CD") (:stem . "10-15") (:form . "10-15") (:end . 86) (:start . 81)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 88) (:start . 87)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.97) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501707@unknown@formal@none@1@S@Arrow indicates the lane in which the Runt domain concentration approximates K2.@(((:tag . "NNP") (:stem . "Arrow") (:form . "Arrow") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 49)\n  (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 63) (:start . 50) (:id . 51))\n ((:tag . "VBZ") (:stem . "approximate") (:form . "approximates") (:end . 76)\n  (:start . 64) (:id . 52))\n ((:tag . "NN") (:stem . "k2") (:form . "K2") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.98) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501708@unknown@formal@none@1@S@(E) Isothermal titration calorimetric measurements of CBFß binding to the wild-type, T161A, and Y113A/T161A mutant Runt domains.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "isothermal") (:form . "Isothermal") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "titration") (:form . "titration") (:end . 24)\n  (:start . 15) (:id . 46))\n ((:tag . "JJ") (:stem . "calorimetric") (:form . "calorimetric") (:end . 37)\n  (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . "measurement") (:form . "measurements") (:end . 50)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 83)\n  (:start . 74) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 90) (:start . 85)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 107)\n  (:start . 96) (:id . 59))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 114)\n  (:start . 108) (:id . 60))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 119) (:start . 115)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 127)\n  (:start . 120) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.99) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501709@unknown@formal@none@1@S@Wild-type Runt domain (45 µM) was titrated with 440 µM CBFß at 26°C, and 42 µM T161A or 38 µM Y113A/T161A were titrated with 396 µM CBFß at 22°C.@(((:tag . "JJ") (:stem . "wild-type") (:form . "Wild-type") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "µM") (:form . "µM") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 33) (:start . 30)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "titrate") (:form . "titrated") (:end . 42)\n  (:start . 34) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "CD") (:stem . "440") (:form . "440") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "µM") (:form . "µM") (:end . 54) (:start . 52)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 59) (:start . 55)\n  (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 62) (:start . 60)\n  (:id . 55))\n ((:tag . "NN") (:stem . "26°c") (:form . "26°C") (:end . 67) (:start . 63)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 58))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 75) (:start . 73)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "µM") (:form . "µM") (:end . 78) (:start . 76)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 84) (:start . 79)\n  (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 87) (:start . 85)\n  (:id . 62))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 90) (:start . 88)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "µM") (:form . "µM") (:end . 93) (:start . 91)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 105)\n  (:start . 94) (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 110) (:start . 106)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "titrate") (:form . "titrated") (:end . 119)\n  (:start . 111) (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 124) (:start . 120)\n  (:id . 68))\n ((:tag . "CD") (:stem . "396") (:form . "396") (:end . 128) (:start . 125)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "µM") (:form . "µM") (:end . 131) (:start . 129)\n  (:id . 70))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 136) (:start . 132)\n  (:id . 71))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 139) (:start . 137)\n  (:id . 72))\n ((:tag . "NN") (:stem . "22°c") (:form . "22°C") (:end . 144) (:start . 140)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x6.100.1) (:span 85 87)))\n (:hscopes ((:id . :x6.100.1) (:span 73 105)))\n (:identifiers (:sid . :s6.100) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501710@unknown@formal@none@1@S@In each panel, the top portion is the raw data, and the bottom panel is a plot of the binding corrected for dilution enthalpy.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 30)\n  (:start . 23) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "raw") (:form . "raw") (:end . 41) (:start . 38)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 46) (:start . 42)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "bottom") (:form . "bottom") (:end . 62)\n  (:start . 56) (:id . 56))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 68) (:start . 63)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 59))\n ((:tag . "NN") (:stem . "plot") (:form . "plot") (:end . 78) (:start . 74)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 62))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 93)\n  (:start . 86) (:id . 63))\n ((:tag . "VBN") (:stem . "correct") (:form . "corrected") (:end . 103)\n  (:start . 94) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 107) (:start . 104)\n  (:id . 65))\n ((:tag . "NN") (:stem . "dilution") (:form . "dilution") (:end . 116)\n  (:start . 108) (:id . 66))\n ((:tag . "NN") (:stem . "enthalpy") (:form . "enthalpy") (:end . 125)\n  (:start . 117) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s6.101) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501711@unknown@formal@none@1@S@Experimental data (squares) are fit to a one-site binding model (line).@(((:tag . "JJ") (:stem . "experimental") (:form . "Experimental") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 17) (:start . 13)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 19) (:start . 18)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "square") (:form . "squares") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "fit") (:form . "fit") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "one-site") (:form . "one-site") (:end . 49)\n  (:start . 41) (:id . 51))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 63) (:start . 58)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 69) (:start . 65)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s6.102) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501712@unknown@formal@none@1@S@The equilibrium dissociation constants (K1) are indicated in the plots.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "equilibrium") (:form . "equilibrium") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "dissociation") (:form . "dissociation") (:end . 28)\n  (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "constant") (:form . "constants") (:end . 38)\n  (:start . 29) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "K1") (:form . "K1") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "plot") (:form . "plots") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.103) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501713@unknown@formal@none@1@S@The average values from 2 independent measurements (± standard deviation [SD]) are given.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "measurement") (:form . "measurements") (:end . 50)\n  (:start . 38) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "±") (:form . "±") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . "NN") (:stem . "deviation") (:form . "deviation") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 74) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "SD") (:form . "SD") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 77) (:start . 76)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 88) (:start . 83)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.104) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501714@unknown@formal@none@1@S@We measured the affinity of the T161A and Y113A/T161A mutant Runt domains for CBFß by isothermal titration calorimetry (Figure 1E).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "measure") (:form . "measured") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 53)\n  (:start . 42) (:id . 50))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 73)\n  (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "isothermal") (:form . "isothermal") (:end . 96)\n  (:start . 86) (:id . 57))\n ((:tag . "NN") (:stem . "titration") (:form . "titration") (:end . 106)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "calorimetry") (:form . "calorimetry") (:end . 118)\n  (:start . 107) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 120) (:start . 119)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 126)\n  (:start . 120) (:id . 61))\n ((:tag . "NN") (:stem . "1e") (:form . "1E") (:end . 129) (:start . 127)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.105) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501715@unknown@formal@none@1@S@The dissociation constant (K1 in Figure 1C) for the T161A mutant Runt domain was increased by 63-fold, and for the Y113A/T161A mutant by 430-fold (Figure 1E).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "dissociation") (:form . "dissociation") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "constant") (:form . "constant") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "k1") (:form . "K1") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "1c") (:form . "1C") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 57) (:start . 52)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 64)\n  (:start . 58) (:id . 54))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 69) (:start . 65)\n  (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 76)\n  (:start . 70) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 90)\n  (:start . 81) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "63-fold") (:form . "63-fold") (:end . 101)\n  (:start . 94) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 126)\n  (:start . 115) (:id . 65))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 133)\n  (:start . 127) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 136) (:start . 134)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "430-fold") (:form . "430-fold") (:end . 145)\n  (:start . 137) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 153)\n  (:start . 147) (:id . 70))\n ((:tag . "NN") (:stem . "1e") (:form . "1E") (:end . 156) (:start . 154)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s6.106) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501716@unknown@formal@none@1@S@Whereas binding of the wild-type Runt domain to CBFß is exothermic (release of heat upon binding), that of the mutant Runt domains is endothermic (absorption of heat upon binding).@(((:tag . "IN") (:stem . "whereas") (:form . "Whereas") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "exothermic") (:form . "exothermic") (:end . 66)\n  (:start . 56) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "release") (:form . "release") (:end . 75)\n  (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "heat") (:form . "heat") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 96)\n  (:start . 89) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 60))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 103) (:start . 99)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 117)\n  (:start . 111) (:id . 64))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 122) (:start . 118)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 130)\n  (:start . 123) (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 133) (:start . 131)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "endothermic") (:form . "endothermic") (:end . 145)\n  (:start . 134) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . "NN") (:stem . "absorption") (:form . "absorption") (:end . 157)\n  (:start . 147) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n  (:id . 71))\n ((:tag . "NN") (:stem . "heat") (:form . "heat") (:end . 165) (:start . 161)\n  (:id . 72))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 170) (:start . 166)\n  (:id . 73))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 178)\n  (:start . 171) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.107) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501717@unknown@formal@none@1@S@For this reason, the raw heat data in Figure 1E switches from being negative for the wild-type to positive for the T161A and Y113A/T161A mutant Runt domains.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "reason") (:form . "reason") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "raw") (:form . "raw") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "heat") (:form . "heat") (:end . 29) (:start . 25)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 34) (:start . 30)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 44)\n  (:start . 38) (:id . 51))\n ((:tag . "NN") (:stem . "1e") (:form . "1E") (:end . 47) (:start . 45)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "switch") (:form . "switches") (:end . 56)\n  (:start . 48) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 67) (:start . 62)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 76)\n  (:start . 68) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 94)\n  (:start . 85) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 106)\n  (:start . 98) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 110) (:start . 107)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 120)\n  (:start . 115) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 136)\n  (:start . 125) (:id . 66))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 143)\n  (:start . 137) (:id . 67))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 148) (:start . 144)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 156)\n  (:start . 149) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.108) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501718@unknown@formal@none@1@S@Apparently, the interactions mediated by T161 contribute strongly to the enthalpy of binding, and loss of these interactions results in a binding process that is no longer enthalpically favorable but remains entropically favorable, albeit of weaker affinity.@(((:tag . "RB") (:stem . "apparently") (:form . "Apparently") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 28)\n  (:start . 16) (:id . 45))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "T161") (:form . "T161") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "contribute") (:form . "contribute") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 65)\n  (:start . 57) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "enthalpy") (:form . "enthalpy") (:end . 81)\n  (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 92)\n  (:start . 85) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 57))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 102) (:start . 98)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 59))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 111)\n  (:start . 106) (:id . 60))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 124)\n  (:start . 112) (:id . 61))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 132)\n  (:start . 125) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 137) (:start . 136)\n  (:id . 64))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 145)\n  (:start . 138) (:id . 65))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 153)\n  (:start . 146) (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 158) (:start . 154)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 161) (:start . 159)\n  (:id . 68))\n ((:tag . "RB") (:stem . "no") (:form . "no") (:end . 164) (:start . 162)\n  (:id . 69))\n ((:tag . "RB") (:stem . "longer") (:form . "longer") (:end . 171)\n  (:start . 165) (:id . 70))\n ((:tag . "RB") (:stem . "enthalpically") (:form . "enthalpically")\n  (:end . 185) (:start . 172) (:id . 71))\n ((:tag . "JJ") (:stem . "favorable") (:form . "favorable") (:end . 195)\n  (:start . 186) (:id . 72))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 199) (:start . 196)\n  (:id . 73))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 207)\n  (:start . 200) (:id . 74))\n ((:tag . "RB") (:stem . "entropically") (:form . "entropically") (:end . 220)\n  (:start . 208) (:id . 75))\n ((:tag . "JJ") (:stem . "favorable") (:form . "favorable") (:end . 230)\n  (:start . 221) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 231) (:start . 230)\n  (:id . 77))\n ((:tag . "IN") (:stem . "albeit") (:form . "albeit") (:end . 238)\n  (:start . 232) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 241) (:start . 239)\n  (:id . 79))\n ((:tag . "JJR") (:stem . "weak") (:form . "weaker") (:end . 248)\n  (:start . 242) (:id . 80))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 257)\n  (:start . 249) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 258) (:start . 257)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s6.109) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501719@unknown@formal@none@1@S@Disruption of DNA or CBFß binding impairs AML1-ETO's ability to repress granulocyte differentiation.@(((:tag . "NN") (:stem . "disruption") (:form . "Disruption") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "VBZ") (:stem . "impair") (:form . "impairs") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 50)\n  (:start . 42) (:id . 49))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "VB") (:stem . "repress") (:form . "repress") (:end . 71)\n  (:start . 64) (:id . 53))\n ((:tag . "NN") (:stem . "granulocyte") (:form . "granulocyte") (:end . 83)\n  (:start . 72) (:id . 54))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 99) (:start . 84) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s6.110) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501720@unknown@formal@none@1@S@We introduced the R174Q, T161A, and Y113A/T161A mutations into AML1-ETO (Figure 2A) and expressed AML1-ETO and its mutated derivates in lineage negative (CD5-, B220-, Mac-1-, Gr-1-, Ter119-) mouse BM cells (Lin- BM).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "introduce") (:form . "introduced") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 47)\n  (:start . 36) (:id . 50))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 57)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 71)\n  (:start . 63) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 79)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "2a") (:form . "2A") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "express") (:form . "expressed") (:end . 97)\n  (:start . 88) (:id . 59))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 106)\n  (:start . 98) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 114) (:start . 111)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 122)\n  (:start . 115) (:id . 63))\n ((:tag . "NNS") (:stem . "derivate") (:form . "derivates") (:end . 132)\n  (:start . 123) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 143)\n  (:start . 136) (:id . 66))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 152)\n  (:start . 144) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "CD5-") (:form . "CD5-") (:end . 158) (:start . 154)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n  (:id . 70))\n ((:tag . "NN") (:stem . "b220-") (:form . "B220-") (:end . 165)\n  (:start . 160) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 72))\n ((:tag . "NN") (:stem . "mac-1-") (:form . "Mac-1-") (:end . 173)\n  (:start . 167) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Gr-1-") (:form . "Gr-1-") (:end . 180)\n  (:start . 175) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 181) (:start . 180)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Ter119-") (:form . "Ter119-") (:end . 189)\n  (:start . 182) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n  (:id . 78))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 196)\n  (:start . 191) (:id . 79))\n ((:tag . "NN") (:stem . "bm") (:form . "BM") (:end . 199) (:start . 197)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 205)\n  (:start . 200) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 207) (:start . 206)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Lin-") (:form . "Lin-") (:end . 211) (:start . 207)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 214) (:start . 212)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 215) (:start . 214)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s6.111) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501721@unknown@formal@none@1@S@The retroviruses also expressed the enhanced green fluorescent protein (EGFP) from an internal ribosomal entry site.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "retrovirus") (:form . "retroviruses") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "express") (:form . "expressed") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 50) (:start . 45)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "fluorescent") (:form . "fluorescent") (:end . 62)\n  (:start . 51) (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 70)\n  (:start . 63) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 76) (:start . 72)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 82) (:start . 78)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 94)\n  (:start . 86) (:id . 56))\n ((:tag . "JJ") (:stem . "ribosomal") (:form . "ribosomal") (:end . 104)\n  (:start . 95) (:id . 57))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 110)\n  (:start . 105) (:id . 58))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.112) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501722@unknown@formal@none@1@S@We cultured cells following transduction in the presence of IL-3, IL-6, and SCF for 2 days, in the same cytokines plus granulocyte colony-stimulating factor (G-CSF) for an additional 7 days to induce granulocyte differentiation, and then analyzed EGFP+ cells for Mac-1 and Gr-1 expression (Figure 2B,C).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "culture") (:form . "cultured") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 40)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . 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5501723@unknown@formal@none@1@S@Approximately 32% of cells expressing EGFP alone were Mac-1+Gr-1+ (Figure 2C) versus 10% of those expressing AML1-ETO.@(((:tag . "RB") (:stem . "approximately") (:form . "Approximately")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 16) (:start . 14)\n  (:id . 43))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 48) (:start . 43)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "mac-1+gr-1+") (:form . "Mac-1+Gr-1+") (:end . 65)\n  (:start . 54) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 55))\n ((:tag . "IN") (:stem . "versus") (:form . "versus") (:end . 84)\n  (:start . 78) (:id . 56))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 88) (:start . 87)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 97) (:start . 92)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 108)\n  (:start . 98) (:id . 61))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 117)\n  (:start . 109) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.114) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501724@unknown@formal@none@1@S@Disruption of DNA binding (R174Q) or impairment of CBFß heterodimerization (Y113A/T161A) increased the percentage of Mac-1+Gr-1+ cells.@(((:tag . "NN") (:stem . "disruption") (:form . "Disruption") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "impairment") (:form . "impairment") (:end . 47)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "heterodimerization") (:form . "heterodimerization")\n  (:end . 74) (:start . 56) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 87)\n  (:start . 76) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 98)\n  (:start . 89) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 113)\n  (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "mac-1+gr-1+") (:form . "Mac-1+Gr-1+") (:end . 128)\n  (:start . 117) (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 134)\n  (:start . 129) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.115) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501725@unknown@formal@none@1@S@A triple Y113A/T161A/R174Q mutation in AML1-ETO did not further increase the percentage of Mac-1+Gr-1+cells compared with the individually mutated AML1-ETO proteins, indicating that the residual inhibitory effect of AML1-ETO resides in more C-terminal ETO sequences, and is not mediated through CBF binding sites.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "triple") (:form . "triple") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Y113A/T161A/R174Q") (:form . "Y113A/T161A/R174Q")\n  (:end . 26) (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 35)\n  (:start . 27) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 47)\n  (:start . 39) (:id . 47))\n ((:tag . "VBD") (:stem . "do") (:form . 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5501726@unknown@formal@none@1@S@The mutated AML1-ETO proteins accumulated to similar steady state levels in transduced NIH3T3 cells (Figure 2E).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "VBD") (:stem . "accumulate") (:form . "accumulated") (:end . 41)\n  (:start . 30) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "JJ") (:stem . "steady") (:form . "steady") (:end . 59)\n  (:start . 53) (:id . 49))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 65) (:start . 60)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 72)\n  (:start . 66) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "transduce") (:form . "transduced") (:end . 86)\n  (:start . 76) (:id . 53))\n ((:tag . "NN") (:stem . "nih3t3") (:form . "NIH3T3") (:end . 93)\n  (:start . 87) (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 99) (:start . 94)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 107)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "2e") (:form . "2E") (:end . 110) (:start . 108)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.117) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501727@unknown@formal@none@1@S@AML1-ETO function is impaired by mutations that disrupt DNA or CBFß binding.@(((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "impair") (:form . "impaired") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "disrupt") (:form . "disrupt") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 75)\n  (:start . 68) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.118) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501728@unknown@formal@none@1@S@(A) Diagram of AML1-ETO and location of the mutations affecting DNA (R174Q) and CBFß binding (T161A and Y113A/T161A).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Diagram") (:form . "Diagram") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 23)\n  (:start . 15) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n  (:id . 48))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 36)\n  (:start . 28) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 53)\n  (:start . 44) (:id . 52))\n ((:tag . "VBG") (:stem . "affect") (:form . "affecting") (:end . 63)\n  (:start . 54) (:id . 53))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 74) (:start . 69)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n  (:id . 58))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 84) (:start . 80)\n  (:id . 59))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 92)\n  (:start . 85) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 99) (:start . 94)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 115)\n  (:start . 104) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.119) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501729@unknown@formal@none@1@S@(B) Lin- BM cells infected with MigR1 retroviruses expressing AML1-ETO and mutated derivatives after 7 days of culture in the presence of IL-3, IL-6, SCF, and G-CSF.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Lin-") (:form . "Lin-") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 11) (:start . 9)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 17) (:start . 12)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "infect") (:form . "infected") (:end . 26)\n  (:start . 18) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 31) (:start . 27)\n  (:id . 49))\n ((:tag . "NN") (:stem . "migr1") (:form . "MigR1") (:end . 37) (:start . 32)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "retrovirus") (:form . "retroviruses") (:end . 50)\n  (:start . 38) (:id . 51))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 61)\n  (:start . 51) (:id . 52))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 70)\n  (:start . 62) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 82)\n  (:start . 75) (:id . 55))\n ((:tag . "NNS") (:stem . "derivative") (:form . "derivatives") (:end . 94)\n  (:start . 83) (:id . 56))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 100) (:start . 95)\n  (:id . 57))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 107) (:start . 103)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 118)\n  (:start . 111) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 134)\n  (:start . 126) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "IL-3") (:form . "IL-3") (:end . 142) (:start . 138)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 148) (:start . 144)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "SCF") (:form . "SCF") (:end . 153) (:start . 150)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 158) (:start . 155)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "G-CSF") (:form . "G-CSF") (:end . 164)\n  (:start . 159) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.120) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501730@unknown@formal@none@1@S@EGFP+ gated cells (not shown) were analyzed for Gr-1 and Mac-1 expression.@(((:tag . "JJ") (:stem . "egfp+") (:form . "EGFP+") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "gate") (:form . "gated") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 43)\n  (:start . 35) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gr-1") (:form . "Gr-1") (:end . 52) (:start . 48)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "mac-1") (:form . "Mac-1") (:end . 62) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 73)\n  (:start . 63) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s6.121) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501731@unknown@formal@none@1@S@(C) Summary of data illustrated in panel B compiled from 2 experiments, each with triplicate samples.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Summary") (:form . "Summary") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 19) (:start . 15)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "illustrate") (:form . "illustrated") (:end . 31)\n  (:start . 20) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 40) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "b") (:form . "B") (:end . 42) (:start . 41)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "compile") (:form . "compiled") (:end . 51)\n  (:start . 43) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 56) (:start . 52)\n  (:id . 53))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 58) (:start . 57)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 70)\n  (:start . 59) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 76) (:start . 72)\n  (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 81) (:start . 77)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "triplicate") (:form . "triplicate") (:end . 92)\n  (:start . 82) (:id . 59))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 100)\n  (:start . 93) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.122) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501732@unknown@formal@none@1@S@**P ≤ .01 compared with AML1-ETO (#); ***P ≤ .001 (Dunnett test and analysis of variance [ANOVA]).@(((:tag . "NNP") (:stem . "**P") (:form . "**P") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "CD") (:stem . ".01") (:form . ".01") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 18)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "#") (:stem . "#") (:form . "#") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 37) (:start . 36)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "***P") (:form . "***P") (:end . 42) (:start . 38)\n  (:id . 52))\n ((:tag . "NN") (:stem . "≤") (:form . "≤") (:end . 44) (:start . 43)\n  (:id . 53))\n ((:tag . "CD") (:stem . ".001") (:form . ".001") (:end . 49) (:start . 45)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Dunnett") (:form . "Dunnett") (:end . 58)\n  (:start . 51) (:id . 56))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 63) (:start . 59)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 58))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 76)\n  (:start . 68) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 60))\n ((:tag . "NN") (:stem . "variance") (:form . "variance") (:end . 88)\n  (:start . 80) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 90) (:start . 89)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "ANOVA") (:form . "ANOVA") (:end . 95) (:start . 90)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 96) (:start . 95)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.123) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501733@unknown@formal@none@1@S@(D) Serial replating analysis.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "serial") (:form . "Serial") (:end . 10) (:start . 4)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "replate") (:form . "replating") (:end . 20)\n  (:start . 11) (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 30) (:start . 29)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s6.124) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501734@unknown@formal@none@1@S@Graphs represent the average number of colonies from each round of replating in the presence of IL-3, IL-6, and SCF.@(((:tag . "NNS") (:stem . "graph") (:form . "Graphs") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 16)\n  (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 35)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "colony") (:form . "colonies") (:end . 47)\n  (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "NN") (:stem . "round") (:form . "round") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "replate") (:form . "replating") (:end . 76)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "IL-3") (:form . "IL-3") (:end . 100) (:start . 96)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "IL-6") (:form . "IL-6") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "SCF") (:form . "SCF") (:end . 115) (:start . 112)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.125) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501735@unknown@formal@none@1@S@Week 1 represents colony numbers per 103 cells plated, weeks 2 and 3 are from 104 plated cells.@(((:tag . "NNP") (:stem . "Week") (:form . "Week") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "colony") (:form . "colony") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "CD") (:stem . "103") (:form . "103") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "plat") (:form . "plated") (:end . 53) (:start . 47)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "week") (:form . "weeks") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 77) (:start . 73)\n  (:id . 57))\n ((:tag . "CD") (:stem . "104") (:form . "104") (:end . 81) (:start . 78)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "plat") (:form . "plated") (:end . 88) (:start . 82)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 94) (:start . 89)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.126) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501736@unknown@formal@none@1@S@Numbers are averaged from 2 experiments, each containing triplicate samples.@(((:tag . "NNPS") (:stem . "Number") (:form . "Numbers") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "average") (:form . "averaged") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 39)\n  (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "triplicate") (:form . "triplicate") (:end . 67)\n  (:start . 57) (:id . 51))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 75)\n  (:start . 68) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.127) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501737@unknown@formal@none@1@S@(E) Western blot analysis probed with an antibody to the Runt domain, demonstrating expression of AML1-ETO and its mutated derivatives in MigR1-transduced NIH3T3 cells.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 16) (:start . 12)\n  (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 25)\n  (:start . 17) (:id . 47))\n ((:tag . "VBD") (:stem . "probe") (:form . "probed") (:end . 32)\n  (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 49)\n  (:start . 41) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 68)\n  (:start . 62) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating") (:end . 83)\n  (:start . 70) (:id . 57))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 94)\n  (:start . 84) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 106)\n  (:start . 98) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 114) (:start . 111)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 122)\n  (:start . 115) (:id . 63))\n ((:tag . "NNS") (:stem . "derivative") (:form . "derivatives") (:end . 134)\n  (:start . 123) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 137) (:start . 135)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "migr1-transduced") (:form . "MigR1-transduced")\n  (:end . 154) (:start . 138) (:id . 66))\n ((:tag . "NN") (:stem . "nih3t3") (:form . "NIH3T3") (:end . 161)\n  (:start . 155) (:id . 67))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 167)\n  (:start . 162) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s6.128) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501738@unknown@formal@none@1@S@(F) BrdU incorporation 48 hours after transduction of Lin- BM cells with AML1-ETO and its mutants.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "BrdU") (:form . "BrdU") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "incorporation") (:form . "incorporation")\n  (:end . 22) (:start . 9) (:id . 46))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 31) (:start . 26)\n  (:id . 48))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 50)\n  (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Lin-") (:form . "Lin-") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 81)\n  (:start . 73) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 57))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 97)\n  (:start . 90) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.129) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501739@unknown@formal@none@1@S@EGFP+ cells were analyzed after a 1 hour BrdU pulse for BrdU and 7-AAD incorporation.@(((:tag . "JJ") (:stem . "egfp+") (:form . "EGFP+") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 35) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "hour") (:form . "hour") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "BrdU") (:form . "BrdU") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "pulse") (:form . "pulse") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "BrdU") (:form . "BrdU") (:end . 60) (:start . 56)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "7-aad") (:form . "7-AAD") (:end . 70) (:start . 65)\n  (:id . 55))\n ((:tag . "NN") (:stem . "incorporation") (:form . "incorporation")\n  (:end . 84) (:start . 71) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s6.130) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501740@unknown@formal@none@1@S@Shown is a representative of 3 experiments.@(((:tag . "NNP") (:stem . "Shown") (:form . "Shown") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "representative") (:form . "representative")\n  (:end . 25) (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 42)\n  (:start . 31) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.131) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501741@unknown@formal@none@1@S@(G) Average percentages of gated BrdU+ (S phase) cells from scatter plots in panel F (n = 3).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "percentage") (:form . "percentages") (:end . 23)\n  (:start . 12) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "gate") (:form . "gated") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "brdu+") (:form . "BrdU+") (:end . 38) (:start . 33)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 41) (:start . 40)\n  (:id . 51))\n ((:tag . "NN") (:stem . "phase") (:form . "phase") (:end . 47) (:start . 42)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 54) (:start . 49)\n  (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 59) (:start . 55)\n  (:id . 55))\n ((:tag . "NN") (:stem . "scatter") (:form . "scatter") (:end . 67)\n  (:start . 60) (:id . 56))\n ((:tag . "NNS") (:stem . "plot") (:form . "plots") (:end . 73) (:start . 68)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 58))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 82) (:start . 77)\n  (:id . 59))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 84) (:start . 83)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 61))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 87) (:start . 86)\n  (:id . 62))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 89) (:start . 88)\n  (:id . 63))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 91) (:start . 90)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.132) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501742@unknown@formal@none@1@S@Error bars indicate 95% confidence intervals.@(((:tag . "NN") (:stem . "error") (:form . "Error") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "CD") (:stem . "95") (:form . "95") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 34)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.133) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501743@unknown@formal@none@1@S@**P ≤ .01 compared with AML1-ETO (Dunnett test and ANOVA).@(((:tag . "NNP") (:stem . "**P") (:form . "**P") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "CD") (:stem . ".01") (:form . ".01") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 18)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Dunnett") (:form . "Dunnett") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "ANOVA") (:form . "ANOVA") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.134) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501744@unknown@formal@none@1@S@Disruption of DNA binding or CBFß binding abrogates AML1-ETO's ability to promote self-renewal and inhibit proliferation.@(((:tag . "NN") (:stem . "disruption") (:form . "Disruption") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "VBZ") (:stem . "abrogate") (:form . "abrogates") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 60)\n  (:start . 52) (:id . 50))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 70)\n  (:start . 63) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 81)\n  (:start . 74) (:id . 54))\n ((:tag . "JJ") (:stem . "self-renewal") (:form . "self-renewal") (:end . 94)\n  (:start . 82) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "inhibit") (:form . "inhibit") (:end . 106)\n  (:start . 99) (:id . 57))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 120) (:start . 107) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s6.135) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501745@unknown@formal@none@1@S@We assessed the importance of DNA binding and heterodimerization with CBFß for AML1-ETO's ability to confer increased self-renewal capacity to hematopoietic progenitors in vitro.69–71@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "assess") (:form . "assessed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "heterodimerization") (:form . "heterodimerization")\n  (:end . 64) (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 97)\n  (:start . 90) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "VB") (:stem . "confer") (:form . "confer") (:end . 107)\n  (:start . 101) (:id . 58))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 117)\n  (:start . 108) (:id . 59))\n ((:tag . "JJ") (:stem . "self-renewal") (:form . "self-renewal") (:end . 130)\n  (:start . 118) (:id . 60))\n ((:tag . "NN") (:stem . "capacity") (:form . "capacity") (:end . 139)\n  (:start . 131) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "hematopoietic") (:form . "hematopoietic")\n  (:end . 156) (:start . 143) (:id . 63))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 168)\n  (:start . 157) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 171) (:start . 169)\n  (:id . 65))\n ((:tag . "NN") (:stem . "vitro.69–71") (:form . "vitro.69–71") (:end . 183)\n  (:start . 172) (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.136) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501746@unknown@formal@none@1@S@Cells expressing AML1-ETO could be propagated for at least 3 weeks in methylcellulose cultures (Figure 2D) and yielded primarily immature myeloid lineage cells and a smaller percentage of differentiated macrophages15,70 (not shown).@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 31) (:start . 26)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "propagate") (:form . "propagated") (:end . 45)\n  (:start . 35) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 58) (:start . 53)\n  (:id . 50))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 60) (:start . 59)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "week") (:form . "weeks") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "methylcellulose") (:form . "methylcellulose")\n  (:end . 85) (:start . 70) (:id . 54))\n ((:tag . "NNS") (:stem . "culture") (:form . "cultures") (:end . 94)\n  (:start . 86) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 102)\n  (:start . 96) (:id . 57))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "yield") (:form . "yielded") (:end . 118)\n  (:start . 111) (:id . 61))\n ((:tag . "RB") (:stem . "primarily") (:form . "primarily") (:end . 128)\n  (:start . 119) (:id . 62))\n ((:tag . "JJ") (:stem . "immature") (:form . "immature") (:end . 137)\n  (:start . 129) (:id . 63))\n ((:tag . "JJ") (:stem . "myeloid") (:form . "myeloid") (:end . 145)\n  (:start . 138) (:id . 64))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 153)\n  (:start . 146) (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 159)\n  (:start . 154) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 163) (:start . 160)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 165) (:start . 164)\n  (:id . 68))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 173)\n  (:start . 166) (:id . 69))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 184)\n  (:start . 174) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "differentiate") (:form . "differentiated")\n  (:end . 202) (:start . 188) (:id . 72))\n ((:tag . "CD") (:stem . "macrophages15,70") (:form . "macrophages15,70")\n  (:end . 219) (:start . 203) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 221) (:start . 220)\n  (:id . 74))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 224) (:start . 221)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 230)\n  (:start . 225) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 231) (:start . 230)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s6.137) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501747@unknown@formal@none@1@S@Impaired DNA or CBFß binding caused by the R174Q or Y113A/T161A mutations, respectively, completely abolished AML1-ETO's ability to sustain this clonogenic activity (Figure 2D).@(((:tag . "JJ") (:stem . "impaired") (:form . "Impaired") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 63)\n  (:start . 52) (:id . 52))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 73)\n  (:start . 64) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 87)\n  (:start . 75) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 99)\n  (:start . 89) (:id . 57))\n ((:tag . "VBD") (:stem . "abolish") (:form . "abolished") (:end . 109)\n  (:start . 100) (:id . 58))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 118)\n  (:start . 110) (:id . 59))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 120) (:start . 118)\n  (:id . 60))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 128)\n  (:start . 121) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 131) (:start . 129)\n  (:id . 62))\n ((:tag . "VB") (:stem . "sustain") (:form . "sustain") (:end . 139)\n  (:start . 132) (:id . 63))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 144) (:start . 140)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "clonogenic") (:form . "clonogenic") (:end . 155)\n  (:start . 145) (:id . 65))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 164)\n  (:start . 156) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 166) (:start . 165)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 172)\n  (:start . 166) (:id . 68))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 175) (:start . 173)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s6.138) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501748@unknown@formal@none@1@S@Interestingly, it appears that the threshold level above which AML1-ETO cannot tolerate disruption of CBFß binding and maintain clonogenicity lies above 60-fold, as the T161A mutant retains activity for at least 3 weeks in this assay (Figure 2D).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 56) (:start . 51)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 62) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 71)\n  (:start . 63) (:id . 52))\n ((:tag . "VB") (:stem . "cannot") (:form . "cannot") (:end . 78)\n  (:start . 72) (:id . 53))\n ((:tag . "VB") (:stem . "tolerate") (:form . "tolerate") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "NN") (:stem . "disruption") (:form . "disruption") (:end . 98)\n  (:start . 88) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 106) (:start . 102)\n  (:id . 57))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 114)\n  (:start . 107) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 59))\n ((:tag . "NN") (:stem . "maintain") (:form . "maintain") (:end . 127)\n  (:start . 119) (:id . 60))\n ((:tag . "NN") (:stem . "clonogenicity") (:form . "clonogenicity")\n  (:end . 141) (:start . 128) (:id . 61))\n ((:tag . "VBZ") (:stem . "lie") (:form . "lies") (:end . 146) (:start . 142)\n  (:id . 62))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 152)\n  (:start . 147) (:id . 63))\n ((:tag . "JJ") (:stem . "60-fold") (:form . "60-fold") (:end . 160)\n  (:start . 153) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 164) (:start . 162)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 174)\n  (:start . 169) (:id . 68))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 181)\n  (:start . 175) (:id . 69))\n ((:tag . "VBZ") (:stem . "retain") (:form . "retains") (:end . 189)\n  (:start . 182) (:id . 70))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 198)\n  (:start . 190) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 202) (:start . 199)\n  (:id . 72))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 205) (:start . 203)\n  (:id . 73))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 211)\n  (:start . 206) (:id . 74))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 213) (:start . 212)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "week") (:form . "weeks") (:end . 219)\n  (:start . 214) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 222) (:start . 220)\n  (:id . 77))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 227) (:start . 223)\n  (:id . 78))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 233)\n  (:start . 228) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 235) (:start . 234)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 241)\n  (:start . 235) (:id . 81))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 244) (:start . 242)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 245) (:start . 244)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x6.139.1) (:span 18 25)))\n (:hscopes ((:id . :x6.139.1) (:span 18 233)))\n (:identifiers (:sid . :s6.139) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501749@unknown@formal@none@1@S@AML1-ETO inhibits the short-term proliferation of human and mouse primary BM cells.70,71@(((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "short-term") (:form . "short-term") (:end . 32)\n  (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 46) (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 55) (:start . 50)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 49))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 65) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 73)\n  (:start . 66) (:id . 51))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 76) (:start . 74)\n  (:id . 52))\n ((:tag . "CD") (:stem . "cells.70,71") (:form . "cells.70,71") (:end . 88)\n  (:start . 77) (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.140) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501750@unknown@formal@none@1@S@The R174Q, T161A, and Y113A/T161A mutations alleviated this repressive effect, although the percentage of cells in S phase was still significantly lower than in MigR1 transduced cells (Figure 2F,G).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 33)\n  (:start . 22) (:id . 48))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "VBD") (:stem . "alleviate") (:form . "alleviated") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "repressive") (:form . "repressive") (:end . 70)\n  (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 77)\n  (:start . 71) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 87)\n  (:start . 79) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 102)\n  (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 111)\n  (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . "NN") (:stem . "phase") (:form . "phase") (:end . 122)\n  (:start . 117) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 126) (:start . 123)\n  (:id . 63))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 132)\n  (:start . 127) (:id . 64))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 146) (:start . 133) (:id . 65))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 152) (:start . 147)\n  (:id . 66))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 157) (:start . 153)\n  (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 160) (:start . 158)\n  (:id . 68))\n ((:tag . "NN") (:stem . "migr1") (:form . "MigR1") (:end . 166)\n  (:start . 161) (:id . 69))\n ((:tag . "VBN") (:stem . "transduce") (:form . "transduced") (:end . 177)\n  (:start . 167) (:id . 70))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 183)\n  (:start . 178) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 191)\n  (:start . 185) (:id . 73))\n ((:tag . "CD") (:stem . "2F,G") (:form . "2F,G") (:end . 196) (:start . 192)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 197) (:start . 196)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.141) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5501752@unknown@formal@none@1@S@Numerous murine models have demonstrated that full-length AML1-ETO alone is not capable of causing AML.69,72–76@(((:tag . "JJ") (:stem . "numerous") (:form . "Numerous") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "murine") (:form . "murine") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 22)\n  (:start . 16) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "demonstrate") (:form . "demonstrated") (:end . 40)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 45) (:start . 41)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 57)\n  (:start . 46) (:id . 48))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 66)\n  (:start . 58) (:id . 49))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 72) (:start . 67)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 75) (:start . 73)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 79) (:start . 76)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "capable") (:form . "capable") (:end . 87)\n  (:start . 80) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "cause") (:form . "causing") (:end . 98)\n  (:start . 91) (:id . 55))\n ((:tag . "NNP") (:stem . "AML.69,72–76") (:form . "AML.69,72–76")\n  (:end . 111) (:start . 99) (:id . 56)))@@@1@15@((:identifiers (:sid . :s6.143) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5501754@unknown@formal@none@1@S@Both aforementioned mouse studies reported that mutation of leucine 148 to aspartic acid (L148D) within the Runt domain of AML1-ETO, which disrupts DNA binding16 and presumably causes a severe disruption of domain stability,30,65 resulted in a loss of cooperation with either oncogene.82,83@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "aforementioned") (:form . "aforementioned")\n  (:end . 19) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 25) (:start . 20)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 33)\n  (:start . 26) (:id . 45))\n ((:tag . "VBD") (:stem . "report") (:form . "reported") (:end . 42)\n  (:start . 34) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 47) (:start . 43)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 56)\n  (:start . 48) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 49))\n ((:tag . "NN") (:stem . "leucine") (:form . "leucine") (:end . 67)\n  (:start . 60) (:id . 50))\n ((:tag . "CD") (:stem . "148") (:form . "148") (:end . 71) (:start . 68)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "aspartic") (:form . "aspartic") (:end . 83)\n  (:start . 75) (:id . 53))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 88) (:start . 84)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "L148D") (:form . "L148D") (:end . 95) (:start . 90)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "NN") (:stem . "runt") (:form . "Runt") (:end . 112) (:start . 108)\n  (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 119)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 131)\n  (:start . 123) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 138)\n  (:start . 133) (:id . 65))\n ((:tag . "VBZ") (:stem . "disrupt") (:form . "disrupts") (:end . 147)\n  (:start . 139) (:id . 66))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 151) (:start . 148)\n  (:id . 67))\n ((:tag . "NN") (:stem . "binding16") (:form . "binding16") (:end . 161)\n  (:start . 152) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 69))\n ((:tag . "RB") (:stem . "presumably") (:form . "presumably") (:end . 176)\n  (:start . 166) (:id . 70))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 183)\n  (:start . 177) (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 185) (:start . 184)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 192)\n  (:start . 186) (:id . 73))\n ((:tag . "NN") (:stem . "disruption") (:form . "disruption") (:end . 203)\n  (:start . 193) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 206) (:start . 204)\n  (:id . 75))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 213)\n  (:start . 207) (:id . 76))\n ((:tag . "CD") (:stem . "stability,30,65") (:form . "stability,30,65")\n  (:end . 229) (:start . 214) (:id . 77))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 238)\n  (:start . 230) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 241) (:start . 239)\n  (:id . 79))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 243) (:start . 242)\n  (:id . 80))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 248) (:start . 244)\n  (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 251) (:start . 249)\n  (:id . 82))\n ((:tag . "NN") (:stem . "cooperation") (:form . "cooperation") (:end . 263)\n  (:start . 252) (:id . 83))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 268) (:start . 264)\n  (:id . 84))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 275)\n  (:start . 269) (:id . 85))\n ((:tag . "CD") (:stem . "oncogene.82,83") (:form . "oncogene.82,83")\n  (:end . 290) (:start . 276) (:id . 86)))@@@1@45@((:hcues ((:id . :x6.145.1) (:span 166 176)))\n (:hscopes ((:id . :x6.145.1) (:span 166 284)))\n (:identifiers (:sid . :s6.145) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501755@unknown@formal@none@1@S@These studies underscored the importance of the Runt domain for AML1-ETO's cooperative activity, but did not address whether disruption of DNA binding, CBFß heterodimerization, or both were responsible for the observed effect.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "underscore") (:form . "underscored") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "NN") (:stem . "runt") (:form . "Runt") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 72)\n  (:start . 64) (:id . 52))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "cooperative") (:form . "cooperative") (:end . 86)\n  (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 95)\n  (:start . 87) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "VB") (:stem . "address") (:form . "address") (:end . 116)\n  (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 124)\n  (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "disruption") (:form . "disruption") (:end . 135)\n  (:start . 125) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 142) (:start . 139)\n  (:id . 64))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 150)\n  (:start . 143) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n  (:id . 66))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 156) (:start . 152)\n  (:id . 67))\n ((:tag . "NN") (:stem . "heterodimerization") (:form . "heterodimerization")\n  (:end . 175) (:start . 157) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 176) (:start . 175)\n  (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 179) (:start . 177)\n  (:id . 70))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 184) (:start . 180)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 189) (:start . 185)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "responsible") (:form . "responsible") (:end . 201)\n  (:start . 190) (:id . 73))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 205) (:start . 202)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 218)\n  (:start . 210) (:id . 76))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 225)\n  (:start . 219) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x6.146.1) (:span 177 179))\n  ((:id . :x6.146.2) (:span 117 124)))\n (:hscopes ((:id . :x6.146.1) (:span 125 184))\n  ((:id . :x6.146.2) (:span 117 225)))\n (:identifiers (:sid . :s6.146) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501756@unknown@formal@none@1@S@We retrovirally transduced AML1-ETO (and derivative mutants) and TEL-PDGFßR into BM cells from 5-FU–treated mice (Figure 3A).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "retrovirally") (:form . "retrovirally") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "transduce") (:form . "transduced") (:end . 26)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 35)\n  (:start . 27) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "derivative") (:form . "derivative") (:end . 51)\n  (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 59)\n  (:start . 52) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 75)\n  (:start . 65) (:id . 52))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 80) (:start . 76)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 83) (:start . 81)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 89) (:start . 84)\n  (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "5-fu–treated") (:form . "5-FU–treated") (:end . 107)\n  (:start . 95) (:id . 57))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 112)\n  (:start . 108) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 120)\n  (:start . 114) (:id . 60))\n ((:tag . "NN") (:stem . "3a") (:form . "3A") (:end . 123) (:start . 121)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.147) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501757@unknown@formal@none@1@S@The retrovirus expressing AML1-ETO produced EGFP from an internal ribosome entry site, and the TEL-PDGFßR virus produced hCD4.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "retrovirus") (:form . "retrovirus") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 34)\n  (:start . 26) (:id . 45))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 43)\n  (:start . 35) (:id . 46))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 48) (:start . 44)\n  (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 53) (:start . 49)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 56) (:start . 54)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 65)\n  (:start . 57) (:id . 50))\n ((:tag . "NN") (:stem . "ribosome") (:form . "ribosome") (:end . 74)\n  (:start . 66) (:id . 51))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 80) (:start . 75)\n  (:id . 52))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 85) (:start . 81)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 105)\n  (:start . 95) (:id . 57))\n ((:tag . "NN") (:stem . "virus") (:form . "virus") (:end . 111)\n  (:start . 106) (:id . 58))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 120)\n  (:start . 112) (:id . 59))\n ((:tag . "NN") (:stem . "hcd4") (:form . "hCD4") (:end . 125) (:start . 121)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.148) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501758@unknown@formal@none@1@S@The percentages of doubly transduced cells (EGFP+hCD4+) were similar for AML1-ETO and various mutants thereof at 2 days after spinfection (Figure 3B).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "percentage") (:form . "percentages") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "RB") (:stem . "doubly") (:form . "doubly") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . "VBN") (:stem . "transduce") (:form . "transduced") (:end . 36)\n  (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 42) (:start . 37)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "EGFP+hCD4+") (:form . "EGFP+hCD4+") (:end . 54)\n  (:start . 44) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 93)\n  (:start . 86) (:id . 56))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 101)\n  (:start . 94) (:id . 57))\n ((:tag . "RB") (:stem . "thereof") (:form . "thereof") (:end . 109)\n  (:start . 102) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 112) (:start . 110)\n  (:id . 59))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 114) (:start . 113)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 119) (:start . 115)\n  (:id . 61))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 125)\n  (:start . 120) (:id . 62))\n ((:tag . "NN") (:stem . "spinfection") (:form . "spinfection") (:end . 137)\n  (:start . 126) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 145)\n  (:start . 139) (:id . 65))\n ((:tag . "NN") (:stem . "3b") (:form . "3B") (:end . 148) (:start . 146)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s6.149) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501759@unknown@formal@none@1@S@We transplanted lethally irradiated primary recipient animals with 106 retrovirally transduced, unsorted cells and monitored the animals for disease.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "transplant") (:form . "transplanted") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "RB") (:stem . "lethally") (:form . "lethally") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "VBN") (:stem . "irradiate") (:form . "irradiated") (:end . 35)\n  (:start . 25) (:id . 45))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 43)\n  (:start . 36) (:id . 46))\n ((:tag . "JJ") (:stem . "recipient") (:form . "recipient") (:end . 53)\n  (:start . 44) (:id . 47))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 61)\n  (:start . 54) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 49))\n ((:tag . "CD") (:stem . "106") (:form . "106") (:end . 70) (:start . 67)\n  (:id . 50))\n ((:tag . "RB") (:stem . "retrovirally") (:form . "retrovirally") (:end . 83)\n  (:start . 71) (:id . 51))\n ((:tag . "VBN") (:stem . "transduce") (:form . "transduced") (:end . 94)\n  (:start . 84) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "unsorted") (:form . "unsorted") (:end . 104)\n  (:start . 96) (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 110)\n  (:start . 105) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "monitor") (:form . "monitored") (:end . 124)\n  (:start . 115) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 136)\n  (:start . 129) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 140) (:start . 137)\n  (:id . 60))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 148)\n  (:start . 141) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.150) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501760@unknown@formal@none@1@S@The AML that develops in mice transplanted with BM cells expressing both AML1-ETO and TEL-PDGFßR is marked clinically by splenomegaly, hepatomegaly, thrombocytopenia, and anemia with an accumulation of myeloid blasts in the BM and an infiltration thereof in the spleen and liver.82@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "AML") (:form . "AML") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "develop") (:form . "develops") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 42)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 96)\n  (:start . 86) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 106)\n  (:start . 100) (:id . 58))\n ((:tag . "RB") (:stem . "clinically") (:form . "clinically") (:end . 117)\n  (:start . 107) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 120) (:start . 118)\n  (:id . 60))\n ((:tag . "NN") (:stem . "splenomegaly") (:form . "splenomegaly") (:end . 133)\n  (:start . 121) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 62))\n ((:tag . "NN") (:stem . "hepatomegaly") (:form . "hepatomegaly") (:end . 147)\n  (:start . 135) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 64))\n ((:tag . "NN") (:stem . "thrombocytopenia") (:form . "thrombocytopenia")\n  (:end . 165) (:start . 149) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 170) (:start . 167)\n  (:id . 67))\n ((:tag . "NN") (:stem . "anemia") (:form . "anemia") (:end . 177)\n  (:start . 171) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 182) (:start . 178)\n  (:id . 69))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 185) (:start . 183)\n  (:id . 70))\n ((:tag . "NN") (:stem . "accumulation") (:form . "accumulation") (:end . 198)\n  (:start . 186) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 201) (:start . 199)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "myeloid") (:form . "myeloid") (:end . 209)\n  (:start . 202) (:id . 73))\n ((:tag . "NNS") (:stem . "blast") (:form . "blasts") (:end . 216)\n  (:start . 210) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 219) (:start . 217)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 223) (:start . 220)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 226) (:start . 224)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 230) (:start . 227)\n  (:id . 78))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 233) (:start . 231)\n  (:id . 79))\n ((:tag . "NN") (:stem . "infiltration") (:form . "infiltration") (:end . 246)\n  (:start . 234) (:id . 80))\n ((:tag . "RB") (:stem . "thereof") (:form . "thereof") (:end . 254)\n  (:start . 247) (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 257) (:start . 255)\n  (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 261) (:start . 258)\n  (:id . 83))\n ((:tag . "NN") (:stem . "spleen") (:form . "spleen") (:end . 268)\n  (:start . 262) (:id . 84))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 272) (:start . 269)\n  (:id . 85))\n ((:tag . "NN") (:stem . "liver.82") (:form . "liver.82") (:end . 281)\n  (:start . 273) (:id . 86)))@@@1@45@((:identifiers (:sid . :s6.151) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501761@unknown@formal@none@1@S@TEL-PDGFßR will independently generate a chronic myeloproliferative disorder (CMPD) marked by splenomegaly, hepatomegaly, and neutrophilic leukocytosis.84@(((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n  (:end . 29) (:start . 16) (:id . 44))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 38)\n  (:start . 30) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "chronic") (:form . "chronic") (:end . 48)\n  (:start . 41) (:id . 47))\n ((:tag . "JJ") (:stem . "myeloproliferative") (:form . "myeloproliferative")\n  (:end . 67) (:start . 49) (:id . 48))\n ((:tag . "NN") (:stem . "disorder") (:form . "disorder") (:end . 76)\n  (:start . 68) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "CMPD") (:form . "CMPD") (:end . 82) (:start . 78)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 90) (:start . 84)\n  (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 93) (:start . 91)\n  (:id . 54))\n ((:tag . "NN") (:stem . "splenomegaly") (:form . "splenomegaly") (:end . 106)\n  (:start . 94) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 56))\n ((:tag . "NN") (:stem . "hepatomegaly") (:form . "hepatomegaly") (:end . 120)\n  (:start . 108) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "neutrophilic") (:form . "neutrophilic") (:end . 138)\n  (:start . 126) (:id . 60))\n ((:tag . "NN") (:stem . "leukocytosis.84") (:form . "leukocytosis.84")\n  (:end . 154) (:start . 139) (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.152) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501762@unknown@formal@none@1@S@We predicted that if mutations in AML1-ETO impaired its leukemogenic activity, the disease would more closely resemble the CMPD caused by TEL-PDGFßR alone.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "predict") (:form . "predicted") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "VBD") (:stem . "impair") (:form . "impaired") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "leukemogenic") (:form . "leukemogenic") (:end . 68)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 77)\n  (:start . 69) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 90)\n  (:start . 83) (:id . 55))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 101) (:start . 97)\n  (:id . 57))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 109)\n  (:start . 102) (:id . 58))\n ((:tag . "VB") (:stem . "resemble") (:form . "resemble") (:end . 118)\n  (:start . 110) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "CMPD") (:form . "CMPD") (:end . 127) (:start . 123)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 134)\n  (:start . 128) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 137) (:start . 135)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 148)\n  (:start . 138) (:id . 64))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 154)\n  (:start . 149) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x6.153.1) (:span 3 12)))\n (:hscopes ((:id . :x6.153.1) (:span 3 154)))\n (:identifiers (:sid . :s6.153) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501763@unknown@formal@none@1@S@Mutations that disrupt DNA or CBFß binding impair AML1-ETO's leukemogenic activity.@(((:tag . "NNS") (:stem . "mutation") (:form . "Mutations") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "disrupt") (:form . "disrupt") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "impair") (:form . "impair") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 58)\n  (:start . 50) (:id . 50))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "leukemogenic") (:form . "leukemogenic") (:end . 73)\n  (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 82)\n  (:start . 74) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.154) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501764@unknown@formal@none@1@S@(A) Schematic of transplantation scheme.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "NN") (:stem . "transplantation") (:form . "transplantation")\n  (:end . 32) (:start . 17) (:id . 47))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 40) (:start . 39)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.155) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501765@unknown@formal@none@1@S@BM mononuclear cells harvested from 5-FU–treated C57BL/6 mice were co-infected with MigR1 expressing AML1-ETO (and its mutated derivatives) and TEL-PDGFßR.@(((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "mononuclear") (:form . "mononuclear") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "harvest") (:form . "harvested") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "5-fu–treated") (:form . "5-FU–treated") (:end . 48)\n  (:start . 36) (:id . 47))\n ((:tag . "NN") (:stem . "c57bl/6") (:form . "C57BL/6") (:end . 56)\n  (:start . 49) (:id . 48))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 61) (:start . 57)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "co-infecte") (:form . "co-infected") (:end . 78)\n  (:start . 67) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 83) (:start . 79)\n  (:id . 52))\n ((:tag . "NN") (:stem . "migr1") (:form . "MigR1") (:end . 89) (:start . 84)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 100)\n  (:start . 90) (:id . 54))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 109)\n  (:start . 101) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 57))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 126)\n  (:start . 119) (:id . 59))\n ((:tag . "NNS") (:stem . "derivative") (:form . "derivatives") (:end . 138)\n  (:start . 127) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 154)\n  (:start . 144) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.156) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501766@unknown@formal@none@1@S@Internal ribosome entry site (IRES)–mediated expression of EGFP marks AML1-ETO expressing cells, while hCD4 marks TEL-PDGFßR expressing cells.@(((:tag . "JJ") (:stem . "internal") (:form . "Internal") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "ribosome") (:form . "ribosome") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "IRES)–mediated") (:form . "IRES)–mediated")\n  (:end . 44) (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 55)\n  (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 63) (:start . 59)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "mark") (:form . "marks") (:end . 69) (:start . 64)\n  (:id . 51))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 78)\n  (:start . 70) (:id . 52))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 89)\n  (:start . 79) (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 95) (:start . 90)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 55))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 102) (:start . 97)\n  (:id . 56))\n ((:tag . "NN") (:stem . "hcd4") (:form . "hCD4") (:end . 107) (:start . 103)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "mark") (:form . "marks") (:end . 113)\n  (:start . 108) (:id . 58))\n ((:tag . "NN") (:stem . "tel-pdgfßr") (:form . "TEL-PDGFßR") (:end . 124)\n  (:start . 114) (:id . 59))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 135)\n  (:start . 125) (:id . 60))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 141)\n  (:start . 136) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.157) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501767@unknown@formal@none@1@S@Retrovirally transduced cells (106) were transplanted along with 2 × 105 normal BM cells into lethally irradiated mice.@(((:tag . "RB") (:stem . "retrovirally") (:form . "Retrovirally") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "VBN") (:stem . "transduce") (:form . "transduced") (:end . 23)\n  (:start . 13) (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 29) (:start . 24)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 45))\n ((:tag . "CD") (:stem . "106") (:form . "106") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 53)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "IN") (:stem . "×") (:form . "×") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "CD") (:stem . "105") (:form . "105") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 79)\n  (:start . 73) (:id . 55))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 88) (:start . 83)\n  (:id . 57))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "RB") (:stem . "lethally") (:form . "lethally") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . "JJ") (:stem . "irradiated") (:form . "irradiated") (:end . 113)\n  (:start . 103) (:id . 60))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 118)\n  (:start . 114) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.158) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501768@unknown@formal@none@1@S@(B) FACS plots of BM cells 2 days after transduction to show that all were equivalently infected.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "FACS") (:form . "FACS") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "plot") (:form . "plots") (:end . 14) (:start . 9)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 20) (:start . 18)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 26) (:start . 21)\n  (:id . 49))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 28) (:start . 27)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 33) (:start . 29)\n  (:id . 51))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 39) (:start . 34)\n  (:id . 52))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 52)\n  (:start . 40) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n  (:id . 54))\n ((:tag . "VB") (:stem . "show") (:form . "show") (:end . 60) (:start . 56)\n  (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 65) (:start . 61)\n  (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 69) (:start . 66)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 74) (:start . 70)\n  (:id . 58))\n ((:tag . "RB") (:stem . "equivalently") (:form . "equivalently") (:end . 87)\n  (:start . 75) (:id . 59))\n ((:tag . "JJ") (:stem . "infected") (:form . "infected") (:end . 96)\n  (:start . 88) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.159) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501769@unknown@formal@none@1@S@(C) Kaplan-Meier survival curve of mice after transplantation with retroviruses expressing AML1-ETO (AE) or its mutated derivatives and TEL-PDGFßR (TP).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Kaplan-Meier") (:form . "Kaplan-Meier") (:end . 16)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "curve") (:form . "curve") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "transplantation") (:form . "transplantation")\n  (:end . 61) (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "retrovirus") (:form . "retroviruses") (:end . 79)\n  (:start . 67) (:id . 53))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 90)\n  (:start . 80) (:id . 54))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 99)\n  (:start . 91) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "AE") (:form . "AE") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 111) (:start . 108)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 119)\n  (:start . 112) (:id . 61))\n ((:tag . "NNS") (:stem . "derivative") (:form . "derivatives") (:end . 131)\n  (:start . 120) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 146)\n  (:start . 136) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "TP") (:form . "TP") (:end . 150) (:start . 148)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s6.160) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501770@unknown@formal@none@1@S@The study end point was 63 days.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 32) (:start . 31)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.161) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501771@unknown@formal@none@1@S@The number of mice in each group is indicated.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 45)\n  (:start . 36) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.162) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501772@unknown@formal@none@1@S@(D) Spleen weights of mice upon sacrifice.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Spleen") (:form . "Spleen") (:end . 10)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "weight") (:form . "weights") (:end . 18)\n  (:start . 11) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 26) (:start . 22)\n  (:id . 48))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 31) (:start . 27)\n  (:id . 49))\n ((:tag . "NN") (:stem . "sacrifice") (:form . "sacrifice") (:end . 41)\n  (:start . 32) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.163) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501773@unknown@formal@none@1@S@Significant differences from AML1-ETO plus TEL-PDGFßR recipients (#) are indicated with * (Dunnett test and ANOVA).@(((:tag . "JJ") (:stem . "significant") (:form . "Significant") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 23)\n  (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 37)\n  (:start . 29) (:id . 45))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 42) (:start . 38)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 53)\n  (:start . 43) (:id . 47))\n ((:tag . "NNS") (:stem . "recipient") (:form . "recipients") (:end . 64)\n  (:start . 54) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 49))\n ((:tag . "#") (:stem . "#") (:form . "#") (:end . 67) (:start . 66)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 87) (:start . 83)\n  (:id . 54))\n ((:tag . "SYM") (:stem . "*") (:form . "*") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Dunnett") (:form . "Dunnett") (:end . 98)\n  (:start . 91) (:id . 57))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 103) (:start . 99)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "ANOVA") (:form . "ANOVA") (:end . 113)\n  (:start . 108) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.164) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501774@unknown@formal@none@1@S@(E) Representative plots of BM cells in transplant recipients upon sacrifice demonstrating the presence of EGFP+ and hCD4+ cells.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "representative") (:form . "Representative")\n  (:end . 18) (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "plot") (:form . "plots") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "bm") (:form . "BM") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 36) (:start . 31)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "transplant") (:form . "transplant") (:end . 50)\n  (:start . 40) (:id . 51))\n ((:tag . "NNS") (:stem . "recipient") (:form . "recipients") (:end . 61)\n  (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sacrifice") (:form . "sacrifice") (:end . 76)\n  (:start . 67) (:id . 54))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating") (:end . 90)\n  (:start . 77) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 103)\n  (:start . 95) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "egfp+") (:form . "EGFP+") (:end . 112)\n  (:start . 107) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "hcd4+") (:form . "hCD4+") (:end . 122)\n  (:start . 117) (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 128)\n  (:start . 123) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.165) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501775@unknown@formal@none@1@S@The relatively high EGFP fluorescence in the AML1-ETO (Y113A/T161A) plus TEL-PDGFßR BM cells was observed in 19 of 24 mice.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 37)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 53)\n  (:start . 45) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 66)\n  (:start . 55) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 83)\n  (:start . 73) (:id . 54))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 92) (:start . 87)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 96) (:start . 93)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 105)\n  (:start . 97) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 117) (:start . 115)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 122)\n  (:start . 118) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.166) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501776@unknown@formal@none@1@S@(F) Average percentage of EGFP- hCD4+ and EGFP+ hCD4+ BM cells in transplant recipients upon sacrifice.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 22)\n  (:start . 12) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "EGFP-") (:form . "EGFP-") (:end . 31) (:start . 26)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "hCD4+") (:form . "hCD4+") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "egfp+") (:form . "EGFP+") (:end . 47) (:start . 42)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "hcd4+") (:form . "hCD4+") (:end . 53) (:start . 48)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 62) (:start . 57)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "transplant") (:form . "transplant") (:end . 76)\n  (:start . 66) (:id . 56))\n ((:tag . "NNS") (:stem . "recipient") (:form . "recipients") (:end . 87)\n  (:start . 77) (:id . 57))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . "NN") (:stem . "sacrifice") (:form . "sacrifice") (:end . 102)\n  (:start . 93) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.167) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501777@unknown@formal@none@1@S@Error bars indicate 95% confidence intervals.@(((:tag . "NN") (:stem . "error") (:form . "Error") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "CD") (:stem . "95") (:form . "95") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 34)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.168) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501778@unknown@formal@none@1@S@Differences relative to AML1-ETO plus TEL-PDGFßR (#) for each group were determined using Dunnett test and ANOVA.@(((:tag . "NNS") (:stem . "difference") (:form . "Differences") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 48)\n  (:start . 38) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 48))\n ((:tag . "#") (:stem . "#") (:form . "#") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 83)\n  (:start . 73) (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 89) (:start . 84)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Dunnett") (:form . "Dunnett") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 102) (:start . 98)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "ANOVA") (:form . "ANOVA") (:end . 112)\n  (:start . 107) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.169) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501779@unknown@formal@none@1@S@(G) Cytospin preparations of BM cells from an AML1-ETO plus TEL-PDGFßR leukemic mouse purified based on hCD4 and EGFP expression.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Cytospin") (:form . "Cytospin") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "preparation") (:form . "preparations") (:end . 25)\n  (:start . 13) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "bm") (:form . "BM") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 45) (:start . 43)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 54)\n  (:start . 46) (:id . 52))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 59) (:start . 55)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 70)\n  (:start . 60) (:id . 54))\n ((:tag . "JJ") (:stem . "leukemic") (:form . "leukemic") (:end . 79)\n  (:start . 71) (:id . 55))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 94)\n  (:start . 86) (:id . 57))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 100) (:start . 95)\n  (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "hcd4") (:form . "hCD4") (:end . 108) (:start . 104)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 117) (:start . 113)\n  (:id . 62))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 128)\n  (:start . 118) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s6.170) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501780@unknown@formal@none@1@S@Mice transplanted with BM cells expressing both AML1-ETO and TEL-PDGFßR developed a completely penetrant lethal leukemia, as reported previously,82 and succumbed to their disease within 4 weeks (Figure 3C).@(((:tag . "NNS") (:stem . "mouse") (:form . "Mice") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 17)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 42)\n  (:start . 32) (:id . 47))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 56)\n  (:start . 48) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "VBD") (:stem . "develop") (:form . "developed") (:end . 81)\n  (:start . 72) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 83) (:start . 82)\n  (:id . 53))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 94)\n  (:start . 84) (:id . 54))\n ((:tag . "JJ") (:stem . "penetrant") (:form . "penetrant") (:end . 104)\n  (:start . 95) (:id . 55))\n ((:tag . "JJ") (:stem . "lethal") (:form . "lethal") (:end . 111)\n  (:start . 105) (:id . 56))\n ((:tag . "NN") (:stem . "leukemia") (:form . "leukemia") (:end . 120)\n  (:start . 112) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 124) (:start . 122)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 133)\n  (:start . 125) (:id . 60))\n ((:tag . "CD") (:stem . "previously,82") (:form . "previously,82")\n  (:end . 147) (:start . 134) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 151) (:start . 148)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "succumb") (:form . "succumbed") (:end . 161)\n  (:start . 152) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 164) (:start . 162)\n  (:id . 64))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 170)\n  (:start . 165) (:id . 65))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 178)\n  (:start . 171) (:id . 66))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 185)\n  (:start . 179) (:id . 67))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 187) (:start . 186)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "week") (:form . "weeks") (:end . 193)\n  (:start . 188) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 195) (:start . 194)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 201)\n  (:start . 195) (:id . 71))\n ((:tag . "NN") (:stem . "3c") (:form . "3C") (:end . 204) (:start . 202)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 205) (:start . 204)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.171) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501781@unknown@formal@none@1@S@In contrast, most control mice transplanted with cells expressing AML1-ETO alone (8/8), or TEL-PDGFßR alone (7/8) survived for 63 days, at which point they were killed for analysis.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 43)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 65)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 74)\n  (:start . 66) (:id . 52))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 80) (:start . 75)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 54))\n ((:tag . "CD") (:stem . "8/8") (:form . "8/8") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 101)\n  (:start . 91) (:id . 59))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 107)\n  (:start . 102) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . "CD") (:stem . "7/8") (:form . "7/8") (:end . 112) (:start . 109)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "survive") (:form . "survived") (:end . 122)\n  (:start . 114) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 126) (:start . 123)\n  (:id . 65))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 129) (:start . 127)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 134) (:start . 130)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 68))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 138) (:start . 136)\n  (:id . 69))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 144)\n  (:start . 139) (:id . 70))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 150)\n  (:start . 145) (:id . 71))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 155) (:start . 151)\n  (:id . 72))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 160) (:start . 156)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "kill") (:form . "killed") (:end . 167)\n  (:start . 161) (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 171) (:start . 168)\n  (:id . 75))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 180)\n  (:start . 172) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s6.172) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501782@unknown@formal@none@1@S@Diseased AML1-ETO plus TEL-PDGFßR transplanted mice presented with anemia, splenomegaly, and pale livers (not shown).@(((:tag . "VBN") (:stem . "disease") (:form . "Diseased") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 33)\n  (:start . 23) (:id . 45))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 46)\n  (:start . 34) (:id . 46))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 51) (:start . 47)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "present") (:form . "presented") (:end . 61)\n  (:start . 52) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 49))\n ((:tag . "NN") (:stem . "anemia") (:form . "anemia") (:end . 73)\n  (:start . 67) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 51))\n ((:tag . "NN") (:stem . "splenomegaly") (:form . "splenomegaly") (:end . 87)\n  (:start . 75) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "pale") (:form . "pale") (:end . 97) (:start . 93)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "liver") (:form . "livers") (:end . 104)\n  (:start . 98) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 109) (:start . 106)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 115)\n  (:start . 110) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.173) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501783@unknown@formal@none@1@S@Their BM contained blast cells characterized by a high nucleocytoplasmic ratio, heterochromatic nuclei, occasional cytoplasmic vacuoles, irregular nuclear contours, and prominent nucleoli (not shown).@(((:tag . "PRP$") (:stem . "their") (:form . "Their") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bm") (:form . "BM") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "blast") (:form . "blast") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n  (:end . 44) (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "nucleocytoplasmic") (:form . "nucleocytoplasmic")\n  (:end . 72) (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 78) (:start . 73)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "heterochromatic") (:form . "heterochromatic")\n  (:end . 95) (:start . 80) (:id . 54))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 102)\n  (:start . 96) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "occasional") (:form . "occasional") (:end . 114)\n  (:start . 104) (:id . 57))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 126)\n  (:start . 115) (:id . 58))\n ((:tag . "NNS") (:stem . "vacuole") (:form . "vacuoles") (:end . 135)\n  (:start . 127) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "irregular") (:form . "irregular") (:end . 146)\n  (:start . 137) (:id . 61))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 154)\n  (:start . 147) (:id . 62))\n ((:tag . "NNS") (:stem . "contour") (:form . "contours") (:end . 163)\n  (:start . 155) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "prominent") (:form . "prominent") (:end . 178)\n  (:start . 169) (:id . 66))\n ((:tag . "NNS") (:stem . "nucleolus") (:form . "nucleoli") (:end . 187)\n  (:start . 179) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n  (:id . 68))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 192) (:start . 189)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 198)\n  (:start . 193) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s6.174) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501784@unknown@formal@none@1@S@Blast cells were also present in peripheral blood (not shown).@(((:tag . "NN") (:stem . "blast") (:form . "Blast") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "peripheral") (:form . "peripheral") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "blood") (:form . "blood") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s6.175) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501785@unknown@formal@none@1@S@However the BM contained many more differentiated myeloid cells such as neutrophils with ring-shaped nuclei (characteristic of CMPD), presumably arising from the large population of EGFP-hCD4+ cells expressing TEL-PDGFßR alone (Figure 3E,F).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "differentiate") (:form . "differentiated")\n  (:end . 49) (:start . 35) (:id . 48))\n ((:tag . "JJ") (:stem . "myeloid") (:form . "myeloid") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 63) (:start . 58)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "neutrophil") (:form . "neutrophils") (:end . 83)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 88) (:start . 84)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "ring-shaped") (:form . "ring-shaped") (:end . 100)\n  (:start . 89) (:id . 55))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 107)\n  (:start . 101) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 123) (:start . 109) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "CMPD") (:form . "CMPD") (:end . 131) (:start . 127)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 62))\n ((:tag . "RB") (:stem . "presumably") (:form . "presumably") (:end . 144)\n  (:start . 134) (:id . 63))\n ((:tag . "VBG") (:stem . "arise") (:form . "arising") (:end . 152)\n  (:start . 145) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 157) (:start . 153)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 167)\n  (:start . 162) (:id . 67))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 178)\n  (:start . 168) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 181) (:start . 179)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "egfp-hcd4+") (:form . "EGFP-hCD4+") (:end . 192)\n  (:start . 182) (:id . 70))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 198)\n  (:start . 193) (:id . 71))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 209)\n  (:start . 199) (:id . 72))\n ((:tag . "NN") (:stem . "tel-pdgfßr") (:form . "TEL-PDGFßR") (:end . 220)\n  (:start . 210) (:id . 73))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 226)\n  (:start . 221) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 228) (:start . 227)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 234)\n  (:start . 228) (:id . 76))\n ((:tag . "CD") (:stem . "3E,F") (:form . "3E,F") (:end . 239) (:start . 235)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 240) (:start . 239)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 241) (:start . 240)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x6.176.1) (:span 134 144)))\n (:hscopes ((:id . :x6.176.1) (:span 134 226)))\n (:identifiers (:sid . :s6.176) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501786@unknown@formal@none@1@S@As a result of the mixed diseases in these mice, BM differentials and histology were not useful diagnostic aids.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mixed") (:form . "mixed") (:end . 24) (:start . 19)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 33)\n  (:start . 25) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 42) (:start . 37)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 51) (:start . 49)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "differential") (:form . "differentials")\n  (:end . 65) (:start . 52) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "NN") (:stem . "histology") (:form . "histology") (:end . 79)\n  (:start . 70) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 88) (:start . 85)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 95)\n  (:start . 89) (:id . 59))\n ((:tag . "JJ") (:stem . "diagnostic") (:form . "diagnostic") (:end . 106)\n  (:start . 96) (:id . 60))\n ((:tag . "NNS") (:stem . "aid") (:form . "aids") (:end . 111) (:start . 107)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.177) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501787@unknown@formal@none@1@S@We therefore isolated EGFP-hCD4+ and EGFP+hCD4+ cells from the BM of leukemic AML1-ETO plus TEL-PDGFßR mice and analyzed their morphology.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "isolate") (:form . "isolated") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "JJ") (:stem . "egfp-hcd4+") (:form . "EGFP-hCD4+") (:end . 32)\n  (:start . 22) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "egfp+hcd4+") (:form . "EGFP+hCD4+") (:end . 47)\n  (:start . 37) (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 53) (:start . 48)\n  (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 58) (:start . 54)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "bm") (:form . "BM") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "leukemic") (:form . "leukemic") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 86)\n  (:start . 78) (:id . 54))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 91) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "tel-pdgfßr") (:form . "TEL-PDGFßR") (:end . 102)\n  (:start . 92) (:id . 56))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 107)\n  (:start . 103) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 120)\n  (:start . 112) (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 126)\n  (:start . 121) (:id . 60))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 137)\n  (:start . 127) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.178) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501788@unknown@formal@none@1@S@The EGFP+hCD4+ population (expressing AML1-ETO plus TEL-PDGFßR) contained a markedly greater percentage of blast cells, consistent with AML, in comparison to the EGFP-hCD4+ population (Figure 3G).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "egfp+hcd4+") (:form . "EGFP+hCD4+") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 46)\n  (:start . 38) (:id . 47))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 62)\n  (:start . 52) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 73)\n  (:start . 64) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . "RB") (:stem . "markedly") (:form . "markedly") (:end . 84)\n  (:start . 76) (:id . 53))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 92)\n  (:start . 85) (:id . 54))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 103)\n  (:start . 93) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 56))\n ((:tag . "NN") (:stem . "blast") (:form . "blast") (:end . 112)\n  (:start . 107) (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 118)\n  (:start . 113) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 130)\n  (:start . 120) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 135) (:start . 131)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "AML") (:form . "AML") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 143) (:start . 141)\n  (:id . 64))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 154)\n  (:start . 144) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 157) (:start . 155)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "egfp-hcd4+") (:form . "EGFP-hCD4+") (:end . 172)\n  (:start . 162) (:id . 68))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 183)\n  (:start . 173) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 191)\n  (:start . 185) (:id . 71))\n ((:tag . "NN") (:stem . "3g") (:form . "3G") (:end . 194) (:start . 192)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.179) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501789@unknown@formal@none@1@S@We were able to transplant AML1-ETO plus TEL-PDGFßR expressing cells into secondary recipients and reconstitute the disease, but only using large numbers (> 2 × 106) of freshly isolated splenocytes, and not with frozen cells (not shown), indicating that the percentage of leukemia initiating cells was low.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "transplant") (:form . "transplant") (:end . 26)\n  (:start . 16) (:id . 46))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . "plus") (:form . 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5501790@unknown@formal@none@1@S@Most mice transplanted with BM expressing TEL-PDGFßR plus either the non-DNA binding or non-CBFß binding AML1-ETO mutants (R174Q and Y113A/T161A, respectively) survived until the study end point of 63 days (Figure 3C).@(((:tag . "JJS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 22)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "tel-pdgfßr") (:form . "TEL-PDGFßR") (:end . 52)\n  (:start . 42) (:id . 48))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 64)\n  (:start . 58) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "non-dna") (:form . "non-DNA") (:end . 76)\n  (:start . 69) (:id . 52))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 84)\n  (:start . 77) (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 87) (:start . 85)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "non-cbfß") (:form . "non-CBFß") (:end . 96)\n  (:start . 88) (:id . 55))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 104)\n  (:start . 97) (:id . 56))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 113)\n  (:start . 105) (:id . 57))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 121)\n  (:start . 114) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 128)\n  (:start . 123) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 144)\n  (:start . 133) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 63))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 158)\n  (:start . 146) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "survive") (:form . "survived") (:end . 168)\n  (:start . 160) (:id . 66))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 174)\n  (:start . 169) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 68))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 184)\n  (:start . 179) (:id . 69))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 188) (:start . 185)\n  (:id . 70))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 194)\n  (:start . 189) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 197) (:start . 195)\n  (:id . 72))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 200) (:start . 198)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 205) (:start . 201)\n  (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 207) (:start . 206)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 213)\n  (:start . 207) (:id . 76))\n ((:tag . "NN") (:stem . "3c") (:form . "3C") (:end . 216) (:start . 214)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 217) (:start . 216)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.181) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501791@unknown@formal@none@1@S@The majority of these mice had evidence of disease as manifested by enlarged spleens [15/22 for AML1-ETO (R174Q) and 22/24 for AML1-ETO (Y113A/T161A)].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 50)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "manifest") (:form . "manifested") (:end . 64)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "enlarged") (:form . "enlarged") (:end . 76)\n  (:start . 68) (:id . 54))\n ((:tag . "NNS") (:stem . "spleen") (:form . "spleens") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 86) (:start . 85)\n  (:id . 56))\n ((:tag . "CD") (:stem . "15/22") (:form . "15/22") (:end . 91) (:start . 86)\n  (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 104)\n  (:start . 96) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 111)\n  (:start . 106) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 63))\n ((:tag . "CD") (:stem . "22/24") (:form . "22/24") (:end . 122)\n  (:start . 117) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 126) (:start . 123)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 135)\n  (:start . 127) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 148)\n  (:start . 137) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 150) (:start . 149)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s6.182) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501792@unknown@formal@none@1@S@Their average spleen sizes were similar to those of mice transplanted with BM expressing AML1-ETO plus TEL-PDGFßR or TEL-PDGFßR alone, and were significantly greater than those of mice transplanted with BM expressing AML1-ETO alone (Figure 3D), indicating that TEL-PDGFßR contributed significantly to the splenomegaly.@(((:tag . "PRP$") (:stem . "their") (:form . "Their") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "spleen") (:form . "spleen") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "size") (:form . "sizes") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . 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5501793@unknown@formal@none@1@S@A minority of the mice were anemic as evidenced by pale livers [2/22 for AML1-ETO (R174Q) and 6/24 for AML1-ETO (Y113A/T161A)], whereas anemia was more prevalent in the AML1-ETO plus TEL-PDGFßR mice (16/22).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "minority") (:form . "minority") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "anemic") (:form . "anemic") (:end . 34)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "evidence") (:form . "evidenced") (:end . 47)\n  (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "pale") (:form . "pale") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "liver") (:form . "livers") (:end . 62)\n  (:start . 56) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . "CD") (:stem . "2/22") (:form . "2/22") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 81)\n  (:start . 73) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 88) (:start . 83)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 61))\n ((:tag . "CD") (:stem . "6/24") (:form . "6/24") (:end . 98) (:start . 94)\n  (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 102) (:start . 99)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 111)\n  (:start . 103) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 124)\n  (:start . 113) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 126) (:start . 125)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 69))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 135)\n  (:start . 128) (:id . 70))\n ((:tag . "NN") (:stem . "anemia") (:form . "anemia") (:end . 142)\n  (:start . 136) (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 146) (:start . 143)\n  (:id . 72))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 151) (:start . 147)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "prevalent") (:form . "prevalent") (:end . 161)\n  (:start . 152) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 164) (:start . 162)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 177)\n  (:start . 169) (:id . 77))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 182) (:start . 178)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 193)\n  (:start . 183) (:id . 79))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 198)\n  (:start . 194) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 200) (:start . 199)\n  (:id . 81))\n ((:tag . "CD") (:stem . "16/22") (:form . "16/22") (:end . 205)\n  (:start . 200) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s6.184) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501794@unknown@formal@none@1@S@The BM of all groups contained EGFP-hCD4+ and EGFP+hCD4+ cells, but relatively few cells expressing EGFP (AML1-ETO) alone, suggesting a competitive advantage for cells that expressed TEL-PDGFßR (Figure 3E).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bm") (:form . "BM") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 20)\n  (:start . 14) (:id . 46))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 30)\n  (:start . 21) (:id . 47))\n ((:tag . "JJ") (:stem . "egfp-hcd4+") (:form . "EGFP-hCD4+") (:end . 41)\n  (:start . 31) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "egfp+hcd4+") (:form . "EGFP+hCD4+") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 62) (:start . 57)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 78)\n  (:start . 68) (:id . 54))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 88) (:start . 83)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 99)\n  (:start . 89) (:id . 57))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 104) (:start . 100)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 114)\n  (:start . 106) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 121)\n  (:start . 116) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 133)\n  (:start . 123) (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 135) (:start . 134)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "competitive") (:form . "competitive") (:end . 147)\n  (:start . 136) (:id . 66))\n ((:tag . "NN") (:stem . "advantage") (:form . "advantage") (:end . 157)\n  (:start . 148) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 161) (:start . 158)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 167)\n  (:start . 162) (:id . 69))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 172) (:start . 168)\n  (:id . 70))\n ((:tag . "VBD") (:stem . "express") (:form . "expressed") (:end . 182)\n  (:start . 173) (:id . 71))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 193)\n  (:start . 183) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 195) (:start . 194)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 201)\n  (:start . 195) (:id . 74))\n ((:tag . "NN") (:stem . "3e") (:form . "3E") (:end . 204) (:start . 202)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 205) (:start . 204)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x6.185.1) (:span 123 133)))\n (:hscopes ((:id . :x6.185.1) (:span 123 193)))\n (:identifiers (:sid . :s6.185) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501795@unknown@formal@none@1@S@Interestingly, most mice (19/24) transplanted with cells expressing the AML1-ETO (Y113A/T161A) mutant contained an EGFPhihCD4+ BM population, presumably resulting from a selection for cells expressing high AML1-ETO (Y113A/T161A) levels (Figure 3E).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "CD") (:stem . "19/24") (:form . "19/24") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 45)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 80)\n  (:start . 72) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 93)\n  (:start . 82) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 101)\n  (:start . 95) (:id . 58))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 111)\n  (:start . 102) (:id . 59))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "egfphihcd4+") (:form . "EGFPhihCD4+") (:end . 126)\n  (:start . 115) (:id . 61))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 129) (:start . 127)\n  (:id . 62))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 140)\n  (:start . 130) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 64))\n ((:tag . "RB") (:stem . "presumably") (:form . "presumably") (:end . 152)\n  (:start . 142) (:id . 65))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 162)\n  (:start . 153) (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 167) (:start . 163)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 169) (:start . 168)\n  (:id . 68))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 179)\n  (:start . 170) (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 183) (:start . 180)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 189)\n  (:start . 184) (:id . 71))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 200)\n  (:start . 190) (:id . 72))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 205) (:start . 201)\n  (:id . 73))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 214)\n  (:start . 206) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 216) (:start . 215)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 227)\n  (:start . 216) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 228) (:start . 227)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 235)\n  (:start . 229) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 237) (:start . 236)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 243)\n  (:start . 237) (:id . 80))\n ((:tag . "NN") (:stem . "3e") (:form . "3E") (:end . 246) (:start . 244)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 247) (:start . 246)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 248) (:start . 247)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x6.186.1) (:span 142 152)))\n (:hscopes ((:id . :x6.186.1) (:span 142 235)))\n (:identifiers (:sid . :s6.186) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501796@unknown@formal@none@1@S@We speculate that the Y113A/T161A mutant has residual activity and that more highly expressing cells partially overcome the effects of the mutations and thus are positively selected.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "speculate") (:form . "speculate") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 33)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "residual") (:form . "residual") (:end . 53)\n  (:start . 45) (:id . 49))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 83)\n  (:start . 77) (:id . 54))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 94)\n  (:start . 84) (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 100) (:start . 95)\n  (:id . 56))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 110)\n  (:start . 101) (:id . 57))\n ((:tag . "VBP") (:stem . "overcome") (:form . "overcome") (:end . 119)\n  (:start . 111) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 131)\n  (:start . 124) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 148)\n  (:start . 139) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 64))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 157) (:start . 153)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 161) (:start . 158)\n  (:id . 66))\n ((:tag . "RB") (:stem . "positively") (:form . "positively") (:end . 172)\n  (:start . 162) (:id . 67))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 181)\n  (:start . 173) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x6.187.1) (:span 3 12)))\n (:hscopes ((:id . :x6.187.1) (:span 3 181)))\n (:identifiers (:sid . :s6.187) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501797@unknown@formal@none@1@S@Despite having more EGFP+hCD4+ cells and higher AML1-ETO levels, the AML1-ETO (Y113A/T161A) plus TEL-PDGFßR group survived longer than the AML1-ETO plus TEL-PDGFßR group, thus AML1-ETO deficient for CBFß binding has greatly attenuated activity.@(((:tag . "IN") (:stem . "despite") (:form . "Despite") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBG") (:stem . "have") (:form . "having") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "egfp+hcd4+") (:form . "EGFP+hCD4+") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 36) (:start . 31)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 47) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 56)\n  (:start . 48) (:id . 49))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 63)\n  (:start . 57) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 90)\n  (:start . 79) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 56))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 107)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 113)\n  (:start . 108) (:id . 59))\n ((:tag . "VBD") (:stem . "survive") (:form . "survived") (:end . 122)\n  (:start . 114) (:id . 60))\n ((:tag . "RBR") (:stem . "longer") (:form . "longer") (:end . 129)\n  (:start . 123) (:id . 61))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 134) (:start . 130)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 147)\n  (:start . 139) (:id . 64))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 152) (:start . 148)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 163)\n  (:start . 153) (:id . 66))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 169)\n  (:start . 164) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 170) (:start . 169)\n  (:id . 68))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 175) (:start . 171)\n  (:id . 69))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 184)\n  (:start . 176) (:id . 70))\n ((:tag . "JJ") (:stem . "deficient") (:form . "deficient") (:end . 194)\n  (:start . 185) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 198) (:start . 195)\n  (:id . 72))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 203) (:start . 199)\n  (:id . 73))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 211)\n  (:start . 204) (:id . 74))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 215) (:start . 212)\n  (:id . 75))\n ((:tag . "RB") (:stem . "greatly") (:form . "greatly") (:end . 223)\n  (:start . 216) (:id . 76))\n ((:tag . "VBN") (:stem . "attenuate") (:form . "attenuated") (:end . 234)\n  (:start . 224) (:id . 77))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 243)\n  (:start . 235) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s6.188) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501798@unknown@formal@none@1@S@We were unable to detect AML1-ETO protein in spleen samples from any of the transplanted mice using antibodies that recognize either ETO or the Runt domain from Runx1, although we could detect the protein in Kasumi-1 cells which contain the t(8;21), and actin was clearly visible in all of the samples (not shown).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "unable") (:form . "unable") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . 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5501799@unknown@formal@none@1@S@We suspect our inability to detect AML1-ETO was due to the relatively low percentage of AML1-ETO expressing spleen cells (Figure 3F).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "suspect") (:form . "suspect") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "inability") (:form . "inability") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 84)\n  (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 96)\n  (:start . 88) (:id . 57))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 107)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "spleen") (:form . "spleen") (:end . 114)\n  (:start . 108) (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 120)\n  (:start . 115) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 128)\n  (:start . 122) (:id . 62))\n ((:tag . "NN") (:stem . "3f") (:form . "3F") (:end . 131) (:start . 129)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x6.190.1) (:span 3 10)))\n (:hscopes ((:id . :x6.190.1) (:span 3 120)))\n (:identifiers (:sid . :s6.190) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501800@unknown@formal@none@1@S@EGFP+hCD4+ BM cells (expressing AML1-ETO plus TEL-PDGFßR) from the AML1-ETO plus TEL-PDGFßR recipients contained significantly higher percentages of c-kit+ Sca-1+ cells than those expressing either of the mutated AML1-ETO proteins or TEL-PDGFßR alone (Figure 4A,B).@(((:tag . "JJ") (:stem . "egfp+hcd4+") (:form . "EGFP+hCD4+") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 75)\n  (:start . 67) (:id . 53))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 91)\n  (:start . 81) (:id . 55))\n ((:tag . "NNS") (:stem . "recipient") (:form . "recipients") (:end . 102)\n  (:start . 92) (:id . 56))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 112)\n  (:start . 103) (:id . 57))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 126) (:start . 113) (:id . 58))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 133)\n  (:start . 127) (:id . 59))\n ((:tag . "NNS") (:stem . "percentage") (:form . "percentages") (:end . 145)\n  (:start . 134) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "c-kit+") (:form . "c-kit+") (:end . 155)\n  (:start . 149) (:id . 62))\n ((:tag . "JJ") (:stem . "sca-1+") (:form . "Sca-1+") (:end . 162)\n  (:start . 156) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 168)\n  (:start . 163) (:id . 64))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 173) (:start . 169)\n  (:id . 65))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 179)\n  (:start . 174) (:id . 66))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 190)\n  (:start . 180) (:id . 67))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 197)\n  (:start . 191) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 200) (:start . 198)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 204) (:start . 201)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 212)\n  (:start . 205) (:id . 71))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 221)\n  (:start . 213) (:id . 72))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 230)\n  (:start . 222) (:id . 73))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 233) (:start . 231)\n  (:id . 74))\n ((:tag . "NN") (:stem . "tel-pdgfßr") (:form . "TEL-PDGFßR") (:end . 244)\n  (:start . 234) (:id . 75))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 250)\n  (:start . 245) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 252) (:start . 251)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 258)\n  (:start . 252) (:id . 78))\n ((:tag . "CD") (:stem . "4A,B") (:form . "4A,B") (:end . 263) (:start . 259)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 264) (:start . 263)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s6.191) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501801@unknown@formal@none@1@S@The percentage of Gr1+Mac1+ cells in the EGFP+hCD4+ BM population was correspondingly lower in the AML1-ETO plus TEL-PDGFßR group than in any other, reflective of impaired granulocyte differentiation (Figure 4A,C).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "gr1+mac1+") (:form . "Gr1+Mac1+") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "egfp+hcd4+") (:form . "EGFP+hCD4+") (:end . 51)\n  (:start . 41) (:id . 49))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 65)\n  (:start . 55) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "RB") (:stem . "correspondingly") (:form . "correspondingly")\n  (:end . 85) (:start . 70) (:id . 53))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 91) (:start . 86)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 107)\n  (:start . 99) (:id . 57))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 112) (:start . 108)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 123)\n  (:start . 113) (:id . 59))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 129)\n  (:start . 124) (:id . 60))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 134) (:start . 130)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 137) (:start . 135)\n  (:id . 62))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 141) (:start . 138)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 147)\n  (:start . 142) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "reflective") (:form . "reflective") (:end . 159)\n  (:start . 149) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 162) (:start . 160)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "impaired") (:form . "impaired") (:end . 171)\n  (:start . 163) (:id . 68))\n ((:tag . "NN") (:stem . "granulocyte") (:form . "granulocyte") (:end . 183)\n  (:start . 172) (:id . 69))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 199) (:start . 184) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 201) (:start . 200)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 207)\n  (:start . 201) (:id . 72))\n ((:tag . "CD") (:stem . "4A,C") (:form . "4A,C") (:end . 212) (:start . 208)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s6.192) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501802@unknown@formal@none@1@S@Interestingly, the FACS profiles of EGFP+hCD4+ BM cells from the AML1-ETO (Y113A/T161A) plus TEL-PDGFßR group were not identical to those of the AML1-ETO (R174Q) plus TEL-PDGFßR group and appeared to be intermediate between CMPD and AML.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "FACS") (:form . "FACS") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "egfp+hcd4+") (:form . "EGFP+hCD4+") (:end . 46)\n  (:start . 36) (:id . 48))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 73)\n  (:start . 65) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 86)\n  (:start . 75) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 92) (:start . 88)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 103)\n  (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 109)\n  (:start . 104) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 114) (:start . 110)\n  (:id . 60))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 118) (:start . 115)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 128)\n  (:start . 119) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 131) (:start . 129)\n  (:id . 63))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 137)\n  (:start . 132) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 153)\n  (:start . 145) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 160)\n  (:start . 155) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n  (:id . 70))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 166) (:start . 162)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 177)\n  (:start . 167) (:id . 72))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 183)\n  (:start . 178) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 187) (:start . 184)\n  (:id . 74))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 196)\n  (:start . 188) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 199) (:start . 197)\n  (:id . 76))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 202) (:start . 200)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 215)\n  (:start . 203) (:id . 78))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 223)\n  (:start . 216) (:id . 79))\n ((:tag . "NNP") (:stem . "CMPD") (:form . "CMPD") (:end . 228) (:start . 224)\n  (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 232) (:start . 229)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "AML") (:form . "AML") (:end . 236) (:start . 233)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 237) (:start . 236)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x6.193.1) (:span 188 196)))\n (:hscopes ((:id . :x6.193.1) (:span 188 236)))\n (:identifiers (:sid . :s6.193) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501803@unknown@formal@none@1@S@For instance, there were fewer Gr1hiMac1hi cells in the AML1-ETO (Y113A/T161A) plus TEL-PDGFßR group, suggesting that granulocyte differentiation was somewhat more impaired (Figure 4A).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Gr1hiMac1hi") (:form . "Gr1hiMac1hi") (:end . 42)\n  (:start . 31) (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 48) (:start . 43)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 77)\n  (:start . 66) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 94)\n  (:start . 84) (:id . 57))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 100) (:start . 95)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 112)\n  (:start . 102) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 117) (:start . 113)\n  (:id . 61))\n ((:tag . "NN") (:stem . "granulocyte") (:form . "granulocyte") (:end . 129)\n  (:start . 118) (:id . 62))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 145) (:start . 130) (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 149) (:start . 146)\n  (:id . 64))\n ((:tag . "RB") (:stem . "somewhat") (:form . "somewhat") (:end . 158)\n  (:start . 150) (:id . 65))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 163) (:start . 159)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "impaired") (:form . "impaired") (:end . 172)\n  (:start . 164) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 180)\n  (:start . 174) (:id . 69))\n ((:tag . "NN") (:stem . "4a") (:form . "4A") (:end . 183) (:start . 181)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x6.194.1) (:span 102 112)))\n (:hscopes ((:id . :x6.194.1) (:span 102 172)))\n (:identifiers (:sid . :s6.194) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501804@unknown@formal@none@1@S@Flow cytometric analysis of BM from primary transplant recipients.@(((:tag . "NNP") (:stem . "Flow") (:form . "Flow") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "cytometric") (:form . "cytometric") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "transplant") (:form . "transplant") (:end . 54)\n  (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "recipient") (:form . "recipients") (:end . 65)\n  (:start . 55) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.195) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501805@unknown@formal@none@1@S@(A) Whole BM of diseased mice was gated based on forward and side scatter characteristics and subsequently analyzed for expression of hCD4 (TEL-PDGFßR) and EGFP (AML1-ETO).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "whole") (:form . "Whole") (:end . 9) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "bm") (:form . "BM") (:end . 12) (:start . 10)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "diseased") (:form . "diseased") (:end . 24)\n  (:start . 16) (:id . 48))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 29) (:start . 25)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 33) (:start . 30)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "gate") (:form . "gated") (:end . 39) (:start . 34)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 45) (:start . 40)\n  (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 48) (:start . 46)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "forward") (:form . "forward") (:end . 56)\n  (:start . 49) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 55))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 65) (:start . 61)\n  (:id . 56))\n ((:tag . "NN") (:stem . "scatter") (:form . "scatter") (:end . 73)\n  (:start . 66) (:id . 57))\n ((:tag . "NNS") (:stem . "characteristic") (:form . "characteristics")\n  (:end . 89) (:start . 74) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 106)\n  (:start . 94) (:id . 60))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 115)\n  (:start . 107) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 119) (:start . 116)\n  (:id . 62))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 130)\n  (:start . 120) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 64))\n ((:tag . "NN") (:stem . "hcd4") (:form . "hCD4") (:end . 138) (:start . 134)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 150)\n  (:start . 140) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 155) (:start . 152)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 160) (:start . 156)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 170)\n  (:start . 162) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 171) (:start . 170)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.196) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501806@unknown@formal@none@1@S@EGFP+hCD4+ cells were then analyzed for the expression of myeloid and progenitor markers.@(((:tag . "JJ") (:stem . "egfp+hcd4+") (:form . "EGFP+hCD4+") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 16) (:start . 11)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 54)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "myeloid") (:form . "myeloid") (:end . 65)\n  (:start . 58) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "progenitor") (:form . "progenitor") (:end . 80)\n  (:start . 70) (:id . 53))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 88)\n  (:start . 81) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s6.197) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501807@unknown@formal@none@1@S@Plots are from a single animal that is representative of the experimental group.@(((:tag . "NNS") (:stem . "plot") (:form . "Plots") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "animal") (:form . "animal") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 53) (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 73)\n  (:start . 61) (:id . 53))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s6.198) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501808@unknown@formal@none@1@S@(B) Differences in the percentage of EGFP+hCD4+ BM cells that were positive for both c-kit and Sca-1.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "difference") (:form . "Differences") (:end . 15)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 33)\n  (:start . 23) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "egfp+hcd4+") (:form . "EGFP+hCD4+") (:end . 47)\n  (:start . 37) (:id . 50))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 75)\n  (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . "NN") (:stem . "c-kit") (:form . "c-kit") (:end . 90) (:start . 85)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . "NN") (:stem . "sca-1") (:form . "Sca-1") (:end . 100) (:start . 95)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.199) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501809@unknown@formal@none@1@S@Error bars indicate 95% confidence intervals.@(((:tag . "NN") (:stem . "error") (:form . "Error") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "CD") (:stem . "95") (:form . "95") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 34)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.200) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501810@unknown@formal@none@1@S@AE + TP, n = 21 mice; R174Q + TP, n = 22; Y113A/T161A, n = 24; TP, n = 8; AE, n = 8.@(((:tag . "NNP") (:stem . "AE") (:form . "AE") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "TP") (:form . "TP") (:end . 7) (:start . 5)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 45))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 10) (:start . 9)\n  (:id . 46))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 12) (:start . 11)\n  (:id . 47))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 15) (:start . 13)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 20) (:start . 16)\n  (:id . 49))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 21) (:start . 20)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 27) (:start . 22)\n  (:id . 51))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 29) (:start . 28)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "TP") (:form . "TP") (:end . 32) (:start . 30)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 54))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 35) (:start . 34)\n  (:id . 55))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 37) (:start . 36)\n  (:id . 56))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 40) (:start . 38)\n  (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 41) (:start . 40)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 53)\n  (:start . 42) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 60))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 56) (:start . 55)\n  (:id . 61))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 58) (:start . 57)\n  (:id . 62))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 61) (:start . 59)\n  (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 62) (:start . 61)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "TP") (:form . "TP") (:end . 65) (:start . 63)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 66))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 68) (:start . 67)\n  (:id . 67))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 70) (:start . 69)\n  (:id . 68))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 72) (:start . 71)\n  (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 73) (:start . 72)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "AE") (:form . "AE") (:end . 76) (:start . 74)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 72))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 79) (:start . 78)\n  (:id . 73))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 81) (:start . 80)\n  (:id . 74))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 83) (:start . 82)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.201) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501811@unknown@formal@none@1@S@Differences relative to AML1-ETO plus TEL-PDGFßR (#) for each group were determined using Dunnett test and ANOVA.@(((:tag . "NNS") (:stem . "difference") (:form . "Differences") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 48)\n  (:start . 38) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 48))\n ((:tag . "#") (:stem . "#") (:form . "#") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 83)\n  (:start . 73) (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 89) (:start . 84)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Dunnett") (:form . "Dunnett") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 102) (:start . 98)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "ANOVA") (:form . "ANOVA") (:end . 112)\n  (:start . 107) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.202) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501812@unknown@formal@none@1@S@(C) Differences in the percentage of EGFP+hCD4+ BM cells that were positive for both Gr-1 and Mac-1.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "difference") (:form . "Differences") (:end . 15)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 33)\n  (:start . 23) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "egfp+hcd4+") (:form . "EGFP+hCD4+") (:end . 47)\n  (:start . 37) (:id . 50))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 75)\n  (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . "NN") (:stem . "gr-1") (:form . "Gr-1") (:end . 89) (:start . 85)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "NN") (:stem . "mac-1") (:form . "Mac-1") (:end . 99) (:start . 94)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.203) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501813@unknown@formal@none@1@S@Error bars indicate 95% confidence intervals.@(((:tag . "NN") (:stem . "error") (:form . "Error") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "CD") (:stem . "95") (:form . "95") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 34)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s6.204) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501814@unknown@formal@none@1@S@Differences relative to AML1-ETO plus TEL-PDGFßR (#) for each group were determined using Dunnett test and ANOVA.@(((:tag . "NNS") (:stem . "difference") (:form . "Differences") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 48)\n  (:start . 38) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 48))\n ((:tag . "#") (:stem . "#") (:form . "#") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 83)\n  (:start . 73) (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 89) (:start . 84)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Dunnett") (:form . "Dunnett") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 102) (:start . 98)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "ANOVA") (:form . "ANOVA") (:end . 112)\n  (:start . 107) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.205) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501815@unknown@formal@none@1@S@The percentage of Gr-1+Mac-1+ cells in mice transplanted with AML1-ETO (Y113A/T161A) plus TEL-PDGFßR transduced cells was significantly lower (P < .001) than in mice transplanted with BM expressing AML1-ETO (R174Q) plus TEL-PDGFßR or TEL-PDGFßR alone.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "gr-1+mac-1+") (:form . "Gr-1+Mac-1+") (:end . 29)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 56)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 61) (:start . 57)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 70)\n  (:start . 62) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 83)\n  (:start . 72) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 89) (:start . 85)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 100)\n  (:start . 90) (:id . 56))\n ((:tag . "VBN") (:stem . "transduce") (:form . "transduced") (:end . 111)\n  (:start . 101) (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 117)\n  (:start . 112) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 121) (:start . 118)\n  (:id . 59))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 135) (:start . 122) (:id . 60))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 141) (:start . 136)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 62))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 144) (:start . 143)\n  (:id . 63))\n ((:tag . "JJR") (:stem . "<") (:form . "<") (:end . 146) (:start . 145)\n  (:id . 64))\n ((:tag . "CD") (:stem . ".001") (:form . ".001") (:end . 151) (:start . 147)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 66))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 157) (:start . 153)\n  (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 160) (:start . 158)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 165)\n  (:start . 161) (:id . 69))\n ((:tag . "VBN") (:stem . "transplant") (:form . "transplanted") (:end . 178)\n  (:start . 166) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 183) (:start . 179)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "BM") (:form . "BM") (:end . 186) (:start . 184)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 197)\n  (:start . 187) (:id . 73))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 206)\n  (:start . 198) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 208) (:start . 207)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "R174Q") (:form . "R174Q") (:end . 213)\n  (:start . 208) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n  (:id . 77))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 219) (:start . 215)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 230)\n  (:start . 220) (:id . 79))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 233) (:start . 231)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 244)\n  (:start . 234) (:id . 81))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 250)\n  (:start . 245) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 251) (:start . 250)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s6.206) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501816@unknown@formal@none@1@S@In summary, cells expressing AML1-ETO plus TEL-PDGFßR gave rise to a rapid AML as reported previously.82@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "summary") (:form . "summary") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 53)\n  (:start . 43) (:id . 49))\n ((:tag . "VBD") (:stem . "give") (:form . "gave") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "rise") (:form . "rise") (:end . 63) (:start . 59)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "AML") (:form . "AML") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 90)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "previously.82") (:form . "previously.82")\n  (:end . 104) (:start . 91) (:id . 58)))@@@1@17@((:identifiers (:sid . :s6.207) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501817@unknown@formal@none@1@S@Mutations in AML1-ETO that impaired DNA binding significantly weakened its activity, resulting in an extended latency and disease specificity more closely resembling that caused by TEL-PDGFßR alone.@(((:tag . "NNS") (:stem . "mutation") (:form . "Mutations") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "impair") (:form . "impaired") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 47)\n  (:start . 40) (:id . 48))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 61) (:start . 48) (:id . 49))\n ((:tag . "VBD") (:stem . "weaken") (:form . "weakened") (:end . 70)\n  (:start . 62) (:id . 50))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 74) (:start . 71)\n  (:id . 51))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 83)\n  (:start . 75) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 94)\n  (:start . 85) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 97) (:start . 95)\n  (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "extend") (:form . "extended") (:end . 109)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "latency") (:form . "latency") (:end . 117)\n  (:start . 110) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 59))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 129)\n  (:start . 122) (:id . 60))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 141)\n  (:start . 130) (:id . 61))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 146) (:start . 142)\n  (:id . 62))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 154)\n  (:start . 147) (:id . 63))\n ((:tag . "VBG") (:stem . "resemble") (:form . "resembling") (:end . 165)\n  (:start . 155) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 170) (:start . 166)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 177)\n  (:start . 171) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 180) (:start . 178)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "TEL-PDGFßR") (:form . "TEL-PDGFßR") (:end . 191)\n  (:start . 181) (:id . 68))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 197)\n  (:start . 192) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s6.208) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501818@unknown@formal@none@1@S@Loss of CBFß binding also weakened AML1-ETO's activity, resulting in an extended disease latency, selection of higher AML1-ETO expressing cells, and a cell surface phenotype intermediate between AML and CMPD.@(((:tag . "NN") (:stem . "loss") (:form . "Loss") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "weaken") (:form . "weakened") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 65)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "extend") (:form . "extended") (:end . 80)\n  (:start . 72) (:id . 55))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 88)\n  (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "latency") (:form . "latency") (:end . 96)\n  (:start . 89) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 107)\n  (:start . 98) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 117)\n  (:start . 111) (:id . 61))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 126)\n  (:start . 118) (:id . 62))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 137)\n  (:start . 127) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 143)\n  (:start . 138) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 150) (:start . 149)\n  (:id . 67))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 155) (:start . 151)\n  (:id . 68))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 163)\n  (:start . 156) (:id . 69))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 173)\n  (:start . 164) (:id . 70))\n ((:tag . "NN") (:stem . "intermediate") (:form . "intermediate") (:end . 186)\n  (:start . 174) (:id . 71))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 194)\n  (:start . 187) (:id . 72))\n ((:tag . "NNP") (:stem . "AML") (:form . "AML") (:end . 198) (:start . 195)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 202) (:start . 199)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "CMPD") (:form . "CMPD") (:end . 207) (:start . 203)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.209) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501819@unknown@formal@none@1@S@These results indicate that the mutated AML1-ETO proteins were unable to appropriately regulate a subset of genes required for the development of AML.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "unable") (:form . "unable") (:end . 69)\n  (:start . 63) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "RB") (:stem . "appropriately") (:form . "appropriately")\n  (:end . 86) (:start . 73) (:id . 53))\n ((:tag . "VB") (:stem . "regulate") (:form . "regulate") (:end . 95)\n  (:start . 87) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n  (:id . 55))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 104)\n  (:start . 98) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 113)\n  (:start . 108) (:id . 58))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 122)\n  (:start . 114) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 126) (:start . 123)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 61))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 142)\n  (:start . 131) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "AML") (:form . "AML") (:end . 149) (:start . 146)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x6.210.1) (:span 14 27)))\n (:hscopes ((:id . :x6.210.1) (:span 14 149)))\n (:identifiers (:sid . :s6.210) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501820@unknown@formal@none@1@S@Disruption of CBFß binding by the Runt domain of TEL-AML1 abrogates its ability to enhance self-renewal of B-cell progenitors.@(((:tag . "NN") (:stem . "disruption") (:form . "Disruption") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "runt") (:form . "Runt") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "VBZ") (:stem . "abrogate") (:form . "abrogates") (:end . 67)\n  (:start . 58) (:id . 52))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 90)\n  (:start . 83) (:id . 56))\n ((:tag . "NN") (:stem . "self-renewal") (:form . "self-renewal") (:end . 103)\n  (:start . 91) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "b-cell") (:form . "B-cell") (:end . 113)\n  (:start . 107) (:id . 59))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 125)\n  (:start . 114) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s6.211) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5501821@unknown@formal@none@1@S@TEL-AML1 is critically dependent upon DNA binding to enhance the self-renewal of B-cell progenitors in culture.61@(((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "RB") (:stem . "critically") (:form . "critically") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "JJ") (:stem . "dependent") (:form . "dependent") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "self-renewal") (:form . "self-renewal") (:end . 77)\n  (:start . 65) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 53))\n ((:tag . "NN") (:stem . "b-cell") (:form . "B-cell") (:end . 87)\n  (:start . 81) (:id . 54))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 99)\n  (:start . 88) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n  (:id . 56))\n ((:tag . "NN") (:stem . "culture.61") (:form . "culture.61") (:end . 113)\n  (:start . 103) (:id . 57)))@@@1@16@((:identifiers (:sid . :s6.212) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501822@unknown@formal@none@1@S@To determine whether disrupting CBFß binding above a specific threshold results in functional impairment, we introduced mutations analogous to T161A and Y113A/T161A (T188A and Y140A/T188A) into TEL-AML1.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "VBG") (:stem . "disrupt") (:form . "disrupting") (:end . 31)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 50) (:start . 45)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 71)\n  (:start . 62) (:id . 51))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 79)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 93)\n  (:start . 83) (:id . 54))\n ((:tag . "NN") (:stem . "impairment") (:form . "impairment") (:end . 104)\n  (:start . 94) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 108) (:start . 106)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "introduce") (:form . "introduced") (:end . 119)\n  (:start . 109) (:id . 58))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 129)\n  (:start . 120) (:id . 59))\n ((:tag . "JJ") (:stem . "analogous") (:form . "analogous") (:end . 139)\n  (:start . 130) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "T161A") (:form . "T161A") (:end . 148)\n  (:start . 143) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Y113A/T161A") (:form . "Y113A/T161A") (:end . 164)\n  (:start . 153) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 166) (:start . 165)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "T188A") (:form . "T188A") (:end . 171)\n  (:start . 166) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Y140A/T188A") (:form . "Y140A/T188A") (:end . 187)\n  (:start . 176) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 69))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 193) (:start . 189)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 202)\n  (:start . 194) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x6.213.1) (:span 13 20)))\n (:hscopes ((:id . :x6.213.1) (:span 13 104)))\n (:identifiers (:sid . :s6.213) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501823@unknown@formal@none@1@S@As the Runt domains of AML1-ETO and TEL-AML1 are identical, we would expect the biophysical characteristics of the mutated proteins to be comparable.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "runt") (:form . "Runt") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "VB") (:stem . "expect") (:form . "expect") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "biophysical") (:form . "biophysical") (:end . 91)\n  (:start . 80) (:id . 57))\n ((:tag . "NNS") (:stem . "characteristic") (:form . "characteristics")\n  (:end . 107) (:start . 92) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 122)\n  (:start . 115) (:id . 61))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 131)\n  (:start . 123) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 134) (:start . 132)\n  (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "comparable") (:form . "comparable") (:end . 148)\n  (:start . 138) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x6.214.1) (:span 63 68)))\n (:hscopes ((:id . :x6.214.1) (:span 63 148)))\n (:identifiers (:sid . :s6.214) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501824@unknown@formal@none@1@S@We transduced c-Kit+ fetal liver cells from embryonic day 12 C57BL/6 mice with retroviruses expressing TEL-AML1 or its mutated derivatives and EGFP,61,66 and serially replated them in methylcellulose under conditions that promote B-cell differentiation.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "transduce") (:form . "transduced") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "c-kit+") (:form . "c-Kit+") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "JJ") (:stem . "fetal") (:form . "fetal") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "liver") (:form . "liver") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "c57bl/6") (:form . "C57BL/6") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "retrovirus") (:form . "retroviruses") (:end . 91)\n  (:start . 79) (:id . 55))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 102)\n  (:start . 92) (:id . 56))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 111)\n  (:start . 103) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 114) (:start . 112)\n  (:id . 58))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 118) (:start . 115)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 126)\n  (:start . 119) (:id . 60))\n ((:tag . "NNS") (:stem . "derivative") (:form . "derivatives") (:end . 138)\n  (:start . 127) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "EGFP,61,66") (:form . "EGFP,61,66") (:end . 153)\n  (:start . 143) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 64))\n ((:tag . "RB") (:stem . "serially") (:form . "serially") (:end . 166)\n  (:start . 158) (:id . 65))\n ((:tag . "VBD") (:stem . "replate") (:form . "replated") (:end . 175)\n  (:start . 167) (:id . 66))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 180) (:start . 176)\n  (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 183) (:start . 181)\n  (:id . 68))\n ((:tag . "NN") (:stem . "methylcellulose") (:form . "methylcellulose")\n  (:end . 199) (:start . 184) (:id . 69))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 205)\n  (:start . 200) (:id . 70))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 216)\n  (:start . 206) (:id . 71))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 221) (:start . 217)\n  (:id . 72))\n ((:tag . "VBP") (:stem . "promote") (:form . "promote") (:end . 229)\n  (:start . 222) (:id . 73))\n ((:tag . "NN") (:stem . "b-cell") (:form . "B-cell") (:end . 236)\n  (:start . 230) (:id . 74))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 252) (:start . 237) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 253) (:start . 252)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.215) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501825@unknown@formal@none@1@S@Expression of similar steady-state levels of the TEL-AML1 mutant proteins in transduced NIH3T3 cells was confirmed by Western blot analysis, and retroviral transduction of c-kit+ cells was measured by EGFP fluorescence (Figure 5A,B).@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "JJ") (:stem . "steady-state") (:form . "steady-state") (:end . 34)\n  (:start . 22) (:id . 45))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 41)\n  (:start . 35) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . "NN") (:stem . "tel-aml1") (:form . "TEL-AML1") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 64)\n  (:start . 58) (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 73)\n  (:start . 65) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "transduce") (:form . "transduced") (:end . 87)\n  (:start . 77) (:id . 53))\n ((:tag . "NN") (:stem . "nih3t3") (:form . "NIH3T3") (:end . 94)\n  (:start . 88) (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 100) (:start . 95)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 104) (:start . 101)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 114)\n  (:start . 105) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 117) (:start . 115)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 125)\n  (:start . 118) (:id . 59))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 130) (:start . 126)\n  (:id . 60))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 139)\n  (:start . 131) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "retroviral") (:form . "retroviral") (:end . 155)\n  (:start . 145) (:id . 64))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 168)\n  (:start . 156) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "c-kit+") (:form . "c-kit+") (:end . 178)\n  (:start . 172) (:id . 67))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 184)\n  (:start . 179) (:id . 68))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 188) (:start . 185)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 197)\n  (:start . 189) (:id . 70))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 200) (:start . 198)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 205) (:start . 201)\n  (:id . 72))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 218)\n  (:start . 206) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 220) (:start . 219)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 226)\n  (:start . 220) (:id . 75))\n ((:tag . "CD") (:stem . "5A,B") (:form . "5A,B") (:end . 231) (:start . 227)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 232) (:start . 231)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 233) (:start . 232)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s6.216) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501826@unknown@formal@none@1@S@Cells expressing TEL-AML1 generated increased numbers of colonies and cells, which are B220 enriched, more than multiple rounds of replating relative to cells expressing EGFP alone (Figure 5C-E).@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "tel-aml1") (:form . "TEL-AML1") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 35)\n  (:start . 26) (:id . 45))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 45)\n  (:start . 36) (:id . 46))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 53)\n  (:start . 46) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "colony") (:form . "colonies") (:end . 65)\n  (:start . 57) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 75) (:start . 70)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 82) (:start . 77)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 86) (:start . 83)\n  (:id . 54))\n ((:tag . "NN") (:stem . "b220") (:form . "B220") (:end . 91) (:start . 87)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 100)\n  (:start . 92) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 57))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 106) (:start . 102)\n  (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 111) (:start . 107)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 120)\n  (:start . 112) (:id . 60))\n ((:tag . "NNS") (:stem . "round") (:form . "rounds") (:end . 127)\n  (:start . 121) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "replate") (:form . "replating") (:end . 140)\n  (:start . 131) (:id . 63))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 149)\n  (:start . 141) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 152) (:start . 150)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 158)\n  (:start . 153) (:id . 66))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 169)\n  (:start . 159) (:id . 67))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 174) (:start . 170)\n  (:id . 68))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 180)\n  (:start . 175) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 182) (:start . 181)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 188)\n  (:start . 182) (:id . 71))\n ((:tag . "NN") (:stem . "5c-e") (:form . "5C-E") (:end . 193) (:start . 189)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.217) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501827@unknown@formal@none@1@S@A reduction in CBFß heterodimerization by greater than 400-fold through introduction of the Y140A/T188A mutations severely impaired TEL-AML1's ability to enhance the clonogenic potential of these B-cell precursors, as the numbers of cells and colonies were very similar to those of EGFP-transduced cells.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 11)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "heterodimerization") (:form . "heterodimerization")\n  (:end . 38) (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "RB") (:stem . "400-fold") (:form . "400-fold") (:end . 63)\n  (:start . 55) (:id . 50))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 71)\n  (:start . 64) (:id . 51))\n ((:tag . "NN") (:stem . "introduction") (:form . "introduction") (:end . 84)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Y140A/T188A") (:form . "Y140A/T188A") (:end . 103)\n  (:start . 92) (:id . 55))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 113)\n  (:start . 104) (:id . 56))\n ((:tag . "RB") (:stem . "severely") (:form . "severely") (:end . 122)\n  (:start . 114) (:id . 57))\n ((:tag . "VBD") (:stem . "impair") (:form . "impaired") (:end . 131)\n  (:start . 123) (:id . 58))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 140)\n  (:start . 132) (:id . 59))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 142) (:start . 140)\n  (:id . 60))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 150)\n  (:start . 143) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 153) (:start . 151)\n  (:id . 62))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 161)\n  (:start . 154) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "clonogenic") (:form . "clonogenic") (:end . 176)\n  (:start . 166) (:id . 65))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 186)\n  (:start . 177) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 189) (:start . 187)\n  (:id . 67))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 195)\n  (:start . 190) (:id . 68))\n ((:tag . "NN") (:stem . "b-cell") (:form . "B-cell") (:end . 202)\n  (:start . 196) (:id . 69))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 213)\n  (:start . 203) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 214) (:start . 213)\n  (:id . 71))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 217) (:start . 215)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 221) (:start . 218)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 229)\n  (:start . 222) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 232) (:start . 230)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 238)\n  (:start . 233) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 242) (:start . 239)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "colony") (:form . "colonies") (:end . 251)\n  (:start . 243) (:id . 78))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 256) (:start . 252)\n  (:id . 79))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 261) (:start . 257)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 269)\n  (:start . 262) (:id . 81))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 272) (:start . 270)\n  (:id . 82))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 278)\n  (:start . 273) (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 281) (:start . 279)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "egfp-transduced") (:form . "EGFP-transduced")\n  (:end . 297) (:start . 282) (:id . 85))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 303)\n  (:start . 298) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 304) (:start . 303)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s6.218) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501828@unknown@formal@none@1@S@Cells expressing the T188A TEL-AML1 mutant, which is expected to have an approximately 60-fold reduction in CBFß binding, produced numbers of colonies and cells similar to those of TEL-AML1–expressing cells during secondary replating, however, the numbers from the third round of replating were very significantly decreased and therefore somewhat intermediate between the TEL-AML1 and TEL-AML1 (Y140A/T188A) expressing cells.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "T188A") (:form . "T188A") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "mutant") (:form . 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5501829@unknown@formal@none@1@S@It appears that, as was the case for AML1-ETO, a decrease in CBFß binding from 60- to 400-fold is accompanied by a progressive impairment in TEL-AML1's clonogenic activity.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 48))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 32) (:start . 28)\n  (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 45)\n  (:start . 37) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 53))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 57)\n  (:start . 49) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 65) (:start . 61)\n  (:id . 56))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 73)\n  (:start . 66) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 78) (:start . 74)\n  (:id . 58))\n ((:tag . "CD") (:stem . "60-") (:form . "60-") (:end . 82) (:start . 79)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "400-fold") (:form . "400-fold") (:end . 94)\n  (:start . 86) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 97) (:start . 95)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "accompany") (:form . "accompanied") (:end . 109)\n  (:start . 98) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 112) (:start . 110)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 114) (:start . 113)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "progressive") (:form . "progressive") (:end . 126)\n  (:start . 115) (:id . 66))\n ((:tag . "NN") (:stem . "impairment") (:form . "impairment") (:end . 137)\n  (:start . 127) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 149)\n  (:start . 141) (:id . 69))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 151) (:start . 149)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "clonogenic") (:form . "clonogenic") (:end . 162)\n  (:start . 152) (:id . 71))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 171)\n  (:start . 163) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x6.220.1) (:span 3 10)))\n (:hscopes ((:id . :x6.220.1) (:span 3 171)))\n (:identifiers (:sid . :s6.220) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501830@unknown@formal@none@1@S@As the thermodynamic stability and DNA binding affinity of the T118A and Y140A/T188A mutant Runt domains are identical, the decreased activity can only be explained by more severely impaired CBFß binding.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "thermodynamic") (:form . "thermodynamic")\n  (:end . 20) (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "stability") (:form . "stability") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "T118A") (:form . "T118A") (:end . 68) (:start . 63)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Y140A/T188A") (:form . "Y140A/T188A") (:end . 84)\n  (:start . 73) (:id . 54))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 91)\n  (:start . 85) (:id . 55))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 96) (:start . 92)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 104)\n  (:start . 97) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 108) (:start . 105)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 118)\n  (:start . 109) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "decrease") (:form . "decreased") (:end . 133)\n  (:start . 124) (:id . 62))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 142)\n  (:start . 134) (:id . 63))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 146) (:start . 143)\n  (:id . 64))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 151) (:start . 147)\n  (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 154) (:start . 152)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "explain") (:form . "explained") (:end . 164)\n  (:start . 155) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 167) (:start . 165)\n  (:id . 68))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 172) (:start . 168)\n  (:id . 69))\n ((:tag . "RB") (:stem . "severely") (:form . "severely") (:end . 181)\n  (:start . 173) (:id . 70))\n ((:tag . "JJ") (:stem . "impaired") (:form . "impaired") (:end . 190)\n  (:start . 182) (:id . 71))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 195) (:start . 191)\n  (:id . 72))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 203)\n  (:start . 196) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.221) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501831@unknown@formal@none@1@S@Disrupting heterodimerization with CBFß substantially abrogates TEL-AML1's ability to enhance the clonogenic potential of c-kit+ B-cell precursors.@(((:tag . "VBG") (:stem . "disrupt") (:form . "Disrupting") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "heterodimerization") (:form . "heterodimerization")\n  (:end . 29) (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 39) (:start . 35)\n  (:id . 45))\n ((:tag . "RB") (:stem . "substantially") (:form . "substantially")\n  (:end . 53) (:start . 40) (:id . 46))\n ((:tag . "VBZ") (:stem . "abrogate") (:form . "abrogates") (:end . 63)\n  (:start . 54) (:id . 47))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 72)\n  (:start . 64) (:id . 48))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 74) (:start . 72)\n  (:id . 49))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 82)\n  (:start . 75) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n  (:id . 51))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 93)\n  (:start . 86) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "clonogenic") (:form . "clonogenic") (:end . 108)\n  (:start . 98) (:id . 54))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 118)\n  (:start . 109) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "c-kit+") (:form . "c-kit+") (:end . 128)\n  (:start . 122) (:id . 57))\n ((:tag . "NN") (:stem . "b-cell") (:form . "B-cell") (:end . 135)\n  (:start . 129) (:id . 58))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 146)\n  (:start . 136) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s6.222) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501832@unknown@formal@none@1@S@(A) Detection of hemagglutinin (HA)–tagged TEL-AML1 and the T188A and Y140A/T188A mutants in NIH3T3 cells 48 hours after retroviral (murine stem cell virus [MSCV]) transduction.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "detection") (:form . "Detection") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "NN") (:stem . "hemagglutinin") (:form . "hemagglutinin")\n  (:end . 30) (:start . 17) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "HA)–tagged") (:form . "HA)–tagged") (:end . 42)\n  (:start . 32) (:id . 49))\n ((:tag . "NN") (:stem . "tel-aml1") (:form . "TEL-AML1") (:end . 51)\n  (:start . 43) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "T188A") (:form . "T188A") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Y140A/T188A") (:form . "Y140A/T188A") (:end . 81)\n  (:start . 70) (:id . 55))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "nih3t3") (:form . "NIH3T3") (:end . 99)\n  (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 105)\n  (:start . 100) (:id . 59))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 114)\n  (:start . 109) (:id . 61))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 120)\n  (:start . 115) (:id . 62))\n ((:tag . "JJ") (:stem . "retroviral") (:form . "retroviral") (:end . 131)\n  (:start . 121) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "murine") (:form . "murine") (:end . 139)\n  (:start . 133) (:id . 65))\n ((:tag . "NN") (:stem . "stem") (:form . "stem") (:end . 144) (:start . 140)\n  (:id . 66))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 149) (:start . 145)\n  (:id . 67))\n ((:tag . "NN") (:stem . "virus") (:form . "virus") (:end . 155)\n  (:start . 150) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 157) (:start . 156)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "MSCV") (:form . "MSCV") (:end . 161) (:start . 157)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 162) (:start . 161)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 163) (:start . 162)\n  (:id . 72))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 176)\n  (:start . 164) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s6.223) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501833@unknown@formal@none@1@S@Vertical lines have been inserted to indicate a repositioned gel lane.@(((:tag . "JJ") (:stem . "vertical") (:form . "Vertical") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "VB") (:stem . "indicate") (:form . "indicate") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "repositioned") (:form . "repositioned") (:end . 60)\n  (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 69) (:start . 65)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s6.224) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501834@unknown@formal@none@1@S@(B) Flow cytometric analysis of EGFP expression in c-kit+ fetal liver cells 48 hours after infection with viral supernatants.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Flow") (:form . "Flow") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "cytometric") (:form . "cytometric") (:end . 19)\n  (:start . 9) (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 36) (:start . 32)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 47)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "c-kit+") (:form . "c-kit+") (:end . 57)\n  (:start . 51) (:id . 52))\n ((:tag . "JJ") (:stem . "fetal") (:form . "fetal") (:end . 63) (:start . 58)\n  (:id . 53))\n ((:tag . "NN") (:stem . "liver") (:form . "liver") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 75) (:start . 70)\n  (:id . 55))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 84) (:start . 79)\n  (:id . 57))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 90) (:start . 85)\n  (:id . 58))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 100)\n  (:start . 91) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 105) (:start . 101)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "viral") (:form . "viral") (:end . 111)\n  (:start . 106) (:id . 61))\n ((:tag . "NNS") (:stem . "supernatant") (:form . "supernatants") (:end . 124)\n  (:start . 112) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.225) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501835@unknown@formal@none@1@S@(C) Transduced c-kit+ cells grown in methylcellulose serial replating assays in conditions promoting B-cell differentiation (IL-7, SCF, and FLT3 ligand).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "VBD") (:stem . "transduce") (:form . "Transduced") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "JJ") (:stem . "c-kit+") (:form . "c-kit+") (:end . 21)\n  (:start . 15) (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "grow") (:form . "grown") (:end . 33) (:start . 28)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "methylcellulose") (:form . "methylcellulose")\n  (:end . 52) (:start . 37) (:id . 50))\n ((:tag . "JJ") (:stem . "serial") (:form . "serial") (:end . 59)\n  (:start . 53) (:id . 51))\n ((:tag . "VBG") (:stem . "replate") (:form . "replating") (:end . 69)\n  (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 76)\n  (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 90)\n  (:start . 80) (:id . 55))\n ((:tag . "VBG") (:stem . "promote") (:form . "promoting") (:end . 100)\n  (:start . 91) (:id . 56))\n ((:tag . "NN") (:stem . "b-cell") (:form . "B-cell") (:end . 107)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 123) (:start . 108) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "IL-7") (:form . "IL-7") (:end . 129) (:start . 125)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "SCF") (:form . "SCF") (:end . 134) (:start . 131)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 64))\n ((:tag . "NN") (:stem . "flt3") (:form . "FLT3") (:end . 144) (:start . 140)\n  (:id . 65))\n ((:tag . "NN") (:stem . "ligand") (:form . "ligand") (:end . 151)\n  (:start . 145) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s6.226) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501836@unknown@formal@none@1@S@The number of colonies harvested from each culture, per 104 cells plated, is shown for the first (), second (), and third (¦) rounds of plating.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "colony") (:form . "colonies") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "VBN") (:stem . "harvest") (:form . "harvested") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "CD") (:stem . "104") (:form . "104") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "plat") (:form . "plated") (:end . 72) (:start . 66)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 82) (:start . 77)\n  (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 96) (:start . 91)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 107)\n  (:start . 101) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 121)\n  (:start . 116) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "¦") (:form . "¦") (:end . 124) (:start . 123)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "round") (:form . "rounds") (:end . 132)\n  (:start . 126) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 74))\n ((:tag . "NN") (:stem . "plating") (:form . "plating") (:end . 143)\n  (:start . 136) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s6.227) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501837@unknown@formal@none@1@S@Plots show means and SDs of duplicate cultures.@(((:tag . "NNS") (:stem . "plot") (:form . "Plots") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "mean") (:form . "means") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "sd") (:form . "SDs") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "duplicate") (:form . "duplicate") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "NNS") (:stem . "culture") (:form . "cultures") (:end . 46)\n  (:start . 38) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s6.228) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501838@unknown@formal@none@1@S@The data shown are representative of 5 independent experiments.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 33) (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 50)\n  (:start . 39) (:id . 49))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 62)\n  (:start . 51) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s6.229) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501839@unknown@formal@none@1@S@(D) Total number of cells, as in panel C. (E) Number of B220+ cells as in panel C.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "total") (:form . "Total") (:end . 9) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 16)\n  (:start . 10) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 25) (:start . 20)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 29) (:start . 27)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 51))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 38) (:start . 33)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 41) (:start . 39)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 44) (:start . 43)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Number") (:form . "Number") (:end . 52)\n  (:start . 46) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "b220+") (:form . "B220+") (:end . 61) (:start . 56)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 67) (:start . 62)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 70) (:start . 68)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 62))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 79) (:start . 74)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 81) (:start . 80)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s6.230) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5501840@unknown@formal@none@1@S@Discussion@(((:tag . "NN") (:stem . "discussion") (:form . "Discussion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s6.231) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501841@unknown@formal@none@1@S@Assessing which protein-protein interactions mediated by oncogenic transcription factors are essential for their leukemogenic activity, and determining the structures of the domains responsible for those interactions will greatly facilitate the development of specific inhibitors by structure-aided drug design.@(((:tag . "VBG") (:stem . "assess") (:form . "Assessing") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "protein-protein") (:form . "protein-protein")\n  (:end . 31) (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 44)\n  (:start . 32) (:id . 45))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 53)\n  (:start . 45) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 56) (:start . 54)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "oncogenic") (:form . "oncogenic") (:end . 66)\n  (:start . 57) (:id . 48))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 80) (:start . 67) (:id . 49))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 88)\n  (:start . 81) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 92) (:start . 89)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 102)\n  (:start . 93) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 106) (:start . 103)\n  (:id . 53))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 112)\n  (:start . 107) (:id . 54))\n ((:tag . "JJ") (:stem . "leukemogenic") (:form . "leukemogenic") (:end . 125)\n  (:start . 113) (:id . 55))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 134)\n  (:start . 126) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "determine") (:form . "determining") (:end . 151)\n  (:start . 140) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 166)\n  (:start . 156) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 169) (:start . 167)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 173) (:start . 170)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 181)\n  (:start . 174) (:id . 64))\n ((:tag . "JJ") (:stem . "responsible") (:form . "responsible") (:end . 193)\n  (:start . 182) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 197) (:start . 194)\n  (:id . 66))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 203)\n  (:start . 198) (:id . 67))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 216)\n  (:start . 204) (:id . 68))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 221) (:start . 217)\n  (:id . 69))\n ((:tag . "RB") (:stem . "greatly") (:form . "greatly") (:end . 229)\n  (:start . 222) (:id . 70))\n ((:tag . "VB") (:stem . "facilitate") (:form . "facilitate") (:end . 240)\n  (:start . 230) (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 244) (:start . 241)\n  (:id . 72))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 256)\n  (:start . 245) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 259) (:start . 257)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 268)\n  (:start . 260) (:id . 75))\n ((:tag . "NNS") (:stem . "inhibitor") (:form . "inhibitors") (:end . 279)\n  (:start . 269) (:id . 76))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 282) (:start . 280)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "structure-aided") (:form . "structure-aided")\n  (:end . 298) (:start . 283) (:id . 78))\n ((:tag . "NN") (:stem . "drug") (:form . "drug") (:end . 303) (:start . 299)\n  (:id . 79))\n ((:tag . "NN") (:stem . "design") (:form . "design") (:end . 310)\n  (:start . 304) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 311) (:start . 310)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s6.232) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501842@unknown@formal@none@1@S@Here, we show that ablation of DNA binding by 40000 fold30,49 or reduction of CBFß heterodimerization by greater than 400-fold partially impaired AML1-ETO's ability to inhibit granulocyte differentiation, almost completely reversed its acute inhibition of proliferation, eliminated its ability to confer serial replating to myeloid progenitors, and severely compromised its cooperation with TEL-PDGFßR to cause AML, and thus impaired or delayed AML disease.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 13) (:start . 9)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 46))\n ((:tag . "NN") (:stem . "ablation") (:form . 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"serial") (:end . 310)\n  (:start . 304) (:id . 87))\n ((:tag . "NN") (:stem . "replating") (:form . "replating") (:end . 320)\n  (:start . 311) (:id . 88))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 323) (:start . 321)\n  (:id . 89))\n ((:tag . "JJ") (:stem . "myeloid") (:form . "myeloid") (:end . 331)\n  (:start . 324) (:id . 90))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 343)\n  (:start . 332) (:id . 91))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 344) (:start . 343)\n  (:id . 92))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 348) (:start . 345)\n  (:id . 93))\n ((:tag . "RB") (:stem . "severely") (:form . "severely") (:end . 357)\n  (:start . 349) (:id . 94))\n ((:tag . "VBD") (:stem . "compromise") (:form . "compromised") (:end . 369)\n  (:start . 358) (:id . 95))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 373) (:start . 370)\n  (:id . 96))\n ((:tag . "NN") (:stem . "cooperation") (:form . 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"or") (:end . 436) (:start . 434)\n  (:id . 107))\n ((:tag . "VBN") (:stem . "delay") (:form . "delayed") (:end . 444)\n  (:start . 437) (:id . 108))\n ((:tag . "NN") (:stem . "aml") (:form . "AML") (:end . 448) (:start . 445)\n  (:id . 109))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 456)\n  (:start . 449) (:id . 110))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 457) (:start . 456)\n  (:id . 111)))@@@1@70@((:identifiers (:sid . :s6.233) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501843@unknown@formal@none@1@S@Similarly, inhibition of both DNA61 and CBFß binding by TEL-AML1 eliminated its ability to enhance the self-renewal of B-cell progenitors.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dna61") (:form . "DNA61") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . "VBD") (:stem . "eliminate") (:form . "eliminated") (:end . 75)\n  (:start . 65) (:id . 53))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 87)\n  (:start . 80) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 98)\n  (:start . 91) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "NN") (:stem . "self-renewal") (:form . "self-renewal") (:end . 115)\n  (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n  (:id . 60))\n ((:tag . "NN") (:stem . "b-cell") (:form . "B-cell") (:end . 125)\n  (:start . 119) (:id . 61))\n ((:tag . "NNS") (:stem . "progenitor") (:form . "progenitors") (:end . 137)\n  (:start . 126) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s6.234) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501844@unknown@formal@none@1@S@We are optimistic that targeted disruption of either function may provide an effective therapeutic modality.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "optimistic") (:form . "optimistic") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "target") (:form . "targeted") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "disruption") (:form . "disruption") (:end . 42)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 52)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 73)\n  (:start . 66) (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 86)\n  (:start . 77) (:id . 54))\n ((:tag . "JJ") (:stem . "therapeutic") (:form . "therapeutic") (:end . 98)\n  (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "modality") (:form . "modality") (:end . 107)\n  (:start . 99) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x6.235.1) (:span 62 65)))\n (:hscopes ((:id . :x6.235.1) (:span 62 107)))\n (:identifiers (:sid . :s6.235) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501845@unknown@formal@none@1@S@The more promising of the 2 interactions for small molecule inhibitors is that between the Runt domain and CBFß, since the Runt domain-DNA interface is highly charged and may be difficult to target with a small molecule.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "promising") (:form . "promising") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 40)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "molecule") (:form . "molecule") (:end . 59)\n  (:start . 51) (:id . 51))\n ((:tag . "NNS") (:stem . "inhibitor") (:form . "inhibitors") (:end . 70)\n  (:start . 60) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 86)\n  (:start . 79) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 95) (:start . 91)\n  (:id . 57))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 102)\n  (:start . 96) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 111) (:start . 107)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 118)\n  (:start . 113) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 127) (:start . 123)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "domain-DNA") (:form . "domain-DNA") (:end . 138)\n  (:start . 128) (:id . 65))\n ((:tag . "NN") (:stem . "interface") (:form . "interface") (:end . 148)\n  (:start . 139) (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 151) (:start . 149)\n  (:id . 67))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 158)\n  (:start . 152) (:id . 68))\n ((:tag . "VBN") (:stem . "charge") (:form . "charged") (:end . 166)\n  (:start . 159) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 170) (:start . 167)\n  (:id . 70))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 174) (:start . 171)\n  (:id . 71))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 177) (:start . 175)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 187)\n  (:start . 178) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 190) (:start . 188)\n  (:id . 74))\n ((:tag . "VB") (:stem . "target") (:form . "target") (:end . 197)\n  (:start . 191) (:id . 75))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 202) (:start . 198)\n  (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 204) (:start . 203)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 210)\n  (:start . 205) (:id . 78))\n ((:tag . "NN") (:stem . "molecule") (:form . "molecule") (:end . 219)\n  (:start . 211) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x6.236.1) (:span 171 174)))\n (:hscopes ((:id . :x6.236.1) (:span 171 219)))\n (:identifiers (:sid . :s6.236) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501846@unknown@formal@none@1@S@The Runt domain-CBFß interface, on the other hand, contains a large hydrophobic area,36,62 which should be more conducive for binding small molecules with drug-like properties.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "domain-CBFß") (:form . "domain-CBFß") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "interface") (:form . "interface") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "hand") (:form . "hand") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 59)\n  (:start . 51) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "hydrophobic") (:form . "hydrophobic") (:end . 79)\n  (:start . 68) (:id . 55))\n ((:tag . "CD") (:stem . "area,36,62") (:form . "area,36,62") (:end . 90)\n  (:start . 80) (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 111) (:start . 107)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "conducive") (:form . "conducive") (:end . 121)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 125) (:start . 122)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 133)\n  (:start . 126) (:id . 63))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 139)\n  (:start . 134) (:id . 64))\n ((:tag . "NNS") (:stem . "molecule") (:form . "molecules") (:end . 149)\n  (:start . 140) (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 154) (:start . 150)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "drug-like") (:form . "drug-like") (:end . 164)\n  (:start . 155) (:id . 67))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 175)\n  (:start . 165) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x6.237.1) (:span 97 103)))\n (:hscopes ((:id . :x6.237.1) (:span 97 175)))\n (:identifiers (:sid . :s6.237) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501847@unknown@formal@none@1@S@Although small molecules targeting protein-protein interactions are relatively limited thus far, there has been an increase in activity and reported success in developing these inhibitors.85@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "molecule") (:form . "molecules") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . "JJ") (:stem . "protein-protein") (:form . "protein-protein")\n  (:end . 50) (:start . 35) (:id . 46))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 63)\n  (:start . 51) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 67) (:start . 64)\n  (:id . 48))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 78)\n  (:start . 68) (:id . 49))\n ((:tag . "JJ") (:stem . "limited") (:form . "limited") (:end . 86)\n  (:start . 79) (:id . 50))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 91) (:start . 87)\n  (:id . 51))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 95) (:start . 92)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 53))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 102) (:start . 97)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 106) (:start . 103)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 111) (:start . 107)\n  (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 114) (:start . 112)\n  (:id . 57))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 123)\n  (:start . 115) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 126) (:start . 124)\n  (:id . 59))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 135)\n  (:start . 127) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "report") (:form . "reported") (:end . 148)\n  (:start . 140) (:id . 62))\n ((:tag . "NN") (:stem . "success") (:form . "success") (:end . 156)\n  (:start . 149) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 159) (:start . 157)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 170)\n  (:start . 160) (:id . 65))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 176)\n  (:start . 171) (:id . 66))\n ((:tag . "NN") (:stem . "inhibitors.85") (:form . "inhibitors.85")\n  (:end . 190) (:start . 177) (:id . 67)))@@@1@26@((:identifiers (:sid . :s6.238) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501848@unknown@formal@none@1@S@For example, we recently developed a small molecule that binds CBFß and allosterically inhibits CBFß binding to the Runt domain, supporting the notion that disrupting this interaction with drug-like molecules is feasible.86@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "VBD") (:stem . "develop") (:form . "developed") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "molecule") (:form . "molecule") (:end . 51)\n  (:start . 43) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "bind") (:form . "binds") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "RB") (:stem . "allosterically") (:form . "allosterically")\n  (:end . 86) (:start . 72) (:id . 55))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 95)\n  (:start . 87) (:id . 56))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 100) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 108)\n  (:start . 101) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 120) (:start . 116)\n  (:id . 61))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 127)\n  (:start . 121) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "support") (:form . "supporting") (:end . 139)\n  (:start . 129) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 65))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 150)\n  (:start . 144) (:id . 66))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 155) (:start . 151)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "disrupt") (:form . "disrupting") (:end . 166)\n  (:start . 156) (:id . 68))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 171) (:start . 167)\n  (:id . 69))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 183)\n  (:start . 172) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 188) (:start . 184)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "drug-like") (:form . "drug-like") (:end . 198)\n  (:start . 189) (:id . 72))\n ((:tag . "NNS") (:stem . "molecule") (:form . "molecules") (:end . 208)\n  (:start . 199) (:id . 73))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 211) (:start . 209)\n  (:id . 74))\n ((:tag . "NN") (:stem . "feasible.86") (:form . "feasible.86") (:end . 223)\n  (:start . 212) (:id . 75)))@@@1@34@((:identifiers (:sid . :s6.239) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501849@unknown@formal@none@1@S@A potential drawback to this approach is that the inhibitors would also further impair the function of the normal core binding factors, in which case there would need to be a therapeutic window for them to be clinically useful.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 11)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "drawback") (:form . "drawback") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "inhibitor") (:form . "inhibitors") (:end . 60)\n  (:start . 50) (:id . 51))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "VB") (:stem . "impair") (:form . "impair") (:end . 86)\n  (:start . 80) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 99)\n  (:start . 91) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 113)\n  (:start . 107) (:id . 60))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 118) (:start . 114)\n  (:id . 61))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 126)\n  (:start . 119) (:id . 62))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 134)\n  (:start . 127) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 138) (:start . 136)\n  (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 144)\n  (:start . 139) (:id . 66))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 149) (:start . 145)\n  (:id . 67))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 155)\n  (:start . 150) (:id . 68))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 161)\n  (:start . 156) (:id . 69))\n ((:tag . "VB") (:stem . "need") (:form . "need") (:end . 166) (:start . 162)\n  (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 169) (:start . 167)\n  (:id . 71))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 172) (:start . 170)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 174) (:start . 173)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "therapeutic") (:form . "therapeutic") (:end . 186)\n  (:start . 175) (:id . 74))\n ((:tag . "NN") (:stem . "window") (:form . "window") (:end . 193)\n  (:start . 187) (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 197) (:start . 194)\n  (:id . 76))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 202) (:start . 198)\n  (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 205) (:start . 203)\n  (:id . 78))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 208) (:start . 206)\n  (:id . 79))\n ((:tag . "RB") (:stem . "clinically") (:form . "clinically") (:end . 219)\n  (:start . 209) (:id . 80))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 226)\n  (:start . 220) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x6.240.1) (:span 156 161)) ((:id . :x6.240.2) (:span 61 66)))\n (:hscopes ((:id . :x6.240.1) (:span 156 226))\n  ((:id . :x6.240.2) (:span 61 226)))\n (:identifiers (:sid . :s6.240) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501850@unknown@formal@none@1@S@Alternatively, combined therapies using inhibitors targeting other functions specific for AML1-ETO (eg, oligomerization 15,49,87) may provide specificity.@(((:tag . "RB") (:stem . "alternatively") (:form . "Alternatively")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "combined") (:form . "combined") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "therapy") (:form . "therapies") (:end . 33)\n  (:start . 24) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 39) (:start . 34)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "inhibitor") (:form . "inhibitors") (:end . 50)\n  (:start . 40) (:id . 47))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 60)\n  (:start . 51) (:id . 48))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 66) (:start . 61)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 76)\n  (:start . 67) (:id . 50))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 85)\n  (:start . 77) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 89) (:start . 86)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 98)\n  (:start . 90) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 54))\n ((:tag . "FW") (:stem . "eg") (:form . "eg") (:end . 102) (:start . 100)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 56))\n ((:tag . "NN") (:stem . "oligomerization") (:form . "oligomerization")\n  (:end . 119) (:start . 104) (:id . 57))\n ((:tag . "CD") (:stem . "15,49,87") (:form . "15,49,87") (:end . 128)\n  (:start . 120) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 59))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 133) (:start . 130)\n  (:id . 60))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 141)\n  (:start . 134) (:id . 61))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 153)\n  (:start . 142) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x6.241.1) (:span 130 133)))\n (:hscopes ((:id . :x6.241.1) (:span 130 153)))\n (:identifiers (:sid . :s6.241) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501851@unknown@formal@none@1@S@We find it encouraging that both AML1-ETO and TEL-AML1 rely on CBFß for their activity, and therefore a single compound may prove efficacious in both disease settings.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "encouraging") (:form . "encouraging") (:end . 22)\n  (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "TEL-AML1") (:form . "TEL-AML1") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "VBP") (:stem . "rely") (:form . "rely") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 77)\n  (:start . 72) (:id . 55))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 101)\n  (:start . 92) (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 110)\n  (:start . 104) (:id . 61))\n ((:tag . "NN") (:stem . "compound") (:form . "compound") (:end . 119)\n  (:start . 111) (:id . 62))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . "VB") (:stem . "prove") (:form . "prove") (:end . 129)\n  (:start . 124) (:id . 64))\n ((:tag . "JJ") (:stem . "efficacious") (:form . "efficacious") (:end . 141)\n  (:start . 130) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n  (:id . 66))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 149) (:start . 145)\n  (:id . 67))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 157)\n  (:start . 150) (:id . 68))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 166)\n  (:start . 158) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x6.242.1) (:span 120 123)))\n (:hscopes ((:id . :x6.242.1) (:span 120 166)))\n (:identifiers (:sid . :s6.242) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501852@unknown@formal@none@1@S@In fact, we predict that all the Runx1 fusion proteins will require CBFß for their activity and that an inhibitor of the Runt domain-CBFß interaction may be useful for targeting all of these proteins.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "predict") (:form . "predict") (:end . 19)\n  (:start . 12) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 47))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 49))\n ((:tag . "NN") (:stem . "runx1") (:form . "Runx1") (:end . 38) (:start . 33)\n  (:id . 50))\n ((:tag . "NN") (:stem . "fusion") (:form . "fusion") (:end . 45)\n  (:start . 39) (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 54)\n  (:start . 46) (:id . 52))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 59) (:start . 55)\n  (:id . 53))\n ((:tag . "VB") (:stem . "require") (:form . "require") (:end . 67)\n  (:start . 60) (:id . 54))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 82)\n  (:start . 77) (:id . 57))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 91)\n  (:start . 83) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 103) (:start . 101)\n  (:id . 61))\n ((:tag . "NN") (:stem . "inhibitor") (:form . "inhibitor") (:end . 113)\n  (:start . 104) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 125) (:start . 121)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "domain-CBFß") (:form . "domain-CBFß") (:end . 137)\n  (:start . 126) (:id . 66))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 149)\n  (:start . 138) (:id . 67))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 153) (:start . 150)\n  (:id . 68))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 156) (:start . 154)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 163)\n  (:start . 157) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 167) (:start . 164)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 177)\n  (:start . 168) (:id . 72))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 181) (:start . 178)\n  (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n  (:id . 74))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 190)\n  (:start . 185) (:id . 75))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 199)\n  (:start . 191) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x6.243.1) (:span 150 153)) ((:id . :x6.243.2) (:span 12 19)))\n (:hscopes ((:id . :x6.243.1) (:span 150 199))\n  ((:id . :x6.243.2) (:span 12 199)))\n (:identifiers (:sid . :s6.243) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501853@unknown@formal@none@1@S@Although CBFß is clearly important for AML1-ETO and TEL-AML1 function, the nature of its activity is not completely understood.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 47)\n  (:start . 39) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "tel-aml1") (:form . "TEL-AML1") (:end . 60)\n  (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 69)\n  (:start . 61) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 53))\n ((:tag . "NN") (:stem . "nature") (:form . "nature") (:end . 81)\n  (:start . 75) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 97)\n  (:start . 89) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 115)\n  (:start . 105) (:id . 60))\n ((:tag . "VBN") (:stem . "understand") (:form . "understood") (:end . 126)\n  (:start . 116) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s6.244) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501854@unknown@formal@none@1@S@It has long been known that CBFß increases the Runx proteins' affinity for DNA,88,89 and it was more recently shown that it protects them from ubiquitin-mediated proteolysis.37,90@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 42)\n  (:start . 33) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Runx") (:form . "Runx") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 60)\n  (:start . 52) (:id . 52))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 70)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "DNA,88,89") (:form . "DNA,88,89") (:end . 84)\n  (:start . 75) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 109)\n  (:start . 101) (:id . 61))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 115)\n  (:start . 110) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 120) (:start . 116)\n  (:id . 63))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . "VBZ") (:stem . "protect") (:form . "protects") (:end . 132)\n  (:start . 124) (:id . 65))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 137) (:start . 133)\n  (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 142) (:start . 138)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "ubiquitin-mediated") (:form . "ubiquitin-mediated")\n  (:end . 161) (:start . 143) (:id . 68))\n ((:tag . "CD") (:stem . "proteolysis.37,90") (:form . "proteolysis.37,90")\n  (:end . 179) (:start . 162) (:id . 69)))@@@1@28@((:identifiers (:sid . :s6.245) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501855@unknown@formal@none@1@S@However, genetic data in both flies and worms hint at other functions.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "worm") (:form . "worms") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "hint") (:form . "hint") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 59) (:start . 54)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 69)\n  (:start . 60) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s6.246) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501856@unknown@formal@none@1@S@For example, overexpression of a Drosophila Runt protein that could bind DNA but not CBFß dominantly inhibited its wild-type counterpart, suggesting that it was occupying its DNA binding sites but forming nonfunctional complexes.91@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 27) (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "NNP") (:stem . "Runt") (:form . "Runt") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "VB") (:stem . "bind") (:form . "bind") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 89) (:start . 85)\n  (:id . 57))\n ((:tag . "RB") (:stem . "dominantly") (:form . "dominantly") (:end . 100)\n  (:start . 90) (:id . 58))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 110)\n  (:start . 101) (:id . 59))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 114) (:start . 111)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 124)\n  (:start . 115) (:id . 61))\n ((:tag . "NN") (:stem . "counterpart") (:form . "counterpart") (:end . 136)\n  (:start . 125) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 148)\n  (:start . 138) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 153) (:start . 149)\n  (:id . 65))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 156) (:start . 154)\n  (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 160) (:start . 157)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "occupy") (:form . "occupying") (:end . 170)\n  (:start . 161) (:id . 68))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 174) (:start . 171)\n  (:id . 69))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 178) (:start . 175)\n  (:id . 70))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 186)\n  (:start . 179) (:id . 71))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 192)\n  (:start . 187) (:id . 72))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 196) (:start . 193)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 204)\n  (:start . 197) (:id . 74))\n ((:tag . "JJ") (:stem . "nonfunctional") (:form . "nonfunctional")\n  (:end . 218) (:start . 205) (:id . 75))\n ((:tag . "NN") (:stem . "complexes.91") (:form . "complexes.91") (:end . 231)\n  (:start . 219) (:id . 76)))@@@1@35@((:hcues ((:id . :x6.247.1) (:span 138 148)) ((:id . :x6.247.2) (:span 62 67)))\n (:hscopes ((:id . :x6.247.1) (:span 138 228))\n  ((:id . :x6.247.2) (:span 62 89)))\n (:identifiers (:sid . :s6.247) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501857@unknown@formal@none@1@S@More recently, it was shown that ectopic overexpression of CBFß (BRO-1) could partially restore a Runx (RNT)–deficient defect in Caenorhabditis elegans.92@(((:tag . "RBR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 40)\n  (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 55) (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "CBFß") (:form . "CBFß") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "bro-1") (:form . "BRO-1") (:end . 70) (:start . 65)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 77) (:start . 72)\n  (:id . 56))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 87)\n  (:start . 78) (:id . 57))\n ((:tag . "VB") (:stem . "restore") (:form . "restore") (:end . 95)\n  (:start . 88) (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Runx") (:form . "Runx") (:end . 102) (:start . 98)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "RNT)–deficient") (:form . "RNT)–deficient")\n  (:end . 118) (:start . 104) (:id . 62))\n ((:tag . "NN") (:stem . "defect") (:form . "defect") (:end . 125)\n  (:start . 119) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Caenorhabditis") (:form . "Caenorhabditis")\n  (:end . 143) (:start . 129) (:id . 65))\n ((:tag . "NN") (:stem . "elegans.92") (:form . "elegans.92") (:end . 154)\n  (:start . 144) (:id . 66)))@@@1@25@((:identifiers (:sid . :s6.248) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501858@unknown@formal@none@1@S@Thus we speculate that CBFß participates in the formation of protein complexes that are necessary for AML1-ETO and TEL-AML1 function in vivo.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "speculate") (:form . "speculate") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cbfß") (:form . "CBFß") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "participate") (:form . "participates") (:end . 40)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 97)\n  (:start . 88) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 101) (:start . 98)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 110)\n  (:start . 102) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 59))\n ((:tag . "NN") (:stem . "tel-aml1") (:form . "TEL-AML1") (:end . 123)\n  (:start . 115) (:id . 60))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 132)\n  (:start . 124) (:id . 61))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 62))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 140) (:start . 136)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x6.249.1) (:span 8 17)))\n (:hscopes ((:id . :x6.249.1) (:span 8 140)))\n (:identifiers (:sid . :s6.249) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501859@unknown@formal@none@1@S@If this is the case, and if the nature of those complexes differs from those formed by the wild-type Runx1-CBFß heterodimer then other protein-protein interactions specific for the fusion protein complexes could lend themselves to targeting with small molecules.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 48))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 27) (:start . 25)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 50))\n ((:tag . "NN") (:stem . "nature") (:form . "nature") (:end . 38)\n  (:start . 32) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 52))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 47) (:start . 42)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 57)\n  (:start . 48) (:id . 54))\n ((:tag . "VBZ") (:stem . "differ") (:form . "differs") (:end . 65)\n  (:start . 58) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 70) (:start . 66)\n  (:id . 56))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 76) (:start . 71)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "form") (:form . "formed") (:end . 83) (:start . 77)\n  (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 86) (:start . 84)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 100)\n  (:start . 91) (:id . 61))\n ((:tag . "NN") (:stem . "runx1-cbfß") (:form . "Runx1-CBFß") (:end . 111)\n  (:start . 101) (:id . 62))\n ((:tag . "NN") (:stem . "heterodimer") (:form . "heterodimer") (:end . 123)\n  (:start . 112) (:id . 63))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 128) (:start . 124)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 134)\n  (:start . 129) (:id . 65))\n ((:tag . "JJ") (:stem . "protein-protein") (:form . "protein-protein")\n  (:end . 150) (:start . 135) (:id . 66))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 163)\n  (:start . 151) (:id . 67))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 172)\n  (:start . 164) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 176) (:start . 173)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 180) (:start . 177)\n  (:id . 70))\n ((:tag . "NN") (:stem . "fusion") (:form . "fusion") (:end . 187)\n  (:start . 181) (:id . 71))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 195)\n  (:start . 188) (:id . 72))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 205)\n  (:start . 196) (:id . 73))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 211)\n  (:start . 206) (:id . 74))\n ((:tag . "VB") (:stem . "lend") (:form . "lend") (:end . 216) (:start . 212)\n  (:id . 75))\n ((:tag . "PRP") (:stem . "themselves") (:form . "themselves") (:end . 227)\n  (:start . 217) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 230) (:start . 228)\n  (:id . 77))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 240)\n  (:start . 231) (:id . 78))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 245) (:start . 241)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 251)\n  (:start . 246) (:id . 80))\n ((:tag . "NNS") (:stem . "molecule") (:form . "molecules") (:end . 261)\n  (:start . 252) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 262) (:start . 261)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x6.250.1) (:span 206 211)))\n (:hscopes ((:id . :x6.250.1) (:span 206 261)))\n (:identifiers (:sid . :s6.250) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501860@unknown@formal@none@1@S@It has been suggested that much of AML1-ETO's activity may be mediated in a manner that does not require binding to Runx-dependent promoters.13@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "suggest") (:form . "suggested") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "much") (:form . "much") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 43)\n  (:start . 35) (:id . 49))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 70)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 75) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 82)\n  (:start . 76) (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 87) (:start . 83)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 92) (:start . 88)\n  (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 96) (:start . 93)\n  (:id . 60))\n ((:tag . "VB") (:stem . "require") (:form . "require") (:end . 104)\n  (:start . 97) (:id . 61))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 112)\n  (:start . 105) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "runx-dependent") (:form . "Runx-dependent")\n  (:end . 130) (:start . 116) (:id . 64))\n ((:tag . "NN") (:stem . "promoters.13") (:form . "promoters.13") (:end . 143)\n  (:start . 131) (:id . 65)))@@@1@24@((:hcues ((:id . :x6.251.1) (:span 55 58)) ((:id . :x6.251.2) (:span 12 21)))\n (:hscopes ((:id . :x6.251.1) (:span 27 140))\n  ((:id . :x6.251.2) (:span 0 140)))\n (:identifiers (:sid . :s6.251) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501861@unknown@formal@none@1@S@Our data support the notion that some of AML1-ETO's activity indeed does not require either DNA or CBFß binding, in that ectopic (retroviral) expression of a mutant defective in both functions could still significantly repress granulocyte differentiation of BM cells in vitro.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . 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5501862@unknown@formal@none@1@S@Although repression of granulocyte differentiation is a consistent feature of AML1-ETO overexpression,15,25,70,73,75 it is not entirely clear how important it is to AML1-ETO's leukemogenic function.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "repression") (:form . "repression") (:end . 19)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NN") (:stem . "granulocyte") (:form . "granulocyte") (:end . 34)\n  (:start . 23) (:id . 45))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 50) (:start . 35) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 53) (:start . 51)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 55) (:start . 54)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 66)\n  (:start . 56) (:id . 49))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 74)\n  (:start . 67) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 86)\n  (:start . 78) (:id . 52))\n ((:tag . "CD") (:stem . "overexpression,15,25,70,73,75")\n  (:form . "overexpression,15,25,70,73,75") (:end . 116) (:start . 87)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 119) (:start . 117)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 122) (:start . 120)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 126) (:start . 123)\n  (:id . 56))\n ((:tag . "RB") (:stem . "entirely") (:form . "entirely") (:end . 135)\n  (:start . 127) (:id . 57))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 141)\n  (:start . 136) (:id . 58))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 145) (:start . 142)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 155)\n  (:start . 146) (:id . 60))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 158) (:start . 156)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 161) (:start . 159)\n  (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 164) (:start . 162)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 173)\n  (:start . 165) (:id . 64))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 175) (:start . 173)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "leukemogenic") (:form . "leukemogenic") (:end . 188)\n  (:start . 176) (:id . 66))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 197)\n  (:start . 189) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s6.253) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501863@unknown@formal@none@1@S@We found several AML1-ETO mutants that were able to partially repress granulocyte differentiation but had no leukemogenic activity, nor was a granulocyte differentiation defect observed in a conditional AML1-ETO knock-in model.69@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "VB") (:stem . "repress") (:form . "repress") (:end . 69)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "granulocyte") (:form . "granulocyte") (:end . 81)\n  (:start . 70) (:id . 53))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 97) (:start . 82) (:id . 54))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 101) (:start . 98)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 105) (:start . 102)\n  (:id . 56))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 108) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "leukemogenic") (:form . "leukemogenic") (:end . 121)\n  (:start . 109) (:id . 58))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 130)\n  (:start . 122) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 60))\n ((:tag . "CC") (:stem . "nor") (:form . "nor") (:end . 135) (:start . 132)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 141) (:start . 140)\n  (:id . 63))\n ((:tag . "NN") (:stem . "granulocyte") (:form . "granulocyte") (:end . 153)\n  (:start . 142) (:id . 64))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 169) (:start . 154) (:id . 65))\n ((:tag . "NN") (:stem . "defect") (:form . "defect") (:end . 176)\n  (:start . 170) (:id . 66))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 185)\n  (:start . 177) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 188) (:start . 186)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 190) (:start . 189)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "conditional") (:form . "conditional") (:end . 202)\n  (:start . 191) (:id . 70))\n ((:tag . "NN") (:stem . "aml1-eto") (:form . "AML1-ETO") (:end . 211)\n  (:start . 203) (:id . 71))\n ((:tag . "NN") (:stem . "knock-in") (:form . "knock-in") (:end . 220)\n  (:start . 212) (:id . 72))\n ((:tag . "NN") (:stem . "model.69") (:form . "model.69") (:end . 229)\n  (:start . 221) (:id . 73)))@@@1@32@((:identifiers (:sid . :s6.254) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501864@unknown@formal@none@1@S@What is clear, however, from our data and that of Yan et al,49 is that DNA binding by AML1-ETO is essential for its leukemogenic activity and that this observation must be incorporated into any mechanistic model for AML1-ETO function.@(((:tag . "WP") (:stem . "what") (:form . "What") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 22)\n  (:start . 15) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 32) (:start . 29)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 37) (:start . 33)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 51))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Yan") (:form . "Yan") (:end . 53) (:start . 50)\n  (:id . 54))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 56) (:start . 54)\n  (:id . 55))\n ((:tag . "CD") (:stem . "al,49") (:form . "al,49") (:end . 62) (:start . 57)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n  (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 70) (:start . 66)\n  (:id . 58))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 74) (:start . 71)\n  (:id . 59))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 82)\n  (:start . 75) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 85) (:start . 83)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 94)\n  (:start . 86) (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 97) (:start . 95)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 107)\n  (:start . 98) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 111) (:start . 108)\n  (:id . 65))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 115) (:start . 112)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "leukemogenic") (:form . "leukemogenic") (:end . 128)\n  (:start . 116) (:id . 67))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 137)\n  (:start . 129) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 69))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 146) (:start . 142)\n  (:id . 70))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 151) (:start . 147)\n  (:id . 71))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 163)\n  (:start . 152) (:id . 72))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 168) (:start . 164)\n  (:id . 73))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 171) (:start . 169)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "incorporate") (:form . "incorporated") (:end . 184)\n  (:start . 172) (:id . 75))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 189) (:start . 185)\n  (:id . 76))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 193) (:start . 190)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "mechanistic") (:form . "mechanistic") (:end . 205)\n  (:start . 194) (:id . 78))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 211)\n  (:start . 206) (:id . 79))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 215) (:start . 212)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "AML1-ETO") (:form . "AML1-ETO") (:end . 224)\n  (:start . 216) (:id . 81))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 233)\n  (:start . 225) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s6.255) (:did . :pmc2662647) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501865@unknown@formal@none@1@S@O-Linked N-Acetylglucosaminylation of Sp1 Inhibits the Human Immunodeficiency Virus Type 1 Promoter@(((:tag . "JJ") (:stem . "o-linked") (:form . "O-Linked") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "n-acetylglucosaminylation")\n  (:form . "N-Acetylglucosaminylation") (:end . 34) (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 41) (:start . 38)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "Inhibits") (:end . 50)\n  (:start . 42) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "human") (:form . "Human") (:end . 60) (:start . 55)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Immunodeficiency") (:form . "Immunodeficiency")\n  (:end . 77) (:start . 61) (:id . 49))\n ((:tag . "NNP") (:stem . "Virus") (:form . "Virus") (:end . 83) (:start . 78)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Type") (:form . "Type") (:end . 88) (:start . 84)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 90) (:start . 89)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Promoter") (:form . "Promoter") (:end . 99)\n  (:start . 91) (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.1) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5501866@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s7.2) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501867@unknown@formal@none@1@S@Human immunodeficiency virus type 1 (HIV-1) gene expression and replication are regulated by the promoter/enhancer located in the U3 region of the proviral 5' long terminal repeat (LTR).@(((:tag . "JJ") (:stem . "human") (:form . "Human") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "immunodeficiency") (:form . "immunodeficiency")\n  (:end . 22) (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "virus") (:form . "virus") (:end . 28) (:start . 23)\n  (:id . 44))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 33) (:start . 29)\n  (:id . 45))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 35) (:start . 34)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 59)\n  (:start . 49) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 75)\n  (:start . 64) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 89)\n  (:start . 80) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "promoter/enhancer") (:form . "promoter/enhancer")\n  (:end . 114) (:start . 97) (:id . 58))\n ((:tag . "VBN") (:stem . "locate") (:form . "located") (:end . 122)\n  (:start . 115) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 125) (:start . 123)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 61))\n ((:tag . "NN") (:stem . "u3") (:form . "U3") (:end . 132) (:start . 130)\n  (:id . 62))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 139)\n  (:start . 133) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "proviral") (:form . "proviral") (:end . 155)\n  (:start . 147) (:id . 66))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 158) (:start . 157)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 163) (:start . 159)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 172)\n  (:start . 164) (:id . 70))\n ((:tag . "NN") (:stem . "repeat") (:form . "repeat") (:end . 179)\n  (:start . 173) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 181) (:start . 180)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 184) (:start . 181)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 185) (:start . 184)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s7.3) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501868@unknown@formal@none@1@S@The binding of cellular transcription factors to specific regulatory sites in the 5' LTR is a key event in the replication cycle of HIV-1.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 37) (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 68)\n  (:start . 58) (:id . 50))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 74) (:start . 69)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 53))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "ltr") (:form . "LTR") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 103) (:start . 98)\n  (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 62))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 122)\n  (:start . 111) (:id . 63))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 128)\n  (:start . 123) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 137)\n  (:start . 132) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.4) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501869@unknown@formal@none@1@S@Since transcriptional activity is regulated by the posttranslational modification of transcription factors with the monosaccharide O-linked N-acetyl-d-glucosamine (O-GlcNAc), we evaluated whether increased O-GlcNAcylation affects HIV-1 transcription.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 21) (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 30)\n  (:start . 22) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 33) (:start . 31)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 43)\n  (:start . 34) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 46) (:start . 44)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "posttranslational") (:form . "posttranslational")\n  (:end . 68) (:start . 51) (:id . 49))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 81)\n  (:start . 69) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 51))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 98) (:start . 85) (:id . 52))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 106)\n  (:start . 99) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 111) (:start . 107)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 55))\n ((:tag . "NN") (:stem . "monosaccharide") (:form . "monosaccharide")\n  (:end . 130) (:start . 116) (:id . 56))\n ((:tag . "JJ") (:stem . "o-linked") (:form . "O-linked") (:end . 139)\n  (:start . 131) (:id . 57))\n ((:tag . "NNP") (:stem . "N-acetyl-d-glucosamine")\n  (:form . "N-acetyl-d-glucosamine") (:end . 162) (:start . 140) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 172)\n  (:start . 164) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 173) (:start . 172)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 62))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 177) (:start . 175)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "evaluate") (:form . "evaluated") (:end . 187)\n  (:start . 178) (:id . 64))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 195)\n  (:start . 188) (:id . 65))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 205)\n  (:start . 196) (:id . 66))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 221) (:start . 206) (:id . 67))\n ((:tag . "VBZ") (:stem . "affect") (:form . "affects") (:end . 229)\n  (:start . 222) (:id . 68))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 235)\n  (:start . 230) (:id . 69))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 249) (:start . 236) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 250) (:start . 249)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x7.5.1) (:span 188 195)))\n (:hscopes ((:id . :x7.5.1) (:span 188 249)))\n (:identifiers (:sid . :s7.5) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501870@unknown@formal@none@1@S@In the present study we demonstrate that treatment of HIV-1-infected lymphocytes with the O-GlcNAcylation-enhancing agent glucosamine (GlcN) repressed viral transcription in a dose-dependent manner.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 35)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "hiv-1-infected") (:form . "HIV-1-infected")\n  (:end . 68) (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 80)\n  (:start . 69) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 85) (:start . 81)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "o-glcnacylation-enhancing")\n  (:form . "O-GlcNAcylation-enhancing") (:end . 115) (:start . 90) (:id . 55))\n ((:tag . "NN") (:stem . "agent") (:form . "agent") (:end . 121)\n  (:start . 116) (:id . 56))\n ((:tag . "NN") (:stem . "glucosamine") (:form . "glucosamine") (:end . 133)\n  (:start . 122) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 139) (:start . 135)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "repress") (:form . "repressed") (:end . 150)\n  (:start . 141) (:id . 61))\n ((:tag . "JJ") (:stem . "viral") (:form . "viral") (:end . 156)\n  (:start . 151) (:id . 62))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 170) (:start . 157) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 173) (:start . 171)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 175) (:start . 174)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "dose-dependent") (:form . "dose-dependent")\n  (:end . 190) (:start . 176) (:id . 66))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 197)\n  (:start . 191) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.6) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501871@unknown@formal@none@1@S@Overexpression of O-GlcNAc transferase (OGT), the sole known enzyme catalyzing the addition of O-GlcNAc to proteins, specifically inhibited the activity of the HIV-1 LTR promoter in different T-cell lines and in primary CD4+ T lymphocytes.@(((:tag . "NNP") (:stem . "Overexpression") (:form . "Overexpression")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 26)\n  (:start . 18) (:id . 44))\n ((:tag . "NN") (:stem . "transferase") (:form . "transferase") (:end . 38)\n  (:start . 27) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "sole") (:form . "sole") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "enzyme") (:form . "enzyme") (:end . 67)\n  (:start . 61) (:id . 53))\n ((:tag . "VBG") (:stem . "catalyze") (:form . "catalyzing") (:end . 78)\n  (:start . 68) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 91)\n  (:start . 83) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 103)\n  (:start . 95) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 115)\n  (:start . 107) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 129)\n  (:start . 117) (:id . 62))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 139)\n  (:start . 130) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 64))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 152)\n  (:start . 144) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 165)\n  (:start . 160) (:id . 68))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 169) (:start . 166)\n  (:id . 69))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 178)\n  (:start . 170) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 181) (:start . 179)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 191)\n  (:start . 182) (:id . 72))\n ((:tag . "NN") (:stem . "t-cell") (:form . "T-cell") (:end . 198)\n  (:start . 192) (:id . 73))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 204)\n  (:start . 199) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 208) (:start . 205)\n  (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 211) (:start . 209)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 219)\n  (:start . 212) (:id . 77))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 224) (:start . 220)\n  (:id . 78))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 226) (:start . 225)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 238)\n  (:start . 227) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s7.7) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501872@unknown@formal@none@1@S@Inhibition of HIV-1 LTR activity in infected T cells was most efficient (>95%) when OGT was recombinantly overexpressed prior to infection.@(((:tag . "NNP") (:stem . "Inhibition") (:form . "Inhibition") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "infected") (:form . "infected") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 71)\n  (:start . 62) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "CD") (:stem . ">95") (:form . ">95") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 57))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 83) (:start . 79)\n  (:id . 58))\n ((:tag . "NN") (:stem . "ogt") (:form . "OGT") (:end . 87) (:start . 84)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 91) (:start . 88)\n  (:id . 60))\n ((:tag . "RB") (:stem . "recombinantly") (:form . "recombinantly")\n  (:end . 105) (:start . 92) (:id . 61))\n ((:tag . "VBN") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 119) (:start . 106) (:id . 62))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 125)\n  (:start . 120) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 128) (:start . 126)\n  (:id . 64))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 138)\n  (:start . 129) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.8) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501873@unknown@formal@none@1@S@O-GlcNAcylation of the transcription factor Sp1 and the presence of Sp1-binding sites in the LTR were found to be crucial for this inhibitory effect.@(((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 36) (:start . 23) (:id . 45))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 43)\n  (:start . 37) (:id . 46))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 47) (:start . 44)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 79)\n  (:start . 68) (:id . 52))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 85) (:start . 80)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "ltr") (:form . "LTR") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 101) (:start . 97)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 107)\n  (:start . 102) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 121)\n  (:start . 114) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 125) (:start . 122)\n  (:id . 62))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 130) (:start . 126)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 141)\n  (:start . 131) (:id . 64))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 148)\n  (:start . 142) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.9) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501874@unknown@formal@none@1@S@From this study, we conclude that O-GlcNAcylation of Sp1 inhibits the activity of the HIV-1 LTR promoter.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 49) (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 65)\n  (:start . 57) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 91) (:start . 86)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 104)\n  (:start . 96) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.10) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501875@unknown@formal@none@1@S@Modulation of Sp1 O-GlcNAcylation may play a role in the regulation of HIV-1 latency and activation and links viral replication to the glucose metabolism of the host cell.@(((:tag . "NN") (:stem . "modulation") (:form . "Modulation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 33) (:start . 18) (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 76) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "latency") (:form . "latency") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 99)\n  (:start . 89) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "link") (:form . "links") (:end . 109)\n  (:start . 104) (:id . 59))\n ((:tag . "JJ") (:stem . "viral") (:form . "viral") (:end . 115)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 127)\n  (:start . 116) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "NN") (:stem . "glucose") (:form . "glucose") (:end . 142)\n  (:start . 135) (:id . 64))\n ((:tag . "NN") (:stem . "metabolism") (:form . "metabolism") (:end . 153)\n  (:start . 143) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 156) (:start . 154)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 160) (:start . 157)\n  (:id . 67))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 165) (:start . 161)\n  (:id . 68))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 170) (:start . 166)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x7.11.1) (:span 34 37)))\n (:hscopes ((:id . :x7.11.1) (:span 34 99)))\n (:identifiers (:sid . :s7.11) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501876@unknown@formal@none@1@S@Hence, the establishment of a metabolic treatment might supplement the repertoire of antiretroviral therapies against AIDS.@(((:tag . "RB") (:stem . "hence") (:form . "Hence") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "establishment") (:form . "establishment")\n  (:end . 24) (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "metabolic") (:form . "metabolic") (:end . 39)\n  (:start . 30) (:id . 48))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "VB") (:stem . "supplement") (:form . "supplement") (:end . 66)\n  (:start . 56) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "repertoire") (:form . "repertoire") (:end . 81)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "antiretroviral") (:form . "antiretroviral")\n  (:end . 99) (:start . 85) (:id . 55))\n ((:tag . "NNS") (:stem . "therapy") (:form . "therapies") (:end . 109)\n  (:start . 100) (:id . 56))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 117)\n  (:start . 110) (:id . 57))\n ((:tag . "NNP") (:stem . "AIDS") (:form . "AIDS") (:end . 122) (:start . 118)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x7.12.1) (:span 50 55)))\n (:hscopes ((:id . :x7.12.1) (:span 50 122)))\n (:identifiers (:sid . :s7.12) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501877@unknown@formal@none@1@S@ @(((:tag . "LS") (:stem . " ") (:form . " ") (:end . 1) (:start . 0)\n  (:id . 42)))@@@1@1@((:identifiers (:sid . :s7.13) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501878@unknown@formal@none@1@S@Human immunodeficiency virus type 1 (HIV-1) gene expression is regulated by the long terminal repeat (LTR) promoter, which is composed of three regions: U3 (unique 3' end), R (repeated), and U5 (unique 5' end).@(((:tag . "JJ") (:stem . "human") (:form . "Human") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "immunodeficiency") (:form . "immunodeficiency")\n  (:end . 22) (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "virus") (:form . "virus") (:end . 28) (:start . 23)\n  (:id . 44))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 33) (:start . 29)\n  (:id . 45))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 35) (:start . 34)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . 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5501879@unknown@formal@none@1@S@The U3 region contains an upstream regulatory element including binding sites for several cellular transcription factors such as the nuclear factor of activated T cells 1 (NFATc1) and the activator protein 1 (AP-1), an enhancer with two binding sites for the nuclear factor κB (NF-κB), and the core promoter composed of three tandem binding sites for specificity protein 1 (Sp1) and a TATA box.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "u3") (:form . "U3") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . 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5501880@unknown@formal@none@1@S@While NF-κB is a strong enhancer of HIV-1 transcription (8), Sp1 is essential for basal transcription and Tat-mediated activation of HIV-1 (25, 69).@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "enhancer") (:form . "enhancer") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 55) (:start . 42) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 64) (:start . 61)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 67) (:start . 65)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 77)\n  (:start . 68) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 81) (:start . 78)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "basal") (:form . "basal") (:end . 87) (:start . 82)\n  (:id . 59))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 101) (:start . 88) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "tat-mediated") (:form . "Tat-mediated") (:end . 118)\n  (:start . 106) (:id . 62))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 129)\n  (:start . 119) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 138)\n  (:start . 133) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 66))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 142) (:start . 140)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 68))\n ((:tag . "CD") (:stem . "69") (:form . "69") (:end . 146) (:start . 144)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.16) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501881@unknown@formal@none@1@S@This is concordant with the fact that Sp1 is upregulated in activated T cells (43), which compose the primary reservoir for HIV-1 replication (68).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "concordant") (:form . "concordant") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "upregulate") (:form . "upregulated") (:end . 56)\n  (:start . 45) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 69)\n  (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 81) (:start . 79)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 89) (:start . 84)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "compose") (:form . "compose") (:end . 97)\n  (:start . 90) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 109)\n  (:start . 102) (:id . 63))\n ((:tag . "NN") (:stem . "reservoir") (:form . "reservoir") (:end . 119)\n  (:start . 110) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 123) (:start . 120)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 129)\n  (:start . 124) (:id . 66))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 141)\n  (:start . 130) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 68))\n ((:tag . "CD") (:stem . "68") (:form . "68") (:end . 145) (:start . 143)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.17) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501882@unknown@formal@none@1@S@Importantly, deletion of all three Sp1-binding sites reduces viral replication in human T-cell cultures (58).@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 46)\n  (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "reduce") (:form . "reduces") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . "JJ") (:stem . "viral") (:form . "viral") (:end . 66) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 78)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 87) (:start . 82)\n  (:id . 54))\n ((:tag . "NN") (:stem . "t-cell") (:form . "T-cell") (:end . 94)\n  (:start . 88) (:id . 55))\n ((:tag . "NNS") (:stem . "culture") (:form . "cultures") (:end . 103)\n  (:start . 95) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n  (:id . 57))\n ((:tag . "CD") (:stem . "58") (:form . "58") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.18) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501883@unknown@formal@none@1@S@In eukaryotic cells, myriad cytoplasmic and nuclear proteins are posttranslationally modified at the hydroxyl groups of specific serine and threonine residues by a single monosaccharide, N-acetyl-d-glucosamine (GlcNAc) (26, 80).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "eukaryotic") (:form . "eukaryotic") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "myriad") (:form . "myriad") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 39)\n  (:start . 28) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 60)\n  (:start . 52) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "RB") (:stem . "posttranslationally")\n  (:form . "posttranslationally") (:end . 84) (:start . 65) (:id . 52))\n ((:tag . "VBN") (:stem . "modify") (:form . "modified") (:end . 93)\n  (:start . 85) (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 96) (:start . 94)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 55))\n ((:tag . "NN") (:stem . "hydroxyl") (:form . "hydroxyl") (:end . 109)\n  (:start . 101) (:id . 56))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 116)\n  (:start . 110) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 128)\n  (:start . 120) (:id . 59))\n ((:tag . "NN") (:stem . "serine") (:form . "serine") (:end . 135)\n  (:start . 129) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 61))\n ((:tag . "NN") (:stem . "threonine") (:form . "threonine") (:end . 149)\n  (:start . 140) (:id . 62))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 158)\n  (:start . 150) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 161) (:start . 159)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 163) (:start . 162)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 170)\n  (:start . 164) (:id . 66))\n ((:tag . "NN") (:stem . "monosaccharide") (:form . "monosaccharide")\n  (:end . 185) (:start . 171) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 186) (:start . 185)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "N-acetyl-d-glucosamine")\n  (:form . "N-acetyl-d-glucosamine") (:end . 209) (:start . 187) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 211) (:start . 210)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "GlcNAc") (:form . "GlcNAc") (:end . 217)\n  (:start . 211) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 218) (:start . 217)\n  (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 220) (:start . 219)\n  (:id . 73))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 222) (:start . 220)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 223) (:start . 222)\n  (:id . 75))\n ((:tag . "CD") (:stem . "80") (:form . "80") (:end . 226) (:start . 224)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 227) (:start . 226)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s7.19) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501884@unknown@formal@none@1@S@The O-glycosidic linkage of GlcNAc to proteins is a highly dynamic and reversible posttranslational modification and differs from other glycosylation events in that it occurs in the cytosol and the nucleus rather than in the Golgi apparatus or the endoplasmic reticulum.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "o-glycosidic") (:form . "O-glycosidic") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "linkage") (:form . "linkage") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "GlcNAc") (:form . "GlcNAc") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 58)\n  (:start . 52) (:id . 51))\n ((:tag . "JJ") (:stem . "dynamic") (:form . "dynamic") (:end . 66)\n  (:start . 59) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "reversible") (:form . "reversible") (:end . 81)\n  (:start . 71) (:id . 54))\n ((:tag . "JJ") (:stem . "posttranslational") (:form . "posttranslational")\n  (:end . 99) (:start . 82) (:id . 55))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 112)\n  (:start . 100) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "differ") (:form . "differs") (:end . 124)\n  (:start . 117) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 129) (:start . 125)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 135)\n  (:start . 130) (:id . 60))\n ((:tag . "NN") (:stem . "glycosylation") (:form . "glycosylation")\n  (:end . 149) (:start . 136) (:id . 61))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 156)\n  (:start . 150) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 159) (:start . 157)\n  (:id . 63))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 164) (:start . 160)\n  (:id . 64))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 167) (:start . 165)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 174)\n  (:start . 168) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 177) (:start . 175)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 181) (:start . 178)\n  (:id . 68))\n ((:tag . "NN") (:stem . "cytosol") (:form . "cytosol") (:end . 189)\n  (:start . 182) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 193) (:start . 190)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n  (:id . 71))\n ((:tag . "NN") (:stem . "nucleus") (:form . "nucleus") (:end . 205)\n  (:start . 198) (:id . 72))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 212)\n  (:start . 206) (:id . 73))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 217) (:start . 213)\n  (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 220) (:start . 218)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 224) (:start . 221)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Golgi") (:form . "Golgi") (:end . 230)\n  (:start . 225) (:id . 77))\n ((:tag . "NN") (:stem . "apparatus") (:form . "apparatus") (:end . 240)\n  (:start . 231) (:id . 78))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 243) (:start . 241)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 247) (:start . 244)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "endoplasmic") (:form . "endoplasmic") (:end . 259)\n  (:start . 248) (:id . 81))\n ((:tag . "NN") (:stem . "reticulum") (:form . "reticulum") (:end . 269)\n  (:start . 260) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s7.20) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501885@unknown@formal@none@1@S@Protein O-linked N-acetyl-d-glucosaminylation (O-GlcNAcylation) is catalyzed by O-GlcNAc transferase (OGT) and reversed by O-GlcNAc hexosaminidase (O-GlcNAcase) (30).@(((:tag . "NN") (:stem . "protein") (:form . "Protein") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "o-linked") (:form . "O-linked") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "NNP") (:stem . "N-acetyl-d-glucosaminylation")\n  (:form . "N-acetyl-d-glucosaminylation") (:end . 45) (:start . 17)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 47) (:start . 46)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "O-GlcNAcylation") (:form . "O-GlcNAcylation")\n  (:end . 62) (:start . 47) (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 66) (:start . 64)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "catalyze") (:form . "catalyzed") (:end . 76)\n  (:start . 67) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 79) (:start . 77)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 88)\n  (:start . 80) (:id . 51))\n ((:tag . "NN") (:stem . "transferase") (:form . "transferase") (:end . 100)\n  (:start . 89) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 105) (:start . 102)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "reverse") (:form . "reversed") (:end . 119)\n  (:start . 111) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 122) (:start . 120)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 131)\n  (:start . 123) (:id . 59))\n ((:tag . "NNP") (:stem . "hexosaminidase") (:form . "hexosaminidase")\n  (:end . 146) (:start . 132) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "O-GlcNAcase") (:form . "O-GlcNAcase") (:end . 159)\n  (:start . 148) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 64))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 164) (:start . 162)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.21) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501886@unknown@formal@none@1@S@The substrate for protein O-GlcNAcylation is UDP-GlcNAc.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "substrate") (:form . "substrate") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 41) (:start . 26) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "UDP-GlcNAc") (:form . "UDP-GlcNAc") (:end . 55)\n  (:start . 45) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s7.22) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501887@unknown@formal@none@1@S@Therefore, O- GlcNAcylation is regulated by the cellular levels of OGT and O-GlcNAcase and by the availability of UDP-GlcNAc (81).@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "O-") (:form . "O-") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "GlcNAcylation") (:form . "GlcNAcylation")\n  (:end . 27) (:start . 14) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 40)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 63)\n  (:start . 57) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "O-GlcNAcase") (:form . "O-GlcNAcase") (:end . 86)\n  (:start . 75) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "availability") (:form . "availability") (:end . 110)\n  (:start . 98) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "UDP-GlcNAc") (:form . "UDP-GlcNAc") (:end . 124)\n  (:start . 114) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 62))\n ((:tag . "CD") (:stem . "81") (:form . "81") (:end . 128) (:start . 126)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.23) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501888@unknown@formal@none@1@S@As UDP-GlcNAc is synthesized de novo from glucose via the hexosamine biosynthetic pathway, glucose flux through the hexosamine biosynthetic pathway increases O-GlcNAcylation of proteins.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "UDP-GlcNAc") (:form . "UDP-GlcNAc") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "synthesize") (:form . "synthesized") (:end . 28)\n  (:start . 17) (:id . 45))\n ((:tag . "FW") (:stem . "de") (:form . "de") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "FW") (:stem . "novo") (:form . "novo") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "glucose") (:form . "glucose") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "hexosamine") (:form . "hexosamine") (:end . 68)\n  (:start . 58) (:id . 52))\n ((:tag . "JJ") (:stem . "biosynthetic") (:form . "biosynthetic") (:end . 81)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 89)\n  (:start . 82) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "glucose") (:form . "glucose") (:end . 98)\n  (:start . 91) (:id . 56))\n ((:tag . "NN") (:stem . "flux") (:form . "flux") (:end . 103) (:start . 99)\n  (:id . 57))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 111)\n  (:start . 104) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 59))\n ((:tag . "NN") (:stem . "hexosamine") (:form . "hexosamine") (:end . 126)\n  (:start . 116) (:id . 60))\n ((:tag . "JJ") (:stem . "biosynthetic") (:form . "biosynthetic") (:end . 139)\n  (:start . 127) (:id . 61))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 147)\n  (:start . 140) (:id . 62))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 157)\n  (:start . 148) (:id . 63))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 173) (:start . 158) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 185)\n  (:start . 177) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.24) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501889@unknown@formal@none@1@S@Furthermore, compounds like glucosamine (GlcN), streptozotocin, O-(2-acetamido-2-deoxy-d-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc), and 2-deoxyglucose enhance O-GlcNAcylation of proteins either by increasing the availability of UDP-GlcNAc or by inhibiting the enzyme O-GlcNAcase (23, 37, 63).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "compound") (:form . "compounds") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "glucosamine") (:form . "glucosamine") (:end . 39)\n  (:start . 28) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "streptozotocin") (:form . "streptozotocin")\n  (:end . 62) (:start . 48) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "NNP")\n  (:stem\n   . "O-(2-acetamido-2-deoxy-d-glucopyranosylidene)amino-N-phenylcarbamate")\n  (:form\n   . "O-(2-acetamido-2-deoxy-d-glucopyranosylidene)amino-N-phenylcarbamate")\n  (:end . 132) (:start . 64) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "PUGNAc") (:form . "PUGNAc") (:end . 140)\n  (:start . 134) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 146) (:start . 143)\n  (:id . 58))\n ((:tag . "NN") (:stem . "2-deoxyglucose") (:form . "2-deoxyglucose")\n  (:end . 161) (:start . 147) (:id . 59))\n ((:tag . "VBP") (:stem . "enhance") (:form . "enhance") (:end . 169)\n  (:start . 162) (:id . 60))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 185) (:start . 170) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 188) (:start . 186)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 197)\n  (:start . 189) (:id . 63))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 204)\n  (:start . 198) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 207) (:start . 205)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 218)\n  (:start . 208) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 222) (:start . 219)\n  (:id . 67))\n ((:tag . "NN") (:stem . "availability") (:form . "availability") (:end . 235)\n  (:start . 223) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 238) (:start . 236)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "UDP-GlcNAc") (:form . "UDP-GlcNAc") (:end . 249)\n  (:start . 239) (:id . 70))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 252) (:start . 250)\n  (:id . 71))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 255) (:start . 253)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "inhibit") (:form . "inhibiting") (:end . 266)\n  (:start . 256) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 270) (:start . 267)\n  (:id . 74))\n ((:tag . "NN") (:stem . "enzyme") (:form . "enzyme") (:end . 277)\n  (:start . 271) (:id . 75))\n ((:tag . "NN") (:stem . "o-glcnacase") (:form . "O-GlcNAcase") (:end . 289)\n  (:start . 278) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 291) (:start . 290)\n  (:id . 77))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 293) (:start . 291)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 294) (:start . 293)\n  (:id . 79))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 297) (:start . 295)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 298) (:start . 297)\n  (:id . 81))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 301) (:start . 299)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 302) (:start . 301)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 303) (:start . 302)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s7.25) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501890@unknown@formal@none@1@S@Protein O-GlcNAcylation has been shown to modulate (i) enzyme activity, (ii) protein-protein interactions, (iii) DNA-binding affinity, (iv) subcellular localization, and (v) the half-life and proteolytic processing of proteins (81).@(((:tag . "NN") (:stem . "protein") (:form . "Protein") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 23) (:start . 8) (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 27) (:start . 24)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 32) (:start . 28)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 38) (:start . 33)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "VB") (:stem . "modulate") (:form . "modulate") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "LS") (:stem . "i") (:form . "i") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "enzyme") (:form . "enzyme") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 70)\n  (:start . 62) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "LS") (:stem . "ii") (:form . "ii") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "protein-protein") (:form . "protein-protein")\n  (:end . 92) (:start . 77) (:id . 58))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 105)\n  (:start . 93) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . "LS") (:stem . "iii") (:form . "iii") (:end . 111) (:start . 108)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "dna-binding") (:form . "DNA-binding") (:end . 124)\n  (:start . 113) (:id . 64))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 133)\n  (:start . 125) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 136) (:start . 135)\n  (:id . 67))\n ((:tag . "LS") (:stem . "iv") (:form . "iv") (:end . 138) (:start . 136)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "subcellular") (:form . "subcellular") (:end . 151)\n  (:start . 140) (:id . 70))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 164)\n  (:start . 152) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 169) (:start . 166)\n  (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 171) (:start . 170)\n  (:id . 74))\n ((:tag . "LS") (:stem . "v") (:form . "v") (:end . 172) (:start . 171)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 173) (:start . 172)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 77))\n ((:tag . "NN") (:stem . "half-life") (:form . "half-life") (:end . 187)\n  (:start . 178) (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 191) (:start . 188)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "proteolytic") (:form . "proteolytic") (:end . 203)\n  (:start . 192) (:id . 80))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 214)\n  (:start . 204) (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 217) (:start . 215)\n  (:id . 82))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 226)\n  (:start . 218) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 228) (:start . 227)\n  (:id . 84))\n ((:tag . "CD") (:stem . "81") (:form . "81") (:end . 230) (:start . 228)\n  (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 231) (:start . 230)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s7.26) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501891@unknown@formal@none@1@S@Furthermore, O-GlcNAcylation often plays an antagonistic role in relation to phosphorylation (36).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "O-GlcNAcylation") (:form . "O-GlcNAcylation")\n  (:end . 28) (:start . 13) (:id . 44))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 34) (:start . 29)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "play") (:form . "plays") (:end . 40) (:start . 35)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "antagonistic") (:form . "antagonistic") (:end . 56)\n  (:start . 44) (:id . 48))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 61) (:start . 57)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "NN") (:stem . "relation") (:form . "relation") (:end . 73)\n  (:start . 65) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n  (:id . 52))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 92) (:start . 77) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 54))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 96) (:start . 94)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.27) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501892@unknown@formal@none@1@S@The dynamic interplay between O-GlcNAcylation and phosphorylation has therefore been proposed to control protein-protein interactions and protein functions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "dynamic") (:form . "dynamic") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "interplay") (:form . "interplay") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 45) (:start . 30) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 47))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 65) (:start . 50) (:id . 48))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 69) (:start . 66)\n  (:id . 49))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 79)\n  (:start . 70) (:id . 50))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 84) (:start . 80)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 93)\n  (:start . 85) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 96) (:start . 94)\n  (:id . 53))\n ((:tag . "VB") (:stem . "control") (:form . "control") (:end . 104)\n  (:start . 97) (:id . 54))\n ((:tag . "JJ") (:stem . "protein-protein") (:form . "protein-protein")\n  (:end . 120) (:start . 105) (:id . 55))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 133)\n  (:start . 121) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 145)\n  (:start . 138) (:id . 58))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 155)\n  (:start . 146) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x7.28.1) (:span 85 93)))\n (:hscopes ((:id . :x7.28.1) (:span 0 155)))\n (:identifiers (:sid . :s7.28) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501893@unknown@formal@none@1@S@Furthermore, O-GlcNAc plays a pivotal role in the regulation of gene expression via modification of RNA polymerase II (12, 39) and associated transcription factors (31, 32).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "play") (:form . "plays") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "pivotal") (:form . "pivotal") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 60)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 79)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 96)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 114)\n  (:start . 104) (:id . 59))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 119) (:start . 118)\n  (:id . 61))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . "CD") (:stem . "39") (:form . "39") (:end . 125) (:start . 123)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 141)\n  (:start . 131) (:id . 67))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 155) (:start . 142) (:id . 68))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 163)\n  (:start . 156) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 165) (:start . 164)\n  (:id . 70))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 167) (:start . 165)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 72))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 171) (:start . 169)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s7.29) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501894@unknown@formal@none@1@S@Thus, O-GlcNAc serves as a nutrient sensor to couple the metabolic status to cellular processes, such as protein degradation, signal transduction, and gene transcription.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 14)\n  (:start . 6) (:id . 44))\n ((:tag . "VBZ") (:stem . "serve") (:form . "serves") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "nutrient") (:form . "nutrient") (:end . 35)\n  (:start . 27) (:id . 48))\n ((:tag . "NN") (:stem . "sensor") (:form . "sensor") (:end . 42)\n  (:start . 36) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "VB") (:stem . "couple") (:form . "couple") (:end . 52)\n  (:start . 46) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "metabolic") (:form . "metabolic") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "status") (:form . "status") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 85)\n  (:start . 77) (:id . 56))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 95)\n  (:start . 86) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 101) (:start . 97)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 112)\n  (:start . 105) (:id . 61))\n ((:tag . "NN") (:stem . "degradation") (:form . "degradation") (:end . 124)\n  (:start . 113) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 63))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 132)\n  (:start . 126) (:id . 64))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 145)\n  (:start . 133) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 67))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 155) (:start . 151)\n  (:id . 68))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 169) (:start . 156) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s7.30) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501895@unknown@formal@none@1@S@Some of the transcription factors involved in HIV-1 gene regulation are modified by O-GlcNAc, including AP-1 (67), yin-yang 1 (YY1) (28), NFATc1 (21), NF-κB (21), and Sp1 (31, 62).@(((:tag . "DT") (:stem . "some") (:form . "Some") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 25) (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 51) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 67)\n  (:start . 57) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "modify") (:form . "modified") (:end . 80)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 83) (:start . 81)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 92)\n  (:start . 84) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 103)\n  (:start . 94) (:id . 57))\n ((:tag . "NN") (:stem . "ap-1") (:form . "AP-1") (:end . 108) (:start . 104)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 59))\n ((:tag . "CD") (:stem . "67") (:form . "67") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 62))\n ((:tag . "NN") (:stem . "yin-yang") (:form . "yin-yang") (:end . 123)\n  (:start . 115) (:id . 63))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "YY1") (:form . "YY1") (:end . 130) (:start . 127)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 68))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 135) (:start . 133)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "NFATc1") (:form . "NFATc1") (:end . 144)\n  (:start . 138) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n  (:id . 73))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 148) (:start . 146)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 156)\n  (:start . 151) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 158) (:start . 157)\n  (:id . 78))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 160) (:start . 158)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n  (:id . 82))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 170) (:start . 167)\n  (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 84))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 174) (:start . 172)\n  (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 86))\n ((:tag . "CD") (:stem . "62") (:form . "62") (:end . 178) (:start . 176)\n  (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s7.31) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501896@unknown@formal@none@1@S@Sp1 was the first transcription factor identified as being O-GlcNAcylated (31).@(((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 31) (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 49)\n  (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 58) (:start . 53)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "o-glcnacylate") (:form . "O-GlcNAcylated")\n  (:end . 73) (:start . 59) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.32) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501897@unknown@formal@none@1@S@Sp1 is ubiquitous and belongs to the Sp1-like/Krüppel-like family of transcription factors characterized by three C-terminal Cys2His2 zinc finger motifs (34) and a DNA-binding affinity to GC-rich sites (16).@(((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "ubiquitous") (:form . "ubiquitous") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "belong") (:form . "belongs") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "sp1-like/krüppel-like")\n  (:form . "Sp1-like/Krüppel-like") (:end . 58) (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 65)\n  (:start . 59) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 82) (:start . 69) (:id . 52))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 90)\n  (:start . 83) (:id . 53))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n  (:end . 104) (:start . 91) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 107) (:start . 105)\n  (:id . 55))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 113)\n  (:start . 108) (:id . 56))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 124)\n  (:start . 114) (:id . 57))\n ((:tag . "NN") (:stem . "cys2his2") (:form . "Cys2His2") (:end . 133)\n  (:start . 125) (:id . 58))\n ((:tag . "NN") (:stem . "zinc") (:form . "zinc") (:end . 138) (:start . 134)\n  (:id . 59))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 145)\n  (:start . 139) (:id . 60))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 152)\n  (:start . 146) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 62))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 156) (:start . 154)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 163) (:start . 162)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "dna-binding") (:form . "DNA-binding") (:end . 175)\n  (:start . 164) (:id . 67))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 184)\n  (:start . 176) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 187) (:start . 185)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "gc-rich") (:form . "GC-rich") (:end . 195)\n  (:start . 188) (:id . 70))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 201)\n  (:start . 196) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 203) (:start . 202)\n  (:id . 72))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 205) (:start . 203)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s7.33) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501898@unknown@formal@none@1@S@Two decades ago, Tjian and coworkers showed that Sp1 bears at least eight O-GlcNAc sites and that the O-GlcNAcylated form of Sp1 was more active than the non-O-GlcNAcylated protein (31).@(((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "decade") (:form . "decades") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "ago") (:form . "ago") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "tjian") (:form . "Tjian") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "coworker") (:form . "coworkers") (:end . 36)\n  (:start . 27) (:id . 48))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 43) (:start . 37)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "bear") (:form . "bears") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . "CD") (:stem . "eight") (:form . "eight") (:end . 73) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "o-glcnac") (:form . "O-GlcNAc") (:end . 82)\n  (:start . 74) (:id . 56))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 88) (:start . 83)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 97) (:start . 93)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "o-glcnacylated") (:form . "O-GlcNAcylated")\n  (:end . 116) (:start . 102) (:id . 61))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 121) (:start . 117)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 128) (:start . 125)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 132) (:start . 129)\n  (:id . 65))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 137) (:start . 133)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 144)\n  (:start . 138) (:id . 67))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 149) (:start . 145)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "non-o-glcnacylated") (:form . "non-O-GlcNAcylated")\n  (:end . 172) (:start . 154) (:id . 70))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 180)\n  (:start . 173) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 182) (:start . 181)\n  (:id . 72))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 184) (:start . 182)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 185) (:start . 184)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s7.34) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501899@unknown@formal@none@1@S@In the meantime, other studies revealed that O-GlcNAcylation of Sp1 can also result in a reduction of transcriptional activation (62, 77), indicating that the specific effect of O-GlcNAcylation on Sp1 activity strongly depends on the targeted promoter.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "meantime") (:form . "meantime") (:end . 15)\n  (:start . 7) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 30)\n  (:start . 23) (:id . 47))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 60) (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "VB") (:stem . "result") (:form . "result") (:end . 83)\n  (:start . 77) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 88) (:start . 87)\n  (:id . 57))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 98)\n  (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 117) (:start . 102) (:id . 60))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 128)\n  (:start . 118) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "CD") (:stem . "62") (:form . "62") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "CD") (:stem . "77") (:form . "77") (:end . 136) (:start . 134)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 149)\n  (:start . 139) (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 154) (:start . 150)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 167)\n  (:start . 159) (:id . 71))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 174)\n  (:start . 168) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n  (:id . 73))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 193) (:start . 178) (:id . 74))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 196) (:start . 194)\n  (:id . 75))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 200) (:start . 197)\n  (:id . 76))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 209)\n  (:start . 201) (:id . 77))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 218)\n  (:start . 210) (:id . 78))\n ((:tag . "VBZ") (:stem . "depend") (:form . "depends") (:end . 226)\n  (:start . 219) (:id . 79))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 229) (:start . 227)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 233) (:start . 230)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "target") (:form . "targeted") (:end . 242)\n  (:start . 234) (:id . 82))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 251)\n  (:start . 243) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x7.35.1) (:span 139 154)) ((:id . :x7.35.2) (:span 68 71)))\n (:hscopes ((:id . :x7.35.1) (:span 139 251))\n  ((:id . :x7.35.2) (:span 68 251)))\n (:identifiers (:sid . :s7.35) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501900@unknown@formal@none@1@S@Since Sp1 is critical and important for HIV-1 transcription (25) and Sp1 activity is modulated by O-GlcNAc (42), we investigated the effect of Sp1 O-GlcNAcylation on the activity of the HIV-1 LTR promoter.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 59) (:start . 46) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 51))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 81)\n  (:start . 73) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 84) (:start . 82)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "modulate") (:form . "modulated") (:end . 94)\n  (:start . 85) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 106)\n  (:start . 98) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 115) (:start . 113)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "investigate") (:form . "investigated") (:end . 128)\n  (:start . 116) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 67))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 139)\n  (:start . 133) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 69))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 146) (:start . 143)\n  (:id . 70))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 162) (:start . 147) (:id . 71))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 165) (:start . 163)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n  (:id . 73))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 178)\n  (:start . 170) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 181) (:start . 179)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 191)\n  (:start . 186) (:id . 77))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 195) (:start . 192)\n  (:id . 78))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 204)\n  (:start . 196) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s7.36) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501901@unknown@formal@none@1@S@Here we show that an increased O-GlcNAc level represses the HIV-1 LTR promoter activity.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 30)\n  (:start . 21) (:id . 47))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "repress") (:form . "represses") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 65) (:start . 60)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 87)\n  (:start . 79) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.37) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501902@unknown@formal@none@1@S@This required O-GlcNAcylation of Sp1 and the presence of Sp1-binding sites in the HIV-1 LTR.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "required") (:form . "required") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 29) (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 53)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 68)\n  (:start . 57) (:id . 51))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 87) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.38) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501903@unknown@formal@none@1@S@Thus, modulation of Sp1 O-GlcNAcylation may be useful as a potential therapeutic approach for the inhibition of HIV-1 replication.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "modulation") (:form . "modulation") (:end . 16)\n  (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 39) (:start . 24) (:id . 47))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 53)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 68)\n  (:start . 59) (:id . 53))\n ((:tag . "JJ") (:stem . "therapeutic") (:form . "therapeutic") (:end . 80)\n  (:start . 69) (:id . 54))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 89)\n  (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 93) (:start . 90)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 57))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 108)\n  (:start . 98) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 117)\n  (:start . 112) (:id . 60))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 129)\n  (:start . 118) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x7.39.1) (:span 59 68)) ((:id . :x7.39.2) (:span 40 43)))\n (:hscopes ((:id . :x7.39.1) (:span 59 129)) ((:id . :x7.39.2) (:span 40 129)))\n (:identifiers (:sid . :s7.39) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501904@unknown@formal@none@1@S@MATERIALS AND METHODS@(((:tag . "NNP") (:stem . "MATERIALS") (:form . "MATERIALS") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "AND") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "METHODS") (:form . "METHODS") (:end . 21)\n  (:start . 14) (:id . 44)))@@@1@3@((:identifiers (:sid . :s7.40) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5501905@unknown@formal@none@1@S@Jurkat and T1 (174 × CEM.T1) cells were maintained in very-low-endotoxin-Roswell Park Memorial Institute (RPMI) 1640 medium (Biochrom, Berlin, Germany) supplemented with 10% fetal calf serum (FCS; Biochrom) and 2 mM l-glutamine (PAA, Cölbe, Germany) at 37°C in a humidified atmosphere at 5% CO2.@(((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "T1") (:form . "T1") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "CD") (:stem . "174") (:form . "174") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "×") (:form . "×") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cem.t1") (:form . "CEM.T1") (:end . 27)\n  (:start . 21) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 28) (:start . 27)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 34) (:start . 29)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 39) (:start . 35)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "maintain") (:form . "maintained") (:end . 50)\n  (:start . 40) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "very-low-endotoxin-Roswell")\n  (:form . "very-low-endotoxin-Roswell") (:end . 80) (:start . 54) (:id . 54))\n ((:tag . "NNP") (:stem . "Park") (:form . "Park") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Memorial") (:form . "Memorial") (:end . 94)\n  (:start . 86) (:id . 56))\n ((:tag . "NNP") (:stem . "Institute") (:form . "Institute") (:end . 104)\n  (:start . 95) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "RPMI") (:form . 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"VBN") (:stem . "supplement") (:form . "supplemented") (:end . 164)\n  (:start . 152) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 169) (:start . 165)\n  (:id . 71))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 172) (:start . 170)\n  (:id . 72))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 173) (:start . 172)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "fetal") (:form . "fetal") (:end . 179)\n  (:start . 174) (:id . 74))\n ((:tag . "NN") (:stem . "calf") (:form . "calf") (:end . 184) (:start . 180)\n  (:id . 75))\n ((:tag . "NN") (:stem . "serum") (:form . "serum") (:end . 190)\n  (:start . 185) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 192) (:start . 191)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "FCS") (:form . "FCS") (:end . 195) (:start . 192)\n  (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 196) (:start . 195)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Biochrom") (:form . "Biochrom") (:end . 205)\n  (:start . 197) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 210) (:start . 207)\n  (:id . 82))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 212) (:start . 211)\n  (:id . 83))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 215) (:start . 213)\n  (:id . 84))\n ((:tag . "NN") (:stem . "l-glutamine") (:form . "l-glutamine") (:end . 227)\n  (:start . 216) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 229) (:start . 228)\n  (:id . 86))\n ((:tag . "NNP") (:stem . "PAA") (:form . "PAA") (:end . 232) (:start . 229)\n  (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 233) (:start . 232)\n  (:id . 88))\n ((:tag . "NNP") (:stem . "Cölbe") (:form . "Cölbe") (:end . 239)\n  (:start . 234) (:id . 89))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 240) (:start . 239)\n  (:id . 90))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 248)\n  (:start . 241) (:id . 91))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 249) (:start . 248)\n  (:id . 92))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 252) (:start . 250)\n  (:id . 93))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 257) (:start . 253)\n  (:id . 94))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 260) (:start . 258)\n  (:id . 95))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 262) (:start . 261)\n  (:id . 96))\n ((:tag . "JJ") (:stem . "humidified") (:form . "humidified") (:end . 273)\n  (:start . 263) (:id . 97))\n ((:tag . "NN") (:stem . "atmosphere") (:form . "atmosphere") (:end . 284)\n  (:start . 274) (:id . 98))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 287) (:start . 285)\n  (:id . 99))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 289) (:start . 288)\n  (:id . 100))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 290) (:start . 289)\n  (:id . 101))\n ((:tag . "NN") (:stem . "co2") (:form . "CO2") (:end . 294) (:start . 291)\n  (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 295) (:start . 294)\n  (:id . 103)))@@@1@62@((:identifiers (:sid . :s7.41) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501906@unknown@formal@none@1@S@CD4+ T cells were isolated using anti-CD4 magnetically activated cell sorting beads (Miltenyi, Bergisch Gladbach, Germany) according to the manufacturer's instructions.@(((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "anti-cd4") (:form . "anti-CD4") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "RB") (:stem . "magnetically") (:form . "magnetically") (:end . 54)\n  (:start . 42) (:id . 49))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 64)\n  (:start . 55) (:id . 50))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . "NN") (:stem . "sorting") (:form . "sorting") (:end . 77)\n  (:start . 70) (:id . 52))\n ((:tag . "NNS") (:stem . "bead") (:form . "beads") (:end . 83) (:start . 78)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Miltenyi") (:form . "Miltenyi") (:end . 93)\n  (:start . 85) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Bergisch") (:form . "Bergisch") (:end . 103)\n  (:start . 95) (:id . 57))\n ((:tag . "NNP") (:stem . "Gladbach") (:form . "Gladbach") (:end . 112)\n  (:start . 104) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 121)\n  (:start . 114) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 132)\n  (:start . 123) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 64))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 152)\n  (:start . 140) (:id . 65))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 154) (:start . 152)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 167)\n  (:start . 155) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.42) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501907@unknown@formal@none@1@S@CD4+ T cells were cultured in MLPC medium consisting of RPMI 1640, 10% human serum, 2 mM l-glutamine, 20 mg/liter gentamicin, 10 mM HEPES, 1 mM sodium pyruvate, and 1% minimum essential medium nonessential amino acids (all from PAA, Cölbe, Germany) at 37°C under 5% CO2.@(((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "MLPC") (:form . "MLPC") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "medium") (:form . 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(:end . 270) (:start . 269)\n  (:id . 101)))@@@1@60@((:identifiers (:sid . :s7.43) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501908@unknown@formal@none@1@S@HeLa-Tat-III/LTR/d1EGFP cells were obtained through the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH, from Masahiko Satoh (57).@(((:tag . "NNP") (:stem . "HeLa-Tat-III/LTR/d1EGFP")\n  (:form . "HeLa-Tat-III/LTR/d1EGFP") (:end . 23) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 29) (:start . 24)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 43)\n  (:start . 35) (:id . 45))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 51)\n  (:start . 44) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "AIDS") (:form . "AIDS") (:end . 60) (:start . 56)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Research") (:form . "Research") (:end . 69)\n  (:start . 61) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Reference") (:form . "Reference") (:end . 83)\n  (:start . 74) (:id . 51))\n ((:tag . "NNP") (:stem . "Reagent") (:form . "Reagent") (:end . 91)\n  (:start . 84) (:id . 52))\n ((:tag . "NNP") (:stem . "Program") (:form . "Program") (:end . 99)\n  (:start . 92) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Division") (:form . "Division") (:end . 109)\n  (:start . 101) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "AIDS") (:form . "AIDS") (:end . 117) (:start . 113)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "NIAID") (:form . "NIAID") (:end . 124)\n  (:start . 119) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "NIH") (:form . "NIH") (:end . 129) (:start . 126)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 135) (:start . 131)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Masahiko") (:form . "Masahiko") (:end . 144)\n  (:start . 136) (:id . 64))\n ((:tag . "NNP") (:stem . "Satoh") (:form . "Satoh") (:end . 150)\n  (:start . 145) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 152) (:start . 151)\n  (:id . 66))\n ((:tag . "CD") (:stem . "57") (:form . "57") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.44) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501909@unknown@formal@none@1@S@These cells stably express d1EGFP (which was derived from d2EGFP, a destabilized, redshifted variant of the enhanced green fluorescent protein [EGFP], and has a half-life of approximately 1 hour) under the control of the HIV-1 LTR promoter.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "stably") (:form . "stably") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "d1egfp") (:form . "d1EGFP") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "d2EGFP") (:form . "d2EGFP") (:end . 64)\n  (:start . 58) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "destabilized") (:form . "destabilized") (:end . 80)\n  (:start . 68) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "redshifted") (:form . "redshifted") (:end . 92)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "variant") (:form . "variant") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 116)\n  (:start . 108) (:id . 61))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 122)\n  (:start . 117) (:id . 62))\n ((:tag . "JJ") (:stem . "fluorescent") (:form . "fluorescent") (:end . 134)\n  (:start . 123) (:id . 63))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 142)\n  (:start . 135) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 144) (:start . 143)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 148) (:start . 144)\n  (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 149) (:start . 148)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 69))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 158) (:start . 155)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 160) (:start . 159)\n  (:id . 71))\n ((:tag . "NN") (:stem . "half-life") (:form . "half-life") (:end . 170)\n  (:start . 161) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 73))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 187) (:start . 174) (:id . 74))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 189) (:start . 188)\n  (:id . 75))\n ((:tag . "NN") (:stem . "hour") (:form . "hour") (:end . 194) (:start . 190)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 77))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 201)\n  (:start . 196) (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 205) (:start . 202)\n  (:id . 79))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 213)\n  (:start . 206) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 216) (:start . 214)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 220) (:start . 217)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 226)\n  (:start . 221) (:id . 83))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 230) (:start . 227)\n  (:id . 84))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 239)\n  (:start . 231) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 240) (:start . 239)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s7.45) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501910@unknown@formal@none@1@S@HeLa-Tat-III/LTR/d1EGFP cells were cultivated in Dulbecco's modified Eagle's medium (PAA) supplemented with 10% FCS, 2 mM l-glutamine, and 1 mg/ml G418 at 37°C under 8.5% CO2.@(((:tag . "NNP") (:stem . "HeLa-Tat-III/LTR/d1EGFP")\n  (:form . "HeLa-Tat-III/LTR/d1EGFP") (:end . 23) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 29) (:start . 24)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "cultivate") (:form . "cultivated") (:end . 45)\n  (:start . 35) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Dulbecco") (:form . "Dulbecco") (:end . 57)\n  (:start . 49) (:id . 47))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 59) (:start . 57)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "modify") (:form . "modified") (:end . 68)\n  (:start . 60) (:id . 49))\n ((:tag . "NNP") (:stem . "Eagle") (:form . "Eagle") (:end . 74) (:start . 69)\n  (:id . 50))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 76) (:start . 74)\n  (:id . 51))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 83)\n  (:start . 77) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "PAA") (:form . "PAA") (:end . 88) (:start . 85)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "supplement") (:form . "supplemented") (:end . 102)\n  (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 107) (:start . 103)\n  (:id . 57))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 110) (:start . 108)\n  (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 111) (:start . 110)\n  (:id . 59))\n ((:tag . "NN") (:stem . "fcs") (:form . "FCS") (:end . 115) (:start . 112)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 121) (:start . 119)\n  (:id . 63))\n ((:tag . "NN") (:stem . "l-glutamine") (:form . "l-glutamine") (:end . 133)\n  (:start . 122) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n  (:id . 66))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 140) (:start . 139)\n  (:id . 67))\n ((:tag . "NN") (:stem . "mg/ml") (:form . "mg/ml") (:end . 146)\n  (:start . 141) (:id . 68))\n ((:tag . "NN") (:stem . "g418") (:form . "G418") (:end . 151) (:start . 147)\n  (:id . 69))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 154) (:start . 152)\n  (:id . 70))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 159) (:start . 155)\n  (:id . 71))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 165)\n  (:start . 160) (:id . 72))\n ((:tag . "CD") (:stem . "8.5") (:form . "8.5") (:end . 169) (:start . 166)\n  (:id . 73))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 170) (:start . 169)\n  (:id . 74))\n ((:tag . "NN") (:stem . "co2") (:form . "CO2") (:end . 174) (:start . 171)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s7.46) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501911@unknown@formal@none@1@S@HEK 293T cells were cultivated in Dulbecco's modified Eagle's medium supplemented with 10% FCS and 2 mM l-glutamine at 37°C under 8.5% CO2.@(((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "cultivate") (:form . "cultivated") (:end . 30)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Dulbecco") (:form . "Dulbecco") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "modify") (:form . "modified") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "NNP") (:stem . "Eagle") (:form . "Eagle") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 68)\n  (:start . 62) (:id . 53))\n ((:tag . "VBN") (:stem . "supplement") (:form . "supplemented") (:end . 81)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 86) (:start . 82)\n  (:id . 55))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "fcs") (:form . "FCS") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 103) (:start . 101)\n  (:id . 61))\n ((:tag . "NN") (:stem . "l-glutamine") (:form . "l-glutamine") (:end . 115)\n  (:start . 104) (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 118) (:start . 116)\n  (:id . 63))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 123) (:start . 119)\n  (:id . 64))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 129)\n  (:start . 124) (:id . 65))\n ((:tag . "CD") (:stem . "8.5") (:form . "8.5") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 134) (:start . 133)\n  (:id . 67))\n ((:tag . "NN") (:stem . "co2") (:form . "CO2") (:end . 138) (:start . 135)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.47) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501912@unknown@formal@none@1@S@Pseudoviruses were produced by cotransfection of HEK 293T cells with pNL4-3LucR-E- (obtained through the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH, from Nathaniel Landau [13, 27]) and a vesicular stomatitis virus G protein (VSV-G)-encoding plasmid by using the calcium phosphate technique.@(((:tag . "NNS") (:stem . "pseudovirus") (:form . "Pseudoviruses") (:end . 13)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 27)\n  (:start . 19) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cotransfection") (:form . "cotransfection")\n  (:end . 45) (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "HEK") (:form . 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5501913@unknown@formal@none@1@S@Pseudovirus-containing supernatants were harvested 2 days after transfection, and cellular debris was removed by centrifugation at 300 × g for 5 min.@(((:tag . "JJ") (:stem . "pseudovirus-containing")\n  (:form . "Pseudovirus-containing") (:end . 22) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "supernatant") (:form . "supernatants") (:end . 35)\n  (:start . 23) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 40) (:start . 36)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "harvest") (:form . "harvested") (:end . 50)\n  (:start . 41) (:id . 45))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 52) (:start . 51)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 57) (:start . 53)\n  (:id . 47))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 63) (:start . 58)\n  (:id . 48))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 76)\n  (:start . 64) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 90)\n  (:start . 82) (:id . 52))\n ((:tag . "NN") (:stem . "debris") (:form . "debris") (:end . 97)\n  (:start . 91) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 101) (:start . 98)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "remove") (:form . "removed") (:end . 109)\n  (:start . 102) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 112) (:start . 110)\n  (:id . 56))\n ((:tag . "NN") (:stem . "centrifugation") (:form . "centrifugation")\n  (:end . 127) (:start . 113) (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 130) (:start . 128)\n  (:id . 58))\n ((:tag . "CD") (:stem . "300") (:form . "300") (:end . 134) (:start . 131)\n  (:id . 59))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 136) (:start . 135)\n  (:id . 60))\n ((:tag . "NN") (:stem . "g") (:form . "g") (:end . 138) (:start . 137)\n  (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 142) (:start . 139)\n  (:id . 62))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 144) (:start . 143)\n  (:id . 63))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 148) (:start . 145)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.49) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501914@unknown@formal@none@1@S@HIV-1 p24 concentration was estimated by antigen enzyme-linked immunosorbent assay.@(((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "p24") (:form . "p24") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "antigen") (:form . "antigen") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "JJ") (:stem . "enzyme-linked") (:form . "enzyme-linked")\n  (:end . 62) (:start . 49) (:id . 49))\n ((:tag . "JJ") (:stem . "immunosorbent") (:form . "immunosorbent")\n  (:end . 76) (:start . 63) (:id . 50))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 82) (:start . 77)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.50) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501915@unknown@formal@none@1@S@Pseudovirus-containing supernatants were stored in 1-ml aliquots at -80°C until use.@(((:tag . "JJ") (:stem . "pseudovirus-containing")\n  (:form . "Pseudovirus-containing") (:end . 22) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "supernatant") (:form . "supernatants") (:end . 35)\n  (:start . 23) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 40) (:start . 36)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "store") (:form . "stored") (:end . 47)\n  (:start . 41) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "1-ml") (:form . "1-ml") (:end . 55) (:start . 51)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "aliquot") (:form . "aliquots") (:end . 64)\n  (:start . 56) (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 67) (:start . 65)\n  (:id . 49))\n ((:tag . "NN") (:stem . "-80°c") (:form . "-80°C") (:end . 73) (:start . 68)\n  (:id . 50))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 79) (:start . 74)\n  (:id . 51))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 83) (:start . 80)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.51) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501916@unknown@formal@none@1@S@Jurkat and T1 cells were cultured to a density of 1.5 × 106 cells/ml and split 1:2 on the day prior to infection.@(((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "t1") (:form . "T1") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "density") (:form . "density") (:end . 46)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1.5") (:form . "1.5") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "HYPH") (:stem . "×") (:form . "×") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "CD") (:stem . "106") (:form . "106") (:end . 59) (:start . 56)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cells/ml") (:form . "cells/ml") (:end . 68)\n  (:start . 60) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "split") (:form . "split") (:end . 78) (:start . 73)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "1:2") (:form . "1:2") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 85) (:start . 83)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 60))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 93) (:start . 90)\n  (:id . 61))\n ((:tag . "RB") (:stem . "prior") (:form . "prior") (:end . 99) (:start . 94)\n  (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 102) (:start . 100)\n  (:id . 63))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 112)\n  (:start . 103) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.52) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501917@unknown@formal@none@1@S@Cells were infected with VSV-G env pseudotyped HIV-1NL4-3LucR-E- for 4 h at 37°C, using a concentration of 30 ng p24 per 1 × 106 cells.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "infect") (:form . "infected") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "VSV-G") (:form . "VSV-G") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "env") (:form . "env") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "pseudotype") (:form . "pseudotyped") (:end . 46)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "hiv-1nl4-3lucr-e-") (:form . "HIV-1NL4-3LucR-E-")\n  (:end . 64) (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n  (:id . 50))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 87) (:start . 82)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 103) (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 109) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "ng") (:form . "ng") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "NN") (:stem . "p24") (:form . "p24") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 120) (:start . 117)\n  (:id . 63))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 122) (:start . 121)\n  (:id . 64))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 124) (:start . 123)\n  (:id . 65))\n ((:tag . "CD") (:stem . "106") (:form . "106") (:end . 128) (:start . 125)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 134)\n  (:start . 129) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.53) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501918@unknown@formal@none@1@S@Cells were centrifuged at 300 × g for 5 min to remove excessive pseudovirus and resuspended in 2 ml very-low-endotoxin-RPMI 1640 containing 2 mM l-glutamine and 10% FCS supplemented with the respective concentration of GlcN (Sigma-Aldrich, Munich, Germany) in triplicate.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "centrifuge") (:form . "centrifuged") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "CD") (:stem . "300") (:form . "300") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "g") (:form . "g") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 39) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 46) (:start . 44)\n  (:id . 52))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 53)\n  (:start . 47) (:id . 53))\n ((:tag . "JJ") (:stem . "excessive") (:form . "excessive") (:end . 63)\n  (:start . 54) (:id . 54))\n ((:tag . "NN") (:stem . "pseudovirus") (:form . "pseudovirus") (:end . 75)\n  (:start . 64) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "resuspend") (:form . "resuspended") (:end . 91)\n  (:start . 80) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "ml") (:form . "ml") (:end . 99) (:start . 97)\n  (:id . 60))\n ((:tag . "NN") (:stem . "very-low-endotoxin-rpmi")\n  (:form . "very-low-endotoxin-RPMI") (:end . 123) (:start . 100) (:id . 61))\n ((:tag . "CD") (:stem . "1640") (:form . "1640") (:end . 128) (:start . 124)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 139)\n  (:start . 129) (:id . 63))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 141) (:start . 140)\n  (:id . 64))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "NN") (:stem . "l-glutamine") (:form . "l-glutamine") (:end . 156)\n  (:start . 145) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 67))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 163) (:start . 161)\n  (:id . 68))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 164) (:start . 163)\n  (:id . 69))\n ((:tag . "NN") (:stem . "fcs") (:form . "FCS") (:end . 168) (:start . 165)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "supplement") (:form . "supplemented") (:end . 181)\n  (:start . 169) (:id . 71))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 186) (:start . 182)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 190) (:start . 187)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 201)\n  (:start . 191) (:id . 74))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 215) (:start . 202) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 218) (:start . 216)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 223) (:start . 219)\n  (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 225) (:start . 224)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Sigma-Aldrich") (:form . "Sigma-Aldrich")\n  (:end . 238) (:start . 225) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 239) (:start . 238)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Munich") (:form . "Munich") (:end . 246)\n  (:start . 240) (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 247) (:start . 246)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 255)\n  (:start . 248) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 256) (:start . 255)\n  (:id . 84))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 259) (:start . 257)\n  (:id . 85))\n ((:tag . "NN") (:stem . "triplicate") (:form . "triplicate") (:end . 270)\n  (:start . 260) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 271) (:start . 270)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s7.54) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501919@unknown@formal@none@1@S@CD4+ T cells were stimulated for 6 days with 10 U/ml interleukin-2 (Roche, Mannheim, Germany) and 10 µg/ml phytohemagglutinin P (Sigma-Aldrich) prior to infection.@(((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "U/ml") (:form . "U/ml") (:end . 52) (:start . 48)\n  (:id . 52))\n ((:tag . "NN") (:stem . "interleukin-2") (:form . "interleukin-2")\n  (:end . 66) (:start . 53) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Roche") (:form . "Roche") (:end . 73) (:start . 68)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Mannheim") (:form . "Mannheim") (:end . 83)\n  (:start . 75) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 92)\n  (:start . 85) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 61))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 100) (:start . 98)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "µg/ml") (:form . "µg/ml") (:end . 106)\n  (:start . 101) (:id . 63))\n ((:tag . "NN") (:stem . "phytohemagglutinin") (:form . "phytohemagglutinin")\n  (:end . 125) (:start . 107) (:id . 64))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 127) (:start . 126)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "sigma-aldrich") (:form . "Sigma-Aldrich")\n  (:end . 142) (:start . 129) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 149)\n  (:start . 144) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 152) (:start . 150)\n  (:id . 70))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 162)\n  (:start . 153) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.55) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501920@unknown@formal@none@1@S@Cells were infected with reporter HIV-1 for 4 h at 37°C, using a concentration of 30 ng p24 per 2 × 106 cells.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "infect") (:form . "infected") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 62) (:start . 57)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 78) (:start . 65) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 57))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "NN") (:stem . "ng") (:form . "ng") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "NN") (:stem . "p24") (:form . "p24") (:end . 91) (:start . 88)\n  (:id . 60))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 95) (:start . 92)\n  (:id . 61))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 97) (:start . 96)\n  (:id . 62))\n ((:tag . "HYPH") (:stem . "×") (:form . "×") (:end . 99) (:start . 98)\n  (:id . 63))\n ((:tag . "CD") (:stem . "106") (:form . "106") (:end . 103) (:start . 100)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 109)\n  (:start . 104) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.56) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501921@unknown@formal@none@1@S@Cells were centrifuged at 250 × g for 10 min to remove excessive pseudovirus and resuspended in 1.5 ml MLPC medium supplemented with the respective concentration of GlcN in triplicate.@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "centrifuge") (:form . "centrifuged") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "CD") (:stem . "250") (:form . "250") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "g") (:form . "g") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 44) (:start . 41)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n  (:id . 52))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 54)\n  (:start . 48) (:id . 53))\n ((:tag . "JJ") (:stem . "excessive") (:form . "excessive") (:end . 64)\n  (:start . 55) (:id . 54))\n ((:tag . "NN") (:stem . "pseudovirus") (:form . "pseudovirus") (:end . 76)\n  (:start . 65) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "resuspend") (:form . "resuspended") (:end . 92)\n  (:start . 81) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1.5") (:form . "1.5") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "ml") (:form . "ml") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "MLPC") (:form . "MLPC") (:end . 107) (:start . 103)\n  (:id . 61))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 114)\n  (:start . 108) (:id . 62))\n ((:tag . "VBN") (:stem . "supplement") (:form . "supplemented") (:end . 127)\n  (:start . 115) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 132) (:start . 128)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 147)\n  (:start . 137) (:id . 66))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 161) (:start . 148) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 164) (:start . 162)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 169) (:start . 165)\n  (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 172) (:start . 170)\n  (:id . 70))\n ((:tag . "NN") (:stem . "triplicate") (:form . "triplicate") (:end . 183)\n  (:start . 173) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.57) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501922@unknown@formal@none@1@S@After incubation for 24 h, cells were collected, washed once with phosphate-buffered saline (PBS; Biochrom), lysed in 1× passive lysis buffer (Promega, Mannheim, Germany), and assayed for luciferase activity as described below.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "incubation") (:form . "incubation") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 47)\n  (:start . 38) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "wash") (:form . "washed") (:end . 55) (:start . 49)\n  (:id . 52))\n ((:tag . "RB") (:stem . "once") (:form . "once") (:end . 60) (:start . 56)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "phosphate-buffered") (:form . "phosphate-buffered")\n  (:end . 84) (:start . 66) (:id . 55))\n ((:tag . "NN") (:stem . "saline") (:form . "saline") (:end . 91)\n  (:start . 85) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "PBS") (:form . "PBS") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Biochrom") (:form . "Biochrom") (:end . 106)\n  (:start . 98) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "lyse") (:form . "lysed") (:end . 114)\n  (:start . 109) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n  (:id . 64))\n ((:tag . "CD") (:stem . "1×") (:form . "1×") (:end . 120) (:start . 118)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "passive") (:form . "passive") (:end . 128)\n  (:start . 121) (:id . 66))\n ((:tag . "NN") (:stem . "lysis") (:form . "lysis") (:end . 134)\n  (:start . 129) (:id . 67))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 141)\n  (:start . 135) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Promega") (:form . "Promega") (:end . 150)\n  (:start . 143) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Mannheim") (:form . "Mannheim") (:end . 160)\n  (:start . 152) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 169)\n  (:start . 162) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "assay") (:form . "assayed") (:end . 183)\n  (:start . 176) (:id . 78))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 187) (:start . 184)\n  (:id . 79))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 198)\n  (:start . 188) (:id . 80))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 207)\n  (:start . 199) (:id . 81))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 210) (:start . 208)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 220)\n  (:start . 211) (:id . 83))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 226)\n  (:start . 221) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s7.58) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501923@unknown@formal@none@1@S@Cell viability was measured using the CellTiter 96 nonradioactive cell proliferation assay (MTT [3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide] assay; Promega) according to the manufacturer's protocol.@(((:tag . "NN") (:stem . "cell") (:form . "Cell") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "CellTiter") (:form . "CellTiter") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "CD") (:stem . "96") (:form . "96") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "nonradioactive") (:form . "nonradioactive")\n  (:end . 65) (:start . 51) (:id . 50))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 70) (:start . 66)\n  (:id . 51))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 84) (:start . 71) (:id . 52))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 90) (:start . 85)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "MTT") (:form . "MTT") (:end . 95) (:start . 92)\n  (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 97) (:start . 96)\n  (:id . 56))\n ((:tag . "NN")\n  (:stem . "3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium")\n  (:form . "3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium")\n  (:end . 153) (:start . 97) (:id . 57))\n ((:tag . "NN") (:stem . "bromide") (:form . "bromide") (:end . 161)\n  (:start . 154) (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 162) (:start . 161)\n  (:id . 59))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 168)\n  (:start . 163) (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 169) (:start . 168)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Promega") (:form . "Promega") (:end . 177)\n  (:start . 170) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 178) (:start . 177)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 188)\n  (:start . 179) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 191) (:start . 189)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 195) (:start . 192)\n  (:id . 66))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 208)\n  (:start . 196) (:id . 67))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 210) (:start . 208)\n  (:id . 68))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 219)\n  (:start . 211) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s7.59) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501924@unknown@formal@none@1@S@Briefly, 100-µl cell suspensions containing either 1 × 105 HIV-1-infected Jurkat or T1 cells or 2 × 105 HIV-1-infected CD4+ primary T lymphocytes were applied for the assay.@(((:tag . "RB") (:stem . "briefly") (:form . "Briefly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "100-µl") (:form . "100-µl") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "suspension") (:form . "suspensions") (:end . 32)\n  (:start . 21) (:id . 46))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 50)\n  (:start . 44) (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 54) (:start . 53)\n  (:id . 50))\n ((:tag . "CD") (:stem . "105") (:form . "105") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "hiv-1-infected") (:form . "HIV-1-infected")\n  (:end . 73) (:start . 59) (:id . 52))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 80)\n  (:start . 74) (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 83) (:start . 81)\n  (:id . 54))\n ((:tag . "NN") (:stem . "t1") (:form . "T1") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 92) (:start . 87)\n  (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "CC") (:stem . "×") (:form . "×") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . "CD") (:stem . "105") (:form . "105") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "hiv-1-infected") (:form . "HIV-1-infected")\n  (:end . 118) (:start . 104) (:id . 61))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 123) (:start . 119)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 131)\n  (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 145)\n  (:start . 134) (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 150) (:start . 146)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 158)\n  (:start . 151) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 162) (:start . 159)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 69))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 172)\n  (:start . 167) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.60) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501925@unknown@formal@none@1@S@The coding sequence of OGT was cloned by amplifying 820 bp corresponding to the N terminus of nucleocytoplasmic OGT, GenBank accession number NM_181672 (24, 41), from human cDNA with specific primers containing the restriction sites for BamHI and EcoRV (underlined) and a Kozak sequence (italics) (forward primer, 5'-TAGGGATCCGATATCGCCACCATGGCGTCTTCCGTGGGCAACG-3') and the restriction site for StuI (underlined) (reverse primer, 5'-AGATCTATCAGGCCTTGCTCATAG-3').@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "cod") (:form . "coding") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . 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5501926@unknown@formal@none@1@S@The PCR fragment was then ligated with the StuI restriction site to the part of the Lv4F fragment (also termed mitochondrial OGT; GenBank accession number U77413 [46, 47]) which corresponds to the C terminus of nucleocytoplasmic OGT and harbors a NotI restriction site at the 3' end.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "ligate") (:form . "ligated") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . 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5501927@unknown@formal@none@1@S@The complete sequence for the human nucleocytoplasmic OGT was subsequently inserted into pcDNA4/myc-His B (Invitrogen, Karlsruhe, Germany) at the EcoRV and NotI sites.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "nucleocytoplasmic") (:form . "nucleocytoplasmic")\n  (:end . 53) (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "ogt") (:form . "OGT") (:end . 57) (:start . 54)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 74)\n  (:start . 62) (:id . 51))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 83)\n  (:start . 75) (:id . 52))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 88) (:start . 84)\n  (:id . 53))\n ((:tag . "NN") (:stem . "pcdna4/myc-his") (:form . "pcDNA4/myc-His")\n  (:end . 103) (:start . 89) (:id . 54))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 105) (:start . 104)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 117)\n  (:start . 107) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Karlsruhe") (:form . "Karlsruhe") (:end . 128)\n  (:start . 119) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 137)\n  (:start . 130) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 141) (:start . 139)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "EcoRV") (:form . "EcoRV") (:end . 151)\n  (:start . 146) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 155) (:start . 152)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "NotI") (:form . "NotI") (:end . 160) (:start . 156)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 166)\n  (:start . 161) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.63) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501928@unknown@formal@none@1@S@The rescue mutant resOGT was created by mutagenesis PCR using pcDNA-OGT as template and the QuikChange XL site-directed mutagenesis kit (Stratagene, Amsterdam, The Netherlands) according to the manufacturer's instructions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "resogt") (:form . "resOGT") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "create") (:form . "created") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "mutagenesis") (:form . "mutagenesis") (:end . 51)\n  (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "pcr") (:form . "PCR") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "pcdna-ogt") (:form . "pcDNA-OGT") (:end . 71)\n  (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 83)\n  (:start . 75) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "QuikChange") (:form . "QuikChange") (:end . 102)\n  (:start . 92) (:id . 57))\n ((:tag . "NNP") (:stem . "XL") (:form . "XL") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "site-directed") (:form . "site-directed")\n  (:end . 119) (:start . 106) (:id . 59))\n ((:tag . "NN") (:stem . "mutagenesis") (:form . "mutagenesis") (:end . 131)\n  (:start . 120) (:id . 60))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 135) (:start . 132)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Stratagene") (:form . "Stratagene") (:end . 147)\n  (:start . 137) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Amsterdam") (:form . "Amsterdam") (:end . 158)\n  (:start . 149) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 163) (:start . 160)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Netherlands") (:form . "Netherlands") (:end . 175)\n  (:start . 164) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 186)\n  (:start . 177) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 189) (:start . 187)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 193) (:start . 190)\n  (:id . 72))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 206)\n  (:start . 194) (:id . 73))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 208) (:start . 206)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 221)\n  (:start . 209) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s7.64) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501929@unknown@formal@none@1@S@The mutagenic primers were designed by the QuikChange primer design program: forward primer, 5'-GAGGCACGGCAACCTGTGCTTAGATAAGATCAACGTGCTGCACAAGCCACCATATGAACATCCAAAAGA-3'; reverse primer, 5'-TCTTTTGGATGTTCATATGGTGGCTTGTGCAGCACGTTGATCTTATCTAAGCACAGGTTGCCGTGCCTC-3' (nucleotide changes compared to the wild-type sequence are in bold).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "mutagenic") (:form . "mutagenic") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "QuikChange") (:form . "QuikChange") (:end . 53)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 60)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "design") (:form . "design") (:end . 67)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 75)\n  (:start . 68) (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "RB") (:stem . "forward") (:form . "forward") (:end . 84)\n  (:start . 77) (:id . 54))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 91)\n  (:start . 85) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 56))\n ((:tag . "NN")\n  (:stem\n   . "5'-gaggcacggcaacctgtgcttagataagatcaacgtgctgcacaagccaccatatgaacatccaaaaga-3")\n  (:form\n   . "5’-GAGGCACGGCAACCTGTGCTTAGATAAGATCAACGTGCTGCACAAGCCACCATATGAACATCCAAAAGA-3")\n  (:end . 167) (:start . 93) (:id . 57))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 168) (:start . 167)\n  (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 169) (:start . 168)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 177)\n  (:start . 170) (:id . 60))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 184)\n  (:start . 178) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 62))\n ((:tag . "NNP")\n  (:stem\n   . "5'-TCTTTTGGATGTTCATATGGTGGCTTGTGCAGCACGTTGATCTTATCTAAGCACAGGTTGCCGTGCCTC-3")\n  (:form\n   . "5’-TCTTTTGGATGTTCATATGGTGGCTTGTGCAGCACGTTGATCTTATCTAAGCACAGGTTGCCGTGCCTC-3")\n  (:end . 260) (:start . 186) (:id . 63))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 261) (:start . 260)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 263) (:start . 262)\n  (:id . 65))\n ((:tag . "NN") (:stem . "nucleotide") (:form . "nucleotide") (:end . 273)\n  (:start . 263) (:id . 66))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 281)\n  (:start . 274) (:id . 67))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 290)\n  (:start . 282) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 293) (:start . 291)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 297) (:start . 294)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 307)\n  (:start . 298) (:id . 71))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 316)\n  (:start . 308) (:id . 72))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 320) (:start . 317)\n  (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 323) (:start . 321)\n  (:id . 74))\n ((:tag . "NN") (:stem . "bold") (:form . "bold") (:end . 328) (:start . 324)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 329) (:start . 328)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 330) (:start . 329)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s7.65) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501930@unknown@formal@none@1@S@The expression plasmid for Sp1 was generated by subcloning the XbaI/SmaI fragment of the pBS-Sp1-f1 vector (GenBank accession number AF252284 [35]), representing the open reading frame of Sp1, into the XbaI/EcoRV-digested pcDNA3.1(-) vector (Invitrogen).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "subclone") (:form . "subcloning") (:end . 58)\n  (:start . 48) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "XbaI/SmaI") (:form . "XbaI/SmaI") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 81)\n  (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "pbs-sp1-f1") (:form . "pBS-Sp1-f1") (:end . 99)\n  (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 106)\n  (:start . 100) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 115)\n  (:start . 108) (:id . 59))\n ((:tag . "NN") (:stem . "accession") (:form . "accession") (:end . 125)\n  (:start . 116) (:id . 60))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 132)\n  (:start . 126) (:id . 61))\n ((:tag . "NN") (:stem . "af252284") (:form . "AF252284") (:end . 141)\n  (:start . 133) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 143) (:start . 142)\n  (:id . 63))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 145) (:start . 143)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 146) (:start . 145)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "represent") (:form . "representing") (:end . 161)\n  (:start . 149) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "open") (:form . "open") (:end . 170) (:start . 166)\n  (:id . 70))\n ((:tag . "NN") (:stem . "reading") (:form . "reading") (:end . 178)\n  (:start . 171) (:id . 71))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 184)\n  (:start . 179) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 191) (:start . 188)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 192) (:start . 191)\n  (:id . 75))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 197) (:start . 193)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 201) (:start . 198)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "xbai/ecorv-digested")\n  (:form . "XbaI/EcoRV-digested") (:end . 221) (:start . 202) (:id . 78))\n ((:tag . "JJ") (:stem . "pcDNA3.1(-)") (:form . "pcDNA3.1(-)") (:end . 233)\n  (:start . 222) (:id . 79))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 240)\n  (:start . 234) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 242) (:start . 241)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 252)\n  (:start . 242) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 253) (:start . 252)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 254) (:start . 253)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s7.66) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501931@unknown@formal@none@1@S@The reporter constructs pXP1-LTR-κB-Sp1wt-Luc, pXP1-LTR-κB-Sp1mut-Luc, and pXP1-LTR-Sp1wt-Luc were kindly provided by Manuel López-Cabrera (2, 22).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "pxp1-ltr-κb-sp1wt-luc")\n  (:form . "pXP1-LTR-κB-Sp1wt-Luc") (:end . 45) (:start . 24) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pxp1-ltr-κb-sp1mut-luc")\n  (:form . "pXP1-LTR-κB-Sp1mut-Luc") (:end . 69) (:start . 47) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 49))\n ((:tag . "NN") (:stem . "pxp1-ltr-sp1wt-luc") (:form . "pXP1-LTR-Sp1wt-Luc")\n  (:end . 93) (:start . 75) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 98) (:start . 94)\n  (:id . 51))\n ((:tag . "RB") (:stem . "kindly") (:form . "kindly") (:end . 105)\n  (:start . 99) (:id . 52))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 114)\n  (:start . 106) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 117) (:start . 115)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Manuel") (:form . "Manuel") (:end . 124)\n  (:start . 118) (:id . 55))\n ((:tag . "NNP") (:stem . "López-Cabrera") (:form . "López-Cabrera")\n  (:end . 138) (:start . 125) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 141) (:start . 140)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 59))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 145) (:start . 143)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s7.67) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501932@unknown@formal@none@1@S@The plasmid pcDNA4-LTRwt-d2EGFP (destabilized, redshifted variant of the EGFP with a half-life of approximately 2 hours) was cloned by insertion of d2EGFP into pcDNA4/myc-His B plasmid (Invitrogen) via XhoI and XbaI.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "pcdna4-ltrwt-d2egfp")\n  (:form . "pcDNA4-LTRwt-d2EGFP") (:end . 31) (:start . 12) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 33) (:start . 32)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "destabilize") (:form . "destabilized") (:end . 45)\n  (:start . 33) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "redshifte") (:form . "redshifted") (:end . 57)\n  (:start . 47) (:id . 48))\n ((:tag . "NN") (:stem . "variant") (:form . "variant") (:end . 65)\n  (:start . 58) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 77) (:start . 73)\n  (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 82) (:start . 78)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "NN") (:stem . "half-life") (:form . "half-life") (:end . 94)\n  (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 56))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 111) (:start . 98) (:id . 57))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 113) (:start . 112)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 119)\n  (:start . 114) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 124) (:start . 121)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "clone") (:form . "cloned") (:end . 131)\n  (:start . 125) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 134) (:start . 132)\n  (:id . 63))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 144)\n  (:start . 135) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n  (:id . 65))\n ((:tag . "NN") (:stem . "d2egfp") (:form . "d2EGFP") (:end . 154)\n  (:start . 148) (:id . 66))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 159) (:start . 155)\n  (:id . 67))\n ((:tag . "NN") (:stem . "pcdna4/myc-his") (:form . "pcDNA4/myc-His")\n  (:end . 174) (:start . 160) (:id . 68))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 176) (:start . 175)\n  (:id . 69))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 184)\n  (:start . 177) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 186) (:start . 185)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 196)\n  (:start . 186) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 197) (:start . 196)\n  (:id . 73))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 201) (:start . 198)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "XhoI") (:form . "XhoI") (:end . 206) (:start . 202)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 210) (:start . 207)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "XbaI") (:form . "XbaI") (:end . 215) (:start . 211)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s7.68) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501933@unknown@formal@none@1@S@HIV-1 wild-type LTR (LTRwt) was amplified from pNL4-3, obtained through the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH, from Malcolm Martin (1), using the following primers: forward primer, 5'-GACAATTGAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTC-3'; reverse primer, 5'-ACCTCGAGTTGGCTCACTGCAACCTCTACCTCCTGGGTGCT-3'.@(((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "LTRwt") (:form . "LTRwt") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "amplify") (:form . "amplified") (:end . 41)\n  (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "pnl4-3") (:form . "pNL4-3") (:end . 53)\n  (:start . 47) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 63)\n  (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 71)\n  (:start . 64) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AIDS") (:form . "AIDS") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Research") (:form . "Research") (:end . 89)\n  (:start . 81) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . 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",") (:end . 145) (:start . 144)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "NIH") (:form . "NIH") (:end . 149) (:start . 146)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 70))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 155) (:start . 151)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Malcolm") (:form . "Malcolm") (:end . 163)\n  (:start . 156) (:id . 72))\n ((:tag . "NNP") (:stem . "Martin") (:form . "Martin") (:end . 170)\n  (:start . 164) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 74))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 173) (:start . 172)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 174) (:start . 173)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 77))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 181) (:start . 176)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n  (:id . 79))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 195)\n  (:start . 186) (:id . 80))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 203)\n  (:start . 196) (:id . 81))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 204) (:start . 203)\n  (:id . 82))\n ((:tag . "RB") (:stem . "forward") (:form . "forward") (:end . 212)\n  (:start . 205) (:id . 83))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 219)\n  (:start . 213) (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 220) (:start . 219)\n  (:id . 85))\n ((:tag . "NN") (:stem . "5'-gacaattgaagaaaaggggggactggaagggctaattcactc-3")\n  (:form . "5’-GACAATTGAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTC-3") (:end . 268)\n  (:start . 221) (:id . 86))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 269) (:start . 268)\n  (:id . 87))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 270) (:start . 269)\n  (:id . 88))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 278)\n  (:start . 271) (:id . 89))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 285)\n  (:start . 279) (:id . 90))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 286) (:start . 285)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "5'-ACCTCGAGTTGGCTCACTGCAACCTCTACCTCCTGGGTGCT-3")\n  (:form . "5’-ACCTCGAGTTGGCTCACTGCAACCTCTACCTCCTGGGTGCT-3") (:end . 333)\n  (:start . 287) (:id . 92))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 334) (:start . 333)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 335) (:start . 334)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s7.69) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501934@unknown@formal@none@1@S@The amplified LTRwt DNA was digested with MfeI and XhoI (underlined) and ligated into pcDNA4-d2EGFP.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "amplify") (:form . "amplified") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "LTRwt") (:form . "LTRwt") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "digest") (:form . "digested") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "MfeI") (:form . "MfeI") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "XhoI") (:form . "XhoI") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "underline") (:form . "underlined") (:end . 67)\n  (:start . 57) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "ligate") (:form . "ligated") (:end . 80)\n  (:start . 73) (:id . 56))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "pcDNA4-d2EGFP") (:form . "pcDNA4-d2EGFP")\n  (:end . 99) (:start . 86) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.70) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501935@unknown@formal@none@1@S@The plasmid pcDNA4-LTRmutSp1-d2EGFP contained the Sp1-binding-site-mutated LTR (LTRmutSp1) and was created by QuikChange XL site-directed mutagenesis PCR using the forward primer 5'-GGGGACTTTCCAGGGATTCGTGGCCTGTTCGGGACTGGTTAGTGGCGA-3' and the reverse primer 5'-CTCGCCACTAACCAGTCCCGAACAGGCCACGAATCCCTGGAAAGTCCCC-3' (nucleotide changes compared to the wild-type sequence are in bold).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "pcdna4-ltrmutsp1-d2egfp")\n  (:form . "pcDNA4-LTRmutSp1-d2EGFP") (:end . 35) (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 45)\n  (:start . 36) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "sp1-binding-site-mutated")\n  (:form . "Sp1-binding-site-mutated") (:end . 74) (:start . 50) (:id . 47))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 78) (:start . 75)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "LTRmutSp1") (:form . "LTRmutSp1") (:end . 89)\n  (:start . 80) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 98) (:start . 95)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "create") (:form . "created") (:end . 106)\n  (:start . 99) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 109) (:start . 107)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "QuikChange") (:form . "QuikChange") (:end . 120)\n  (:start . 110) (:id . 56))\n ((:tag . "NNP") (:stem . "XL") (:form . "XL") (:end . 123) (:start . 121)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "site-directed") (:form . "site-directed")\n  (:end . 137) (:start . 124) (:id . 58))\n ((:tag . "NN") (:stem . "mutagenesis") (:form . "mutagenesis") (:end . 149)\n  (:start . 138) (:id . 59))\n ((:tag . "NN") (:stem . "pcr") (:form . "PCR") (:end . 153) (:start . 150)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 159) (:start . 154)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "forward") (:form . "forward") (:end . 171)\n  (:start . 164) (:id . 63))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 178)\n  (:start . 172) (:id . 64))\n ((:tag . "NN")\n  (:stem . "5'-ggggactttccagggattcgtggcctgttcgggactggttagtggcga-3")\n  (:form . "5’-GGGGACTTTCCAGGGATTCGTGGCCTGTTCGGGACTGGTTAGTGGCGA-3")\n  (:end . 232) (:start . 179) (:id . 65))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 233) (:start . 232)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 237) (:start . 234)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 241) (:start . 238)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 249)\n  (:start . 242) (:id . 69))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 256)\n  (:start . 250) (:id . 70))\n ((:tag . "NNP")\n  (:stem . "5'-CTCGCCACTAACCAGTCCCGAACAGGCCACGAATCCCTGGAAAGTCCCC-3")\n  (:form . "5’-CTCGCCACTAACCAGTCCCGAACAGGCCACGAATCCCTGGAAAGTCCCC-3")\n  (:end . 311) (:start . 257) (:id . 71))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 312) (:start . 311)\n  (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 314) (:start . 313)\n  (:id . 73))\n ((:tag . "NN") (:stem . "nucleotide") (:form . "nucleotide") (:end . 324)\n  (:start . 314) (:id . 74))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 332)\n  (:start . 325) (:id . 75))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 341)\n  (:start . 333) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 344) (:start . 342)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 348) (:start . 345)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 358)\n  (:start . 349) (:id . 79))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 367)\n  (:start . 359) (:id . 80))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 371) (:start . 368)\n  (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 374) (:start . 372)\n  (:id . 82))\n ((:tag . "NN") (:stem . "bold") (:form . "bold") (:end . 379) (:start . 375)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 380) (:start . 379)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 381) (:start . 380)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s7.71) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501936@unknown@formal@none@1@S@The Tat expression construct pCEP4-Tat was obtained through the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH, from Lung-Ji Chang (9).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Tat") (:form . "Tat") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "pcep4-tat") (:form . "pCEP4-Tat") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 59)\n  (:start . 52) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "AIDS") (:form . "AIDS") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Research") (:form . "Research") (:end . 77)\n  (:start . 69) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Reference") (:form . "Reference") (:end . 91)\n  (:start . 82) (:id . 54))\n ((:tag . "NNP") (:stem . "Reagent") (:form . "Reagent") (:end . 99)\n  (:start . 92) (:id . 55))\n ((:tag . "NNP") (:stem . "Program") (:form . "Program") (:end . 107)\n  (:start . 100) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Division") (:form . "Division") (:end . 117)\n  (:start . 109) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "AIDS") (:form . "AIDS") (:end . 125) (:start . 121)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "NIAID") (:form . "NIAID") (:end . 132)\n  (:start . 127) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "NIH") (:form . "NIH") (:end . 137) (:start . 134)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 143) (:start . 139)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Lung-Ji") (:form . "Lung-Ji") (:end . 151)\n  (:start . 144) (:id . 67))\n ((:tag . "NNP") (:stem . "Chang") (:form . "Chang") (:end . 157)\n  (:start . 152) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 69))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 160) (:start . 159)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.72) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501937@unknown@formal@none@1@S@The control reporter plasmid pEF1α-Luc was constructed by subcloning the elongation factor 1 alpha (EF1α) promoter from pEF1/Myc-His vector (Invitrogen) into the promoterless pGL3-Basic vector (Promega).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "pef1α-luc") (:form . "pEF1α-Luc") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 54)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "subclone") (:form . "subcloning") (:end . 68)\n  (:start . 58) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 83)\n  (:start . 73) (:id . 52))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 90)\n  (:start . 84) (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 92) (:start . 91)\n  (:id . 54))\n ((:tag . "NN") (:stem . "alpha") (:form . "alpha") (:end . 98) (:start . 93)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 56))\n ((:tag . "NN") (:stem . "ef1α") (:form . "EF1α") (:end . 104) (:start . 100)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 114)\n  (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 119) (:start . 115)\n  (:id . 60))\n ((:tag . "NN") (:stem . "pef1/myc-his") (:form . "pEF1/Myc-His") (:end . 132)\n  (:start . 120) (:id . 61))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 139)\n  (:start . 133) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 151)\n  (:start . 141) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 157) (:start . 153)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "promoterless") (:form . "promoterless") (:end . 174)\n  (:start . 162) (:id . 68))\n ((:tag . "JJ") (:stem . "pgl3-basic") (:form . "pGL3-Basic") (:end . 185)\n  (:start . 175) (:id . 69))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 192)\n  (:start . 186) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 194) (:start . 193)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Promega") (:form . "Promega") (:end . 201)\n  (:start . 194) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 202) (:start . 201)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s7.73) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501938@unknown@formal@none@1@S@pcDNA4-EF1α-d2EGFP was generated by replacing the cytomegalovirus promoter in the plasmid pcDNA4-d2EGFP with the EF1α promoter.@(((:tag . "NNP") (:stem . "pcDNA4-EF1α-d2EGFP") (:form . "pcDNA4-EF1α-d2EGFP")\n  (:end . 18) (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 32)\n  (:start . 23) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 35) (:start . 33)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "replace") (:form . "replacing") (:end . 45)\n  (:start . 36) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cytomegalovirus") (:form . "cytomegalovirus")\n  (:end . 65) (:start . 50) (:id . 48))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 74)\n  (:start . 66) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 51))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 89)\n  (:start . 82) (:id . 52))\n ((:tag . "NN") (:stem . "pcdna4-d2egfp") (:form . "pcDNA4-d2EGFP")\n  (:end . 103) (:start . 90) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 108) (:start . 104)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 55))\n ((:tag . "NN") (:stem . "ef1α") (:form . "EF1α") (:end . 117) (:start . 113)\n  (:id . 56))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 126)\n  (:start . 118) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.74) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501939@unknown@formal@none@1@S@All cloned constructs were confirmed by full-length sequencing and expression experiments.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "clone") (:form . "cloned") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 51)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 62)\n  (:start . 52) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 77)\n  (:start . 67) (:id . 51))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 89)\n  (:start . 78) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.75) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501940@unknown@formal@none@1@S@The plasmid pGEM4Z-OGT-64A was generated by subcloning the OGT gene from pcDNA4-OGT into the RNA production vector pGEM4Z-5'UTR-sig-huSurvivin-DC.LAMP-3'UTR-64A (kindly provided by Kris Thielemans [4]), replacing the huSurvivin-DC.LAMP.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "pgem4z-ogt-64a") (:form . "pGEM4Z-OGT-64A")\n  (:end . 26) (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 40)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "subclone") (:form . "subcloning") (:end . 54)\n  (:start . 44) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 49))\n ((:tag . "NN") (:stem . "ogt") (:form . "OGT") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . "NN") (:stem . "pcdna4-ogt") (:form . "pcDNA4-OGT") (:end . 83)\n  (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 88) (:start . 84)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 107)\n  (:start . 97) (:id . 57))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 114)\n  (:start . 108) (:id . 58))\n ((:tag . "NNP") (:stem . "pGEM4Z-5'UTR-sig-huSurvivin-DC.LAMP-3'UTR-64A")\n  (:form . "pGEM4Z-5’UTR-sig-huSurvivin-DC.LAMP-3’UTR-64A") (:end . 160)\n  (:start . 115) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 60))\n ((:tag . "RB") (:stem . "kindly") (:form . "kindly") (:end . 168)\n  (:start . 162) (:id . 61))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 177)\n  (:start . 169) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 180) (:start . 178)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Kris") (:form . "Kris") (:end . 185) (:start . 181)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Thieleman") (:form . "Thielemans") (:end . 196)\n  (:start . 186) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 198) (:start . 197)\n  (:id . 66))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 199) (:start . 198)\n  (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 200) (:start . 199)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 201) (:start . 200)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 202) (:start . 201)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "replace") (:form . "replacing") (:end . 212)\n  (:start . 203) (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 216) (:start . 213)\n  (:id . 72))\n ((:tag . "NN") (:stem . "husurvivin-dc.lamp") (:form . "huSurvivin-DC.LAMP")\n  (:end . 235) (:start . 217) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 236) (:start . 235)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s7.76) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501941@unknown@formal@none@1@S@The pGEM4Z-EGFP-64A vector was provided by I.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "pgem4z-egfp-64a") (:form . "pGEM4Z-EGFP-64A")\n  (:end . 19) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 26)\n  (:start . 20) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 39)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "i") (:form . "I") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s7.77) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501942@unknown@formal@none@1@S@Tcherepanova, Argos Therapeutics, Durham, NC (66).@(((:tag . "NNP") (:stem . "Tcherepanova") (:form . "Tcherepanova") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Argos") (:form . "Argos") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Therapeutics") (:form . "Therapeutics") (:end . 32)\n  (:start . 20) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Durham") (:form . "Durham") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "NC") (:form . "NC") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "CD") (:stem . "66") (:form . "66") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 50) (:start . 49)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.78) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501943@unknown@formal@none@1@S@The constructs were confirmed by restriction digest and expression experiments.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 29)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "restriction") (:form . "restriction") (:end . 44)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "digest") (:form . "digest") (:end . 51)\n  (:start . 45) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 66)\n  (:start . 56) (:id . 50))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 78)\n  (:start . 67) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.79) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501944@unknown@formal@none@1@S@HeLa-Tat-III/LTR/d1EGFP cells were treated with the respective GlcN concentrations for 5 h in triplicate.@(((:tag . "NNP") (:stem . "HeLa-Tat-III/LTR/d1EGFP")\n  (:form . "HeLa-Tat-III/LTR/d1EGFP") (:end . 23) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 29) (:start . 24)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 42)\n  (:start . 35) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 62)\n  (:start . 52) (:id . 48))\n ((:tag . "NN") (:stem . "glcn") (:form . "GlcN") (:end . 67) (:start . 63)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 82) (:start . 68) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 86) (:start . 83)\n  (:id . 51))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 88) (:start . 87)\n  (:id . 52))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 90) (:start . 89)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 54))\n ((:tag . "NN") (:stem . "triplicate") (:form . "triplicate") (:end . 104)\n  (:start . 94) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.80) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501945@unknown@formal@none@1@S@HEK 293T-LTRwt-d2EGFP and HEK 293T-LTRmutSp1-d2EGFP cells were treated with 16 mM GlcN for 20 h in duplicate.@(((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "293T-LTRwt-d2EGFP") (:form . "293T-LTRwt-d2EGFP")\n  (:end . 21) (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "293T-LTRmutSp1-d2EGFP")\n  (:form . "293T-LTRmutSp1-d2EGFP") (:end . 51) (:start . 30) (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 57) (:start . 52)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 70)\n  (:start . 63) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 75) (:start . 71)\n  (:id . 50))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 78) (:start . 76)\n  (:id . 51))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 81) (:start . 79)\n  (:id . 52))\n ((:tag . "NN") (:stem . "glcn") (:form . "GlcN") (:end . 86) (:start . 82)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 90) (:start . 87)\n  (:id . 54))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 93) (:start . 91)\n  (:id . 55))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "duplicate") (:form . "duplicate") (:end . 108)\n  (:start . 99) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.81) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501946@unknown@formal@none@1@S@The cells were harvested with trypsin-EDTA (PAA), washed twice with FACS-PBS (PBS containing 5% FCS and 0.1% sodium azide [Sigma-Aldrich]) and resuspended in FACS-PBS.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "harvest") (:form . "harvested") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "trypsin-EDTA") (:form . "trypsin-EDTA") (:end . 42)\n  (:start . 30) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PAA") (:form . "PAA") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "wash") (:form . "washed") (:end . 56) (:start . 50)\n  (:id . 52))\n ((:tag . "RB") (:stem . "twice") (:form . "twice") (:end . 62) (:start . 57)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "FACS-PBS") (:form . "FACS-PBS") (:end . 76)\n  (:start . 68) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "PBS") (:form . "PBS") (:end . 81) (:start . 78)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 92)\n  (:start . 82) (:id . 58))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "NN") (:stem . "fcs") (:form . "FCS") (:end . 99) (:start . 96)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 62))\n ((:tag . "CD") (:stem . "0.1") (:form . "0.1") (:end . 107) (:start . 104)\n  (:id . 63))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 108) (:start . 107)\n  (:id . 64))\n ((:tag . "NN") (:stem . "sodium") (:form . "sodium") (:end . 115)\n  (:start . 109) (:id . 65))\n ((:tag . "NN") (:stem . "azide") (:form . "azide") (:end . 121)\n  (:start . 116) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 123) (:start . 122)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "sigma-aldrich") (:form . "Sigma-Aldrich")\n  (:end . 136) (:start . 123) (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 137) (:start . 136)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "resuspend") (:form . "resuspended") (:end . 154)\n  (:start . 143) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 157) (:start . 155)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "FACS-PBS") (:form . "FACS-PBS") (:end . 166)\n  (:start . 158) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s7.82) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501947@unknown@formal@none@1@S@Viable GFP-positive cells (1 × 104) were analyzed for each sample using a FACSCalibur flow cytometer with CellQuest Pro software (both from BD Biosciences, Heidelberg, Germany).@(((:tag . "JJ") (:stem . "viable") (:form . "Viable") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "gfp-positive") (:form . "GFP-positive") (:end . 19)\n  (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 25) (:start . 20)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "CD") (:stem . "104") (:form . "104") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 40) (:start . 36)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 49)\n  (:start . 41) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 58) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 65)\n  (:start . 59) (:id . 54))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 71) (:start . 66)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "FACSCalibur") (:form . "FACSCalibur") (:end . 85)\n  (:start . 74) (:id . 57))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 90) (:start . 86)\n  (:id . 58))\n ((:tag . "NN") (:stem . "cytometer") (:form . "cytometer") (:end . 100)\n  (:start . 91) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 105) (:start . 101)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "CellQuest") (:form . "CellQuest") (:end . 115)\n  (:start . 106) (:id . 61))\n ((:tag . "NN") (:stem . "pro") (:form . "Pro") (:end . 119) (:start . 116)\n  (:id . 62))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 128)\n  (:start . 120) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 134) (:start . 130)\n  (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 139) (:start . 135)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "BD") (:form . "BD") (:end . 142) (:start . 140)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Biosciences") (:form . "Biosciences") (:end . 154)\n  (:start . 143) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Heidelberg") (:form . "Heidelberg") (:end . 166)\n  (:start . 156) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 175)\n  (:start . 168) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s7.83) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501948@unknown@formal@none@1@S@The relative fluorescence intensity is given as a ratio of the geometric mean of untreated cells to that of GlcN-treated cells.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 25)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 35)\n  (:start . 26) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 38) (:start . 36)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 44) (:start . 39)\n  (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "geometric") (:form . "geometric") (:end . 72)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "mean") (:form . "mean") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 90)\n  (:start . 81) (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 104) (:start . 100)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "glcn-treated") (:form . "GlcN-treated") (:end . 120)\n  (:start . 108) (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 126)\n  (:start . 121) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.84) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501949@unknown@formal@none@1@S@The geometric mean of untreated cells was defined as 100%.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "geometric") (:form . "geometric") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "mean") (:form . "mean") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.85) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501950@unknown@formal@none@1@S@In vitro transcription of RNA was performed as described previously (65).@(((:tag . "FW") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 22) (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 56)\n  (:start . 47) (:id . 50))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 67)\n  (:start . 57) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "CD") (:stem . "65") (:form . "65") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.86) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501951@unknown@formal@none@1@S@In short, the pGEM4Z-OGT-64A and pGEM4Z-EGFP-64A vectors were linearized with NotI and SpeI enzyme, respectively, purified by phenol-chloroform extraction and ethanol precipitation, and used as DNA templates.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "NN") (:stem . "pgem4z-ogt-64a") (:form . "pGEM4Z-OGT-64A")\n  (:end . 28) (:start . 14) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "pgem4z-egfp-64a") (:form . "pGEM4Z-EGFP-64A")\n  (:end . 48) (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "vector") (:form . "vectors") (:end . 56)\n  (:start . 49) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 61) (:start . 57)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "linearize") (:form . "linearized") (:end . 72)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 77) (:start . 73)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "NotI") (:form . "NotI") (:end . 82) (:start . 78)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "SpeI") (:form . "SpeI") (:end . 91) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "enzyme") (:form . "enzyme") (:end . 98)\n  (:start . 92) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 112)\n  (:start . 100) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 122)\n  (:start . 114) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 125) (:start . 123)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "phenol-chloroform") (:form . "phenol-chloroform")\n  (:end . 143) (:start . 126) (:id . 62))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 154)\n  (:start . 144) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 158) (:start . 155)\n  (:id . 64))\n ((:tag . "NN") (:stem . "ethanol") (:form . "ethanol") (:end . 166)\n  (:start . 159) (:id . 65))\n ((:tag . "NN") (:stem . "precipitation") (:form . "precipitation")\n  (:end . 180) (:start . 167) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 181) (:start . 180)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 190) (:start . 186)\n  (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 193) (:start . 191)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 197) (:start . 194)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 207)\n  (:start . 198) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s7.87) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501952@unknown@formal@none@1@S@The in vitro transcription was performed with T7 RNA polymerase (mMessage mMachine T7 Ultra kit; Ambion/Applied Biosystems, Austin, TX) according to the manufacturer's instructions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 26) (:start . 13) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 40)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "T7") (:form . "T7") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 63)\n  (:start . 53) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mmessage") (:form . "mMessage") (:end . 73)\n  (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "mmachine") (:form . "mMachine") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . "NNP") (:stem . "T7") (:form . "T7") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Ultra") (:form . "Ultra") (:end . 91) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Ambion/Applied") (:form . "Ambion/Applied")\n  (:end . 111) (:start . 97) (:id . 59))\n ((:tag . "NNP") (:stem . "Biosystems") (:form . "Biosystems") (:end . 122)\n  (:start . 112) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Austin") (:form . "Austin") (:end . 130)\n  (:start . 124) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "TX") (:form . "TX") (:end . 134) (:start . 132)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 135) (:start . 134)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 145)\n  (:start . 136) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 68))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 165)\n  (:start . 153) (:id . 69))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 167) (:start . 165)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 180)\n  (:start . 168) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.88) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501953@unknown@formal@none@1@S@After DNase I (Ambion) digestion and poly(A) tailing (Ambion), the transcribed RNA was recovered on RNeasy columns (Qiagen GmbH, Hilden, Germany) according to the manufacturer's instructions.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "DNase") (:form . "DNase") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "CD") (:stem . "i") (:form . "I") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Ambion") (:form . "Ambion") (:end . 21)\n  (:start . 15) (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "digestion") (:form . "digestion") (:end . 32)\n  (:start . 23) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "NN") (:stem . "poly(A)") (:form . "poly(A)") (:end . 44)\n  (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "tailing") (:form . "tailing") (:end . 52)\n  (:start . 45) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Ambion") (:form . "Ambion") (:end . 60)\n  (:start . 54) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "transcribe") (:form . "transcribed") (:end . 78)\n  (:start . 67) (:id . 57))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 86) (:start . 83)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "recover") (:form . "recovered") (:end . 96)\n  (:start . 87) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 99) (:start . 97)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "rneasy") (:form . "RNeasy") (:end . 106)\n  (:start . 100) (:id . 62))\n ((:tag . "NNS") (:stem . "column") (:form . "columns") (:end . 114)\n  (:start . 107) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Qiagen") (:form . "Qiagen") (:end . 122)\n  (:start . 116) (:id . 65))\n ((:tag . "NNP") (:stem . "GmbH") (:form . "GmbH") (:end . 127) (:start . 123)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Hilden") (:form . "Hilden") (:end . 135)\n  (:start . 129) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 144)\n  (:start . 137) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 155)\n  (:start . 146) (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 158) (:start . 156)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n  (:id . 74))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 175)\n  (:start . 163) (:id . 75))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 177) (:start . 175)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 190)\n  (:start . 178) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s7.89) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501954@unknown@formal@none@1@S@RNA quality was verified by agarose gel electrophoresis, and the RNA concentration was measured spectrophotometrically.@(((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "agarose") (:form . "agarose") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "electrophoresis") (:form . "electrophoresis")\n  (:end . 55) (:start . 40) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 68) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 82) (:start . 69) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 95)\n  (:start . 87) (:id . 56))\n ((:tag . "RB") (:stem . "spectrophotometrically")\n  (:form . "spectrophotometrically") (:end . 118) (:start . 96) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.90) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501955@unknown@formal@none@1@S@The protein concentration was determined in a microplate reader model 680 (Bio-Rad, Munich, Germany) at 750 nm using a detergent-compatible (DC) protein assay kit (Bio-Rad) according to the manufacturer's protocol.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 25) (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "NN") (:stem . "microplate") (:form . "microplate") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "reader") (:form . "reader") (:end . 63)\n  (:start . 57) (:id . 50))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 69) (:start . 64)\n  (:id . 51))\n ((:tag . "CD") (:stem . "680") (:form . "680") (:end . 73) (:start . 70)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Bio-Rad") (:form . "Bio-Rad") (:end . 82)\n  (:start . 75) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Munich") (:form . "Munich") (:end . 90)\n  (:start . 84) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 99)\n  (:start . 92) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 103) (:start . 101)\n  (:id . 60))\n ((:tag . "CD") (:stem . "750") (:form . "750") (:end . 107) (:start . 104)\n  (:id . 61))\n ((:tag . "NN") (:stem . "nm") (:form . "nm") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 116) (:start . 111)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 118) (:start . 117)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "detergent-compatible")\n  (:form . "detergent-compatible") (:end . 139) (:start . 119) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "DC") (:form . "DC") (:end . 143) (:start . 141)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 68))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 152)\n  (:start . 145) (:id . 69))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 158)\n  (:start . 153) (:id . 70))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 162) (:start . 159)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Bio-Rad") (:form . "Bio-Rad") (:end . 171)\n  (:start . 164) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 74))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 182)\n  (:start . 173) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 185) (:start . 183)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 189) (:start . 186)\n  (:id . 77))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 202)\n  (:start . 190) (:id . 78))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 204) (:start . 202)\n  (:id . 79))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 213)\n  (:start . 205) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s7.91) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501956@unknown@formal@none@1@S@Cells were lysed as described under “Cell transfection” and “HIV-1 infection and GlcN treatment.”@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "lyse") (:form . "lysed") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 29)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Cell") (:form . "Cell") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 54)\n  (:start . 42) (:id . 50))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 66) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 76)\n  (:start . 67) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "NN") (:stem . "glcn") (:form . "GlcN") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 95)\n  (:start . 86) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 97) (:start . 96)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.92) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501957@unknown@formal@none@1@S@Samples were prepared in 6× sodium dodecyl sulfate (SDS) buffer (350 mM Tris-HCl, pH 6.8, 30% glycerol, 10% SDS, 0.6 M dithiothreitol, 0.012% bromophenol blue), boiled for 10 min at 99°C, and loaded on 7.5% acrylamide-bisacrylamide gels or 4 to 20% Tris-glycine gradient gels (Anamed, Gross-Bieberau, Germany).@(((:tag . "NNS") (:stem . "sample") (:form . "Samples") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "CD") (:stem . "6×") (:form . "6×") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sodium") (:form . "sodium") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "dodecyl") (:form . 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"gels") (:end . 275) (:start . 271)\n  (:id . 101))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 277) (:start . 276)\n  (:id . 102))\n ((:tag . "NNP") (:stem . "Anamed") (:form . "Anamed") (:end . 283)\n  (:start . 277) (:id . 103))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 284) (:start . 283)\n  (:id . 104))\n ((:tag . "NNP") (:stem . "Gross-Bieberau") (:form . "Gross-Bieberau")\n  (:end . 299) (:start . 285) (:id . 105))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 300) (:start . 299)\n  (:id . 106))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 308)\n  (:start . 301) (:id . 107))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 309) (:start . 308)\n  (:id . 108))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 310) (:start . 309)\n  (:id . 109)))@@@1@68@((:identifiers (:sid . :s7.93) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501958@unknown@formal@none@1@S@Gel-separated proteins were transferred to a polyvinylidene fluoride membrane (Roth, Karlsruhe, Germany), which was blocked with 5% nonfat dry milk in PBS-Tween (PBS containing 0.1% Tween 20) for 2 h, washed with PBS-Tween, and incubated with the primary antibody in 2.5% nonfat dry milk in PBS-Tween at room temperature for 2 h.@(((:tag . "JJ") (:stem . "gel-separated") (:form . "Gel-separated")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 22)\n  (:start . 14) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 27) (:start . 23)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "transfer") (:form . "transferred") (:end . 39)\n  (:start . 28) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 47))\n ((:tag . "NN") (:stem . "polyvinylidene") (:form . 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"at") (:end . 303) (:start . 301)\n  (:id . 100))\n ((:tag . "NN") (:stem . "room") (:form . "room") (:end . 308) (:start . 304)\n  (:id . 101))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 320)\n  (:start . 309) (:id . 102))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 324) (:start . 321)\n  (:id . 103))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 326) (:start . 325)\n  (:id . 104))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 328) (:start . 327)\n  (:id . 105))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 329) (:start . 328)\n  (:id . 106)))@@@1@65@((:identifiers (:sid . :s7.94) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501959@unknown@formal@none@1@S@After washing, the membranes were incubated for 45 min at room temperature with the secondary antibody in 2.5% nonfat dry milk in PBS-Tween (71, 76).@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "wash") (:form . "washing") (:end . 13) (:start . 6)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "room") (:form . "room") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 74)\n  (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 93)\n  (:start . 84) (:id . 57))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 102)\n  (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 59))\n ((:tag . "CD") (:stem . "2.5") (:form . "2.5") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "nonfat") (:form . "nonfat") (:end . 117)\n  (:start . 111) (:id . 62))\n ((:tag . "JJ") (:stem . "dry") (:form . "dry") (:end . 121) (:start . 118)\n  (:id . 63))\n ((:tag . "NN") (:stem . "milk") (:form . "milk") (:end . 126) (:start . 122)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "pbs-tween") (:form . "PBS-Tween") (:end . 139)\n  (:start . 130) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 67))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 143) (:start . 141)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 69))\n ((:tag . "CD") (:stem . "76") (:form . "76") (:end . 147) (:start . 145)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.95) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501960@unknown@formal@none@1@S@In order to prevent cross-reactions with milk proteins, Western blot staining with the O-GlcNAc-recognizing antibody was performed as follows: the membranes were blocked with 10% Western blocking reagent (Roche) in PBS-Tween and the antibody was diluted in 0.5% Western blocking reagent (Roche).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "cross-reaction") (:form . "cross-reactions")\n  (:end . 35) (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "milk") (:form . "milk") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . 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"(") (:end . 288) (:start . 287)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "Roche") (:form . "Roche") (:end . 293)\n  (:start . 288) (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 294) (:start . 293)\n  (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 295) (:start . 294)\n  (:id . 92)))@@@1@51@((:identifiers (:sid . :s7.96) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501961@unknown@formal@none@1@S@Subsequent to the final washing step, chemiluminescence was detected according to the manufacturer's protocol (Pierce Biotechnology, Rockford, IL).@(((:tag . "JJ") (:stem . "subsequent") (:form . "Subsequent") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "washing") (:form . "washing") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "chemiluminescence") (:form . "chemiluminescence")\n  (:end . 55) (:start . 38) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 78)\n  (:start . 69) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 98)\n  (:start . 86) (:id . 55))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 109)\n  (:start . 101) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Pierce") (:form . "Pierce") (:end . 117)\n  (:start . 111) (:id . 59))\n ((:tag . "NNP") (:stem . "Biotechnology") (:form . "Biotechnology")\n  (:end . 131) (:start . 118) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Rockford") (:form . "Rockford") (:end . 141)\n  (:start . 133) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "IL") (:form . "IL") (:end . 145) (:start . 143)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.97) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501962@unknown@formal@none@1@S@The following primary antibodies were used: polyclonal rabbit anti-human Sp1 Pep2 (1:500; Santa Cruz Biotechnology, Heidelberg, Germany), polyclonal goat anti-human lamin A/C N-18 (1:1,000; Santa Cruz Biotechnology), polyclonal rabbit anti-human OGT TI-14 (1:1,000; Sigma-Aldrich), polyclonal rabbit anti-human actin (1:1,000; Sigma-Aldrich), monoclonal mouse anti-human histone H1 (1:1,000; Santa Cruz), monoclonal mouse anti-GFP (1:10,000, Roche); monoclonal mouse anti-eukaryote O-GlcNAc CTD110.6 (1:1,000; Hiss Diagnostics, Freiburg, Germany), and monoclonal mouse anti-human glyceraldehyde-3-phosphate dehydrogenase (GAPDH; 1:70,000, Millipore, Schwalbach, Germany).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . 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5501963@unknown@formal@none@1@S@The monoclonal rat anti-Tat immunoglobulin G2a (IgG2a) antibody (clone 1C9; 1:150) was produced by immunization of LOU/C rats with His-tagged purified recombinant Tat protein (50 µg) according to a previously described procedure (48).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "monoclonal") (:form . "monoclonal") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "rat") (:form . "rat") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "anti-tat") (:form . "anti-Tat") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "immunoglobulin") (:form . "immunoglobulin")\n  (:end . 42) (:start . 28) (:id . 46))\n ((:tag . "NNP") (:stem . "G2a") (:form . "G2a") (:end . 46) (:start . 43)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "IgG2a") (:form . "IgG2a") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 54) (:start . 53)\n  (:id . 50))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "clone") (:form . "clone") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1c9") (:form . "1C9") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . "CD") (:stem . "1:150") (:form . "1:150") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 95)\n  (:start . 87) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 98) (:start . 96)\n  (:id . 60))\n ((:tag . "NN") (:stem . "immunization") (:form . "immunization") (:end . 111)\n  (:start . 99) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "LOU/C") (:form . "LOU/C") (:end . 120)\n  (:start . 115) (:id . 63))\n ((:tag . "NNS") (:stem . "rat") (:form . "rats") (:end . 125) (:start . 121)\n  (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 130) (:start . 126)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "his-tagged") (:form . "His-tagged") (:end . 141)\n  (:start . 131) (:id . 66))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 150)\n  (:start . 142) (:id . 67))\n ((:tag . "JJ") (:stem . "recombinant") (:form . "recombinant") (:end . 162)\n  (:start . 151) (:id . 68))\n ((:tag . "NNP") (:stem . "Tat") (:form . "Tat") (:end . 166) (:start . 163)\n  (:id . 69))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 174)\n  (:start . 167) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n  (:id . 71))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 178) (:start . 176)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "µg") (:form . "µg") (:end . 181) (:start . 179)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 182) (:start . 181)\n  (:id . 74))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 192)\n  (:start . 183) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 195) (:start . 193)\n  (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 197) (:start . 196)\n  (:id . 77))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 208)\n  (:start . 198) (:id . 78))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 218)\n  (:start . 209) (:id . 79))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 228)\n  (:start . 219) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 230) (:start . 229)\n  (:id . 81))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 232) (:start . 230)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 233) (:start . 232)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s7.99) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501964@unknown@formal@none@1@S@The secondary, horseradish peroxidase-coupled antibodies goat anti-rat IgG, donkey anti-rabbit IgG, sheep anti-mouse IgG, and rabbit anti-goat IgG (all from Dako, Hamburg, Germany) were diluted 1:5,000.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "horseradish") (:form . "horseradish") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "JJ") (:stem . "peroxidase-coupled") (:form . "peroxidase-coupled")\n  (:end . 45) (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 56)\n  (:start . 46) (:id . 47))\n ((:tag . "VBP") (:stem . "goat") (:form . "goat") (:end . 61) (:start . 57)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "anti-rat") (:form . "anti-rat") (:end . 70)\n  (:start . 62) (:id . 49))\n ((:tag . "NNP") (:stem . "IgG") (:form . "IgG") (:end . 74) (:start . 71)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 51))\n ((:tag . "NN") (:stem . "donkey") (:form . "donkey") (:end . 82)\n  (:start . 76) (:id . 52))\n ((:tag . "JJ") (:stem . "anti-rabbit") (:form . "anti-rabbit") (:end . 94)\n  (:start . 83) (:id . 53))\n ((:tag . "NNP") (:stem . "IgG") (:form . "IgG") (:end . 98) (:start . 95)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 55))\n ((:tag . "VB") (:stem . "sheep") (:form . "sheep") (:end . 105)\n  (:start . 100) (:id . 56))\n ((:tag . "JJ") (:stem . "anti-mouse") (:form . "anti-mouse") (:end . 116)\n  (:start . 106) (:id . 57))\n ((:tag . "NN") (:stem . "igg") (:form . "IgG") (:end . 120) (:start . 117)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 60))\n ((:tag . "NN") (:stem . "rabbit") (:form . "rabbit") (:end . 132)\n  (:start . 126) (:id . 61))\n ((:tag . "JJ") (:stem . "anti-goat") (:form . "anti-goat") (:end . 142)\n  (:start . 133) (:id . 62))\n ((:tag . "NNP") (:stem . "IgG") (:form . "IgG") (:end . 146) (:start . 143)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 64))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 151) (:start . 148)\n  (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 156) (:start . 152)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Dako") (:form . "Dako") (:end . 161) (:start . 157)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Hamburg") (:form . "Hamburg") (:end . 170)\n  (:start . 163) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 179)\n  (:start . 172) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 72))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 185) (:start . 181)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "dilute") (:form . "diluted") (:end . 193)\n  (:start . 186) (:id . 74))\n ((:tag . "CD") (:stem . "1:5,000") (:form . "1:5,000") (:end . 201)\n  (:start . 194) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s7.100) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501965@unknown@formal@none@1@S@Fractionation was performed with a nuclear/cytosol fractionation kit (BioVision, Wiesbaden, Germany) according to the manufacturer's protocol (64).@(((:tag . "NNP") (:stem . "Fractionation") (:form . "Fractionation")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 17) (:start . 14)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 27)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 32) (:start . 28)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "nuclear/cytosol") (:form . "nuclear/cytosol")\n  (:end . 50) (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "fractionation") (:form . "fractionation")\n  (:end . 64) (:start . 51) (:id . 48))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 68) (:start . 65)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "BioVision") (:form . "BioVision") (:end . 79)\n  (:start . 70) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Wiesbaden") (:form . "Wiesbaden") (:end . 90)\n  (:start . 81) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 99)\n  (:start . 92) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 110)\n  (:start . 101) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 59))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 130)\n  (:start . 118) (:id . 60))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 132) (:start . 130)\n  (:id . 61))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 141)\n  (:start . 133) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 63))\n ((:tag . "CD") (:stem . "64") (:form . "64") (:end . 145) (:start . 143)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.101) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501966@unknown@formal@none@1@S@For gel shift experiments, cells were counted, and the nuclear fractions were lysed in 10 µl nuclear extraction buffer per 1 × 106 HEK 293T cells in order to concentrate the fractions.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 25)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "count") (:form . "counted") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 62)\n  (:start . 55) (:id . 53))\n ((:tag . "NNS") (:stem . "fraction") (:form . "fractions") (:end . 72)\n  (:start . 63) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "lyse") (:form . "lysed") (:end . 83) (:start . 78)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 100)\n  (:start . 93) (:id . 60))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 111)\n  (:start . 101) (:id . 61))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 118)\n  (:start . 112) (:id . 62))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 122) (:start . 119)\n  (:id . 63))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 124) (:start . 123)\n  (:id . 64))\n ((:tag . "HYPH") (:stem . "×") (:form . "×") (:end . 126) (:start . 125)\n  (:id . 65))\n ((:tag . "CD") (:stem . "106") (:form . "106") (:end . 130) (:start . 127)\n  (:id . 66))\n ((:tag . "NN") (:stem . "hek") (:form . "HEK") (:end . 134) (:start . 131)\n  (:id . 67))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 139) (:start . 135)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 145)\n  (:start . 140) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n  (:id . 70))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 154)\n  (:start . 149) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 157) (:start . 155)\n  (:id . 72))\n ((:tag . "VB") (:stem . "concentrate") (:form . "concentrate") (:end . 169)\n  (:start . 158) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 173) (:start . 170)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "fraction") (:form . "fractions") (:end . 183)\n  (:start . 174) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s7.102) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501967@unknown@formal@none@1@S@The protein concentration was determined as described above.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 25) (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 53)\n  (:start . 44) (:id . 48))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 59) (:start . 54)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s7.103) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501968@unknown@formal@none@1@S@Equal protein amounts of each fraction were loaded onto the gel and analyzed by Western blotting or applied to gel shift experiments.@(((:tag . "JJ") (:stem . "equal") (:form . "Equal") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "load") (:form . "loaded") (:end . 50) (:start . 44)\n  (:id . 49))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 76)\n  (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 87)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "blotting") (:form . "blotting") (:end . 96)\n  (:start . 88) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 107)\n  (:start . 100) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 114) (:start . 111)\n  (:id . 61))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 120)\n  (:start . 115) (:id . 62))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 132)\n  (:start . 121) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.104) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501969@unknown@formal@none@1@S@HEK 293T cells (2 × 106) were seeded in 9 ml medium in 10-cm cell culture dishes.@(((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "CC") (:stem . "×") (:form . "×") (:end . 19) (:start . 18)\n  (:id . 47))\n ((:tag . "CD") (:stem . "106") (:form . "106") (:end . 23) (:start . 20)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 24) (:start . 23)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "seed") (:form . "seeded") (:end . 36) (:start . 30)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 52))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 41) (:start . 40)\n  (:id . 53))\n ((:tag . "NN") (:stem . "ml") (:form . "ml") (:end . 44) (:start . 42)\n  (:id . 54))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 51)\n  (:start . 45) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "10-cm") (:form . "10-cm") (:end . 60) (:start . 55)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 65) (:start . 61)\n  (:id . 58))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 73)\n  (:start . 66) (:id . 59))\n ((:tag . "NNS") (:stem . "dish") (:form . "dishes") (:end . 80) (:start . 74)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.105) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501970@unknown@formal@none@1@S@The cells were transfected 24 h later (via the calcium phosphate method) with pcDNA4, pcDNA-Sp1, or pcDNA-Sp1 and pcDNA-OGT.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "RB") (:stem . "later") (:form . "later") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "calcium") (:form . "calcium") (:end . 54)\n  (:start . 47) (:id . 52))\n ((:tag . "NN") (:stem . "phosphate") (:form . "phosphate") (:end . 64)\n  (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 71)\n  (:start . 65) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 77) (:start . 73)\n  (:id . 56))\n ((:tag . "NN") (:stem . "pcdna4") (:form . "pcDNA4") (:end . 84)\n  (:start . 78) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "pcdna-sp1") (:form . "pcDNA-Sp1") (:end . 95)\n  (:start . 86) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 99) (:start . 97)\n  (:id . 61))\n ((:tag . "NN") (:stem . "pcdna-sp1") (:form . "pcDNA-Sp1") (:end . 109)\n  (:start . 100) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 63))\n ((:tag . "NN") (:stem . "pcdna-ogt") (:form . "pcDNA-OGT") (:end . 123)\n  (:start . 114) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.106) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501971@unknown@formal@none@1@S@The total transfected DNA amount was adjusted to 30 µg with the control plasmid pcDNA4.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "adjust") (:form . "adjusted") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 71)\n  (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 79)\n  (:start . 72) (:id . 55))\n ((:tag . "NN") (:stem . "pcdna4") (:form . "pcDNA4") (:end . 86)\n  (:start . 80) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.107) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501972@unknown@formal@none@1@S@At 24 h after transfection, cells were washed with PBS and subsequently lysed in IP lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM MgCl2, and 1% Igepal [all purchased from Sigma-Aldrich]), supplemented with one tablet of Complete Mini, EDTA-free protease inhibitor cocktail (Roche) per 10 ml.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 13) (:start . 8)\n  (:id . 45))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 26)\n  (:start . 14) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 33) (:start . 28)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "wash") (:form . "washed") (:end . 45) (:start . 39)\n  (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "PBS") (:form . "PBS") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 53))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 71)\n  (:start . 59) (:id . 54))\n ((:tag . "VBN") (:stem . "lyse") (:form . "lysed") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "IP") (:form . "IP") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "lysis") (:form . "lysis") (:end . 89) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 96)\n  (:start . 90) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 60))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 100) (:start . 98)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 103) (:start . 101)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Tris-HCl") (:form . "Tris-HCl") (:end . 112)\n  (:start . 104) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "pH") (:form . "pH") (:end . 116) (:start . 114)\n  (:id . 65))\n ((:tag . "CD") (:stem . "7.5") (:form . "7.5") (:end . 120) (:start . 117)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 67))\n ((:tag . "CD") (:stem . "150") (:form . "150") (:end . 125) (:start . 122)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 128) (:start . 126)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "NaCl") (:form . "NaCl") (:end . 133) (:start . 129)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 71))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 136) (:start . 135)\n  (:id . 72))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 139) (:start . 137)\n  (:id . 73))\n ((:tag . "NN") (:stem . "mgcl2") (:form . "MgCl2") (:end . 145)\n  (:start . 140) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 76))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 152) (:start . 151)\n  (:id . 77))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 153) (:start . 152)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Igepal") (:form . "Igepal") (:end . 160)\n  (:start . 154) (:id . 79))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 162) (:start . 161)\n  (:id . 80))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 165) (:start . 162)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "purchase") (:form . "purchased") (:end . 175)\n  (:start . 166) (:id . 82))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 180) (:start . 176)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "sigma-aldrich") (:form . "Sigma-Aldrich")\n  (:end . 194) (:start . 181) (:id . 84))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 195) (:start . 194)\n  (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 196) (:start . 195)\n  (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 87))\n ((:tag . "VBN") (:stem . "supplement") (:form . "supplemented") (:end . 210)\n  (:start . 198) (:id . 88))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 215) (:start . 211)\n  (:id . 89))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 219) (:start . 216)\n  (:id . 90))\n ((:tag . "NN") (:stem . "tablet") (:form . "tablet") (:end . 226)\n  (:start . 220) (:id . 91))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 229) (:start . 227)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "Complete") (:form . "Complete") (:end . 238)\n  (:start . 230) (:id . 93))\n ((:tag . "NNP") (:stem . "Mini") (:form . "Mini") (:end . 243) (:start . 239)\n  (:id . 94))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 244) (:start . 243)\n  (:id . 95))\n ((:tag . "JJ") (:stem . "edta-free") (:form . "EDTA-free") (:end . 254)\n  (:start . 245) (:id . 96))\n ((:tag . "NN") (:stem . "protease") (:form . "protease") (:end . 263)\n  (:start . 255) (:id . 97))\n ((:tag . "NN") (:stem . "inhibitor") (:form . "inhibitor") (:end . 273)\n  (:start . 264) (:id . 98))\n ((:tag . "NN") (:stem . "cocktail") (:form . "cocktail") (:end . 282)\n  (:start . 274) (:id . 99))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 284) (:start . 283)\n  (:id . 100))\n ((:tag . "NNP") (:stem . "Roche") (:form . "Roche") (:end . 289)\n  (:start . 284) (:id . 101))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 290) (:start . 289)\n  (:id . 102))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 294) (:start . 291)\n  (:id . 103))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 297) (:start . 295)\n  (:id . 104))\n ((:tag . "NN") (:stem . "ml") (:form . "ml") (:end . 300) (:start . 298)\n  (:id . 105))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 301) (:start . 300)\n  (:id . 106)))@@@1@65@((:identifiers (:sid . :s7.108) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501973@unknown@formal@none@1@S@The protein concentration was determined, and 1 mg total protein in a maximal volume of 1 ml was used for the immunoprecipitation.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 25) (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "mg") (:form . "mg") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "maximal") (:form . "maximal") (:end . 77)\n  (:start . 70) (:id . 55))\n ((:tag . "NN") (:stem . "volume") (:form . "volume") (:end . 84)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 89) (:start . 88)\n  (:id . 58))\n ((:tag . "NN") (:stem . "ml") (:form . "ml") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 96) (:start . 93)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 101) (:start . 97)\n  (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 105) (:start . 102)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 63))\n ((:tag . "NN") (:stem . "immunoprecipitation")\n  (:form . "immunoprecipitation") (:end . 129) (:start . 110) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.109) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501974@unknown@formal@none@1@S@The lysates were precleared by incubation with 100 µl Sepharose CL-6B (Sigma-Aldrich) at 4°C for 1 h.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "lysate") (:form . "lysates") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "precleare") (:form . "precleared") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "incubation") (:form . "incubation") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sepharose") (:form . "Sepharose") (:end . 63)\n  (:start . 54) (:id . 51))\n ((:tag . "NNP") (:stem . "CL-6B") (:form . "CL-6B") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "sigma-aldrich") (:form . "Sigma-Aldrich")\n  (:end . 84) (:start . 71) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "4°c") (:form . "4°C") (:end . 92) (:start . 89)\n  (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.110) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501975@unknown@formal@none@1@S@The Sp1 protein complex was immunoprecipitated at 4°C for 3 h with 30 µg anti-Sp1 Pep2 antibody covalently coupled to agarose beads (Santa Cruz Biotechnology).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "immunoprecipitate") (:form . "immunoprecipitated")\n  (:end . 46) (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "4°c") (:form . "4°C") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 59) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "anti-sp1") (:form . "anti-Sp1") (:end . 81)\n  (:start . 73) (:id . 56))\n ((:tag . "NN") (:stem . "pep2") (:form . "Pep2") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 95)\n  (:start . 87) (:id . 58))\n ((:tag . "RB") (:stem . "covalently") (:form . "covalently") (:end . 106)\n  (:start . 96) (:id . 59))\n ((:tag . "VBN") (:stem . "couple") (:form . "coupled") (:end . 114)\n  (:start . 107) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n  (:id . 61))\n ((:tag . "VB") (:stem . "agarose") (:form . "agarose") (:end . 125)\n  (:start . 118) (:id . 62))\n ((:tag . "NNS") (:stem . "bead") (:form . "beads") (:end . 131)\n  (:start . 126) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Santa") (:form . "Santa") (:end . 138)\n  (:start . 133) (:id . 65))\n ((:tag . "NNP") (:stem . "Cruz") (:form . "Cruz") (:end . 143) (:start . 139)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Biotechnology") (:form . "Biotechnology")\n  (:end . 157) (:start . 144) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.111) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501976@unknown@formal@none@1@S@Bead-coupled protein complexes were washed twice with 1 ml IP lysis buffer and three times with IP wash buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM MgCl2, and 0.1% Igepal).@(((:tag . "JJ") (:stem . "bead-coupled") (:form . "Bead-coupled") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 20)\n  (:start . 13) (:id . 43))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 30)\n  (:start . 21) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "wash") (:form . "washed") (:end . 42) (:start . 36)\n  (:id . 46))\n ((:tag . "RB") (:stem . "twice") (:form . "twice") (:end . 48) (:start . 43)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 55) (:start . 54)\n  (:id . 49))\n ((:tag . "NN") (:stem . "ml") (:form . "ml") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "IP") (:form . "IP") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "lysis") (:form . "lysis") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 74)\n  (:start . 68) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 84) (:start . 79)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 90) (:start . 85)\n  (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 95) (:start . 91)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "IP") (:form . "IP") (:end . 98) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "wash") (:form . "wash") (:end . 103) (:start . 99)\n  (:id . 59))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 110)\n  (:start . 104) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 117) (:start . 115)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Tris-HCl") (:form . "Tris-HCl") (:end . 126)\n  (:start . 118) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "pH") (:form . "pH") (:end . 130) (:start . 128)\n  (:id . 66))\n ((:tag . "CD") (:stem . "7.5") (:form . "7.5") (:end . 134) (:start . 131)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 68))\n ((:tag . "CD") (:stem . "150") (:form . "150") (:end . 139) (:start . 136)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 142) (:start . 140)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "NaCl") (:form . "NaCl") (:end . 147) (:start . 143)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 72))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 150) (:start . 149)\n  (:id . 73))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 153) (:start . 151)\n  (:id . 74))\n ((:tag . "NN") (:stem . "mgcl2") (:form . "MgCl2") (:end . 159)\n  (:start . 154) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n  (:id . 77))\n ((:tag . "CD") (:stem . "0.1") (:form . "0.1") (:end . 168) (:start . 165)\n  (:id . 78))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 169) (:start . 168)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Igepal") (:form . "Igepal") (:end . 176)\n  (:start . 170) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 177) (:start . 176)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s7.112) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501977@unknown@formal@none@1@S@The immunoprecipitates were analyzed by SDS-polyacrylamide gel electrophoresis and Western blotting as described above.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "immunoprecipitate") (:form . "immunoprecipitates")\n  (:end . 22) (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 27) (:start . 23)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 36)\n  (:start . 28) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sds-polyacrylamide") (:form . "SDS-polyacrylamide")\n  (:end . 58) (:start . 40) (:id . 47))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 62) (:start . 59)\n  (:id . 48))\n ((:tag . "NN") (:stem . "electrophoresis") (:form . "electrophoresis")\n  (:end . 78) (:start . 63) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 50))\n ((:tag . "NN") (:stem . "western") (:form . "Western") (:end . 90)\n  (:start . 83) (:id . 51))\n ((:tag . "NN") (:stem . "blotting") (:form . "blotting") (:end . 99)\n  (:start . 91) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 102) (:start . 100)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 112)\n  (:start . 103) (:id . 54))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 118)\n  (:start . 113) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.113) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501978@unknown@formal@none@1@S@HEK 293T cells were seeded 24 h prior to transfection in 1.5 ml medium at a density of 3 × 105 cells per well in a six-well plate.@(((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "seed") (:form . "seeded") (:end . 26) (:start . 20)\n  (:id . 46))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 53)\n  (:start . 41) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "CD") (:stem . "1.5") (:form . "1.5") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "ml") (:form . "ml") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 70)\n  (:start . 64) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . "NN") (:stem . "density") (:form . "density") (:end . 83)\n  (:start . 76) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 59))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 88) (:start . 87)\n  (:id . 60))\n ((:tag . "HYPH") (:stem . "×") (:form . "×") (:end . 90) (:start . 89)\n  (:id . 61))\n ((:tag . "CD") (:stem . "105") (:form . "105") (:end . 94) (:start . 91)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 100) (:start . 95)\n  (:id . 63))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 104) (:start . 101)\n  (:id . 64))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 109) (:start . 105)\n  (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 114) (:start . 113)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "six-well") (:form . "six-well") (:end . 123)\n  (:start . 115) (:id . 68))\n ((:tag . "NN") (:stem . "plate") (:form . "plate") (:end . 129)\n  (:start . 124) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s7.114) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501979@unknown@formal@none@1@S@Cells were transiently cotransfected (via the calcium phosphate method) in triplicate with 0.5 µg pXP1-LTR-Sp1wt-Luc or 0.5 µg pEF1α-Luc, along with 0.75 µg pcDNA-Sp1 and/or 0.25 µg pCEP4-Tat and 1 µg pcDNA-OGT (unless otherwise indicated).@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "transiently") (:form . "transiently") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "VBN") (:stem . "cotransfecte") (:form . "cotransfected")\n  (:end . 36) (:start . 23) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n  (:id . 46))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "calcium") (:form . "calcium") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "phosphate") (:form . "phosphate") (:end . 63)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 70)\n  (:start . 64) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "triplicate") (:form . "triplicate") (:end . 85)\n  (:start . 75) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n  (:id . 55))\n ((:tag . "CD") (:stem . "0.5") (:form . "0.5") (:end . 94) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "pxp1-ltr-sp1wt-luc") (:form . "pXP1-LTR-Sp1wt-Luc")\n  (:end . 116) (:start . 98) (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 119) (:start . 117)\n  (:id . 59))\n ((:tag . "CD") (:stem . "0.5") (:form . "0.5") (:end . 123) (:start . 120)\n  (:id . 60))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 126) (:start . 124)\n  (:id . 61))\n ((:tag . "NN") (:stem . "pef1α-luc") (:form . "pEF1α-Luc") (:end . 136)\n  (:start . 127) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 63))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 143)\n  (:start . 138) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 148) (:start . 144)\n  (:id . 65))\n ((:tag . "CD") (:stem . "0.75") (:form . "0.75") (:end . 153) (:start . 149)\n  (:id . 66))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 156) (:start . 154)\n  (:id . 67))\n ((:tag . "NN") (:stem . "pcdna-sp1") (:form . "pcDNA-Sp1") (:end . 166)\n  (:start . 157) (:id . 68))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 173)\n  (:start . 167) (:id . 69))\n ((:tag . "CD") (:stem . "0.25") (:form . "0.25") (:end . 178) (:start . 174)\n  (:id . 70))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 181) (:start . 179)\n  (:id . 71))\n ((:tag . "NN") (:stem . "pcep4-tat") (:form . "pCEP4-Tat") (:end . 191)\n  (:start . 182) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 195) (:start . 192)\n  (:id . 73))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 197) (:start . 196)\n  (:id . 74))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 200) (:start . 198)\n  (:id . 75))\n ((:tag . "NN") (:stem . "pcdna-ogt") (:form . "pcDNA-OGT") (:end . 210)\n  (:start . 201) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 212) (:start . 211)\n  (:id . 77))\n ((:tag . "IN") (:stem . "unless") (:form . "unless") (:end . 218)\n  (:start . 212) (:id . 78))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 228)\n  (:start . 219) (:id . 79))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 238)\n  (:start . 229) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 239) (:start . 238)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 240) (:start . 239)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s7.115) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501980@unknown@formal@none@1@S@The total DNA amount was adjusted to 2.5 µg with the control plasmid pcDNA4.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "adjust") (:form . "adjusted") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "CD") (:stem . "2.5") (:form . "2.5") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 43) (:start . 41)\n  (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 48) (:start . 44)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 60)\n  (:start . 53) (:id . 53))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 68)\n  (:start . 61) (:id . 54))\n ((:tag . "NN") (:stem . "pcdna4") (:form . "pcDNA4") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.116) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501981@unknown@formal@none@1@S@For RNA interference experiments, 0.22 µg (amount corresponds to 10 nM) short interfering RNA (siRNA) oligonucleotides specific for human OGT (hsOGT_7 SI02665131; Qiagen), human Sp1 (hsSP1_1 SI00150976; Qiagen), or human GAPDH (Silencer GAPDH siRNA; Ambion, Darmstadt, Germany), or a nontargeting control siRNA (Silencer Negative Control no. 1 siRNA; Ambion) was cotransfected.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "interference") (:form . "interference") (:end . 20)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 32)\n  (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 46))\n ((:tag . "CD") (:stem . "0.22") (:form . "0.22") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 49)\n  (:start . 43) (:id . 50))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 61)\n  (:start . 50) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 77) (:start . 72)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "interfere") (:form . "interfering") (:end . 89)\n  (:start . 78) (:id . 57))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "siRNA") (:form . "siRNA") (:end . 100)\n  (:start . 95) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "oligonucleotide") (:form . "oligonucleotides")\n  (:end . 118) (:start . 102) (:id . 62))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 127)\n  (:start . 119) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 131) (:start . 128)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 137)\n  (:start . 132) (:id . 65))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 141) (:start . 138)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . "NN") (:stem . "hsogt_7") (:form . "hsOGT_7") (:end . 150)\n  (:start . 143) (:id . 68))\n ((:tag . "NN") (:stem . "si02665131") (:form . "SI02665131") (:end . 161)\n  (:start . 151) (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 162) (:start . 161)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Qiagen") (:form . "Qiagen") (:end . 169)\n  (:start . 163) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 177)\n  (:start . 172) (:id . 74))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 181) (:start . 178)\n  (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 183) (:start . 182)\n  (:id . 76))\n ((:tag . "NN") (:stem . "hssp1_1") (:form . "hsSP1_1") (:end . 190)\n  (:start . 183) (:id . 77))\n ((:tag . "NN") (:stem . "si00150976") (:form . "SI00150976") (:end . 201)\n  (:start . 191) (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 202) (:start . 201)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Qiagen") (:form . "Qiagen") (:end . 209)\n  (:start . 203) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 211) (:start . 210)\n  (:id . 82))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 214) (:start . 212)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 220)\n  (:start . 215) (:id . 84))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 226)\n  (:start . 221) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 228) (:start . 227)\n  (:id . 86))\n ((:tag . "NNP") (:stem . "Silencer") (:form . "Silencer") (:end . 236)\n  (:start . 228) (:id . 87))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 242)\n  (:start . 237) (:id . 88))\n ((:tag . "NNP") (:stem . "siRNA") (:form . "siRNA") (:end . 248)\n  (:start . 243) (:id . 89))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 249) (:start . 248)\n  (:id . 90))\n ((:tag . "NNP") (:stem . "Ambion") (:form . "Ambion") (:end . 256)\n  (:start . 250) (:id . 91))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 257) (:start . 256)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "Darmstadt") (:form . "Darmstadt") (:end . 267)\n  (:start . 258) (:id . 93))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 268) (:start . 267)\n  (:id . 94))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 276)\n  (:start . 269) (:id . 95))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 277) (:start . 276)\n  (:id . 96))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 278) (:start . 277)\n  (:id . 97))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 281) (:start . 279)\n  (:id . 98))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 283) (:start . 282)\n  (:id . 99))\n ((:tag . "JJ") (:stem . "nontargeting") (:form . "nontargeting") (:end . 296)\n  (:start . 284) (:id . 100))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 304)\n  (:start . 297) (:id . 101))\n ((:tag . "NNP") (:stem . "siRNA") (:form . "siRNA") (:end . 310)\n  (:start . 305) (:id . 102))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 312) (:start . 311)\n  (:id . 103))\n ((:tag . "NNP") (:stem . "Silencer") (:form . "Silencer") (:end . 320)\n  (:start . 312) (:id . 104))\n ((:tag . "NNP") (:stem . "Negative") (:form . "Negative") (:end . 329)\n  (:start . 321) (:id . 105))\n ((:tag . "NNP") (:stem . "Control") (:form . "Control") (:end . 337)\n  (:start . 330) (:id . 106))\n ((:tag . "RB") (:stem . "no.") (:form . "no.") (:end . 341) (:start . 338)\n  (:id . 107))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 343) (:start . 342)\n  (:id . 108))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 349)\n  (:start . 344) (:id . 109))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 350) (:start . 349)\n  (:id . 110))\n ((:tag . "NNP") (:stem . "Ambion") (:form . "Ambion") (:end . 357)\n  (:start . 351) (:id . 111))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 358) (:start . 357)\n  (:id . 112))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 362) (:start . 359)\n  (:id . 113))\n ((:tag . "VBN") (:stem . "cotransfecte") (:form . "cotransfected")\n  (:end . 376) (:start . 363) (:id . 114))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 377) (:start . 376)\n  (:id . 115)))@@@1@74@((:identifiers (:sid . :s7.117) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501982@unknown@formal@none@1@S@Twenty-four hours later, cells were lysed in 200 µl 1× passive lysis buffer (Promega) and assayed for luciferase activity as described below.@(((:tag . "CD") (:stem . "twenty-four") (:form . "Twenty-four") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 17) (:start . 12)\n  (:id . 43))\n ((:tag . "RB") (:stem . "later") (:form . "later") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "lyse") (:form . "lysed") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "CD") (:stem . "200") (:form . "200") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1×") (:form . "1×") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "passive") (:form . "passive") (:end . 62)\n  (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "lysis") (:form . "lysis") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Promega") (:form . "Promega") (:end . 84)\n  (:start . 77) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "assay") (:form . "assayed") (:end . 97)\n  (:start . 90) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 101) (:start . 98)\n  (:id . 61))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 112)\n  (:start . 102) (:id . 62))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 121)\n  (:start . 113) (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 124) (:start . 122)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 134)\n  (:start . 125) (:id . 65))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 140)\n  (:start . 135) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.118) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501983@unknown@formal@none@1@S@Stable transfection of HEK 293T cells with pcDNA4-LTRwt-d2EGFP and pcDNA4-LTRmutSp1-d2EGFP was performed via the calcium phosphate method.@(((:tag . "JJ") (:stem . "stable") (:form . "Stable") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 19)\n  (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "pcDNA4-LTRwt-d2EGFP")\n  (:form . "pcDNA4-LTRwt-d2EGFP") (:end . 62) (:start . 43) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "pcDNA4-LTRmutSp1-d2EGFP")\n  (:form . "pcDNA4-LTRmutSp1-d2EGFP") (:end . 90) (:start . 67) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 94) (:start . 91)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 104)\n  (:start . 95) (:id . 53))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 108) (:start . 105)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 55))\n ((:tag . "NN") (:stem . "calcium") (:form . "calcium") (:end . 120)\n  (:start . 113) (:id . 56))\n ((:tag . "NN") (:stem . "phosphate") (:form . "phosphate") (:end . 130)\n  (:start . 121) (:id . 57))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 137)\n  (:start . 131) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.119) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501984@unknown@formal@none@1@S@Stably transfected cells were selected with 600 µg/ml Zeocin (Invitrogen).@(((:tag . "RB") (:stem . "stably") (:form . "Stably") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 18)\n  (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 24) (:start . 19)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "CD") (:stem . "600") (:form . "600") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "µg/ml") (:form . "µg/ml") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Zeocin") (:form . "Zeocin") (:end . 60)\n  (:start . 54) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 72)\n  (:start . 62) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.120) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501985@unknown@formal@none@1@S@After 10 days, single colonies were transferred to new culture plates.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 21)\n  (:start . 15) (:id . 46))\n ((:tag . "NNS") (:stem . "colony") (:form . "colonies") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "transfer") (:form . "transferred") (:end . 47)\n  (:start . 36) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "NNS") (:stem . "plate") (:form . "plates") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.121) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501986@unknown@formal@none@1@S@Fluorescence intensity of clones was analyzed by flow cytometry.@(((:tag . "NNP") (:stem . "Fluorescence") (:form . "Fluorescence") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 22)\n  (:start . 13) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 32)\n  (:start . 26) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 53) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cytometry") (:form . "cytometry") (:end . 63)\n  (:start . 54) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s7.122) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501987@unknown@formal@none@1@S@For the final experiment, three clones of each construct, which expressed comparable fluorescence intensities, were selected.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 56)\n  (:start . 47) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 63) (:start . 58)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "express") (:form . "expressed") (:end . 73)\n  (:start . 64) (:id . 54))\n ((:tag . "JJ") (:stem . "comparable") (:form . "comparable") (:end . 84)\n  (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 97)\n  (:start . 85) (:id . 56))\n ((:tag . "NNS") (:stem . "intensity") (:form . "intensities") (:end . 109)\n  (:start . 98) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 124)\n  (:start . 116) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.123) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501988@unknown@formal@none@1@S@Electroporation of Jurkat cells was performed with the Nucleofector II (Amaxa/Lonza, Cologne, Germany).@(((:tag . "NNP") (:stem . "Electroporation") (:form . "Electroporation")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 25)\n  (:start . 19) (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 31) (:start . 26)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 45)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 50) (:start . 46)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Nucleofector") (:form . "Nucleofector") (:end . 67)\n  (:start . 55) (:id . 50))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 70) (:start . 68)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Amaxa/Lonza") (:form . "Amaxa/Lonza") (:end . 83)\n  (:start . 72) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Cologne") (:form . "Cologne") (:end . 92)\n  (:start . 85) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 101)\n  (:start . 94) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.124) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501989@unknown@formal@none@1@S@Therefore, cells were resuspended in 100 µl Nucleofector solution V at a final concentration of 2 × 107 cells/ml and mixed with 50 µg/ml DNA (pcDNA4-EF1α-d2EGFP or pcDNA4-OGT).@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "resuspend") (:form . "resuspended") (:end . 33)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Nucleofector") (:form . "Nucleofector") (:end . 56)\n  (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "solution") (:form . "solution") (:end . 65)\n  (:start . 57) (:id . 51))\n ((:tag . "NNP") (:stem . "V") (:form . "V") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 78) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 92) (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "HYPH") (:stem . "×") (:form . "×") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . "CD") (:stem . "107") (:form . "107") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "cells/ml") (:form . "cells/ml") (:end . 112)\n  (:start . 104) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "mix") (:form . "mixed") (:end . 122) (:start . 117)\n  (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 127) (:start . 123)\n  (:id . 64))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 130) (:start . 128)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "µg/ml") (:form . "µg/ml") (:end . 136)\n  (:start . 131) (:id . 66))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 140) (:start . 137)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "pcDNA4-EF1α-d2EGFP") (:form . "pcDNA4-EF1α-d2EGFP")\n  (:end . 160) (:start . 142) (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 163) (:start . 161)\n  (:id . 70))\n ((:tag . "NN") (:stem . "pcdna4-ogt") (:form . "pcDNA4-OGT") (:end . 174)\n  (:start . 164) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 175) (:start . 174)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s7.125) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501990@unknown@formal@none@1@S@Electroporation was carried out with 100 µl cell DNA suspension using program X-001.@(((:tag . "NNP") (:stem . "Electroporation") (:form . "Electroporation")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 19) (:start . 16)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 27)\n  (:start . 20) (:id . 44))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 31) (:start . 28)\n  (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "suspension") (:form . "suspension") (:end . 63)\n  (:start . 53) (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . "NN") (:stem . "x-001") (:form . "X-001") (:end . 83) (:start . 78)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.126) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501991@unknown@formal@none@1@S@Immediately after transfection, cells were transferred to prewarmed RPMI 1640 medium supplemented with 10% FCS and 4 mM l-glutamine.@(((:tag . "RB") (:stem . "immediately") (:form . "Immediately") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 17) (:start . 12)\n  (:id . 43))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 30)\n  (:start . 18) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 37) (:start . 32)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "transfer") (:form . "transferred") (:end . 54)\n  (:start . 43) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "prewarmed") (:form . "prewarmed") (:end . 67)\n  (:start . 58) (:id . 50))\n ((:tag . "NNP") (:stem . "RPMI") (:form . "RPMI") (:end . 72) (:start . 68)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1640") (:form . "1640") (:end . 77) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 84)\n  (:start . 78) (:id . 53))\n ((:tag . "VBN") (:stem . "supplement") (:form . "supplemented") (:end . 97)\n  (:start . 85) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 102) (:start . 98)\n  (:id . 55))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 105) (:start . 103)\n  (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 106) (:start . 105)\n  (:id . 57))\n ((:tag . "NN") (:stem . "fcs") (:form . "FCS") (:end . 110) (:start . 107)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 59))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 116) (:start . 115)\n  (:id . 60))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . "NN") (:stem . "l-glutamine") (:form . "l-glutamine") (:end . 131)\n  (:start . 120) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.127) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501992@unknown@formal@none@1@S@At 48 h posttransfection, stably transfected Jurkat cells were selected with 400 µg/ml Zeocin (Invitrogen).@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "posttransfection") (:form . "posttransfection")\n  (:end . 24) (:start . 8) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "RB") (:stem . "stably") (:form . "stably") (:end . 32)\n  (:start . 26) (:id . 47))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 44)\n  (:start . 33) (:id . 48))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 71)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "CD") (:stem . "400") (:form . "400") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "µg/ml") (:form . "µg/ml") (:end . 86) (:start . 81)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Zeocin") (:form . "Zeocin") (:end . 93)\n  (:start . 87) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 105)\n  (:start . 95) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.128) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501993@unknown@formal@none@1@S@After initial selection, cells were singularized by limited dilution into 96-well plates.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "singularize") (:form . "singularized") (:end . 48)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "limited") (:form . "limited") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "dilution") (:form . "dilution") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "96-well") (:form . "96-well") (:end . 81)\n  (:start . 74) (:id . 53))\n ((:tag . "NNS") (:stem . "plate") (:form . "plates") (:end . 88)\n  (:start . 82) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.129) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501994@unknown@formal@none@1@S@After 13 days, d2EGFP-expressing Jurkat clones were pooled, while OGT-expressing Jurkat clones were cultivated separately.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "d2egfp-expressing") (:form . "d2EGFP-expressing")\n  (:end . 32) (:start . 15) (:id . 46))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 46)\n  (:start . 40) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 51) (:start . 47)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "pool") (:form . "pooled") (:end . 58) (:start . 52)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 65) (:start . 60)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "ogt-expressing") (:form . "OGT-expressing")\n  (:end . 80) (:start . 66) (:id . 53))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 87)\n  (:start . 81) (:id . 54))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 94)\n  (:start . 88) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "cultivate") (:form . "cultivated") (:end . 110)\n  (:start . 100) (:id . 57))\n ((:tag . "RB") (:stem . "separately") (:form . "separately") (:end . 121)\n  (:start . 111) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.130) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501995@unknown@formal@none@1@S@T lymphocytes were electroporated as described previously (65).@(((:tag . "NN") (:stem . "t") (:form . "T") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 13)\n  (:start . 2) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "electroporate") (:form . "electroporated")\n  (:end . 33) (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 46)\n  (:start . 37) (:id . 47))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 57)\n  (:start . 47) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n  (:id . 49))\n ((:tag . "CD") (:stem . "65") (:form . "65") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.131) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501996@unknown@formal@none@1@S@Briefly, cells were washed once with pure RPMI 1640 and once with OptiMEM without phenol red (Invitrogen) (all at room temperature).@(((:tag . "RB") (:stem . "briefly") (:form . "Briefly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "wash") (:form . "washed") (:end . 26) (:start . 20)\n  (:id . 46))\n ((:tag . "RB") (:stem . "once") (:form . "once") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "pure") (:form . "pure") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "RPMI") (:form . "RPMI") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "CD") (:stem . "1640") (:form . "1640") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "RB") (:stem . "once") (:form . "once") (:end . 60) (:start . 56)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "OptiMEM") (:form . "OptiMEM") (:end . 73)\n  (:start . 66) (:id . 55))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 81)\n  (:start . 74) (:id . 56))\n ((:tag . "NN") (:stem . "phenol") (:form . "phenol") (:end . 88)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 104)\n  (:start . 94) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 62))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 113) (:start . 111)\n  (:id . 64))\n ((:tag . "NN") (:stem . "room") (:form . "room") (:end . 118) (:start . 114)\n  (:id . 65))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 130)\n  (:start . 119) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.132) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501997@unknown@formal@none@1@S@The cells were resuspended in OptiMEM at a concentration of 1 × 108 cells/ml.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "resuspend") (:form . "resuspended") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "OptiMEM") (:form . "OptiMEM") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 56) (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "CD") (:stem . "108") (:form . "108") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cells/ml") (:form . "cells/ml") (:end . 76)\n  (:start . 68) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.133) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501998@unknown@formal@none@1@S@RNA was transferred to a 4-mm cuvette (Molecular Bioproducts, San Diego, CA) at a final concentration of 150 µg/ml.@(((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "transfer") (:form . "transferred") (:end . 19)\n  (:start . 8) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "4-mm") (:form . "4-mm") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cuvette") (:form . "cuvette") (:end . 37)\n  (:start . 30) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Molecular") (:form . "Molecular") (:end . 48)\n  (:start . 39) (:id . 50))\n ((:tag . "NNP") (:stem . "Bioproducts") (:form . "Bioproducts") (:end . 60)\n  (:start . 49) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "San") (:form . "San") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Diego") (:form . "Diego") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "CA") (:form . "CA") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n  (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 79) (:start . 77)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 81) (:start . 80)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 87) (:start . 82)\n  (:id . 60))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 101) (:start . 88) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 62))\n ((:tag . "CD") (:stem . "150") (:form . "150") (:end . 108) (:start . 105)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "µg/ml") (:form . "µg/ml") (:end . 114)\n  (:start . 109) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.134) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5501999@unknown@formal@none@1@S@A volume of 100 µl of cell suspension was added and immediately pulsed in a Gene Pulser Xcell (Bio-Rad).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "volume") (:form . "volume") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µl") (:form . "µl") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 26) (:start . 22)\n  (:id . 48))\n ((:tag . "NN") (:stem . "suspension") (:form . "suspension") (:end . 37)\n  (:start . 27) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 47) (:start . 42)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "RB") (:stem . "immediately") (:form . "immediately") (:end . 63)\n  (:start . 52) (:id . 53))\n ((:tag . "JJ") (:stem . "pulsed") (:form . "pulsed") (:end . 70)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 75) (:start . 74)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 80) (:start . 76)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Pulser") (:form . "Pulser") (:end . 87)\n  (:start . 81) (:id . 58))\n ((:tag . "NNP") (:stem . "Xcell") (:form . "Xcell") (:end . 93) (:start . 88)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Bio-Rad") (:form . "Bio-Rad") (:end . 102)\n  (:start . 95) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 103) (:start . 102)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.135) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502000@unknown@formal@none@1@S@Pulse conditions for CD4+ T lymphocytes were square-wave pulse, 500 V, and 5 ms.@(((:tag . "NN") (:stem . "pulse") (:form . "Pulse") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 39)\n  (:start . 28) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "square-wave") (:form . "square-wave") (:end . 56)\n  (:start . 45) (:id . 49))\n ((:tag . "NN") (:stem . "pulse") (:form . "pulse") (:end . 62) (:start . 57)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "CD") (:stem . "500") (:form . "500") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "V") (:form . "V") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 76) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "ms") (:form . "ms") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.136) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502001@unknown@formal@none@1@S@Immediately after electroporation, cells were transferred to prewarmed MLPC medium.@(((:tag . "RB") (:stem . "immediately") (:form . "Immediately") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 17) (:start . 12)\n  (:id . 43))\n ((:tag . "NN") (:stem . "electroporation") (:form . "electroporation")\n  (:end . 33) (:start . 18) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 40) (:start . 35)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 45) (:start . 41)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "transfer") (:form . "transferred") (:end . 57)\n  (:start . 46) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "prewarmed") (:form . "prewarmed") (:end . 70)\n  (:start . 61) (:id . 50))\n ((:tag . "NNP") (:stem . "MLPC") (:form . "MLPC") (:end . 75) (:start . 71)\n  (:id . 51))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 82)\n  (:start . 76) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.137) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502002@unknown@formal@none@1@S@Cell lysates were centrifuged at 10,000 × g at 4°C for 3 min.@(((:tag . "NN") (:stem . "cell") (:form . "Cell") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "lysate") (:form . "lysates") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "centrifuge") (:form . "centrifuged") (:end . 29)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "CD") (:stem . "10,000") (:form . "10,000") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "g") (:form . "g") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "4°c") (:form . "4°C") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.138) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502003@unknown@formal@none@1@S@Firefly luciferase activity of the supernatants was measured using the luciferase assay system (Promega) in a Luminoskan Ascent instrument (Thermo Fisher Scientific, Langenselbold, Germany).@(((:tag . "JJ") (:stem . "firefly") (:form . "Firefly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 27)\n  (:start . 19) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "supernatant") (:form . "supernatants") (:end . 47)\n  (:start . 35) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 51) (:start . 48)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 60)\n  (:start . 52) (:id . 49))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 66) (:start . 61)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 51))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 81)\n  (:start . 71) (:id . 52))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 87) (:start . 82)\n  (:id . 53))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 94)\n  (:start . 88) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Promega") (:form . "Promega") (:end . 103)\n  (:start . 96) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "luminoskan") (:form . "Luminoskan") (:end . 120)\n  (:start . 110) (:id . 60))\n ((:tag . "JJ") (:stem . "ascent") (:form . "Ascent") (:end . 127)\n  (:start . 121) (:id . 61))\n ((:tag . "NN") (:stem . "instrument") (:form . "instrument") (:end . 138)\n  (:start . 128) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Thermo") (:form . "Thermo") (:end . 146)\n  (:start . 140) (:id . 64))\n ((:tag . "NNP") (:stem . "Fisher") (:form . "Fisher") (:end . 153)\n  (:start . 147) (:id . 65))\n ((:tag . "NNP") (:stem . "Scientific") (:form . "Scientific") (:end . 164)\n  (:start . 154) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Langenselbold") (:form . "Langenselbold")\n  (:end . 179) (:start . 166) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 188)\n  (:start . 181) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.139) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502004@unknown@formal@none@1@S@Each luciferase reporter gene assay was performed in triplicate (except for that shown in Fig. 3).@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 49)\n  (:start . 40) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "triplicate") (:form . "triplicate") (:end . 63)\n  (:start . 53) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 51))\n ((:tag . "IN") (:stem . "except") (:form . "except") (:end . 71)\n  (:start . 65) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 75) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 86) (:start . 81)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 94) (:start . 90)\n  (:id . 57))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.140) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502005@unknown@formal@none@1@S@OGT inhibits HIV-1 LTR promoter activity in infected primary CD4+ T cells.@(((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "infected") (:form . "infected") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 73) (:start . 68)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.141) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502006@unknown@formal@none@1@S@Primary CD4+ T cells from two different donors were infected with VSV-G env pseudotyped HIV-1NL4-3LucR-E-.@(((:tag . "JJ") (:stem . "primary") (:form . "Primary") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 39)\n  (:start . 30) (:id . 48))\n ((:tag . "NNS") (:stem . "donor") (:form . "donors") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "infect") (:form . "infected") (:end . 60)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "VSV-G") (:form . "VSV-G") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "env") (:form . "env") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "pseudotype") (:form . "pseudotyped") (:end . 87)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "hiv-1nl4-3lucr-e-") (:form . "HIV-1NL4-3LucR-E-")\n  (:end . 105) (:start . 88) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.142) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502007@unknown@formal@none@1@S@At 36 h postinfection, cells were electroporated with in vitro-transcribed polyadenylated mRNA encoding either EGFP or OGT.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "postinfection") (:form . "postinfection")\n  (:end . 21) (:start . 8) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "electroporate") (:form . "electroporated")\n  (:end . 48) (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "vitro-transcribed") (:form . "vitro-transcribed")\n  (:end . 74) (:start . 57) (:id . 52))\n ((:tag . "VBN") (:stem . "polyadenylate") (:form . "polyadenylated")\n  (:end . 89) (:start . 75) (:id . 53))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 94) (:start . 90)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "encode") (:form . "encoding") (:end . 103)\n  (:start . 95) (:id . 55))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 110)\n  (:start . 104) (:id . 56))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 115) (:start . 111)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 118) (:start . 116)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 122) (:start . 119)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.143) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502008@unknown@formal@none@1@S@(A) At 8 h postelectroporation, luciferase activity was measured.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "At") (:end . 6) (:start . 4)\n  (:id . 45))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 8) (:start . 7)\n  (:id . 46))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 10) (:start . 9)\n  (:id . 47))\n ((:tag . "NN") (:stem . "postelectroporation")\n  (:form . "postelectroporation") (:end . 30) (:start . 11) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 49))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 42)\n  (:start . 32) (:id . 50))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 51)\n  (:start . 43) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 64)\n  (:start . 56) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.144) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502009@unknown@formal@none@1@S@(B) The O-GlcNAcylation pattern and overexpression of EGFP and OGT were verified by Western blotting.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 23) (:start . 8) (:id . 46))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 50) (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 80)\n  (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 91)\n  (:start . 84) (:id . 57))\n ((:tag . "NN") (:stem . "blotting") (:form . "blotting") (:end . 100)\n  (:start . 92) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.145) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502010@unknown@formal@none@1@S@Staining of GAPDH demonstrates equal loading of proteins.@(((:tag . "NN") (:stem . "staining") (:form . "Staining") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "demonstrate") (:form . "demonstrates") (:end . 30)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 36) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "loading") (:form . "loading") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 56)\n  (:start . 48) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s7.146) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502011@unknown@formal@none@1@S@HEK 293T cells were transfected with the expression constructs for Sp1, OGT, or both, and nuclear proteins were isolated as already described.@(((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 51)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 62)\n  (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 97)\n  (:start . 90) (:id . 60))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 106)\n  (:start . 98) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 111) (:start . 107)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 120)\n  (:start . 112) (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 131)\n  (:start . 124) (:id . 65))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 141)\n  (:start . 132) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.147) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502012@unknown@formal@none@1@S@The electrophoretic mobility shift assay was essentially performed as described previously (54, 56).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "electrophoretic") (:form . "electrophoretic")\n  (:end . 19) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 28)\n  (:start . 20) (:id . 44))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 34) (:start . 29)\n  (:id . 45))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 40) (:start . 35)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "RB") (:stem . "essentially") (:form . "essentially") (:end . 56)\n  (:start . 45) (:id . 48))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 66)\n  (:start . 57) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 69) (:start . 67)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 79)\n  (:start . 70) (:id . 51))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 90)\n  (:start . 80) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 53))\n ((:tag . "CD") (:stem . "54") (:form . "54") (:end . 94) (:start . 92)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 55))\n ((:tag . "CD") (:stem . "56") (:form . "56") (:end . 98) (:start . 96)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.148) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502013@unknown@formal@none@1@S@Briefly, binding reaction mixtures (final volume, 15 µl) contained 10 mM Tris-HCl (pH 7.5), 80 mM NaCl, 1 mM EDTA, 1 mM dithiothreitol, 5% glycerol, 3 µg of poly(dI-dC) · poly(dI-dC) (GE Healthcare), 10 µg of nuclear extract, and 4 × 104 cpm of the 32P-end-labeled double-stranded oligonucleotide probe.@(((:tag . "RB") (:stem . "briefly") (:form . "Briefly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "VBG") (:stem . "bind") (:form . "binding") (:end . 16) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "reaction") (:form . "reaction") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "mixture") (:form . "mixtures") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . 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5502014@unknown@formal@none@1@S@The oligonucleotides corresponded either to the wild-type HIV-1 LTR region containing the three binding sites for Sp1 (wt LTR-Sp1, 5'-GGATCGGGAGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCC-3'; Sp1-binding sites are underlined) or to the Sp1-binding-site-mutated HIV-1 LTR (mut LTR-Sp1, 5'-GGATCGGGATTCGTGGCCTGTTCGGGACTGGTTAGTGGCGAGCCC-3'; nucleotide substitutions in bold).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "oligonucleotide") (:form . "oligonucleotides")\n  (:end . 20) (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "correspond") (:form . "corresponded") (:end . 33)\n  (:start . 21) (:id . 44))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 40)\n  (:start . 34) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 47))\n ((:tag . 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5502015@unknown@formal@none@1@S@After incubation for 45 min on ice, the protein-DNA complexes were resolved on nondenaturing 5% polyacrylamide gels run in 1× Tris-borate-EDTA buffer containing 89 mM Tris, 89 mM boric acid, and 2 mM EDTA (pH 8.0).@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "incubation") (:form . "incubation") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "ice") (:form . "ice") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "protein-dna") (:form . "protein-DNA") (:end . 51)\n  (:start . 40) (:id . 51))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 61)\n  (:start . 52) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "resolve") (:form . "resolved") (:end . 75)\n  (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "nondenature") (:form . "nondenaturing") (:end . 92)\n  (:start . 79) (:id . 56))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "polyacrylamide") (:form . "polyacrylamide")\n  (:end . 110) (:start . 96) (:id . 59))\n ((:tag . "NNS") (:stem . "gel") (:form . "gels") (:end . 115) (:start . 111)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "run") (:form . "run") (:end . 119) (:start . 116)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "CD") (:stem . "1×") (:form . "1×") (:end . 125) (:start . 123)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Tris-borate-EDTA") (:form . "Tris-borate-EDTA")\n  (:end . 142) (:start . 126) (:id . 64))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 149)\n  (:start . 143) (:id . 65))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 160)\n  (:start . 150) (:id . 66))\n ((:tag . "CD") (:stem . "89") (:form . "89") (:end . 163) (:start . 161)\n  (:id . 67))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 166) (:start . 164)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Tris") (:form . "Tris") (:end . 171) (:start . 167)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 70))\n ((:tag . "CD") (:stem . "89") (:form . "89") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 178) (:start . 176)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "boric") (:form . "boric") (:end . 184)\n  (:start . 179) (:id . 73))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 189) (:start . 185)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n  (:id . 76))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 196) (:start . 195)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 199) (:start . 197)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "EDTA") (:form . "EDTA") (:end . 204) (:start . 200)\n  (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 206) (:start . 205)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "pH") (:form . "pH") (:end . 208) (:start . 206)\n  (:id . 81))\n ((:tag . "CD") (:stem . "8.0") (:form . "8.0") (:end . 212) (:start . 209)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s7.151) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5502018@unknown@formal@none@1@S@Supershift antibodies were Sp1 Pep2 sc-59X (Santa Cruz Biotechnology), O-GlcNAc CTD110.6 (Hiss Diagnostics), and OGT TI-14 (Sigma-Aldrich), as well as IgG (NF-κB p50 sc114X [Santa Cruz Biotechnology]) and IgM (heparan sulfate 370255 [Seikagaku Corporation]) isotype controls.@(((:tag . "NNP") (:stem . "Supershift") (:form . "Supershift") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 26) (:start . 22)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Pep2") (:form . "Pep2") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "sc-59X") (:form . "sc-59X") (:end . 42)\n  (:start . 36) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . 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5502019@unknown@formal@none@1@S@All experiments were repeated three times.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "repeat") (:form . "repeated") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s7.155) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502020@unknown@formal@none@1@S@One representative gel shift of each assay is shown.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 51) (:start . 46)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 52) (:start . 51)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s7.156) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502021@unknown@formal@none@1@S@RNA was isolated with RNeasy columns (Qiagen GmbH, Hilden, Germany) according to the manufacturer's instructions.@(((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "rneasy") (:form . "RNeasy") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "column") (:form . "columns") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Qiagen") (:form . "Qiagen") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "NNP") (:stem . "GmbH") (:form . "GmbH") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Hilden") (:form . "Hilden") (:end . 57)\n  (:start . 51) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Germany") (:form . "Germany") (:end . 66)\n  (:start . 59) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 77)\n  (:start . 68) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 97)\n  (:start . 85) (:id . 59))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 99) (:start . 97)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 112)\n  (:start . 100) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s7.157) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502022@unknown@formal@none@1@S@RNA quality was verified by agarose gel electrophoresis, and RNA concentration was measured spectrophotometrically.@(((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "agarose") (:form . "agarose") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "electrophoresis") (:form . "electrophoresis")\n  (:end . 55) (:start . 40) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 78) (:start . 65) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 91)\n  (:start . 83) (:id . 55))\n ((:tag . "RB") (:stem . "spectrophotometrically")\n  (:form . "spectrophotometrically") (:end . 114) (:start . 92) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.158) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502023@unknown@formal@none@1@S@Reverse transcription of total RNA and amplification of OGT and GAPDH cDNA were performed as described previously (53, 72).@(((:tag . "JJ") (:stem . "reverse") (:form . "Reverse") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 21) (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 30) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 52) (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "cDNA") (:form . "cDNA") (:end . 74) (:start . 70)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 89)\n  (:start . 80) (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 102)\n  (:start . 93) (:id . 57))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 113)\n  (:start . 103) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 59))\n ((:tag . "CD") (:stem . "53") (:form . "53") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.159) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502024@unknown@formal@none@1@S@PCR was carried out in a total reaction volume of 25 µl with 1 µl of either undiluted (1) or diluted (1:5 and 1:10) cDNA.@(((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 30) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . "reaction") (:form . "reaction") (:end . 39)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "volume") (:form . "volume") (:end . 46)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 52) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "µl") (:form . "µl") (:end . 55) (:start . 53)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 60) (:start . 56)\n  (:id . 54))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . "NN") (:stem . "µl") (:form . "µl") (:end . 65) (:start . 63)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 57))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 75)\n  (:start . 69) (:id . 58))\n ((:tag . "JJ") (:stem . "undiluted") (:form . "undiluted") (:end . 85)\n  (:start . 76) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 88) (:start . 87)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 62))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 92) (:start . 90)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "dilute") (:form . "diluted") (:end . 100)\n  (:start . 93) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 65))\n ((:tag . "CD") (:stem . "1:5") (:form . "1:5") (:end . 105) (:start . 102)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 67))\n ((:tag . "CD") (:stem . "1:10") (:form . "1:10") (:end . 114) (:start . 110)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "cDNA") (:form . "cDNA") (:end . 120) (:start . 116)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.160) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502025@unknown@formal@none@1@S@Primers specifically amplifying recombinant OGT were selected: the forward primer recognized specifically the vector-encoded 5' untranslated region of the recombinant OGT mRNA (5'-TCCAGTGTGGTGGAATTCTG-3'); the reverse primer was homologous to a sequence corresponding to the N-terminal region of both endogenous and recombinant OGT (5'-TTGCGTCTCAATTGCTTTCA-3').@(((:tag . "NNS") (:stem . "primer") (:form . "Primers") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 20)\n  (:start . 8) (:id . 43))\n ((:tag . "VBG") (:stem . "amplify") (:form . "amplifying") (:end . 31)\n  (:start . 21) (:id . 44))\n ((:tag . "JJ") (:stem . "recombinant") (:form . "recombinant") (:end . 43)\n  (:start . 32) (:id . 45))\n ((:tag . "NN") (:stem . "ogt") (:form . "OGT") (:end . 47) (:start . 44)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 52) (:start . 48)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 61)\n  (:start . 53) (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 62) (:start . 61)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "forward") (:form . "forward") (:end . 74)\n  (:start . 67) (:id . 51))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 81)\n  (:start . 75) (:id . 52))\n ((:tag . "VBD") (:stem . "recognize") (:form . "recognized") (:end . 92)\n  (:start . 82) (:id . 53))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 105)\n  (:start . 93) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "vector-encoded") (:form . "vector-encoded")\n  (:end . 124) (:start . 110) (:id . 56))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 126) (:start . 125)\n  (:id . 57))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 127) (:start . 126)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "untranslated") (:form . "untranslated") (:end . 140)\n  (:start . 128) (:id . 59))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 147)\n  (:start . 141) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "recombinant") (:form . "recombinant") (:end . 166)\n  (:start . 155) (:id . 63))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 170) (:start . 167)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 175) (:start . 171)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "5'-TCCAGTGTGGTGGAATTCTG-3")\n  (:form . "5’-TCCAGTGTGGTGGAATTCTG-3") (:end . 202) (:start . 177)\n  (:id . 67))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 203) (:start . 202)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 204) (:start . 203)\n  (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 205) (:start . 204)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 217)\n  (:start . 210) (:id . 72))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 224)\n  (:start . 218) (:id . 73))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 228) (:start . 225)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 239)\n  (:start . 229) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 242) (:start . 240)\n  (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 244) (:start . 243)\n  (:id . 77))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 253)\n  (:start . 245) (:id . 78))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 267)\n  (:start . 254) (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 270) (:start . 268)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 274) (:start . 271)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 285)\n  (:start . 275) (:id . 82))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 292)\n  (:start . 286) (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 295) (:start . 293)\n  (:id . 84))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 300) (:start . 296)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 311)\n  (:start . 301) (:id . 86))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 315) (:start . 312)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "recombinant") (:form . "recombinant") (:end . 327)\n  (:start . 316) (:id . 88))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 331) (:start . 328)\n  (:id . 89))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 333) (:start . 332)\n  (:id . 90))\n ((:tag . "NNP") (:stem . "5'-TTGCGTCTCAATTGCTTTCA-3")\n  (:form . "5’-TTGCGTCTCAATTGCTTTCA-3") (:end . 358) (:start . 333)\n  (:id . 91))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 359) (:start . 358)\n  (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 360) (:start . 359)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 361) (:start . 360)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s7.161) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502026@unknown@formal@none@1@S@Amplification of GAPDH was performed using the forward primer 5'-AGCCACATCGCTCAGAACAC-3' and the reverse primer 5'-GAGGCATTGCTGATGATCTTG-3' as described previously (44).@(((:tag . "NNP") (:stem . "Amplification") (:form . "Amplification")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 22) (:start . 17)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 42) (:start . 37)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "forward") (:form . "forward") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 61)\n  (:start . 55) (:id . 50))\n ((:tag . "NN") (:stem . "5'-agccacatcgctcagaacac-3")\n  (:form . "5’-AGCCACATCGCTCAGAACAC-3") (:end . 87) (:start . 62) (:id . 51))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 88) (:start . 87)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 104)\n  (:start . 97) (:id . 55))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 111)\n  (:start . 105) (:id . 56))\n ((:tag . "NN") (:stem . "5'-gaggcattgctgatgatcttg-3")\n  (:form . "5’-GAGGCATTGCTGATGATCTTG-3") (:end . 138) (:start . 112)\n  (:id . 57))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 139) (:start . 138)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 142) (:start . 140)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 152)\n  (:start . 143) (:id . 60))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 163)\n  (:start . 153) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 165) (:start . 164)\n  (:id . 62))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 167) (:start . 165)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 168) (:start . 167)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.162) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502027@unknown@formal@none@1@S@Statistical significances were calculated with the Student t test for paired samples using the SPSS 15.0 and 16.0 software for Microsoft Windows (SPSS Inc., Chicago, IL).@(((:tag . "JJ") (:stem . "statistical") (:form . "Statistical") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "significance") (:form . "significances")\n  (:end . 25) (:start . 12) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 41)\n  (:start . 31) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 58)\n  (:start . 51) (:id . 48))\n ((:tag . "NN") (:stem . "t") (:form . "t") (:end . 60) (:start . 59)\n  (:id . 49))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 65) (:start . 61)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "paired") (:form . "paired") (:end . 76)\n  (:start . 70) (:id . 52))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 84)\n  (:start . 77) (:id . 53))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 90) (:start . 85)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "SPSS") (:form . "SPSS") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . "CD") (:stem . "15.0") (:form . "15.0") (:end . 104) (:start . 100)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 58))\n ((:tag . "CD") (:stem . "16.0") (:form . "16.0") (:end . 113) (:start . 109)\n  (:id . 59))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 122)\n  (:start . 114) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Microsoft") (:form . "Microsoft") (:end . 136)\n  (:start . 127) (:id . 62))\n ((:tag . "NNP") (:stem . "Windows") (:form . "Windows") (:end . 144)\n  (:start . 137) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "SPSS") (:form . "SPSS") (:end . 150) (:start . 146)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Inc.") (:form . "Inc.") (:end . 155) (:start . 151)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Chicago") (:form . "Chicago") (:end . 164)\n  (:start . 157) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "IL") (:form . "IL") (:end . 168) (:start . 166)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.163) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502028@unknown@formal@none@1@S@P values smaller than 0.05 were considered statistically significant (*), P values smaller than 0.01 were considered highly significant (**), and P values smaller than 0.001 were considered the most significant (***).@(((:tag . "NN") (:stem . "p") (:form . "P") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "CD") (:stem . "0.05") (:form . "0.05") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n  (:end . 56) (:start . 43) (:id . 49))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 68)\n  (:start . 57) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "SYM") (:stem . "*") (:form . "*") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 82)\n  (:start . 76) (:id . 56))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 90)\n  (:start . 83) (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "CD") (:stem . "0.01") (:form . "0.01") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 105) (:start . 101)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 116)\n  (:start . 106) (:id . 61))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 123)\n  (:start . 117) (:id . 62))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 135)\n  (:start . 124) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 64))\n ((:tag . "SYM") (:stem . "**") (:form . "**") (:end . 139) (:start . 137)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 68))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 154)\n  (:start . 148) (:id . 70))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 162)\n  (:start . 155) (:id . 71))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 167) (:start . 163)\n  (:id . 72))\n ((:tag . "CD") (:stem . "0.001") (:form . "0.001") (:end . 173)\n  (:start . 168) (:id . 73))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 178) (:start . 174)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 189)\n  (:start . 179) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 193) (:start . 190)\n  (:id . 76))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 198) (:start . 194)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 210)\n  (:start . 199) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 212) (:start . 211)\n  (:id . 79))\n ((:tag . "SYM") (:stem . "***") (:form . "***") (:end . 215) (:start . 212)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 216) (:start . 215)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s7.164) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502029@unknown@formal@none@1@S@RESULTS@(((:tag . "NNS") (:stem . "results") (:form . "RESULTS") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s7.165) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5502030@unknown@formal@none@1@S@In order to evaluate whether O-GlcNAcylation affects HIV-1 replication, Jurkat, T1, and primary CD4+ T lymphocytes were infected with HIV-1NL4-3LucR-E-, a replication-deficient HIV-1 clone pseudotyped with the envelope protein VSV-G.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 44) (:start . 29) (:id . 47))\n ((:tag . "VBZ") (:stem . "affect") (:form . "affects") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 58) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 70)\n  (:start . 59) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 78)\n  (:start . 72) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "T1") (:form . "T1") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 95)\n  (:start . 88) (:id . 57))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 100) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 114)\n  (:start . 103) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 119) (:start . 115)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "infect") (:form . "infected") (:end . 128)\n  (:start . 120) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 133) (:start . 129)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "HIV-1NL4-3LucR-E-") (:form . "HIV-1NL4-3LucR-E-")\n  (:end . 151) (:start . 134) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 154) (:start . 153)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "replication-deficient")\n  (:form . "replication-deficient") (:end . 176) (:start . 155) (:id . 67))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 182)\n  (:start . 177) (:id . 68))\n ((:tag . "NN") (:stem . "clone") (:form . "clone") (:end . 188)\n  (:start . 183) (:id . 69))\n ((:tag . "VBN") (:stem . "pseudotype") (:form . "pseudotyped") (:end . 200)\n  (:start . 189) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 205) (:start . 201)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n  (:id . 72))\n ((:tag . "NN") (:stem . "envelope") (:form . "envelope") (:end . 218)\n  (:start . 210) (:id . 73))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 226)\n  (:start . 219) (:id . 74))\n ((:tag . "NN") (:stem . "vsv-g") (:form . "VSV-G") (:end . 232)\n  (:start . 227) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 233) (:start . 232)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s7.166) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502031@unknown@formal@none@1@S@Upon integration, this recombinant virus expresses the firefly luciferase gene driven by the HIV-1 LTR promoter.@(((:tag . "IN") (:stem . "upon") (:form . "Upon") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "recombinant") (:form . "recombinant") (:end . 34)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "virus") (:form . "virus") (:end . 40) (:start . 35)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "express") (:form . "expresses") (:end . 50)\n  (:start . 41) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "firefly") (:form . "firefly") (:end . 62)\n  (:start . 55) (:id . 50))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 73)\n  (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 78) (:start . 74)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 85)\n  (:start . 79) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 111)\n  (:start . 103) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.167) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502032@unknown@formal@none@1@S@Consequently, the luciferase activity in infected cells correlates with the rate of HIV-1 gene transcription.@(((:tag . "RB") (:stem . "consequently") (:form . "Consequently") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "infected") (:form . "infected") (:end . 49)\n  (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "correlate") (:form . "correlates") (:end . 66)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 71) (:start . 67)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 80) (:start . 76)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 89) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 108) (:start . 95) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.168) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502033@unknown@formal@none@1@S@Reporter-HIV-1-infected cells were either left untreated (0 mM) or treated for 24 h with increasing concentrations of GlcN (0.25 mM, 1 mM, 4 mM, and 16 mM), and luciferase activity was measured.@(((:tag . "JJ") (:stem . "reporter-hiv-1-infected")\n  (:form . "Reporter-HIV-1-infected") (:end . 23) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 29) (:start . 24)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n  (:id . 44))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 41)\n  (:start . 35) (:id . 45))\n ((:tag . "VBD") (:stem . "leave") (:form . "left") (:end . 46) (:start . 42)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 56)\n  (:start . 47) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 48))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 59) (:start . 58)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 74)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 99)\n  (:start . 89) (:id . 58))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 114) (:start . 100) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 122) (:start . 118)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n  (:id . 62))\n ((:tag . "CD") (:stem . "0.25") (:form . "0.25") (:end . 128) (:start . 124)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 131) (:start . 129)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 65))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 134) (:start . 133)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 137) (:start . 135)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 68))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 140) (:start . 139)\n  (:id . 69))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 143) (:start . 141)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n  (:id . 72))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 151) (:start . 149)\n  (:id . 73))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 154) (:start . 152)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 77))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 171)\n  (:start . 161) (:id . 78))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 180)\n  (:start . 172) (:id . 79))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 184) (:start . 181)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 193)\n  (:start . 185) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s7.169) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502034@unknown@formal@none@1@S@GlcN significantly inhibited the HIV-1 gene transcription by more than 60% in Jurkat cells and 50% in T1 cells (Fig. 1A and B) without significantly decreasing cell viability (Fig. 1A and B).@(((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 18) (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 28)\n  (:start . 19) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 38) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 57) (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 60) (:start . 58)\n  (:id . 49))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 65) (:start . 61)\n  (:id . 50))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 70) (:start . 66)\n  (:id . 51))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 74) (:start . 73)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 84)\n  (:start . 78) (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 90) (:start . 85)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 57))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 101) (:start . 99)\n  (:id . 60))\n ((:tag . "NN") (:stem . "t1") (:form . "T1") (:end . 104) (:start . 102)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 110)\n  (:start . 105) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 116) (:start . 112)\n  (:id . 64))\n ((:tag . "NN") (:stem . "1a") (:form . "1A") (:end . 119) (:start . 117)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 125) (:start . 124)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 68))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 134)\n  (:start . 127) (:id . 69))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 148) (:start . 135) (:id . 70))\n ((:tag . "VBG") (:stem . "decrease") (:form . "decreasing") (:end . 159)\n  (:start . 149) (:id . 71))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 164) (:start . 160)\n  (:id . 72))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 174)\n  (:start . 165) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 180) (:start . 176)\n  (:id . 75))\n ((:tag . "NN") (:stem . "1a") (:form . "1A") (:end . 183) (:start . 181)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 187) (:start . 184)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 189) (:start . 188)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s7.170) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502035@unknown@formal@none@1@S@Western blot analyses using an antibody which recognizes O-GlcNAcylated proteins demonstrated increased O-GlcNAcylation upon GlcN treatment, whereas expression of OGT remained unchanged (Fig. 1C).@(((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "recognize") (:form . "recognizes") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "JJ") (:stem . "o-glcnacylated") (:form . "O-GlcNAcylated")\n  (:end . 71) (:start . 57) (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 80)\n  (:start . 72) (:id . 51))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 93)\n  (:start . 81) (:id . 52))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 103)\n  (:start . 94) (:id . 53))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 119) (:start . 104) (:id . 54))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 124) (:start . 120)\n  (:id . 55))\n ((:tag . "NN") (:stem . "glcn") (:form . "GlcN") (:end . 129) (:start . 125)\n  (:id . 56))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 139)\n  (:start . 130) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 58))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 148)\n  (:start . 141) (:id . 59))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 159)\n  (:start . 149) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 162) (:start . 160)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 166) (:start . 163)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "remain") (:form . "remained") (:end . 175)\n  (:start . 167) (:id . 63))\n ((:tag . "JJ") (:stem . "unchanged") (:form . "unchanged") (:end . 185)\n  (:start . 176) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 187) (:start . 186)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 191) (:start . 187)\n  (:id . 66))\n ((:tag . "NN") (:stem . "1c") (:form . "1C") (:end . 194) (:start . 192)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.171) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502036@unknown@formal@none@1@S@Detection of GAPDH and actin demonstrated that equal amounts of protein were loaded.@(((:tag . "NNP") (:stem . "Detection") (:form . "Detection") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "actin") (:form . "actin") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 41)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "load") (:form . "loaded") (:end . 83) (:start . 77)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.172) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502037@unknown@formal@none@1@S@Similar results were obtained in primary CD4+ T lymphocytes from two different donors (Fig. 1D and E), although HIV-1 replication in donor 2 (Fig. 1E) was inhibited to a lesser extent than was that in donor 1 (Fig. 1D).@(((:tag . "JJ") (:stem . "similar") (:form . "Similar") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 59)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "donor") (:form . "donors") (:end . 85)\n  (:start . 79) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "1d") (:form . "1D") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 111)\n  (:start . 103) (:id . 62))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 117)\n  (:start . 112) (:id . 63))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 129)\n  (:start . 118) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "NN") (:stem . "donor") (:form . "donor") (:end . 138)\n  (:start . 133) (:id . 66))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 140) (:start . 139)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 146) (:start . 142)\n  (:id . 69))\n ((:tag . "NN") (:stem . "1e") (:form . "1E") (:end . 149) (:start . 147)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 150) (:start . 149)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 154) (:start . 151)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "inhibit") (:form . "inhibited") (:end . 164)\n  (:start . 155) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 167) (:start . 165)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 169) (:start . 168)\n  (:id . 75))\n ((:tag . "JJR") (:stem . "less") (:form . "lesser") (:end . 176)\n  (:start . 170) (:id . 76))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 183)\n  (:start . 177) (:id . 77))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 188) (:start . 184)\n  (:id . 78))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 192) (:start . 189)\n  (:id . 79))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 197) (:start . 193)\n  (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 200) (:start . 198)\n  (:id . 81))\n ((:tag . "NN") (:stem . "donor") (:form . "donor") (:end . 206)\n  (:start . 201) (:id . 82))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 208) (:start . 207)\n  (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 210) (:start . 209)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 214) (:start . 210)\n  (:id . 85))\n ((:tag . "NN") (:stem . "1d") (:form . "1D") (:end . 217) (:start . 215)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 218) (:start . 217)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s7.173) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502038@unknown@formal@none@1@S@This difference is also reflected in smaller amounts of O-GlcNAcylated proteins in the lysates of donor 2 than in lysates of donor 1 (compare donor 1 and donor 2 in Fig. 1F, upper panel).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "reflect") (:form . "reflected") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "o-glcnacylated") (:form . "O-GlcNAcylated")\n  (:end . 70) (:start . 56) (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 79)\n  (:start . 71) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "lysate") (:form . "lysates") (:end . 94)\n  (:start . 87) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 56))\n ((:tag . "NN") (:stem . "donor") (:form . "donor") (:end . 103) (:start . 98)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 110) (:start . 106)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "lysate") (:form . "lysates") (:end . 121)\n  (:start . 114) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 62))\n ((:tag . "NN") (:stem . "donor") (:form . "donor") (:end . 130)\n  (:start . 125) (:id . 63))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 132) (:start . 131)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . "NN") (:stem . "compare") (:form . "compare") (:end . 141)\n  (:start . 134) (:id . 66))\n ((:tag . "NN") (:stem . "donor") (:form . "donor") (:end . 147)\n  (:start . 142) (:id . 67))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 149) (:start . 148)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 153) (:start . 150)\n  (:id . 69))\n ((:tag . "NN") (:stem . "donor") (:form . "donor") (:end . 159)\n  (:start . 154) (:id . 70))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 161) (:start . 160)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 164) (:start . 162)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 169) (:start . 165)\n  (:id . 73))\n ((:tag . "NN") (:stem . "1f") (:form . "1F") (:end . 172) (:start . 170)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 179)\n  (:start . 174) (:id . 76))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 185)\n  (:start . 180) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 186) (:start . 185)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s7.174) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502039@unknown@formal@none@1@S@GlcN inhibits HIV-1 transcription in lymphocytes.@(((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 33) (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 48)\n  (:start . 37) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s7.175) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502040@unknown@formal@none@1@S@Jurkat cells (A), T1 cells (B), and primary CD4+ T cells from two different donors (D and E) were infected with VSV-G env pseudotyped HIV-1NL4-3LucR-E- and cultured in the absence (0 mM) or presence of different concentrations of GlcN (0.25 mM, 1 mM, 4 mM, and 16 mM) for 24 h.@(((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "NN") (:stem . "t1") (:form . "T1") (:end . 20) (:start . 18)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . 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"16") (:end . 263) (:start . 261)\n  (:id . 102))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 266) (:start . 264)\n  (:id . 103))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 267) (:start . 266)\n  (:id . 104))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 271) (:start . 268)\n  (:id . 105))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 274) (:start . 272)\n  (:id . 106))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 276) (:start . 275)\n  (:id . 107))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 277) (:start . 276)\n  (:id . 108)))@@@1@67@((:identifiers (:sid . :s7.176) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502041@unknown@formal@none@1@S@Subsequently, HIV-1 LTR-driven luciferase activity was measured (solid lines).@(((:tag . "RB") (:stem . "subsequently") (:form . "Subsequently") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "ltr-driven") (:form . "LTR-driven") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 41)\n  (:start . 31) (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 50)\n  (:start . 42) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 54) (:start . 51)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 63)\n  (:start . 55) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "solid") (:form . "solid") (:end . 70) (:start . 65)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 76) (:start . 71)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.177) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502042@unknown@formal@none@1@S@The effect of GlcN on cytotoxicity and proliferation was monitored by MTT assay (dashed lines).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "cytotoxicity") (:form . "cytotoxicity") (:end . 34)\n  (:start . 22) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "proliferation") (:form . "proliferation")\n  (:end . 52) (:start . 39) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "monitor") (:form . "monitored") (:end . 66)\n  (:start . 57) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "MTT") (:form . "MTT") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "dash") (:form . "dashed") (:end . 87) (:start . 81)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.178) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502043@unknown@formal@none@1@S@The results are presented in terms of percent activities of untreated control cells.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "percent") (:form . "percent") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 69)\n  (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 83) (:start . 78)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.179) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502044@unknown@formal@none@1@S@The means ± standard deviations from triplicate determinations are indicated.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mean") (:form . "means") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "±") (:form . "±") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "deviation") (:form . "deviations") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "triplicate") (:form . "triplicate") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "determination") (:form . "determinations")\n  (:end . 62) (:start . 48) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 76)\n  (:start . 67) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.180) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502045@unknown@formal@none@1@S@P values are calculated in comparison with control: *, P ≤ 0.05; **, P ≤ 0.@(((:tag . "NN") (:stem . "p") (:form . "P") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "SYM") (:stem . "*") (:form . "*") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 58) (:start . 57)\n  (:id . 54))\n ((:tag . "CD") (:stem . "0.05") (:form . "0.05") (:end . 63) (:start . 59)\n  (:id . 55))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 64) (:start . 63)\n  (:id . 56))\n ((:tag . "SYM") (:stem . "**") (:form . "**") (:end . 67) (:start . 65)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 58))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 70) (:start . 69)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 72) (:start . 71)\n  (:id . 60))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 74) (:start . 73)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s7.181) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502046@unknown@formal@none@1@S@01. (C and F) Western blot analyses of O-GlcNAcylated proteins and OGT in Jurkat and T1 cells (C) and in primary CD4+ T lymphocytes (F).@(((:tag . "LS") (:stem . "01.") (:form . "01.") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 6) (:start . 5)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 12) (:start . 11)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 13) (:start . 12)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 21)\n  (:start . 14) (:id . 48))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 26) (:start . 22)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 35)\n  (:start . 27) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "o-glcnacylated") (:form . "O-GlcNAcylated")\n  (:end . 53) (:start . 39) (:id . 52))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 62)\n  (:start . 54) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 80)\n  (:start . 74) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "NN") (:stem . "t1") (:form . "T1") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 93) (:start . 88)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 96) (:start . 95)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 112)\n  (:start . 105) (:id . 66))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 117) (:start . 113)\n  (:id . 67))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 119) (:start . 118)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 131)\n  (:start . 120) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 70))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 134) (:start . 133)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 135) (:start . 134)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s7.182) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502047@unknown@formal@none@1@S@Actin and GAPDH served as loading controls.@(((:tag . "NNP") (:stem . "Actin") (:form . "Actin") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "serve") (:form . "served") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "load") (:form . "loading") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s7.183) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502048@unknown@formal@none@1@S@To exclude the possibility that reduced HIV-1 gene transcription is caused by impaired nuclear transport of the preintegration complex or reduced proviral integration, we evaluated the impact of GlcN treatment on the HIV-1 LTR promoter activity.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 64) (:start . 51) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 74)\n  (:start . 68) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "impaired") (:form . "impaired") (:end . 86)\n  (:start . 78) (:id . 54))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 94)\n  (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "transport") (:form . "transport") (:end . 104)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 58))\n ((:tag . "NN") (:stem . "preintegration") (:form . "preintegration")\n  (:end . 126) (:start . 112) (:id . 59))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 134)\n  (:start . 127) (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 137) (:start . 135)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 145)\n  (:start . 138) (:id . 62))\n ((:tag . "JJ") (:stem . "proviral") (:form . "proviral") (:end . 154)\n  (:start . 146) (:id . 63))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 166)\n  (:start . 155) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 65))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 170) (:start . 168)\n  (:id . 66))\n ((:tag . "VBD") (:stem . "evaluate") (:form . "evaluated") (:end . 180)\n  (:start . 171) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 184) (:start . 181)\n  (:id . 68))\n ((:tag . "NN") (:stem . "impact") (:form . "impact") (:end . 191)\n  (:start . 185) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 194) (:start . 192)\n  (:id . 70))\n ((:tag . "NN") (:stem . "glcn") (:form . "GlcN") (:end . 199) (:start . 195)\n  (:id . 71))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 209)\n  (:start . 200) (:id . 72))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 212) (:start . 210)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 216) (:start . 213)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 222)\n  (:start . 217) (:id . 75))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 226) (:start . 223)\n  (:id . 76))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 235)\n  (:start . 227) (:id . 77))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 244)\n  (:start . 236) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 245) (:start . 244)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x7.184.1) (:span 15 26)))\n (:hscopes ((:id . :x7.184.1) (:span 15 166)))\n (:identifiers (:sid . :s7.184) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502049@unknown@formal@none@1@S@Therefore, HeLa-Tat-III/LTR/d1EGFP cells, which stably express d1EGFP under the control of the HIV-1 LTR, were either left untreated (0 mM) or treated with increasing concentrations of GlcN (0.25 mM, 1 mM, 4 mM, and 16 mM).@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "HeLa-Tat-III/LTR/d1EGFP")\n  (:form . "HeLa-Tat-III/LTR/d1EGFP") (:end . 34) (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 40) (:start . 35)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 47) (:start . 42)\n  (:id . 47))\n ((:tag . "RB") (:stem . "stably") (:form . "stably") (:end . 54)\n  (:start . 48) (:id . 48))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 62)\n  (:start . 55) (:id . 49))\n ((:tag . "NN") (:stem . "d1egfp") (:form . "d1EGFP") (:end . 69)\n  (:start . 63) (:id . 50))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 75) (:start . 70)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 52))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 87)\n  (:start . 80) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 100)\n  (:start . 95) (:id . 56))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 104) (:start . 101)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 110) (:start . 106)\n  (:id . 59))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 117)\n  (:start . 111) (:id . 60))\n ((:tag . "VBD") (:stem . "leave") (:form . "left") (:end . 122)\n  (:start . 118) (:id . 61))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 132)\n  (:start . 123) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 63))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 135) (:start . 134)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 138) (:start . 136)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 142) (:start . 140)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 150)\n  (:start . 143) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 155) (:start . 151)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 166)\n  (:start . 156) (:id . 70))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 181) (:start . 167) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 189) (:start . 185)\n  (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 191) (:start . 190)\n  (:id . 74))\n ((:tag . "CD") (:stem . "0.25") (:form . "0.25") (:end . 195) (:start . 191)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 198) (:start . 196)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 199) (:start . 198)\n  (:id . 77))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 201) (:start . 200)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 204) (:start . 202)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 205) (:start . 204)\n  (:id . 80))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 207) (:start . 206)\n  (:id . 81))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 210) (:start . 208)\n  (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 211) (:start . 210)\n  (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 215) (:start . 212)\n  (:id . 84))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 218) (:start . 216)\n  (:id . 85))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 221) (:start . 219)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 222) (:start . 221)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 223) (:start . 222)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s7.185) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502050@unknown@formal@none@1@S@Subsequently, fluorescence intensity was measured by flow cytometry.@(((:tag . "RB") (:stem . "subsequently") (:form . "Subsequently") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 26)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 36)\n  (:start . 27) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 40) (:start . 37)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 49)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 52) (:start . 50)\n  (:id . 48))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cytometry") (:form . "cytometry") (:end . 67)\n  (:start . 58) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s7.186) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502051@unknown@formal@none@1@S@GlcN treatment inhibited the HIV-1 LTR-triggered d1EGFP expression in a dose-dependent manner, as detected by the shift of the fluorescence emission peak to a lower fluorescence intensity (Fig. 2A, bar diagram).@(((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "ltr-triggered") (:form . "LTR-triggered")\n  (:end . 48) (:start . 35) (:id . 47))\n ((:tag . "NNP") (:stem . "d1EGFP") (:form . "d1EGFP") (:end . 55)\n  (:start . 49) (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 66)\n  (:start . 56) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "dose-dependent") (:form . "dose-dependent")\n  (:end . 86) (:start . 72) (:id . 52))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 93)\n  (:start . 87) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 97) (:start . 95)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 106)\n  (:start . 98) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 109) (:start . 107)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 58))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 119)\n  (:start . 114) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 139)\n  (:start . 127) (:id . 62))\n ((:tag . "NN") (:stem . "emission") (:form . "emission") (:end . 148)\n  (:start . 140) (:id . 63))\n ((:tag . "NN") (:stem . "peak") (:form . "peak") (:end . 153) (:start . 149)\n  (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 156) (:start . 154)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 158) (:start . 157)\n  (:id . 66))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 164) (:start . 159)\n  (:id . 67))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 177)\n  (:start . 165) (:id . 68))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 187)\n  (:start . 178) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 193) (:start . 189)\n  (:id . 71))\n ((:tag . "NN") (:stem . "2a") (:form . "2A") (:end . 196) (:start . 194)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 73))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 201) (:start . 198)\n  (:id . 74))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 209)\n  (:start . 202) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s7.187) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502052@unknown@formal@none@1@S@Quantification of the different values demonstrated that GlcN significantly decreased the HIV-1 LTR activity by more than 60% (Fig. 2A, bar diagram).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 38)\n  (:start . 32) (:id . 46))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 51)\n  (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 56) (:start . 52)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 61) (:start . 57)\n  (:id . 49))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 75) (:start . 62) (:id . 50))\n ((:tag . "VBD") (:stem . "decrease") (:form . "decreased") (:end . 85)\n  (:start . 76) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 95) (:start . 90)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 99) (:start . 96)\n  (:id . 54))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 108)\n  (:start . 100) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 111) (:start . 109)\n  (:id . 56))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 116) (:start . 112)\n  (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 121) (:start . 117)\n  (:id . 58))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 124) (:start . 122)\n  (:id . 59))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 125) (:start . 124)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 131) (:start . 127)\n  (:id . 62))\n ((:tag . "NN") (:stem . "2a") (:form . "2A") (:end . 134) (:start . 132)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 64))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 139) (:start . 136)\n  (:id . 65))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 147)\n  (:start . 140) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.188) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502053@unknown@formal@none@1@S@Comparable results were obtained after treatment of HeLa-Tat-III/LTR/d1EGFP cells with the UDP-GlcNAc analog streptozotocin (data not shown), which inhibits the O-GlcNAcase activity and thereby increases O-GlcNAcylation (63).@(((:tag . "JJ") (:stem . "comparable") (:form . "Comparable") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 18)\n  (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 38) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 48)\n  (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "HeLa-Tat-III/LTR/d1EGFP")\n  (:form . "HeLa-Tat-III/LTR/d1EGFP") (:end . 75) (:start . 52) (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 81) (:start . 76)\n  (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 86) (:start . 82)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "UDP-GlcNAc") (:form . "UDP-GlcNAc") (:end . 101)\n  (:start . 91) (:id . 53))\n ((:tag . "NN") (:stem . "analog") (:form . "analog") (:end . 108)\n  (:start . 102) (:id . 54))\n ((:tag . "NN") (:stem . "streptozotocin") (:form . "streptozotocin")\n  (:end . 123) (:start . 109) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 129)\n  (:start . 125) (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 133) (:start . 130)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 139)\n  (:start . 134) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 147)\n  (:start . 142) (:id . 62))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 156)\n  (:start . 148) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 160) (:start . 157)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "O-GlcNAcase") (:form . "O-GlcNAcase") (:end . 172)\n  (:start . 161) (:id . 65))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 181)\n  (:start . 173) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n  (:id . 67))\n ((:tag . "RB") (:stem . "thereby") (:form . "thereby") (:end . 193)\n  (:start . 186) (:id . 68))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 203)\n  (:start . 194) (:id . 69))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 219) (:start . 204) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 221) (:start . 220)\n  (:id . 71))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 223) (:start . 221)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 224) (:start . 223)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s7.189) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502054@unknown@formal@none@1@S@GlcN inhibits HIV-1 LTR promoter activity and increases O-GlcNAcylation in HeLa cells.@(((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 55)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 71) (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "HeLa") (:form . "HeLa") (:end . 79) (:start . 75)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 85) (:start . 80)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.190) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502055@unknown@formal@none@1@S@(A) HeLa-Tat-III/LTR/d1EGFP cells were either left untreated (0 mM) or stimulated for 5 h with increasing concentrations of GlcN (0.25 mM, 1 mM, 4 mM, and 16 mM).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "HeLa-Tat-III/LTR/d1EGFP")\n  (:form . "HeLa-Tat-III/LTR/d1EGFP") (:end . 27) (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "VBD") (:stem . "leave") (:form . "left") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 81)\n  (:start . 71) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 85) (:start . 82)\n  (:id . 57))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 89) (:start . 88)\n  (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 94) (:start . 90)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 105)\n  (:start . 95) (:id . 61))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 120) (:start . 106) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 128) (:start . 124)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 65))\n ((:tag . "CD") (:stem . "0.25") (:form . "0.25") (:end . 134) (:start . 130)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 137) (:start . 135)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 68))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 140) (:start . 139)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 143) (:start . 141)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 71))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 146) (:start . 145)\n  (:id . 72))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 149) (:start . 147)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 75))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 157) (:start . 155)\n  (:id . 76))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 160) (:start . 158)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s7.191) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502056@unknown@formal@none@1@S@The HIV-1 LTR activity was assessed by measuring the d1EGFP fluorescence intensity (FI) with flow cytometry analyses.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "measure") (:form . "measuring") (:end . 48)\n  (:start . 39) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "d1egfp") (:form . "d1EGFP") (:end . 59)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 72)\n  (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "FI") (:form . "FI") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 92) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 97) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "cytometry") (:form . "cytometry") (:end . 107)\n  (:start . 98) (:id . 59))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 116)\n  (:start . 108) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.192) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502057@unknown@formal@none@1@S@The shift of the fluorescence emission peak (inset) and the bar diagram of the respective geometric mean values compared to those for unstimulated control cells are shown.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 29)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "emission") (:form . "emission") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "peak") (:form . "peak") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "inset") (:form . "inset") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 71)\n  (:start . 64) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 89)\n  (:start . 79) (:id . 58))\n ((:tag . "JJ") (:stem . "geometric") (:form . "geometric") (:end . 99)\n  (:start . 90) (:id . 59))\n ((:tag . "NN") (:stem . "mean") (:form . "mean") (:end . 104) (:start . 100)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 111)\n  (:start . 105) (:id . 61))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 120)\n  (:start . 112) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 123) (:start . 121)\n  (:id . 63))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 129)\n  (:start . 124) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 133) (:start . 130)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "unstimulated") (:form . "unstimulated") (:end . 146)\n  (:start . 134) (:id . 66))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 154)\n  (:start . 147) (:id . 67))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 160)\n  (:start . 155) (:id . 68))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 164) (:start . 161)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 170)\n  (:start . 165) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.193) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502058@unknown@formal@none@1@S@The means ± standard deviations calculated from triplicate determinations are indicated.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mean") (:form . "means") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "±") (:form . "±") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "deviation") (:form . "deviations") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 42)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "triplicate") (:form . "triplicate") (:end . 58)\n  (:start . 48) (:id . 49))\n ((:tag . "NNS") (:stem . "determination") (:form . "determinations")\n  (:end . 73) (:start . 59) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 77) (:start . 74)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 87)\n  (:start . 78) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.194) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502059@unknown@formal@none@1@S@P values are given for comparison with control: n.s., not significant; **, P ≤ 0.01; ***, P ≤ 0.@(((:tag . "NN") (:stem . "p") (:form . "P") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "LS") (:stem . "n.s.") (:form . "n.s.") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 69)\n  (:start . 58) (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . "SYM") (:stem . "**") (:form . "**") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 57))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 76) (:start . 75)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 78) (:start . 77)\n  (:id . 59))\n ((:tag . "CD") (:stem . "0.01") (:form . "0.01") (:end . 83) (:start . 79)\n  (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 84) (:start . 83)\n  (:id . 61))\n ((:tag . "SYM") (:stem . "***") (:form . "***") (:end . 88) (:start . 85)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 63))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 91) (:start . 90)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 93) (:start . 92)\n  (:id . 65))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 95) (:start . 94)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.195) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502060@unknown@formal@none@1@S@001. (B) Nuclear and cytosolic fractions of unstimulated (control) or stimulated (16 mM GlcN) HeLa-Tat-III/LTR/d1EGFP cells were analyzed by Western blotting to detect O-GlcNAcylated proteins.@(((:tag . "LS") (:stem . "001.") (:form . "001.") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 8) (:start . 7) (:id . 45))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "Nuclear") (:end . 16)\n  (:start . 9) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "cytosolic") (:form . "cytosolic") (:end . 30)\n  (:start . 21) (:id . 48))\n ((:tag . "NNS") (:stem . "fraction") (:form . "fractions") (:end . 40)\n  (:start . 31) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "unstimulated") (:form . "unstimulated") (:end . 56)\n  (:start . 44) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 65)\n  (:start . 58) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 69) (:start . 67)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 80)\n  (:start . 70) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 92) (:start . 88)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "HeLa-Tat-III/LTR/d1EGFP")\n  (:form . "HeLa-Tat-III/LTR/d1EGFP") (:end . 117) (:start . 94) (:id . 62))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 123)\n  (:start . 118) (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 128) (:start . 124)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 137)\n  (:start . 129) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 140) (:start . 138)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 148)\n  (:start . 141) (:id . 67))\n ((:tag . "NN") (:stem . "blotting") (:form . "blotting") (:end . 157)\n  (:start . 149) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 160) (:start . 158)\n  (:id . 69))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 167)\n  (:start . 161) (:id . 70))\n ((:tag . "JJ") (:stem . "o-glcnacylated") (:form . "O-GlcNAcylated")\n  (:end . 182) (:start . 168) (:id . 71))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 191)\n  (:start . 183) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s7.196) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502061@unknown@formal@none@1@S@Arrowheads mark proteins whose O-GlcNAcylation patterns are increased upon GlcN treatment.@(((:tag . "NNS") (:stem . "arrowhead") (:form . "Arrowheads") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "mark") (:form . "mark") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 30) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 46) (:start . 31) (:id . 46))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 55)\n  (:start . 47) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 59) (:start . 56)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 69)\n  (:start . 60) (:id . 49))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 74) (:start . 70)\n  (:id . 50))\n ((:tag . "NN") (:stem . "glcn") (:form . "GlcN") (:end . 79) (:start . 75)\n  (:id . 51))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 89)\n  (:start . 80) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.197) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502062@unknown@formal@none@1@S@Staining of OGT (an example of an O-GlcNAcylated protein) and histone H1 (non-O-GlcNAcylated) shows that protein expression levels were not altered.@(((:tag . "NN") (:stem . "staining") (:form . "Staining") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 27)\n  (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "o-glcnacylated") (:form . "O-GlcNAcylated")\n  (:end . 48) (:start . 34) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "NN") (:stem . "histone") (:form . "histone") (:end . 69)\n  (:start . 62) (:id . 54))\n ((:tag . "NN") (:stem . "h1") (:form . "H1") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "non-o-glcnacylated") (:form . "non-O-GlcNAcylated")\n  (:end . 92) (:start . 74) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 99) (:start . 94)\n  (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 104) (:start . 100)\n  (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 112)\n  (:start . 105) (:id . 61))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 123)\n  (:start . 113) (:id . 62))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 130)\n  (:start . 124) (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 135) (:start . 131)\n  (:id . 64))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 139) (:start . 136)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "alter") (:form . "altered") (:end . 147)\n  (:start . 140) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.198) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502063@unknown@formal@none@1@S@Staining of GAPDH and lamin A/C demonstrates successful fractionation.@(((:tag . "NN") (:stem . "staining") (:form . "Staining") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "lamin") (:form . "lamin") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "A/C") (:form . "A/C") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "demonstrate") (:form . "demonstrates") (:end . 44)\n  (:start . 32) (:id . 48))\n ((:tag . "JJ") (:stem . "successful") (:form . "successful") (:end . 55)\n  (:start . 45) (:id . 49))\n ((:tag . "NN") (:stem . "fractionation") (:form . "fractionation")\n  (:end . 69) (:start . 56) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s7.199) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502064@unknown@formal@none@1@S@To demonstrate O-GlcNAcylation of cellular proteins in the presence of GlcN, cytosolic and nuclear fractions of control-treated versus GlcN-treated (16 mM) HeLa-Tat-III/LTR/d1EGFP cells were analyzed by Western blotting (Fig. 2B).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "demonstrate") (:form . "demonstrate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 30) (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 42)\n  (:start . 34) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 51)\n  (:start . 43) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 49))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 67)\n  (:start . 59) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 75) (:start . 71)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "cytosolic") (:form . "cytosolic") (:end . 86)\n  (:start . 77) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 98)\n  (:start . 91) (:id . 56))\n ((:tag . "NNS") (:stem . "fraction") (:form . "fractions") (:end . 108)\n  (:start . 99) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "control-treated") (:form . "control-treated")\n  (:end . 127) (:start . 112) (:id . 59))\n ((:tag . "CC") (:stem . "versus") (:form . "versus") (:end . 134)\n  (:start . 128) (:id . 60))\n ((:tag . "JJ") (:stem . "glcn-treated") (:form . "GlcN-treated") (:end . 147)\n  (:start . 135) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 149) (:start . 148)\n  (:id . 62))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 151) (:start . 149)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 154) (:start . 152)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "HeLa-Tat-III/LTR/d1EGFP")\n  (:form . "HeLa-Tat-III/LTR/d1EGFP") (:end . 179) (:start . 156) (:id . 66))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 185)\n  (:start . 180) (:id . 67))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 190) (:start . 186)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 199)\n  (:start . 191) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 202) (:start . 200)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 210)\n  (:start . 203) (:id . 71))\n ((:tag . "NN") (:stem . "blotting") (:form . "blotting") (:end . 219)\n  (:start . 211) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 221) (:start . 220)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 225) (:start . 221)\n  (:id . 74))\n ((:tag . "NN") (:stem . "2b") (:form . "2B") (:end . 228) (:start . 226)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 229) (:start . 228)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 230) (:start . 229)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s7.200) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502065@unknown@formal@none@1@S@In both fractions, several proteins showed increased O-GlcNAcylation upon GlcN treatment (Fig. 2B, upper panels), whereas the expression of OGT (example of an O-GlcNAc-modified protein) and of histone H1 (non-O-GlcNAc-modified protein) remained unchanged (Fig. 2B, middle panels).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "fraction") (:form . "fractions") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 42) (:start . 36)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 52)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 68) (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 73) (:start . 69)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 78) (:start . 74)\n  (:id . 52))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 88)\n  (:start . 79) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "2b") (:form . "2B") (:end . 97) (:start . 95)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 104) (:start . 99)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "panel") (:form . 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"DT") (:stem . "an") (:form . "an") (:end . 158) (:start . 156)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "o-glcnac-modified") (:form . "O-GlcNAc-modified")\n  (:end . 176) (:start . 159) (:id . 71))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 184)\n  (:start . 177) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 185) (:start . 184)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 189) (:start . 186)\n  (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 192) (:start . 190)\n  (:id . 75))\n ((:tag . "NN") (:stem . "histone") (:form . "histone") (:end . 200)\n  (:start . 193) (:id . 76))\n ((:tag . "NN") (:stem . "h1") (:form . "H1") (:end . 203) (:start . 201)\n  (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 205) (:start . 204)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "non-o-glcnac-modified")\n  (:form . "non-O-GlcNAc-modified") (:end . 226) (:start . 205) (:id . 79))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 234)\n  (:start . 227) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 235) (:start . 234)\n  (:id . 81))\n ((:tag . "VBD") (:stem . "remain") (:form . "remained") (:end . 244)\n  (:start . 236) (:id . 82))\n ((:tag . "JJ") (:stem . "unchanged") (:form . "unchanged") (:end . 254)\n  (:start . 245) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 256) (:start . 255)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 260) (:start . 256)\n  (:id . 85))\n ((:tag . "NN") (:stem . "2b") (:form . "2B") (:end . 263) (:start . 261)\n  (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 264) (:start . 263)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "middle") (:form . "middle") (:end . 271)\n  (:start . 265) (:id . 88))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 278)\n  (:start . 272) (:id . 89))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 279) (:start . 278)\n  (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 280) (:start . 279)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s7.201) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502066@unknown@formal@none@1@S@Successful fractionation of cytoplasmic and nuclear proteins and loading of equal protein amounts were verified by staining of lamin A/C and GAPDH (Fig. 2B, lower panels).@(((:tag . "JJ") (:stem . "successful") (:form . "Successful") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "fractionation") (:form . "fractionation")\n  (:end . 24) (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 39)\n  (:start . 28) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 51)\n  (:start . 44) (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 60)\n  (:start . 52) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 49))\n ((:tag . "NN") (:stem . "loading") (:form . "loading") (:end . 72)\n  (:start . 65) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 81) (:start . 76)\n  (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 89)\n  (:start . 82) (:id . 53))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 97)\n  (:start . 90) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 102) (:start . 98)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 111)\n  (:start . 103) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 114) (:start . 112)\n  (:id . 57))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 123)\n  (:start . 115) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 59))\n ((:tag . "NN") (:stem . "lamin") (:form . "lamin") (:end . 132)\n  (:start . 127) (:id . 60))\n ((:tag . "NNP") (:stem . "A/C") (:form . "A/C") (:end . 136) (:start . 133)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 146)\n  (:start . 141) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 152) (:start . 148)\n  (:id . 65))\n ((:tag . "NN") (:stem . "2b") (:form . "2B") (:end . 155) (:start . 153)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 67))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 162) (:start . 157)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 169)\n  (:start . 163) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.202) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502067@unknown@formal@none@1@S@Altogether, these results demonstrate that GlcN treatment enhances O-GlcNAcylation of cytoplasmic and nuclear proteins and that this correlates with decreased gene expression from the HIV-1 LTR promoter.@(((:tag . "RB") (:stem . "altogether") (:form . "Altogether") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 37)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "glcn") (:form . "GlcN") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . "VBZ") (:stem . "enhance") (:form . "enhances") (:end . 66)\n  (:start . 58) (:id . 50))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 82) (:start . 67) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 97)\n  (:start . 86) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 109)\n  (:start . 102) (:id . 55))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 118)\n  (:start . 110) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 127) (:start . 123)\n  (:id . 58))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 132) (:start . 128)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "correlate") (:form . "correlates") (:end . 143)\n  (:start . 133) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 148) (:start . 144)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "decrease") (:form . "decreased") (:end . 158)\n  (:start . 149) (:id . 62))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 163) (:start . 159)\n  (:id . 63))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 174)\n  (:start . 164) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 179) (:start . 175)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 189)\n  (:start . 184) (:id . 67))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 193) (:start . 190)\n  (:id . 68))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 202)\n  (:start . 194) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s7.203) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502068@unknown@formal@none@1@S@Since OGT is the only known enzyme to mediate O-GlcNAcylation, we investigated the effect of OGT on HIV-1 transcription in primary lymphocytes.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "enzyme") (:form . "enzyme") (:end . 34)\n  (:start . 28) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "VB") (:stem . "mediate") (:form . "mediate") (:end . 45)\n  (:start . 38) (:id . 50))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 61) (:start . 46) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "investigate") (:form . "investigated") (:end . 78)\n  (:start . 66) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 89)\n  (:start . 83) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 99) (:start . 97)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 105)\n  (:start . 100) (:id . 60))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 119) (:start . 106) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 130)\n  (:start . 123) (:id . 63))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 142)\n  (:start . 131) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.204) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502069@unknown@formal@none@1@S@To this goal, primary CD4+ T lymphocytes from two different donors were infected with pseudotyped reporter HIV-1.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "goal") (:form . "goal") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 21)\n  (:start . 14) (:id . 46))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 40)\n  (:start . 29) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 59)\n  (:start . 50) (:id . 52))\n ((:tag . "NNS") (:stem . "donor") (:form . "donors") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "infect") (:form . "infected") (:end . 80)\n  (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "pseudotype") (:form . "pseudotyped") (:end . 97)\n  (:start . 86) (:id . 57))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 106)\n  (:start . 98) (:id . 58))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 112)\n  (:start . 107) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.205) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502070@unknown@formal@none@1@S@At 36 h postinfection the cells were transfected with in vitro-transcribed polyadenylated mRNA encoding either EGFP or OGT.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "postinfection") (:form . "postinfection")\n  (:end . 21) (:start . 8) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 48)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "vitro-transcribed") (:form . "vitro-transcribed")\n  (:end . 74) (:start . 57) (:id . 52))\n ((:tag . "VBN") (:stem . "polyadenylate") (:form . "polyadenylated")\n  (:end . 89) (:start . 75) (:id . 53))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 94) (:start . 90)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "encode") (:form . "encoding") (:end . 103)\n  (:start . 95) (:id . 55))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 110)\n  (:start . 104) (:id . 56))\n ((:tag . "NNP") (:stem . "EGFP") (:form . "EGFP") (:end . 115) (:start . 111)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 118) (:start . 116)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 122) (:start . 119)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.206) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502071@unknown@formal@none@1@S@OGT expression levels were maximal at 8 h after transfection (data not shown), and the cells were harvested.@(((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "maximal") (:form . "maximal") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 60)\n  (:start . 48) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 92) (:start . 87)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 97) (:start . 93)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "harvest") (:form . "harvested") (:end . 107)\n  (:start . 98) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.207) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502072@unknown@formal@none@1@S@Reporter analyses showed that overexpression of OGT inhibited HIV-1 transcription to an extent similar to that of treatment with 16 mM GlcN (compare Fig. 3A with Fig. 1D and E).@(((:tag . "NN") (:stem . "reporter") (:form . "Reporter") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 24) (:start . 18)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 44) (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 51) (:start . 48)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 61)\n  (:start . 52) (:id . 49))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 67) (:start . 62)\n  (:id . 50))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 81) (:start . 68) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 84) (:start . 82)\n  (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 87) (:start . 85)\n  (:id . 53))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 94)\n  (:start . 88) (:id . 54))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 102)\n  (:start . 95) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n  (:id . 56))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 110) (:start . 106)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 58))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 123)\n  (:start . 114) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 128) (:start . 124)\n  (:id . 60))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 131) (:start . 129)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 134) (:start . 132)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 139) (:start . 135)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 64))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 148)\n  (:start . 141) (:id . 65))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 153) (:start . 149)\n  (:id . 66))\n ((:tag . "NN") (:stem . "3a") (:form . "3A") (:end . 156) (:start . 154)\n  (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 161) (:start . 157)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 166) (:start . 162)\n  (:id . 69))\n ((:tag . "NN") (:stem . "1d") (:form . "1D") (:end . 169) (:start . 167)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 173) (:start . 170)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 175) (:start . 174)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s7.208) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502073@unknown@formal@none@1@S@The inhibition was slightly stronger in the cells of donor 2 than in the cells of donor 1, which correlated well with the increased OGT expression and O-GlcNAcylation level observed in the cells of donor 2 (Fig. 3B, upper panels; compare donor 1 and donor 2).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "JJR") (:stem . "strong") (:form . "stronger") (:end . 36)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . 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5502074@unknown@formal@none@1@S@Assuming that O-GlcNAcylation alters the activity of transcription factors, Sp1 and NF-κB were prime candidates for the O-GlcNAc-mediated inhibition of the HIV-1 LTR.@(((:tag . "VBG") (:stem . "assume") (:form . "Assuming") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 29) (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "alter") (:form . "alters") (:end . 36)\n  (:start . 30) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 49)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 48))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 66) (:start . 53) (:id . 49))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 74)\n  (:start . 67) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 79) (:start . 76)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 89) (:start . 84)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "prime") (:form . "prime") (:end . 100) (:start . 95)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 111)\n  (:start . 101) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 115) (:start . 112)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "o-glcnac-mediated") (:form . "O-GlcNAc-mediated")\n  (:end . 137) (:start . 120) (:id . 60))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 148)\n  (:start . 138) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 161)\n  (:start . 156) (:id . 64))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 165) (:start . 162)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x7.210.1) (:span 0 8)))\n (:hscopes ((:id . :x7.210.1) (:span 0 74)))\n (:identifiers (:sid . :s7.210) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502075@unknown@formal@none@1@S@Binding sites for both factors constitute the core promoter/enhancer of HIV-1, and both have been reported to be modified by O-GlcNAc (21, 31).@(((:tag . "VBG") (:stem . "bind") (:form . "Binding") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "VBP") (:stem . "constitute") (:form . "constitute") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "promoter/enhancer") (:form . "promoter/enhancer")\n  (:end . 68) (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 77) (:start . 72)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 97) (:start . 93)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 106)\n  (:start . 98) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 109) (:start . 107)\n  (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "modify") (:form . "modified") (:end . 121)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 124) (:start . 122)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 133)\n  (:start . 125) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 64))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 137) (:start . 135)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 66))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 141) (:start . 139)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.211) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502076@unknown@formal@none@1@S@In order to prove this hypothesis, luciferase reporter assays were performed using LTR reporters lacking the upstream modulatory region but containing the NF-κB- and/or Sp1-binding sites (either combined or isolated), as well as a TATA box and the trans-activation response (TAR) element for Tat-mediated activation (Fig. 4A, LTR-κB-Sp1wt, LTR-κB-Sp1mut, and LTR-Sp1wt).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "prove") (:form . "prove") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . 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5502077@unknown@formal@none@1@S@HEK 293T cells were cotransfected with the reporter constructs and a Tat-encoding plasmid, along with an OGT-encoding plasmid or a control plasmid (Fig. 4B).@(((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "cotransfecte") (:form . "cotransfected")\n  (:end . 33) (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 62)\n  (:start . 52) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "tat-encoding") (:form . "Tat-encoding") (:end . 81)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 89)\n  (:start . 82) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 101) (:start . 97)\n  (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "ogt-encoding") (:form . "OGT-encoding") (:end . 117)\n  (:start . 105) (:id . 59))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 125)\n  (:start . 118) (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 128) (:start . 126)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 138)\n  (:start . 131) (:id . 63))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 146)\n  (:start . 139) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 152) (:start . 148)\n  (:id . 66))\n ((:tag . "NN") (:stem . "4b") (:form . "4B") (:end . 155) (:start . 153)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.213) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502078@unknown@formal@none@1@S@Overexpression of OGT inhibited the Tat-induced activity of the promoters containing functional Sp1-binding sites (Fig. 4B, LTR-κB-Sp1wt and LTR-Sp1wt).@(((:tag . "NNP") (:stem . "Overexpression") (:form . "Overexpression")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "tat-induced") (:form . "Tat-induced") (:end . 47)\n  (:start . 36) (:id . 47))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 56)\n  (:start . 48) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "promoter") (:form . "promoters") (:end . 73)\n  (:start . 64) (:id . 51))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 84)\n  (:start . 74) (:id . 52))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 95)\n  (:start . 85) (:id . 53))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 107)\n  (:start . 96) (:id . 54))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 113)\n  (:start . 108) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 119) (:start . 115)\n  (:id . 57))\n ((:tag . "NN") (:stem . "4b") (:form . "4B") (:end . 122) (:start . 120)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "LTR-κB-Sp1wt") (:form . "LTR-κB-Sp1wt")\n  (:end . 136) (:start . 124) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 150)\n  (:start . 141) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.214) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502079@unknown@formal@none@1@S@In contrast, the activity of the promoter containing mutated Sp1-binding sites was increased upon overexpression of OGT (Fig. 4B, LTR-κB-Sp1mut).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 72)\n  (:start . 61) (:id . 52))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 78) (:start . 73)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 92)\n  (:start . 83) (:id . 55))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 112) (:start . 98) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 119) (:start . 116)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 125) (:start . 121)\n  (:id . 61))\n ((:tag . "NN") (:stem . "4b") (:form . "4B") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "LTR-κB-Sp1mut") (:form . "LTR-κB-Sp1mut")\n  (:end . 143) (:start . 130) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.215) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502080@unknown@formal@none@1@S@The transient expression of Tat itself was not significantly affected by overexpression of OGT (Fig. 4B, lower panels).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "transient") (:form . "transient") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Tat") (:form . "Tat") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 60) (:start . 47) (:id . 50))\n ((:tag . "VBN") (:stem . "affect") (:form . "affected") (:end . 69)\n  (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 87) (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 94) (:start . 91)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 100) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "4b") (:form . "4B") (:end . 103) (:start . 101)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 110) (:start . 105)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 117)\n  (:start . 111) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.216) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502081@unknown@formal@none@1@S@These findings suggest that the presence of functional Sp1-binding sites is crucial for the inhibitory effect of OGT on the HIV-1 LTR.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 54)\n  (:start . 44) (:id . 49))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 66)\n  (:start . 55) (:id . 50))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 72) (:start . 67)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 75) (:start . 73)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 83)\n  (:start . 76) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 87) (:start . 84)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 102)\n  (:start . 92) (:id . 56))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 109)\n  (:start . 103) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 116) (:start . 113)\n  (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 119) (:start . 117)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 129)\n  (:start . 124) (:id . 62))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 133) (:start . 130)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x7.217.1) (:span 15 22)))\n (:hscopes ((:id . :x7.217.1) (:span 15 133)))\n (:identifiers (:sid . :s7.217) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502082@unknown@formal@none@1@S@The presence of Sp1-binding sites in the HIV-1 LTR promoter is required for OGT-mediated inhibition.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 27)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 59)\n  (:start . 51) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 71)\n  (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "ogt-mediated") (:form . "OGT-mediated") (:end . 88)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 99)\n  (:start . 89) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.218) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502083@unknown@formal@none@1@S@(A) Schematic representation of the promoter constructs used in the luciferase assay in panel B.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "representation") (:form . "representation")\n  (:end . 28) (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 55)\n  (:start . 45) (:id . 50))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 78)\n  (:start . 68) (:id . 54))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 84) (:start . 79)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.219) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502084@unknown@formal@none@1@S@The truncated promoters lack the upstream modulatory region but contain the NF-κB- and/or Sp1-binding sites (either combined or isolated), as well as a TATA box and the TAR element for Tat-mediated activation.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "truncate") (:form . "truncated") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "promoter") (:form . "promoters") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "VBP") (:stem . "lack") (:form . "lack") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "JJ") (:stem . "modulatory") (:form . "modulatory") (:end . 52)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 59)\n  (:start . 53) (:id . 49))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 71)\n  (:start . 64) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "NN") (:stem . "nf-κb-") (:form . "NF-κB-") (:end . 82)\n  (:start . 76) (:id . 53))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 89)\n  (:start . 83) (:id . 54))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 101)\n  (:start . 90) (:id . 55))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 107)\n  (:start . 102) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 57))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 115)\n  (:start . 109) (:id . 58))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 124)\n  (:start . 116) (:id . 59))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 127) (:start . 125)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 136)\n  (:start . 128) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 63))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 141) (:start . 139)\n  (:id . 64))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 146) (:start . 142)\n  (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 149) (:start . 147)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 151) (:start . 150)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "TATA") (:form . "TATA") (:end . 156) (:start . 152)\n  (:id . 68))\n ((:tag . "NN") (:stem . "box") (:form . "box") (:end . 160) (:start . 157)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 71))\n ((:tag . "NN") (:stem . "tar") (:form . "TAR") (:end . 172) (:start . 169)\n  (:id . 72))\n ((:tag . "NN") (:stem . "element") (:form . "element") (:end . 180)\n  (:start . 173) (:id . 73))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 184) (:start . 181)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "tat-mediated") (:form . "Tat-mediated") (:end . 197)\n  (:start . 185) (:id . 75))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 208)\n  (:start . 198) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s7.220) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502085@unknown@formal@none@1@S@Quartered circles represent mutated Sp1-binding sites.@(((:tag . "JJ") (:stem . "quartered") (:form . "Quartered") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "circle") (:form . "circles") (:end . 17)\n  (:start . 10) (:id . 43))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 27)\n  (:start . 18) (:id . 44))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 35)\n  (:start . 28) (:id . 45))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 47)\n  (:start . 36) (:id . 46))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 53) (:start . 48)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s7.221) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502086@unknown@formal@none@1@S@Numbers reflect the positions on the wild-type LTRLAI.@(((:tag . "NNPS") (:stem . "Number") (:form . "Numbers") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "reflect") (:form . "reflect") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 29)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "NNP") (:stem . "LTRLAI") (:form . "LTRLAI") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s7.222) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502087@unknown@formal@none@1@S@(B) Promoter activities were detected by measuring the luciferase activity in the cell lysates of HEK 293T cells transiently transfected with the reporter constructs (LTR-κB-Sp1wt, LTR-κB-Sp1mut, and LTR-Sp1wt) together with plasmids coding for OGT and Tat as indicated.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Promoter") (:form . "Promoter") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 23)\n  (:start . 13) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "measure") (:form . "measuring") (:end . 50)\n  (:start . 41) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 65)\n  (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "lysate") (:form . "lysates") (:end . 94)\n  (:start . 87) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 112)\n  (:start . 107) (:id . 61))\n ((:tag . "RB") (:stem . "transiently") (:form . "transiently") (:end . 124)\n  (:start . 113) (:id . 62))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 136)\n  (:start . 125) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 141) (:start . 137)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 65))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 154)\n  (:start . 146) (:id . 66))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 165)\n  (:start . 155) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "LTR-κB-Sp1wt") (:form . "LTR-κB-Sp1wt")\n  (:end . 179) (:start . 167) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "LTR-κB-Sp1mut") (:form . "LTR-κB-Sp1mut")\n  (:end . 194) (:start . 181) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 199) (:start . 196)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 209)\n  (:start . 200) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 75))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 219)\n  (:start . 211) (:id . 76))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 224) (:start . 220)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "plasmid") (:form . "plasmids") (:end . 233)\n  (:start . 225) (:id . 78))\n ((:tag . "VBG") (:stem . "cod") (:form . "coding") (:end . 240)\n  (:start . 234) (:id . 79))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 244) (:start . 241)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 248) (:start . 245)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 252) (:start . 249)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Tat") (:form . "Tat") (:end . 256) (:start . 253)\n  (:id . 83))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 259) (:start . 257)\n  (:id . 84))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 269)\n  (:start . 260) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s7.223) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502088@unknown@formal@none@1@S@The total DNA amount was adjusted with pcDNA4.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "adjust") (:form . "adjusted") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "pcdna4") (:form . "pcDNA4") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s7.224) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502089@unknown@formal@none@1@S@The values were normalized to the total amount of protein and are presented in terms of percentages of the corresponding Tat-induced promoter activity.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "normalize") (:form . "normalized") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 57)\n  (:start . 50) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 75)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 84) (:start . 79)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "percentage") (:form . "percentages") (:end . 99)\n  (:start . 88) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 120)\n  (:start . 107) (:id . 61))\n ((:tag . "JJ") (:stem . "tat-induced") (:form . "Tat-induced") (:end . 132)\n  (:start . 121) (:id . 62))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 141)\n  (:start . 133) (:id . 63))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 150)\n  (:start . 142) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.225) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502090@unknown@formal@none@1@S@The means ± standard deviations from triplicate determinations are shown (upper panel).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mean") (:form . "means") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "±") (:form . "±") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "deviation") (:form . "deviations") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "triplicate") (:form . "triplicate") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "determination") (:form . "determinations")\n  (:end . 62) (:start . 48) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 72) (:start . 67)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 79) (:start . 74)\n  (:id . 53))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 85) (:start . 80)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.226) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502091@unknown@formal@none@1@S@Western blot analyses of Tat and OGT in transfected cells are shown in the lower panel.@(((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Tat") (:form . "Tat") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 51)\n  (:start . 40) (:id . 50))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 86) (:start . 81)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.227) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502092@unknown@formal@none@1@S@GAPDH staining demonstrates that equal amounts of protein were loaded.@(((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "VBZ") (:stem . "demonstrate") (:form . "demonstrates") (:end . 27)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 38) (:start . 33)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 46)\n  (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "load") (:form . "loaded") (:end . 69) (:start . 63)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.228) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502093@unknown@formal@none@1@S@(C) Schematic representation of the full-length wild-type and full-length Sp1-mutated promoter constructs used for the stable transfection of HEK 293T cells.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "representation") (:form . "representation")\n  (:end . 28) (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 47)\n  (:start . 36) (:id . 49))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 73)\n  (:start . 62) (:id . 52))\n ((:tag . "JJ") (:stem . "sp1-mutated") (:form . "Sp1-mutated") (:end . 85)\n  (:start . 74) (:id . 53))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 94)\n  (:start . 86) (:id . 54))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 105)\n  (:start . 95) (:id . 55))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 110) (:start . 106)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 114) (:start . 111)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "stable") (:form . "stable") (:end . 125)\n  (:start . 119) (:id . 59))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 138)\n  (:start . 126) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 141) (:start . 139)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 145) (:start . 142)\n  (:id . 62))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 150) (:start . 146)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 156)\n  (:start . 151) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.229) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502094@unknown@formal@none@1@S@(D) HEK 293T cells were stably transfected with d2EGFP either under the control of the wild-type HIV-1 LTR (LTRwt) or under the control of the LTR containing mutated Sp1-binding sites in the basal promoter (LTRmutSp1).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 12) (:start . 8)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 18) (:start . 13)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 48))\n ((:tag . "RB") (:stem . "stably") (:form . "stably") (:end . 30)\n  (:start . 24) (:id . 49))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 42)\n  (:start . 31) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "d2EGFP") (:form . "d2EGFP") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 61)\n  (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 79)\n  (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 96)\n  (:start . 87) (:id . 59))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 102)\n  (:start . 97) (:id . 60))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "LTRwt") (:form . "LTRwt") (:end . 113)\n  (:start . 108) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 117) (:start . 115)\n  (:id . 65))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 123)\n  (:start . 118) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 67))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 135)\n  (:start . 128) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n  (:id . 70))\n ((:tag . "NN") (:stem . "ltr") (:form . "LTR") (:end . 146) (:start . 143)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 157)\n  (:start . 147) (:id . 72))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 165)\n  (:start . 158) (:id . 73))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 177)\n  (:start . 166) (:id . 74))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 183)\n  (:start . 178) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 186) (:start . 184)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 190) (:start . 187)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "basal") (:form . "basal") (:end . 196)\n  (:start . 191) (:id . 78))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 205)\n  (:start . 197) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 207) (:start . 206)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "LTRmutSp1") (:form . "LTRmutSp1") (:end . 216)\n  (:start . 207) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 217) (:start . 216)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s7.230) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502095@unknown@formal@none@1@S@The effect of GlcN (16 mM) on the HIV-1 LTR was analyzed by flow cytometry, and the mean fluorescence intensity is represented in the bar diagram.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 22) (:start . 20)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 25) (:start . 23)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 26) (:start . 25)\n  (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 29) (:start . 27)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 39) (:start . 34)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 43) (:start . 40)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 47) (:start . 44)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 56)\n  (:start . 48) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 59) (:start . 57)\n  (:id . 56))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 64) (:start . 60)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cytometry") (:form . "cytometry") (:end . 74)\n  (:start . 65) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "mean") (:form . "mean") (:end . 88) (:start . 84)\n  (:id . 62))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 101)\n  (:start . 89) (:id . 63))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 111)\n  (:start . 102) (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 114) (:start . 112)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 126)\n  (:start . 115) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 68))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 137) (:start . 134)\n  (:id . 69))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 145)\n  (:start . 138) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.231) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502096@unknown@formal@none@1@S@The means ± standard deviations were calculated from duplicate determinations of three independent clones with similar fluorescence intensities.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mean") (:form . "means") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "±") (:form . "±") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "deviation") (:form . "deviations") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "duplicate") (:form . "duplicate") (:end . 62)\n  (:start . 53) (:id . 50))\n ((:tag . "NNS") (:stem . "determination") (:form . "determinations")\n  (:end . 77) (:start . 63) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 52))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 86) (:start . 81)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 98)\n  (:start . 87) (:id . 54))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 105)\n  (:start . 99) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 110) (:start . 106)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 118)\n  (:start . 111) (:id . 57))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 131)\n  (:start . 119) (:id . 58))\n ((:tag . "NNS") (:stem . "intensity") (:form . "intensities") (:end . 143)\n  (:start . 132) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.232) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502097@unknown@formal@none@1@S@P values are given for comparison with control: *, P ≤ 0.05; n.s., not significant.@(((:tag . "NN") (:stem . "p") (:form . "P") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "SYM") (:stem . "*") (:form . "*") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 52))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 54) (:start . 53)\n  (:id . 54))\n ((:tag . "CD") (:stem . "0.05") (:form . "0.05") (:end . 59) (:start . 55)\n  (:id . 55))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "NN") (:stem . "n.s.") (:form . "n.s.") (:end . 65) (:start . 61)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 70) (:start . 67)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 82)\n  (:start . 71) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.233) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502098@unknown@formal@none@1@S@Western blot analyses of one representative clone verify the increased O-GlcNAcylation pattern upon GlcN treatment and constant OGT expression.@(((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 43) (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "clone") (:form . "clone") (:end . 49) (:start . 44)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "verify") (:form . "verify") (:end . 56)\n  (:start . 50) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 70)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 86) (:start . 71) (:id . 52))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 94)\n  (:start . 87) (:id . 53))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 99) (:start . 95)\n  (:id . 54))\n ((:tag . "NN") (:stem . "glcn") (:form . "GlcN") (:end . 104) (:start . 100)\n  (:id . 55))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 114)\n  (:start . 105) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "constant") (:form . "constant") (:end . 127)\n  (:start . 119) (:id . 58))\n ((:tag . "NN") (:stem . "ogt") (:form . "OGT") (:end . 131) (:start . 128)\n  (:id . 59))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 142)\n  (:start . 132) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.234) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502099@unknown@formal@none@1@S@GAPDH staining demonstrates that equal amounts of protein were loaded.@(((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "VBZ") (:stem . "demonstrate") (:form . "demonstrates") (:end . 27)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 38) (:start . 33)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 46)\n  (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "load") (:form . "loaded") (:end . 69) (:start . 63)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.235) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502100@unknown@formal@none@1@S@In a next step, the role of the Sp1-binding sites in the full-length HIV-1 LTR integrated into the cellular genome was analyzed.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 9) (:start . 5)\n  (:id . 44))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 14) (:start . 10)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 47))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 24) (:start . 20)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 43)\n  (:start . 32) (:id . 51))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 49) (:start . 44)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 68)\n  (:start . 57) (:id . 55))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 74) (:start . 69)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 78) (:start . 75)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "integrate") (:form . "integrated") (:end . 89)\n  (:start . 79) (:id . 58))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 94) (:start . 90)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 107)\n  (:start . 99) (:id . 61))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 114)\n  (:start . 108) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 118) (:start . 115)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 127)\n  (:start . 119) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.236) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502101@unknown@formal@none@1@S@Toward this goal, HEK 293T cells were stably transfected with plasmids expressing d2EGFP either under the control of the full-length wild-type HIV-1 LTR (Fig. 4C, LTRwt) or under the control of the full-length LTR containing mutated Sp1-binding sites (Fig. 4C, LTRmutSp1).@(((:tag . "IN") (:stem . "toward") (:form . "Toward") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "goal") (:form . "goal") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . 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"control") (:end . 113)\n  (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 132)\n  (:start . 121) (:id . 62))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 142)\n  (:start . 133) (:id . 63))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 148)\n  (:start . 143) (:id . 64))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 152) (:start . 149)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 158) (:start . 154)\n  (:id . 67))\n ((:tag . "NN") (:stem . "4c") (:form . "4C") (:end . 161) (:start . 159)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . 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"LTR") (:end . 213) (:start . 210)\n  (:id . 79))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 224)\n  (:start . 214) (:id . 80))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 232)\n  (:start . 225) (:id . 81))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 244)\n  (:start . 233) (:id . 82))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 250)\n  (:start . 245) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 252) (:start . 251)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 256) (:start . 252)\n  (:id . 85))\n ((:tag . "NN") (:stem . "4c") (:form . "4C") (:end . 259) (:start . 257)\n  (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 260) (:start . 259)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "LTRmutSp1") (:form . "LTRmutSp1") (:end . 270)\n  (:start . 261) (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 271) (:start . 270)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 272) (:start . 271)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s7.237) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502102@unknown@formal@none@1@S@Three independent HEK 293T cell clones with similar fluorescence intensities were either left untreated or stimulated with 16 mM GlcN.@(((:tag . "CD") (:stem . "three") (:form . "Three") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 17)\n  (:start . 6) (:id . 43))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 64)\n  (:start . 52) (:id . 50))\n ((:tag . "NNS") (:stem . "intensity") (:form . "intensities") (:end . 76)\n  (:start . 65) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 81) (:start . 77)\n  (:id . 52))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 88)\n  (:start . 82) (:id . 53))\n ((:tag . "VBD") (:stem . "leave") (:form . "left") (:end . 93) (:start . 89)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 103)\n  (:start . 94) (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 106) (:start . 104)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "stimulate") (:form . "stimulated") (:end . 117)\n  (:start . 107) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 122) (:start . 118)\n  (:id . 58))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 125) (:start . 123)\n  (:id . 59))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 128) (:start . 126)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 133) (:start . 129)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s7.238) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502103@unknown@formal@none@1@S@Subsequently, the promoter activities were measured by flow cytometry.@(((:tag . "RB") (:stem . "subsequently") (:form . "Subsequently") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cytometry") (:form . "cytometry") (:end . 69)\n  (:start . 60) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.239) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502104@unknown@formal@none@1@S@Mutation of the Sp1-binding sites strongly decreased HIV-1 LTR activity (Fig. 4D, compare fluorescence intensities in the bar diagram).@(((:tag . "NN") (:stem . "mutation") (:form . "Mutation") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 27)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "VBD") (:stem . "decrease") (:form . "decreased") (:end . 52)\n  (:start . 43) (:id . 48))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 58) (:start . 53)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 71)\n  (:start . 63) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "4d") (:form . "4D") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "compare") (:form . "compare") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 102)\n  (:start . 90) (:id . 57))\n ((:tag . "NNS") (:stem . "intensity") (:form . "intensities") (:end . 114)\n  (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 60))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 133)\n  (:start . 126) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.240) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502105@unknown@formal@none@1@S@However, GlcN treatment significantly decreased the fluorescence intensity only in cells expressing d2EGFP under the control of the wild-type HIV-1 LTR and had no significant effect on cells expressing d2EGFP under the control of the Sp1-mutated HIV-1 LTR (Fig. 4D, bar diagram).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "glcn") (:form . "GlcN") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 37) (:start . 24) (:id . 46))\n ((:tag . "VBD") (:stem . "decrease") (:form . "decreased") (:end . 47)\n  (:start . 38) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 48))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 64)\n  (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 74)\n  (:start . 65) (:id . 50))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 79) (:start . 75)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 88) (:start . 83)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 99)\n  (:start . 89) (:id . 54))\n ((:tag . "NN") (:stem . "d2egfp") (:form . "d2EGFP") (:end . 106)\n  (:start . 100) (:id . 55))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 112)\n  (:start . 107) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 57))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 124)\n  (:start . 117) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 141)\n  (:start . 132) (:id . 61))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 147)\n  (:start . 142) (:id . 62))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 151) (:start . 148)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 155) (:start . 152)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 159) (:start . 156)\n  (:id . 65))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 162) (:start . 160)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 174)\n  (:start . 163) (:id . 67))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 181)\n  (:start . 175) (:id . 68))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 184) (:start . 182)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 190)\n  (:start . 185) (:id . 70))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 201)\n  (:start . 191) (:id . 71))\n ((:tag . "NN") (:stem . "d2egfp") (:form . "d2EGFP") (:end . 208)\n  (:start . 202) (:id . 72))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 214)\n  (:start . 209) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 218) (:start . 215)\n  (:id . 74))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 226)\n  (:start . 219) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 229) (:start . 227)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 233) (:start . 230)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "sp1-mutated") (:form . "Sp1-mutated") (:end . 245)\n  (:start . 234) (:id . 78))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 251)\n  (:start . 246) (:id . 79))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 255) (:start . 252)\n  (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 257) (:start . 256)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 261) (:start . 257)\n  (:id . 82))\n ((:tag . "NN") (:stem . "4d") (:form . "4D") (:end . 264) (:start . 262)\n  (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 265) (:start . 264)\n  (:id . 84))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 269) (:start . 266)\n  (:id . 85))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 277)\n  (:start . 270) (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 278) (:start . 277)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 279) (:start . 278)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s7.241) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502106@unknown@formal@none@1@S@Western blot analyses demonstrated that GlcN treatment similarly increased the O-GlcNAcylation pattern in the two cell types, that OGT expression was not altered, and that equal amounts of proteins were loaded (Fig. 4D, right panels).@(((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 34)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "NN") (:stem . "glcn") (:form . "GlcN") (:end . 44) (:start . 40)\n  (:id . 47))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 54)\n  (:start . 45) (:id . 48))\n ((:tag . "RB") (:stem . "similarly") (:form . "similarly") (:end . 64)\n  (:start . 55) (:id . 49))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 74)\n  (:start . 65) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 51))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 94) (:start . 79) (:id . 52))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 102)\n  (:start . 95) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 55))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 113) (:start . 110)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 118) (:start . 114)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 124)\n  (:start . 119) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 130) (:start . 126)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 134) (:start . 131)\n  (:id . 61))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 145)\n  (:start . 135) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 149) (:start . 146)\n  (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 153) (:start . 150)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "alter") (:form . "altered") (:end . 161)\n  (:start . 154) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n  (:id . 67))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 171) (:start . 167)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 177)\n  (:start . 172) (:id . 69))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 185)\n  (:start . 178) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 188) (:start . 186)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 197)\n  (:start . 189) (:id . 72))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 202) (:start . 198)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "load") (:form . "loaded") (:end . 209)\n  (:start . 203) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 211) (:start . 210)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 215) (:start . 211)\n  (:id . 76))\n ((:tag . "NN") (:stem . "4d") (:form . "4D") (:end . 218) (:start . 216)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 219) (:start . 218)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 225)\n  (:start . 220) (:id . 79))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 232)\n  (:start . 226) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 233) (:start . 232)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s7.242) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502107@unknown@formal@none@1@S@Altogether these results demonstrate that the Sp1-binding sites are required for the GlcN-mediated inhibition of the full-length HIV-1 promoter integrated into the cellular genome.@(((:tag . "RB") (:stem . "altogether") (:form . "Altogether") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 16) (:start . 11)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 36)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 57)\n  (:start . 46) (:id . 48))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 63) (:start . 58)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 67) (:start . 64)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 76)\n  (:start . 68) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 80) (:start . 77)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "glcn-mediated") (:form . "GlcN-mediated")\n  (:end . 98) (:start . 85) (:id . 54))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 109)\n  (:start . 99) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 128)\n  (:start . 117) (:id . 58))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 134)\n  (:start . 129) (:id . 59))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 143)\n  (:start . 135) (:id . 60))\n ((:tag . "VBN") (:stem . "integrate") (:form . "integrated") (:end . 154)\n  (:start . 144) (:id . 61))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 159) (:start . 155)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 172)\n  (:start . 164) (:id . 64))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 179)\n  (:start . 173) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.243) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502108@unknown@formal@none@1@S@Since the presence of the Sp1-binding sites is crucial for the inhibitory effect of OGT on the HIV-1 LTR promoter, we investigated whether this is also the case for the Sp1 protein itself.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 73)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 80)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 100)\n  (:start . 95) (:id . 59))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 113)\n  (:start . 105) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 62))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 117) (:start . 115)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "investigate") (:form . "investigated") (:end . 130)\n  (:start . 118) (:id . 64))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 138)\n  (:start . 131) (:id . 65))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 143) (:start . 139)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 146) (:start . 144)\n  (:id . 67))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 151) (:start . 147)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 69))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 160) (:start . 156)\n  (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 164) (:start . 161)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 72))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 172) (:start . 169)\n  (:id . 73))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 180)\n  (:start . 173) (:id . 74))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 187)\n  (:start . 181) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x7.244.1) (:span 131 138)))\n (:hscopes ((:id . :x7.244.1) (:span 131 187)))\n (:identifiers (:sid . :s7.244) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502109@unknown@formal@none@1@S@To this goal, the sensitivity of the Tat-induced LTR-Sp1wt promoter to OGT was analyzed in HEK 293T cells in the absence and presence of Sp1.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "goal") (:form . "goal") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 29)\n  (:start . 18) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "tat-induced") (:form . "Tat-induced") (:end . 48)\n  (:start . 37) (:id . 50))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 67)\n  (:start . 59) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 87)\n  (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 99) (:start . 95)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 105)\n  (:start . 100) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 62))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 120)\n  (:start . 113) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 64))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 133)\n  (:start . 125) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 140) (:start . 137)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.245) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502110@unknown@formal@none@1@S@Sp1 was recombinantly overexpressed, and its expression was inhibited with a specific siRNA.@(((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "recombinantly") (:form . "recombinantly")\n  (:end . 21) (:start . 8) (:id . 44))\n ((:tag . "VBN") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 35) (:start . 22) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 55)\n  (:start . 45) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "inhibit") (:form . "inhibited") (:end . 69)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 85)\n  (:start . 77) (:id . 54))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 91) (:start . 86)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.246) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502111@unknown@formal@none@1@S@A nontargeting siRNA was used as control.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "nontargeting") (:form . "nontargeting") (:end . 14)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 41) (:start . 40)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s7.247) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502112@unknown@formal@none@1@S@Cotransfection of the control siRNA did not affect the OGT-mediated inhibition of the LTR-Sp1wt (Fig. 5A, compare bars 3 and 4).@(((:tag . "NN") (:stem . "cotransfection") (:form . "Cotransfection")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "ogt-mediated") (:form . "OGT-mediated") (:end . 67)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 78)\n  (:start . 68) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 95)\n  (:start . 86) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 101) (:start . 97)\n  (:id . 57))\n ((:tag . "NN") (:stem . "5a") (:form . "5A") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 59))\n ((:tag . "NN") (:stem . "compare") (:form . "compare") (:end . 113)\n  (:start . 106) (:id . 60))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 118) (:start . 114)\n  (:id . 61))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 120) (:start . 119)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 63))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 126) (:start . 125)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 127) (:start . 126)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.248) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502113@unknown@formal@none@1@S@Tat-mediated activation of the LTR-Sp1wt was less pronounced after knockdown of Sp1 (Fig. 5A, compare protein content-normalized relative light unit values given above bars 3 and 7).@(((:tag . "JJ") (:stem . "tat-mediated") (:form . "Tat-mediated") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 23)\n  (:start . 13) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 40)\n  (:start . 31) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "pronounced") (:form . "pronounced") (:end . 60)\n  (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 66) (:start . 61)\n  (:id . 50))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 76)\n  (:start . 67) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 83) (:start . 80)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 89) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "5a") (:form . "5A") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "NN") (:stem . "compare") (:form . "compare") (:end . 101)\n  (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 109)\n  (:start . 102) (:id . 59))\n ((:tag . "JJ") (:stem . "content-normalized") (:form . "content-normalized")\n  (:end . 128) (:start . 110) (:id . 60))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 137)\n  (:start . 129) (:id . 61))\n ((:tag . "JJ") (:stem . "light") (:form . "light") (:end . 143)\n  (:start . 138) (:id . 62))\n ((:tag . "NN") (:stem . "unit") (:form . "unit") (:end . 148) (:start . 144)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 155)\n  (:start . 149) (:id . 64))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 161)\n  (:start . 156) (:id . 65))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 167)\n  (:start . 162) (:id . 66))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 172) (:start . 168)\n  (:id . 67))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 174) (:start . 173)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 178) (:start . 175)\n  (:id . 69))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 180) (:start . 179)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 181) (:start . 180)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.249) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502114@unknown@formal@none@1@S@However, OGT clearly did not inhibit LTR-Sp1wt promoter activity under these conditions (Fig. 5A, compare bars 7 and 8).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "NN") (:stem . "ltr-sp1wt") (:form . "LTR-Sp1wt") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 64)\n  (:start . 56) (:id . 51))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 70) (:start . 65)\n  (:id . 52))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 76) (:start . 71)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 87)\n  (:start . 77) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "NN") (:stem . "5a") (:form . "5A") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "compare") (:form . "compare") (:end . 105)\n  (:start . 98) (:id . 59))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 110) (:start . 106)\n  (:id . 60))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 118) (:start . 117)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.250) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502115@unknown@formal@none@1@S@The expression of OGT and Tat was not altered upon depletion of Sp1 expression (Fig. 5B).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Tat") (:form . "Tat") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "alter") (:form . "altered") (:end . 45)\n  (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "depletion") (:form . "depletion") (:end . 60)\n  (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 78)\n  (:start . 68) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . "NN") (:stem . "5b") (:form . "5B") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.251) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502116@unknown@formal@none@1@S@Thus, in addition to the Sp1-binding sites, the presence of the Sp1 protein itself is also necessary for the OGT-mediated inhibition of the HIV-1 LTR activity.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 17)\n  (:start . 9) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 36)\n  (:start . 25) (:id . 48))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 56)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 75)\n  (:start . 68) (:id . 56))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 82)\n  (:start . 76) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 85) (:start . 83)\n  (:id . 58))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 90) (:start . 86)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 100)\n  (:start . 91) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 104) (:start . 101)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "ogt-mediated") (:form . "OGT-mediated") (:end . 121)\n  (:start . 109) (:id . 63))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 132)\n  (:start . 122) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 145)\n  (:start . 140) (:id . 67))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 149) (:start . 146)\n  (:id . 68))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 158)\n  (:start . 150) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s7.252) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502117@unknown@formal@none@1@S@Sp1 is crucial for the inhibitory effect of OGT on the HIV-1 LTR.@(((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 60) (:start . 55)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.253) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502118@unknown@formal@none@1@S@(A) HIV-1 LTR activity was measured by luciferase assay after cotransfection of HEK 293T cells with an LTR-Sp1wt reporter construct along with Tat-and Sp1-encoding plasmids in the absence or presence of an OGT-encoding vector together with 10 nM control siRNA or an siRNA specifically targeting Sp1.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 9) (:start . 4)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 13) (:start . 10)\n  (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 22)\n  (:start . 14) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 26) (:start . 23)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "measure") (:form . 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"with") (:end . 239) (:start . 235)\n  (:id . 79))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 242) (:start . 240)\n  (:id . 80))\n ((:tag . "NN") (:stem . "nm") (:form . "nM") (:end . 245) (:start . 243)\n  (:id . 81))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 253)\n  (:start . 246) (:id . 82))\n ((:tag . "NNP") (:stem . "siRNA") (:form . "siRNA") (:end . 259)\n  (:start . 254) (:id . 83))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 262) (:start . 260)\n  (:id . 84))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 265) (:start . 263)\n  (:id . 85))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 271)\n  (:start . 266) (:id . 86))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 284)\n  (:start . 272) (:id . 87))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 294)\n  (:start . 285) (:id . 88))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 298) (:start . 295)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 299) (:start . 298)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s7.254) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502119@unknown@formal@none@1@S@Total DNA amount was adjusted with pcDNA4.@(((:tag . "JJ") (:stem . "total") (:form . "Total") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "adjust") (:form . "adjusted") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "pcdna4") (:form . "pcDNA4") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s7.255) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502120@unknown@formal@none@1@S@The relative light units normalized to the total protein content indicate the means ± standard deviations from triplicate determinations (values above the bars).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "light") (:form . "light") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "unit") (:form . "units") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "normalize") (:form . "normalized") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 48) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "content") (:form . "content") (:end . 64)\n  (:start . 57) (:id . 51))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 73)\n  (:start . 65) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "mean") (:form . "means") (:end . 83) (:start . 78)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "±") (:form . "±") (:end . 85) (:start . 84)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 94)\n  (:start . 86) (:id . 56))\n ((:tag . "NNS") (:stem . "deviation") (:form . "deviations") (:end . 105)\n  (:start . 95) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 110) (:start . 106)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "triplicate") (:form . "triplicate") (:end . 121)\n  (:start . 111) (:id . 59))\n ((:tag . "NNS") (:stem . "determination") (:form . "determinations")\n  (:end . 136) (:start . 122) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 144)\n  (:start . 138) (:id . 62))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 150)\n  (:start . 145) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 159) (:start . 155)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.256) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502121@unknown@formal@none@1@S@The results were normalized for each siRNA data set individually and are presented in terms of percentages of control (Tat- and Sp1-induced LTR-Sp1wt activity).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "normalize") (:form . "normalized") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "set") (:form . "set") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "RB") (:stem . "individually") (:form . "individually") (:end . 64)\n  (:start . 52) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 82)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 91) (:start . 86)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "percentage") (:form . "percentages") (:end . 106)\n  (:start . 95) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n  (:id . 59))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 117)\n  (:start . 110) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 119) (:start . 118)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "tat-") (:form . "Tat-") (:end . 123) (:start . 119)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "sp1-induced") (:form . "Sp1-induced") (:end . 139)\n  (:start . 128) (:id . 64))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 149)\n  (:start . 140) (:id . 65))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 158)\n  (:start . 150) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.257) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502122@unknown@formal@none@1@S@P values are given for comparison with control: **, P ≤ 0.01; n.s., not significant.@(((:tag . "NN") (:stem . "p") (:form . "P") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "SYM") (:stem . "**") (:form . "**") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 53) (:start . 52)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 55) (:start . 54)\n  (:id . 54))\n ((:tag . "CD") (:stem . "0.01") (:form . "0.01") (:end . 60) (:start . 56)\n  (:id . 55))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 61) (:start . 60)\n  (:id . 56))\n ((:tag . "NN") (:stem . "n.s.") (:form . "n.s.") (:end . 66) (:start . 62)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 71) (:start . 68)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 83)\n  (:start . 72) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.258) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502123@unknown@formal@none@1@S@(B) Western blot analyses of the lysates verify the knockdown of Sp1 by siRNA and prove that the expression of OGT and Tat remains unaffected upon silencing of Sp1.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 16) (:start . 12)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 25)\n  (:start . 17) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "lysate") (:form . "lysates") (:end . 40)\n  (:start . 33) (:id . 50))\n ((:tag . "VBP") (:stem . "verify") (:form . "verify") (:end . 47)\n  (:start . 41) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 61)\n  (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 71) (:start . 69)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "siRNA") (:form . "siRNA") (:end . 77) (:start . 72)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "prove") (:form . "prove") (:end . 87) (:start . 82)\n  (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 92) (:start . 88)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 61))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 107)\n  (:start . 97) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 114) (:start . 111)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Tat") (:form . "Tat") (:end . 122) (:start . 119)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 130)\n  (:start . 123) (:id . 67))\n ((:tag . "JJ") (:stem . "unaffected") (:form . "unaffected") (:end . 141)\n  (:start . 131) (:id . 68))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 146) (:start . 142)\n  (:id . 69))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 156)\n  (:start . 147) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 159) (:start . 157)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 163) (:start . 160)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s7.259) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502124@unknown@formal@none@1@S@The GAPDH staining demonstrates that equal amounts of protein were loaded.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "demonstrate") (:form . "demonstrates") (:end . 31)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 42) (:start . 37)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "load") (:form . "loaded") (:end . 73) (:start . 67)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.260) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502125@unknown@formal@none@1@S@To investigate the role of Sp1 in the OGT-mediated inhibition of the HIV-1 LTR in more detail, we explored whether overexpression of OGT enhances O-GlcNAcylation of Sp1 (Fig. 6A).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "ogt-mediated") (:form . "OGT-mediated") (:end . 50)\n  (:start . 38) (:id . 50))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 61)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "NN") (:stem . "detail") (:form . "detail") (:end . 93)\n  (:start . 87) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 97) (:start . 95)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "explore") (:form . "explored") (:end . 106)\n  (:start . 98) (:id . 61))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 114)\n  (:start . 107) (:id . 62))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 129) (:start . 115) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 136) (:start . 133)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "enhance") (:form . "enhances") (:end . 145)\n  (:start . 137) (:id . 66))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 161) (:start . 146) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 164) (:start . 162)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 168) (:start . 165)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 170) (:start . 169)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 174) (:start . 170)\n  (:id . 71))\n ((:tag . "NN") (:stem . "6a") (:form . "6A") (:end . 177) (:start . 175)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 178) (:start . 177)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x7.261.1) (:span 107 114)))\n (:hscopes ((:id . :x7.261.1) (:span 107 168)))\n (:identifiers (:sid . :s7.261) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502126@unknown@formal@none@1@S@For this purpose, Sp1 was expressed alone or in combination with OGT (Fig. 6A, input).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "purpose") (:form . "purpose") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 35)\n  (:start . 26) (:id . 48))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 59)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 74) (:start . 70)\n  (:id . 56))\n ((:tag . "NN") (:stem . "6a") (:form . "6A") (:end . 77) (:start . 75)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 58))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 84) (:start . 79)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.262) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502127@unknown@formal@none@1@S@Immunoprecipitation experiments demonstrated that O-GlcNAcylation of Sp1 was substantially increased when OGT was overexpressed (Fig. 6A, Sp1-IP).@(((:tag . "NNP") (:stem . "Immunoprecipitation")\n  (:form . "Immunoprecipitation") (:end . 19) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 31)\n  (:start . 20) (:id . 43))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 44)\n  (:start . 32) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 49) (:start . 45)\n  (:id . 45))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 65) (:start . 50) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 72) (:start . 69)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 76) (:start . 73)\n  (:id . 49))\n ((:tag . "RB") (:stem . "substantially") (:form . "substantially")\n  (:end . 90) (:start . 77) (:id . 50))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 100)\n  (:start . 91) (:id . 51))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 105) (:start . 101)\n  (:id . 52))\n ((:tag . "NN") (:stem . "ogt") (:form . "OGT") (:end . 109) (:start . 106)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 113) (:start . 110)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 127) (:start . 114) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 133) (:start . 129)\n  (:id . 57))\n ((:tag . "NN") (:stem . "6a") (:form . "6A") (:end . 136) (:start . 134)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Sp1-IP") (:form . "Sp1-IP") (:end . 144)\n  (:start . 138) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s7.263) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502128@unknown@formal@none@1@S@Coimmunoprecipitations revealed that OGT physically interacts with Sp1 under these conditions (data not shown).@(((:tag . "NNPS") (:stem . "Coimmunoprecipitation")\n  (:form . "Coimmunoprecipitations") (:end . 22) (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 31)\n  (:start . 23) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 40) (:start . 37)\n  (:id . 45))\n ((:tag . "RB") (:stem . "physically") (:form . "physically") (:end . 51)\n  (:start . 41) (:id . 46))\n ((:tag . "VBZ") (:stem . "interact") (:form . "interacts") (:end . 61)\n  (:start . 52) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 48))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 70) (:start . 67)\n  (:id . 49))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 76) (:start . 71)\n  (:id . 50))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 82) (:start . 77)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 93)\n  (:start . 83) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 99) (:start . 95)\n  (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 103) (:start . 100)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 109)\n  (:start . 104) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.264) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502129@unknown@formal@none@1@S@O-GlcNAcylation of Sp1 selectively inhibits HIV-1 LTR promoter activity in a dose-dependent manner.@(((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 34)\n  (:start . 23) (:id . 45))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 43)\n  (:start . 35) (:id . 46))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 49) (:start . 44)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 53) (:start . 50)\n  (:id . 48))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 62)\n  (:start . 54) (:id . 49))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 71)\n  (:start . 63) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 76) (:start . 75)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dose-dependent") (:form . "dose-dependent")\n  (:end . 91) (:start . 77) (:id . 53))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 98)\n  (:start . 92) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.265) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502130@unknown@formal@none@1@S@(A) HEK 293T cells were transfected with control vector (CV), Sp1, or Sp1- and OGT-expressing vectors.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 12) (:start . 8)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 18) (:start . 13)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 35)\n  (:start . 24) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 40) (:start . 36)\n  (:id . 50))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 48)\n  (:start . 41) (:id . 51))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 55)\n  (:start . 49) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "CV") (:form . "CV") (:end . 59) (:start . 57)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 65) (:start . 62)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 69) (:start . 67)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Sp1-") (:form . "Sp1-") (:end . 74) (:start . 70)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "ogt-expressing") (:form . "OGT-expressing")\n  (:end . 93) (:start . 79) (:id . 62))\n ((:tag . "NNS") (:stem . "vector") (:form . "vectors") (:end . 101)\n  (:start . 94) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.266) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502131@unknown@formal@none@1@S@Total DNA amount was adjusted with pcDNA4.@(((:tag . "JJ") (:stem . "total") (:form . "Total") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "adjust") (:form . "adjusted") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "pcdna4") (:form . "pcDNA4") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s7.267) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502132@unknown@formal@none@1@S@Expression of transfected plasmids and O-GlcNAcylation were assessed via Western blotting of cell lysates (input).@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "plasmid") (:form . "plasmids") (:end . 34)\n  (:start . 26) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 54) (:start . 39) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 59) (:start . 55)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 68)\n  (:start . 60) (:id . 49))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 72) (:start . 69)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 80)\n  (:start . 73) (:id . 51))\n ((:tag . "NN") (:stem . "blotting") (:form . "blotting") (:end . 89)\n  (:start . 81) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 97) (:start . 93)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "lysate") (:form . "lysates") (:end . 105)\n  (:start . 98) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 56))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 112)\n  (:start . 107) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.268) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502133@unknown@formal@none@1@S@Immunoprecipitation of Sp1 (Sp1-IP) and O-GlcNAcylation of Sp1 were verified by Western blotting of Sp1-IPs with anti-Sp1 and anti-O-GlcNAc antibodies, respectively.@(((:tag . "NNP") (:stem . "Immunoprecipitation")\n  (:form . "Immunoprecipitation") (:end . 19) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 26) (:start . 23)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sp1-IP") (:form . "Sp1-IP") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 55) (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 76)\n  (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 87)\n  (:start . 80) (:id . 55))\n ((:tag . "NN") (:stem . "blotting") (:form . "blotting") (:end . 96)\n  (:start . 88) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "sp1-ip") (:form . "Sp1-IPs") (:end . 107)\n  (:start . 100) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 112) (:start . 108)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "anti-sp1") (:form . "anti-Sp1") (:end . 121)\n  (:start . 113) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "anti-o-glcnac") (:form . "anti-O-GlcNAc")\n  (:end . 139) (:start . 126) (:id . 62))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 150)\n  (:start . 140) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n  (:id . 64))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 164)\n  (:start . 152) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.269) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502134@unknown@formal@none@1@S@(B) The effects of OGT on the LTR-Sp1wt and the control promoter EF1α in HEK 293T cells cotransfected with the reporter and an Sp1-encoding plasmid were analyzed by luciferase assay.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 15)\n  (:start . 8) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 22) (:start . 19)\n  (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 25) (:start . 23)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 39)\n  (:start . 30) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 53))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 55)\n  (:start . 48) (:id . 54))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 64)\n  (:start . 56) (:id . 55))\n ((:tag . "NN") (:stem . "ef1α") (:form . "EF1α") (:end . 69) (:start . 65)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 76) (:start . 73)\n  (:id . 58))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 81) (:start . 77)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 87) (:start . 82)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "cotransfecte") (:form . "cotransfected")\n  (:end . 101) (:start . 88) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 106) (:start . 102)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 119)\n  (:start . 111) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 65))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 126) (:start . 124)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "sp1-encoding") (:form . "Sp1-encoding") (:end . 139)\n  (:start . 127) (:id . 67))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 147)\n  (:start . 140) (:id . 68))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 152) (:start . 148)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 161)\n  (:start . 153) (:id . 70))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 164) (:start . 162)\n  (:id . 71))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 175)\n  (:start . 165) (:id . 72))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 181)\n  (:start . 176) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s7.270) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502135@unknown@formal@none@1@S@(C) Luciferase activity of HEK 293T cells transiently cotransfected with the LTR-Sp1wt reporter construct along with Tat- and Sp1-encoding plasmids and increasing concentrations of an OGT-encoding vector (0.05 µg, 0.2 µg, and 1 µg).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Luciferase") (:form . "Luciferase") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 23)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 35) (:start . 31)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 41) (:start . 36)\n  (:id . 50))\n ((:tag . "RB") (:stem . "transiently") (:form . "transiently") (:end . 53)\n  (:start . 42) (:id . 51))\n ((:tag . "VBN") (:stem . "cotransfecte") (:form . "cotransfected")\n  (:end . 67) (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 86)\n  (:start . 77) (:id . 55))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 95)\n  (:start . 87) (:id . 56))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 105)\n  (:start . 96) (:id . 57))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 111)\n  (:start . 106) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 116) (:start . 112)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Tat-") (:form . "Tat-") (:end . 121) (:start . 117)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "sp1-encoding") (:form . "Sp1-encoding") (:end . 138)\n  (:start . 126) (:id . 62))\n ((:tag . "NNS") (:stem . "plasmid") (:form . "plasmids") (:end . 147)\n  (:start . 139) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 151) (:start . 148)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 162)\n  (:start . 152) (:id . 65))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 177) (:start . 163) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 180) (:start . 178)\n  (:id . 67))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 183) (:start . 181)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "ogt-encoding") (:form . "OGT-encoding") (:end . 196)\n  (:start . 184) (:id . 69))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 203)\n  (:start . 197) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 205) (:start . 204)\n  (:id . 71))\n ((:tag . "CD") (:stem . "0.05") (:form . "0.05") (:end . 209) (:start . 205)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "µg") (:form . "µg") (:end . 212) (:start . 210)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 213) (:start . 212)\n  (:id . 74))\n ((:tag . "CD") (:stem . "0.2") (:form . "0.2") (:end . 217) (:start . 214)\n  (:id . 75))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 220) (:start . 218)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 221) (:start . 220)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 225) (:start . 222)\n  (:id . 78))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 227) (:start . 226)\n  (:id . 79))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 230) (:start . 228)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 231) (:start . 230)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s7.271) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502136@unknown@formal@none@1@S@The total DNA amount in panels B and C was adjusted with pcDNA4.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 42) (:start . 39)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "adjust") (:form . "adjusted") (:end . 51)\n  (:start . 43) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 56) (:start . 52)\n  (:id . 53))\n ((:tag . "NN") (:stem . "pcdna4") (:form . "pcDNA4") (:end . 63)\n  (:start . 57) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.272) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502137@unknown@formal@none@1@S@The values were normalized to the total amount of protein and are presented in terms of percentages of control (Sp1 induced [B] and Tat- and Sp1-induced [C] promoter activity).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "normalize") (:form . "normalized") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 57)\n  (:start . 50) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 75)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 84) (:start . 79)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "percentage") (:form . "percentages") (:end . 99)\n  (:start . 88) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 110)\n  (:start . 103) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 115) (:start . 112)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 123)\n  (:start . 116) (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 126) (:start . 125)\n  (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 127) (:start . 126)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Tat-") (:form . "Tat-") (:end . 136) (:start . 132)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "sp1-induced") (:form . "Sp1-induced") (:end . 152)\n  (:start . 141) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 154) (:start . 153)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 155) (:start . 154)\n  (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 156) (:start . 155)\n  (:id . 73))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 165)\n  (:start . 157) (:id . 74))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 174)\n  (:start . 166) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 175) (:start . 174)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s7.273) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502138@unknown@formal@none@1@S@The means ± standard deviations from triplicate determinations are indicated.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mean") (:form . "means") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "±") (:form . "±") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "deviation") (:form . "deviations") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "triplicate") (:form . "triplicate") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "determination") (:form . "determinations")\n  (:end . 62) (:start . 48) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 76)\n  (:start . 67) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.274) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502139@unknown@formal@none@1@S@P values are given for comparison with control: n.s., not significant; *, P ≤ 0.05; **, P ≤ 0.@(((:tag . "NN") (:stem . "p") (:form . "P") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "LS") (:stem . "n.s.") (:form . "n.s.") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 69)\n  (:start . 58) (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . "SYM") (:stem . "*") (:form . "*") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 75) (:start . 74)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 77) (:start . 76)\n  (:id . 59))\n ((:tag . "CD") (:stem . "0.05") (:form . "0.05") (:end . 82) (:start . 78)\n  (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 83) (:start . 82)\n  (:id . 61))\n ((:tag . "SYM") (:stem . "**") (:form . "**") (:end . 86) (:start . 84)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 63))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 89) (:start . 88)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 91) (:start . 90)\n  (:id . 65))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 93) (:start . 92)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.275) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502140@unknown@formal@none@1@S@In order to determine whether O-GlcNAcylation of Sp1 inhibits solely HIV-1 LTR activity or transcription in general, luciferase reporter assays were performed using LTR-Sp1wt and an EF1α promoter construct.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 45) (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "RB") (:stem . "solely") (:form . "solely") (:end . 68)\n  (:start . 62) (:id . 51))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 90) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 104) (:start . 91) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 115)\n  (:start . 108) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 59))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 127)\n  (:start . 117) (:id . 60))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 136)\n  (:start . 128) (:id . 61))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 143)\n  (:start . 137) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 148) (:start . 144)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 158)\n  (:start . 149) (:id . 64))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 164) (:start . 159)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 174)\n  (:start . 165) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 178) (:start . 175)\n  (:id . 67))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 181) (:start . 179)\n  (:id . 68))\n ((:tag . "NN") (:stem . "ef1α") (:form . "EF1α") (:end . 186) (:start . 182)\n  (:id . 69))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 195)\n  (:start . 187) (:id . 70))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 205)\n  (:start . 196) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x7.276.1) (:span 88 90)) ((:id . :x7.276.2) (:span 22 29)))\n (:hscopes ((:id . :x7.276.1) (:span 62 115))\n  ((:id . :x7.276.2) (:span 22 115)))\n (:identifiers (:sid . :s7.276) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502141@unknown@formal@none@1@S@The latter triggers the expression of the housekeeping gene EF1α and harbors Sp1-binding sites.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "trigger") (:form . "triggers") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "housekeeping") (:form . "housekeeping") (:end . 54)\n  (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "ef1α") (:form . "EF1α") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "harbor") (:form . "harbors") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 88)\n  (:start . 77) (:id . 54))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 94) (:start . 89)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.277) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502142@unknown@formal@none@1@S@Unlike the LTR-Sp1wt promoter, the EF1α promoter has no TAR element.@(((:tag . "IN") (:stem . "unlike") (:form . "Unlike") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "ef1α") (:form . "EF1α") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tar") (:form . "TAR") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "NN") (:stem . "element") (:form . "element") (:end . 67)\n  (:start . 60) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.278) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502143@unknown@formal@none@1@S@In order to ensure comparable induction levels, both reporter promoters were activated with Sp1 alone (Fig. 6B).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "JJ") (:stem . "comparable") (:form . "comparable") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "induction") (:form . "induction") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 46)\n  (:start . 40) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 61)\n  (:start . 53) (:id . 51))\n ((:tag . "NNS") (:stem . "promoter") (:form . "promoters") (:end . 71)\n  (:start . 62) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 86)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 91) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 95) (:start . 92)\n  (:id . 56))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 101) (:start . 96)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 107) (:start . 103)\n  (:id . 59))\n ((:tag . "NN") (:stem . "6b") (:form . "6B") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s7.279) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502144@unknown@formal@none@1@S@In agreement with the results above, overexpression of OGT significantly inhibited the Sp1-triggered expression of LTR-Sp1wt (Fig. 6B, LTR-Sp1wt).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 51) (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 72) (:start . 59) (:id . 52))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "sp1-triggered") (:form . "Sp1-triggered")\n  (:end . 100) (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 111)\n  (:start . 101) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 124)\n  (:start . 115) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 130) (:start . 126)\n  (:id . 60))\n ((:tag . "NN") (:stem . "6b") (:form . "6B") (:end . 133) (:start . 131)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 144)\n  (:start . 135) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.280) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502145@unknown@formal@none@1@S@In contrast, the activity of the EF1α promoter was not repressed but significantly increased by OGT (Fig. 6B, EF1α), suggesting that OGT selectively inhibits the HIV-1 LTR promoter and does not generally repress Sp1-regulated gene expression.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "ef1α") (:form . "EF1α") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "repress") (:form . "repressed") (:end . 64)\n  (:start . 55) (:id . 53))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 82) (:start . 69) (:id . 55))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 92)\n  (:start . 83) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 105) (:start . 101)\n  (:id . 60))\n ((:tag . "NN") (:stem . "6b") (:form . "6B") (:end . 108) (:start . 106)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "EF1α") (:form . "EF1α") (:end . 114) (:start . 110)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 127)\n  (:start . 117) (:id . 66))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 132) (:start . 128)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 136) (:start . 133)\n  (:id . 68))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 148)\n  (:start . 137) (:id . 69))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 157)\n  (:start . 149) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 167)\n  (:start . 162) (:id . 72))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 171) (:start . 168)\n  (:id . 73))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 180)\n  (:start . 172) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 184) (:start . 181)\n  (:id . 75))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 189) (:start . 185)\n  (:id . 76))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 193) (:start . 190)\n  (:id . 77))\n ((:tag . "RB") (:stem . "generally") (:form . "generally") (:end . 203)\n  (:start . 194) (:id . 78))\n ((:tag . "VB") (:stem . "repress") (:form . "repress") (:end . 211)\n  (:start . 204) (:id . 79))\n ((:tag . "JJ") (:stem . "sp1-regulated") (:form . "Sp1-regulated")\n  (:end . 225) (:start . 212) (:id . 80))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 230) (:start . 226)\n  (:id . 81))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 241)\n  (:start . 231) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 242) (:start . 241)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x7.281.1) (:span 117 127)))\n (:hscopes ((:id . :x7.281.1) (:span 117 241)))\n (:identifiers (:sid . :s7.281) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502146@unknown@formal@none@1@S@Furthermore, we evaluated by luciferase reporter assay whether the inhibitory effect of OGT on the Sp1-regulated HIV-1 LTR promoter is dose dependent.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "evaluate") (:form . "evaluated") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 39)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 54) (:start . 49)\n  (:id . 49))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 62)\n  (:start . 55) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 77)\n  (:start . 67) (:id . 52))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 84)\n  (:start . 78) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "sp1-regulated") (:form . "Sp1-regulated")\n  (:end . 112) (:start . 99) (:id . 58))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 118)\n  (:start . 113) (:id . 59))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 122) (:start . 119)\n  (:id . 60))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 131)\n  (:start . 123) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 134) (:start . 132)\n  (:id . 62))\n ((:tag . "NN") (:stem . "dose") (:form . "dose") (:end . 139) (:start . 135)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "dependent") (:form . "dependent") (:end . 149)\n  (:start . 140) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x7.282.1) (:span 55 62)))\n (:hscopes ((:id . :x7.282.1) (:span 55 149)))\n (:identifiers (:sid . :s7.282) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502147@unknown@formal@none@1@S@To this end, the reporter LTR-Sp1wt was cotransfected with Sp1- and Tat-encoding constructs in HEK 293T cells together with increasing amounts of OGT-encoding plasmid (0.05 µg, 0.2 µg, and 1 µg).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 25)\n  (:start . 17) (:id . 47))\n ((:tag . "NNP") (:stem . "LTR-Sp1wt") (:form . "LTR-Sp1wt") (:end . 35)\n  (:start . 26) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "cotransfecte") (:form . "cotransfected")\n  (:end . 53) (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Sp1-") (:form . "Sp1-") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "tat-encoding") (:form . "Tat-encoding") (:end . 80)\n  (:start . 68) (:id . 54))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 91)\n  (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 103) (:start . 99)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 109)\n  (:start . 104) (:id . 59))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 118)\n  (:start . 110) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 134)\n  (:start . 124) (:id . 62))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 142)\n  (:start . 135) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "ogt-encoding") (:form . "OGT-encoding") (:end . 158)\n  (:start . 146) (:id . 65))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 166)\n  (:start . 159) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 168) (:start . 167)\n  (:id . 67))\n ((:tag . "CD") (:stem . "0.05") (:form . "0.05") (:end . 172) (:start . 168)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "µg") (:form . "µg") (:end . 175) (:start . 173)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 176) (:start . 175)\n  (:id . 70))\n ((:tag . "CD") (:stem . "0.2") (:form . "0.2") (:end . 180) (:start . 177)\n  (:id . 71))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 183) (:start . 181)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 188) (:start . 185)\n  (:id . 74))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 190) (:start . 189)\n  (:id . 75))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 193) (:start . 191)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s7.283) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502148@unknown@formal@none@1@S@OGT clearly inhibited dose dependently the HIV-1 LTR promoter activity (Fig. 6C).@(((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "dose") (:form . "dose") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "RB") (:stem . "dependently") (:form . "dependently") (:end . 38)\n  (:start . 27) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 70)\n  (:start . 62) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "6c") (:form . "6C") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.284) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502149@unknown@formal@none@1@S@The inhibitory effect of OGT on the HIV-1 LTR may rely on impaired nuclear translocation or decreased DNA-binding affinity of Sp1 upon O-GlcNAcylation.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "VB") (:stem . "rely") (:form . "rely") (:end . 54) (:start . 50)\n  (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "impaired") (:form . "impaired") (:end . 66)\n  (:start . 58) (:id . 54))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 74)\n  (:start . 67) (:id . 55))\n ((:tag . "NN") (:stem . "translocation") (:form . "translocation")\n  (:end . 88) (:start . 75) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "decrease") (:form . "decreased") (:end . 101)\n  (:start . 92) (:id . 58))\n ((:tag . "JJ") (:stem . "dna-binding") (:form . "DNA-binding") (:end . 113)\n  (:start . 102) (:id . 59))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 122)\n  (:start . 114) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 61))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 134) (:start . 130)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "O-GlcNAcylation") (:form . "O-GlcNAcylation")\n  (:end . 150) (:start . 135) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x7.285.1) (:span 89 91)) ((:id . :x7.285.2) (:span 46 49)))\n (:hscopes ((:id . :x7.285.1) (:span 58 150))\n  ((:id . :x7.285.2) (:span 46 150)))\n (:identifiers (:sid . :s7.285) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502150@unknown@formal@none@1@S@The impact of OGT on the nuclear translocation of Sp1 was investigated by comparing the nuclear amounts of Sp1 in cells expressing endogenous or increased levels of OGT.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "impact") (:form . "impact") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 32)\n  (:start . 25) (:id . 48))\n ((:tag . "NN") (:stem . "translocation") (:form . "translocation")\n  (:end . 46) (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 70)\n  (:start . 58) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "compare") (:form . "comparing") (:end . 83)\n  (:start . 74) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 95)\n  (:start . 88) (:id . 57))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 103)\n  (:start . 96) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 119)\n  (:start . 114) (:id . 62))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 130)\n  (:start . 120) (:id . 63))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 141)\n  (:start . 131) (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 154)\n  (:start . 145) (:id . 66))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 161)\n  (:start . 155) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 164) (:start . 162)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 168) (:start . 165)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s7.286) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502151@unknown@formal@none@1@S@The amount of nuclear Sp1 was not decreased upon overexpression of OGT (Fig. 7A) but rather increased, suggesting that the observed decrease in the HIV-1 LTR promoter activity was not due to impaired nuclear translocation of Sp1.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "decrease") (:form . "decreased") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 63) (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "7a") (:form . "7A") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 91)\n  (:start . 85) (:id . 59))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 101)\n  (:start . 92) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 113)\n  (:start . 103) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 118) (:start . 114)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 131)\n  (:start . 123) (:id . 65))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 140)\n  (:start . 132) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 143) (:start . 141)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 153)\n  (:start . 148) (:id . 69))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 157) (:start . 154)\n  (:id . 70))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 166)\n  (:start . 158) (:id . 71))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 175)\n  (:start . 167) (:id . 72))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 179) (:start . 176)\n  (:id . 73))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 183) (:start . 180)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 187) (:start . 184)\n  (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 190) (:start . 188)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "impaired") (:form . "impaired") (:end . 199)\n  (:start . 191) (:id . 77))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 207)\n  (:start . 200) (:id . 78))\n ((:tag . "NN") (:stem . "translocation") (:form . "translocation")\n  (:end . 221) (:start . 208) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 224) (:start . 222)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 228) (:start . 225)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x7.287.1) (:span 103 113)))\n (:hscopes ((:id . :x7.287.1) (:span 103 228)))\n (:identifiers (:sid . :s7.287) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502152@unknown@formal@none@1@S@OGT does not interfere with Sp1 expression and DNA binding of Sp1.@(((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "interfere") (:form . "interfere") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 58)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.288) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502153@unknown@formal@none@1@S@(A) HEK 293T cells were transfected with an Sp1-encoding plasmid, along with an OGT-encoding plasmid or control plasmid.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 12) (:start . 8)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 18) (:start . 13)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 35)\n  (:start . 24) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 40) (:start . 36)\n  (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 43) (:start . 41)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "sp1-encoding") (:form . "Sp1-encoding") (:end . 56)\n  (:start . 44) (:id . 52))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 64)\n  (:start . 57) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 71) (:start . 66)\n  (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 76) (:start . 72)\n  (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "ogt-encoding") (:form . "OGT-encoding") (:end . 92)\n  (:start . 80) (:id . 58))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 100)\n  (:start . 93) (:id . 59))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 103) (:start . 101)\n  (:id . 60))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 111)\n  (:start . 104) (:id . 61))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 119)\n  (:start . 112) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.289) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502154@unknown@formal@none@1@S@Protein expression was detected in nuclear protein extracts via Western blotting.@(((:tag . "NN") (:stem . "protein") (:form . "Protein") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 42)\n  (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "NNS") (:stem . "extract") (:form . "extracts") (:end . 59)\n  (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 71)\n  (:start . 64) (:id . 51))\n ((:tag . "NN") (:stem . "blotting") (:form . "blotting") (:end . 80)\n  (:start . 72) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.290) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502155@unknown@formal@none@1@S@Staining of lamin A/C was used as a loading control.@(((:tag . "NN") (:stem . "staining") (:form . "Staining") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "lamin") (:form . "lamin") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "A/C") (:form . "A/C") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "loading") (:form . "loading") (:end . 43)\n  (:start . 36) (:id . 50))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 51)\n  (:start . 44) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 52) (:start . 51)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.291) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502156@unknown@formal@none@1@S@(B) Electrophoretic mobility shift assays were carried out with 32P-end-labeled double-stranded oligonucleotides corresponding to the Sp1-binding sites in the HIV-1 LTR promoter (wt LTR-Sp1) or with oligonucleotides containing mutated Sp1-binding sites in order to prevent binding (mut LTR-Sp1).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "electrophoretic") (:form . "Electrophoretic")\n  (:end . 19) (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "32p-end-labeled") (:form . "32P-end-labeled")\n  (:end . 79) (:start . 64) (:id . 53))\n ((:tag . "JJ") (:stem . "double-stranded") (:form . "double-stranded")\n  (:end . 95) (:start . 80) (:id . 54))\n ((:tag . "NNS") (:stem . "oligonucleotide") (:form . "oligonucleotides")\n  (:end . 112) (:start . 96) (:id . 55))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 126)\n  (:start . 113) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 129) (:start . 127)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 145)\n  (:start . 134) (:id . 59))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 151)\n  (:start . 146) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 164)\n  (:start . 159) (:id . 63))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 168) (:start . 165)\n  (:id . 64))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 177)\n  (:start . 169) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 179) (:start . 178)\n  (:id . 66))\n ((:tag . "NN") (:stem . "wt") (:form . "wt") (:end . 181) (:start . 179)\n  (:id . 67))\n ((:tag . "NN") (:stem . "ltr-sp1") (:form . "LTR-Sp1") (:end . 189)\n  (:start . 182) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n  (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 193) (:start . 191)\n  (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 198) (:start . 194)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "oligonucleotide") (:form . "oligonucleotides")\n  (:end . 215) (:start . 199) (:id . 72))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 226)\n  (:start . 216) (:id . 73))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 234)\n  (:start . 227) (:id . 74))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 246)\n  (:start . 235) (:id . 75))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 252)\n  (:start . 247) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 255) (:start . 253)\n  (:id . 77))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 261)\n  (:start . 256) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 264) (:start . 262)\n  (:id . 79))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 272)\n  (:start . 265) (:id . 80))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 280)\n  (:start . 273) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 282) (:start . 281)\n  (:id . 82))\n ((:tag . "NN") (:stem . "mut") (:form . "mut") (:end . 285) (:start . 282)\n  (:id . 83))\n ((:tag . "NN") (:stem . "ltr-sp1") (:form . "LTR-Sp1") (:end . 293)\n  (:start . 286) (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 294) (:start . 293)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 295) (:start . 294)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s7.292) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502157@unknown@formal@none@1@S@One representative gel shift assay out of three is shown.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s7.293) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502158@unknown@formal@none@1@S@Reactions were performed either without nuclear extracts (free) or with lysates from cells transfected with an Sp1-encoding plasmid alone (Sp1) or in combination with an OGT-encoding plasmid (Sp1+OGT).@(((:tag . "NNS") (:stem . "reaction") (:form . "Reactions") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 31)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 39)\n  (:start . 32) (:id . 46))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 47)\n  (:start . 40) (:id . 47))\n ((:tag . "NNS") (:stem . "extract") (:form . "extracts") (:end . 56)\n  (:start . 48) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "free") (:form . "free") (:end . 62) (:start . 58)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "lysate") (:form . "lysates") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 90) (:start . 85)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 102)\n  (:start . 91) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 107) (:start . 103)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "sp1-encoding") (:form . "Sp1-encoding") (:end . 123)\n  (:start . 111) (:id . 60))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 131)\n  (:start . 124) (:id . 61))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 137)\n  (:start . 132) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 63))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 142) (:start . 139)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 65))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 146) (:start . 144)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 67))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 161)\n  (:start . 150) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 166) (:start . 162)\n  (:id . 69))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 169) (:start . 167)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "ogt-encoding") (:form . "OGT-encoding") (:end . 182)\n  (:start . 170) (:id . 71))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 190)\n  (:start . 183) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 192) (:start . 191)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Sp1+OGT") (:form . "Sp1+OGT") (:end . 199)\n  (:start . 192) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 200) (:start . 199)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s7.294) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502159@unknown@formal@none@1@S@The Sp1-oligonucleotide complex is indicated as Sp1-C.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "sp1-oligonucleotide")\n  (:form . "Sp1-oligonucleotide") (:end . 23) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 31)\n  (:start . 24) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 34) (:start . 32)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 44)\n  (:start . 35) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 47) (:start . 45)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sp1-C") (:form . "Sp1-C") (:end . 53) (:start . 48)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s7.295) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502160@unknown@formal@none@1@S@(C) Competition experiments were carried out with 10-, 20-, and 50-fold molar excesses of unlabeled wild-type (wt LTR-Sp1) or mutated (mut LTR-Sp1) oligonucleotides.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "competition") (:form . "Competition") (:end . 15)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 27)\n  (:start . 16) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "CD") (:stem . "10-") (:form . "10-") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "CD") (:stem . "20-") (:form . "20-") (:end . 58) (:start . 55)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "50-fold") (:form . "50-fold") (:end . 71)\n  (:start . 64) (:id . 56))\n ((:tag . "JJ") (:stem . "molar") (:form . "molar") (:end . 77) (:start . 72)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "excess") (:form . "excesses") (:end . 86)\n  (:start . 78) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "unlabeled") (:form . "unlabeled") (:end . 99)\n  (:start . 90) (:id . 60))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 109)\n  (:start . 100) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 62))\n ((:tag . "NN") (:stem . "wt") (:form . "wt") (:end . 113) (:start . 111)\n  (:id . 63))\n ((:tag . "NN") (:stem . "ltr-sp1") (:form . "LTR-Sp1") (:end . 121)\n  (:start . 114) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 65))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 125) (:start . 123)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 133)\n  (:start . 126) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 68))\n ((:tag . "NN") (:stem . "mut") (:form . "mut") (:end . 138) (:start . 135)\n  (:id . 69))\n ((:tag . "NN") (:stem . "ltr-sp1") (:form . "LTR-Sp1") (:end . 146)\n  (:start . 139) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "oligonucleotide") (:form . "oligonucleotides")\n  (:end . 164) (:start . 148) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s7.296) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502161@unknown@formal@none@1@S@(D) Supershift analyses were performed using 1 µg, 2 µg, or 5 µg anti-Sp1, anti-O-GlcNAc, or anti-OGT antibodies as well as 5 µg anti-IgG or anti-IgM as an isotype control.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Supershift") (:form . "Supershift") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 23)\n  (:start . 15) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 38)\n  (:start . 29) (:id . 48))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 52))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . "NN") (:stem . "µg") (:form . "µg") (:end . 55) (:start . 53)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 59) (:start . 57)\n  (:id . 56))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 61) (:start . 60)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "µg") (:form . "µg") (:end . 64) (:start . 62)\n  (:id . 58))\n ((:tag . "NN") (:stem . "anti-sp1") (:form . "anti-Sp1") (:end . 73)\n  (:start . 65) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 60))\n ((:tag . "NN") (:stem . "anti-o-glcnac") (:form . "anti-O-GlcNAc")\n  (:end . 88) (:start . 75) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 62))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 92) (:start . 90)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "anti-ogt") (:form . "anti-OGT") (:end . 101)\n  (:start . 93) (:id . 64))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 112)\n  (:start . 102) (:id . 65))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 115) (:start . 113)\n  (:id . 66))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 120) (:start . 116)\n  (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 123) (:start . 121)\n  (:id . 68))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 125) (:start . 124)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "µg") (:form . "µg") (:end . 128) (:start . 126)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "anti-igg") (:form . "anti-IgG") (:end . 137)\n  (:start . 129) (:id . 71))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 140) (:start . 138)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "anti-igm") (:form . "anti-IgM") (:end . 149)\n  (:start . 141) (:id . 73))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 152) (:start . 150)\n  (:id . 74))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 155) (:start . 153)\n  (:id . 75))\n ((:tag . "NN") (:stem . "isotype") (:form . "isotype") (:end . 163)\n  (:start . 156) (:id . 76))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 171)\n  (:start . 164) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s7.297) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502162@unknown@formal@none@1@S@To investigate whether OGT interferes with the DNA-binding affinity of Sp1, gel shift assays were carried out with templates corresponding to the Sp1-binding sites in the HIV-1 LTR promoter (Fig. 7B, wt LTR-Sp1).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "interfere") (:form . "interferes") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dna-binding") (:form . "DNA-binding") (:end . 58)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 67)\n  (:start . 59) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 74) (:start . 71)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 85) (:start . 80)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 92)\n  (:start . 86) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 97) (:start . 93)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 105)\n  (:start . 98) (:id . 58))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 114) (:start . 110)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 124)\n  (:start . 115) (:id . 61))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 138)\n  (:start . 125) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 141) (:start . 139)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 157)\n  (:start . 146) (:id . 65))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 163)\n  (:start . 158) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 166) (:start . 164)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 176)\n  (:start . 171) (:id . 69))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 180) (:start . 177)\n  (:id . 70))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 189)\n  (:start . 181) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 191) (:start . 190)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 195) (:start . 191)\n  (:id . 73))\n ((:tag . "NN") (:stem . "7b") (:form . "7B") (:end . 198) (:start . 196)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 199) (:start . 198)\n  (:id . 75))\n ((:tag . "NN") (:stem . "wt") (:form . "wt") (:end . 202) (:start . 200)\n  (:id . 76))\n ((:tag . "NN") (:stem . "ltr-sp1") (:form . "LTR-Sp1") (:end . 210)\n  (:start . 203) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 211) (:start . 210)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x7.298.1) (:span 15 22)))\n (:hscopes ((:id . :x7.298.1) (:span 15 74)))\n (:identifiers (:sid . :s7.298) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502163@unknown@formal@none@1@S@No decrease in the formation of protein-oligonucleotide complexes was detected upon overexpression of OGT (Fig. 7B, compare lane 3 and 5).@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "protein-oligonucleotide")\n  (:form . "protein-oligonucleotide") (:end . 55) (:start . 32) (:id . 48))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 65)\n  (:start . 56) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 69) (:start . 66)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 78)\n  (:start . 70) (:id . 51))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 83) (:start . 79)\n  (:id . 52))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 98) (:start . 84) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 105) (:start . 102)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 111) (:start . 107)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "7B") (:form . "7B") (:end . 114) (:start . 112)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 59))\n ((:tag . "NN") (:stem . "compare") (:form . "compare") (:end . 123)\n  (:start . 116) (:id . 60))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 128) (:start . 124)\n  (:id . 61))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.299) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502164@unknown@formal@none@1@S@As a specificity control, gel shift experiments were performed using templates containing mutated Sp1-binding sites (Fig. 7B, mut LTR-Sp1).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 16)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 47)\n  (:start . 36) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 62)\n  (:start . 53) (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 68) (:start . 63)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 89)\n  (:start . 79) (:id . 54))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 97)\n  (:start . 90) (:id . 55))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 109)\n  (:start . 98) (:id . 56))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 115)\n  (:start . 110) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 121) (:start . 117)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "7B") (:form . "7B") (:end . 124) (:start . 122)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "NN") (:stem . "mut") (:form . "mut") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "NN") (:stem . "ltr-sp1") (:form . "LTR-Sp1") (:end . 137)\n  (:start . 130) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.300) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502165@unknown@formal@none@1@S@The specific Sp1 complex (Fig. 7B, Sp1-C) was not detectable with these oligonucleotides (Fig. 7B, lanes 4 and 6).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "7b") (:form . "7B") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Sp1-C") (:form . "Sp1-C") (:end . 40) (:start . 35)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 41) (:start . 40)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 45) (:start . 42)\n  (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 49) (:start . 46)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 60)\n  (:start . 50) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 65) (:start . 61)\n  (:id . 55))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 71) (:start . 66)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "oligonucleotide") (:form . "oligonucleotides")\n  (:end . 88) (:start . 72) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 94) (:start . 90)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "7B") (:form . "7B") (:end . 97) (:start . 95)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 104) (:start . 99)\n  (:id . 62))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 106) (:start . 105)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 64))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 112) (:start . 111)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.301) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502166@unknown@formal@none@1@S@The specificity of Sp1-C was confirmed by competition experiments with increasing molar excess of unlabeled wt LTR-Sp1 (Fig. 7C, lanes 2 to 4) and mut LTR-Sp1 oligonucleotides (Fig. 7C, lanes 5 to 7).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sp1-C") (:form . "Sp1-C") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "competition") (:form . "competition") (:end . 53)\n  (:start . 42) (:id . 49))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 65)\n  (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 70) (:start . 66)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 81)\n  (:start . 71) (:id . 52))\n ((:tag . "JJ") (:stem . "molar") (:form . "molar") (:end . 87) (:start . 82)\n  (:id . 53))\n ((:tag . "NN") (:stem . "excess") (:form . "excess") (:end . 94)\n  (:start . 88) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "unlabeled") (:form . "unlabeled") (:end . 107)\n  (:start . 98) (:id . 56))\n ((:tag . "NN") (:stem . "wt") (:form . "wt") (:end . 110) (:start . 108)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "LTR-Sp1") (:form . "LTR-Sp1") (:end . 118)\n  (:start . 111) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 120) (:start . 119)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 124) (:start . 120)\n  (:id . 60))\n ((:tag . "NN") (:stem . "7c") (:form . "7C") (:end . 127) (:start . 125)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 134)\n  (:start . 129) (:id . 63))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n  (:id . 65))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 141) (:start . 140)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 146) (:start . 143)\n  (:id . 68))\n ((:tag . "NN") (:stem . "mut") (:form . "mut") (:end . 150) (:start . 147)\n  (:id . 69))\n ((:tag . "NN") (:stem . "ltr-sp1") (:form . "LTR-Sp1") (:end . 158)\n  (:start . 151) (:id . 70))\n ((:tag . "NNS") (:stem . "oligonucleotide") (:form . "oligonucleotides")\n  (:end . 175) (:start . 159) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 181) (:start . 177)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "7C") (:form . "7C") (:end . 184) (:start . 182)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 191)\n  (:start . 186) (:id . 76))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 193) (:start . 192)\n  (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 196) (:start . 194)\n  (:id . 78))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 198) (:start . 197)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s7.302) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502167@unknown@formal@none@1@S@In addition, the presence of O-GlcNAc-modified Sp1 in Sp1-C was confirmed by supershift analyses using increasing amounts of anti-Sp1 (Fig. 7D, lanes 2 to 4) and anti-O-GlcNAc (Fig. 7D, lanes 5 to 7) antibodies.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "o-glcnac-modified") (:form . "O-GlcNAc-modified")\n  (:end . 46) (:start . 29) (:id . 48))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sp1-C") (:form . "Sp1-C") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 73)\n  (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "supershift") (:form . "supershift") (:end . 87)\n  (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 96)\n  (:start . 88) (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 102) (:start . 97)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 113)\n  (:start . 103) (:id . 58))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 121)\n  (:start . 114) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 60))\n ((:tag . "NN") (:stem . "anti-sp1") (:form . "anti-Sp1") (:end . 133)\n  (:start . 125) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 139) (:start . 135)\n  (:id . 63))\n ((:tag . "NN") (:stem . "7d") (:form . "7D") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 149)\n  (:start . 144) (:id . 66))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 151) (:start . 150)\n  (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 154) (:start . 152)\n  (:id . 68))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 156) (:start . 155)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "anti-o-glcnac") (:form . "anti-O-GlcNAc")\n  (:end . 175) (:start . 162) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 181) (:start . 177)\n  (:id . 74))\n ((:tag . "NN") (:stem . "7d") (:form . "7D") (:end . 184) (:start . 182)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 191)\n  (:start . 186) (:id . 77))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 193) (:start . 192)\n  (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 196) (:start . 194)\n  (:id . 79))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 198) (:start . 197)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 210)\n  (:start . 200) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s7.303) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502168@unknown@formal@none@1@S@Both antibodies shifted Sp1-C almost completely (Fig. 7D, lanes 4 and 7), suggesting that most of the DNA-bound Sp1 is O-GlcNAcylated in OGT-overexpressing cells.@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "shift") (:form . "shifted") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "NNP") (:stem . "Sp1-C") (:form . "Sp1-C") (:end . 29) (:start . 24)\n  (:id . 45))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 36)\n  (:start . 30) (:id . 46))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 47)\n  (:start . 37) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 53) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "7D") (:form . "7D") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 84)\n  (:start . 74) (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 89) (:start . 85)\n  (:id . 59))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 94) (:start . 90)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "dna-bound") (:form . "DNA-bound") (:end . 111)\n  (:start . 102) (:id . 63))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 115) (:start . 112)\n  (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 118) (:start . 116)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "o-glcnacylate") (:form . "O-GlcNAcylated")\n  (:end . 133) (:start . 119) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "ogt-overexpressing") (:form . "OGT-overexpressing")\n  (:end . 155) (:start . 137) (:id . 68))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 161)\n  (:start . 156) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x7.304.1) (:span 74 84)))\n (:hscopes ((:id . :x7.304.1) (:span 74 161)))\n (:identifiers (:sid . :s7.304) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502169@unknown@formal@none@1@S@Addition of an anti-OGT antibody did not shift Sp1-C (Fig. 7D, lanes 8 to 10).@(((:tag . "NN") (:stem . "addition") (:form . "Addition") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "anti-ogt") (:form . "anti-OGT") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "VB") (:stem . "shift") (:form . "shift") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Sp1-C") (:form . "Sp1-C") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "7d") (:form . "7D") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "lane") (:form . "lanes") (:end . 68) (:start . 63)\n  (:id . 55))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 57))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 76) (:start . 74)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.305) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502170@unknown@formal@none@1@S@Isotype control anti-IgG (Fig. 7D, lane 11) and anti-IgM (Fig. 7D, lane 12) antibodies had no effect on Sp1-C.@(((:tag . "NN") (:stem . "isotype") (:form . "Isotype") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "anti-igg") (:form . "anti-IgG") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "7d") (:form . "7D") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "anti-igm") (:form . "anti-IgM") (:end . 56)\n  (:start . 48) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 62) (:start . 58)\n  (:id . 55))\n ((:tag . "NN") (:stem . "7d") (:form . "7D") (:end . 65) (:start . 63)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 57))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 71) (:start . 67)\n  (:id . 58))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 74) (:start . 72)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 86)\n  (:start . 76) (:id . 61))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 90) (:start . 87)\n  (:id . 62))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 93) (:start . 91)\n  (:id . 63))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 100)\n  (:start . 94) (:id . 64))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 103) (:start . 101)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Sp1-C") (:form . "Sp1-C") (:end . 109)\n  (:start . 104) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.306) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502171@unknown@formal@none@1@S@These results demonstrate that increased O-GlcNAcylation of Sp1 inhibits neither the ability of Sp1 to translocate into the nucleus nor the DNA-binding affinity of Sp1.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 40)\n  (:start . 31) (:id . 46))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 56) (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 63) (:start . 60)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 72)\n  (:start . 64) (:id . 50))\n ((:tag . "CC") (:stem . "neither") (:form . "neither") (:end . 80)\n  (:start . 73) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 52))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 92)\n  (:start . 85) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 99) (:start . 96)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 102) (:start . 100)\n  (:id . 56))\n ((:tag . "VB") (:stem . "translocate") (:form . "translocate") (:end . 114)\n  (:start . 103) (:id . 57))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 119) (:start . 115)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 59))\n ((:tag . "NN") (:stem . "nucleus") (:form . "nucleus") (:end . 131)\n  (:start . 124) (:id . 60))\n ((:tag . "CC") (:stem . "nor") (:form . "nor") (:end . 135) (:start . 132)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "dna-binding") (:form . "DNA-binding") (:end . 151)\n  (:start . 140) (:id . 63))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 160)\n  (:start . 152) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 167) (:start . 164)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.307) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502172@unknown@formal@none@1@S@To confirm that the inhibition of the HIV-1 LTR is dependent on Sp1 O-GlcNAcylation, a specific siRNA was used to deplete the expression of OGT.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "confirm") (:form . "confirm") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 30)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "dependent") (:form . "dependent") (:end . 60)\n  (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "O-GlcNAcylation") (:form . "O-GlcNAcylation")\n  (:end . 83) (:start . 68) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 95)\n  (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 110) (:start . 106)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n  (:id . 62))\n ((:tag . "VB") (:stem . "deplete") (:form . "deplete") (:end . 121)\n  (:start . 114) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 64))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 136)\n  (:start . 126) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 139) (:start . 137)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 143) (:start . 140)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.308) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502173@unknown@formal@none@1@S@The specificity of the siRNA was verified with an OGT rescue mutant (resOGT)-encoding plasmid, which contains six silent nucleotide exchanges in the siRNA-binding site (Fig. 8A).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "siRNA") (:form . "siRNA") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 60)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 67)\n  (:start . 61) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "resOGT)-encoding") (:form . "resOGT)-encoding")\n  (:end . 85) (:start . 69) (:id . 55))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 93)\n  (:start . 86) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 100)\n  (:start . 95) (:id . 58))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 109)\n  (:start . 101) (:id . 59))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 113) (:start . 110)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "silent") (:form . "silent") (:end . 120)\n  (:start . 114) (:id . 61))\n ((:tag . "NN") (:stem . "nucleotide") (:form . "nucleotide") (:end . 131)\n  (:start . 121) (:id . 62))\n ((:tag . "NNS") (:stem . "exchange") (:form . "exchanges") (:end . 141)\n  (:start . 132) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "sirna-binding") (:form . "siRNA-binding")\n  (:end . 162) (:start . 149) (:id . 66))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 167) (:start . 163)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 173) (:start . 169)\n  (:id . 69))\n ((:tag . "NN") (:stem . "8a") (:form . "8A") (:end . 176) (:start . 174)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 177) (:start . 176)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.309) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502174@unknown@formal@none@1@S@Western blot analyses proved that overexpression of wild-type OGT (wtOGT) was inhibited in HEK 293T cells cotransfected with the wtOGT-specific siRNA (Fig. 8B, top panel, lanes 2 and 4), whereas expression of resOGT was not affected (Fig. 8B, top panel, lanes 3 and 5).@(((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "prove") (:form . "proved") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 48) (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 48))\n ((:tag . 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5502175@unknown@formal@none@1@S@Staining of O-GlcNAc-modified proteins served as an additional control for the functionality of resOGT (Fig. 8B, middle panel).@(((:tag . "NN") (:stem . "staining") (:form . "Staining") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "o-glcnac-modified") (:form . "O-GlcNAc-modified")\n  (:end . 29) (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 38)\n  (:start . 30) (:id . 45))\n ((:tag . "VBD") (:stem . "serve") (:form . "served") (:end . 45)\n  (:start . 39) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 48) (:start . 46)\n  (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 51) (:start . 49)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 62)\n  (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 70)\n  (:start . 63) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 74) (:start . 71)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 52))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 92) (:start . 79) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 54))\n ((:tag . "NN") (:stem . "resogt") (:form . "resOGT") (:end . 102)\n  (:start . 96) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 108) (:start . 104)\n  (:id . 57))\n ((:tag . "NN") (:stem . "8b") (:form . "8B") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "middle") (:form . "middle") (:end . 119)\n  (:start . 113) (:id . 60))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 125)\n  (:start . 120) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.311) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502176@unknown@formal@none@1@S@Sp1 O-GlcNAcylation is necessary for the inhibition of the HIV-1 LTR.@(((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "O-GlcNAcylation") (:form . "O-GlcNAcylation")\n  (:end . 19) (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 51)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 64) (:start . 59)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.312) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502177@unknown@formal@none@1@S@(A) Generation of a plasmid encoding an OGT rescue mutant in order to escape silencing by the siRNA targeting wild-type OGT: six silent mutations (bold) were introduced into the siRNA-binding sequence of OGT.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Generation") (:form . "Generation") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n  (:id . 47))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 27)\n  (:start . 20) (:id . 48))\n ((:tag . "VBG") (:stem . "encode") (:form . "encoding") (:end . 36)\n  (:start . 28) (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 50)\n  (:start . 44) (:id . 52))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 57)\n  (:start . 51) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 54))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 66) (:start . 61)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 56))\n ((:tag . "VB") (:stem . "escape") (:form . "escape") (:end . 76)\n  (:start . 70) (:id . 57))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 86)\n  (:start . 77) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 89) (:start . 87)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 60))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 99) (:start . 94)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 109)\n  (:start . 100) (:id . 62))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 119)\n  (:start . 110) (:id . 63))\n ((:tag . "NN") (:stem . "ogt") (:form . "OGT") (:end . 123) (:start . 120)\n  (:id . 64))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 124) (:start . 123)\n  (:id . 65))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 128) (:start . 125)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "silent") (:form . "silent") (:end . 135)\n  (:start . 129) (:id . 67))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 145)\n  (:start . 136) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . "NN") (:stem . "bold") (:form . "bold") (:end . 151) (:start . 147)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 157) (:start . 153)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "introduce") (:form . "introduced") (:end . 168)\n  (:start . 158) (:id . 73))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 173) (:start . 169)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "sirna-binding") (:form . "siRNA-binding")\n  (:end . 191) (:start . 178) (:id . 76))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 200)\n  (:start . 192) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 203) (:start . 201)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 207) (:start . 204)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s7.313) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502178@unknown@formal@none@1@S@(B) Western blot analyses of wild-type (wt) and rescue mutant (res) OGT were performed after transfection with the siRNA specifically targeting wtOGT.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "western") (:form . "Western") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 16) (:start . 12)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 25)\n  (:start . 17) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 38)\n  (:start . 29) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "NN") (:stem . "wt") (:form . "wt") (:end . 42) (:start . 40)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 53))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 54)\n  (:start . 48) (:id . 54))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 61)\n  (:start . 55) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "re") (:form . "res") (:end . 66) (:start . 63)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 71) (:start . 68)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 76) (:start . 72)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 86)\n  (:start . 77) (:id . 61))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 92) (:start . 87)\n  (:id . 62))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 105)\n  (:start . 93) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 110) (:start . 106)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 65))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 120)\n  (:start . 115) (:id . 66))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 133)\n  (:start . 121) (:id . 67))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 143)\n  (:start . 134) (:id . 68))\n ((:tag . "NN") (:stem . "wtogt") (:form . "wtOGT") (:end . 149)\n  (:start . 144) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s7.314) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502179@unknown@formal@none@1@S@Detection of O-GlcNAcylation levels was used as a control for the functionality of the rescue mutant.@(((:tag . "NN") (:stem . "detection") (:form . "Detection") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 28) (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 35)\n  (:start . 29) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 39) (:start . 36)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 44) (:start . 40)\n  (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 79) (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 93)\n  (:start . 87) (:id . 56))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 100)\n  (:start . 94) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.315) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502180@unknown@formal@none@1@S@Immunodetection of GAPDH demonstrates that equal amounts of protein were loaded.@(((:tag . "NNP") (:stem . "Immunodetection") (:form . "Immunodetection")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 24) (:start . 19)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "demonstrate") (:form . "demonstrates") (:end . 37)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 42) (:start . 38)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 48) (:start . 43)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "amount") (:form . "amounts") (:end . 56)\n  (:start . 49) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 67)\n  (:start . 60) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 72) (:start . 68)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "load") (:form . "loaded") (:end . 79) (:start . 73)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.316) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502181@unknown@formal@none@1@S@(C) HEK 293T cells were transfected with the reporter construct LTR-Sp1wt along with plasmids encoding Sp1 and OGT (wild type or rescue mutant).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "HEK") (:form . "HEK") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "293t") (:form . "293T") (:end . 12) (:start . 8)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 18) (:start . 13)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 35)\n  (:start . 24) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 40) (:start . 36)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 51))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 53)\n  (:start . 45) (:id . 52))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 63)\n  (:start . 54) (:id . 53))\n ((:tag . "NN") (:stem . "ltr-sp1wt") (:form . "LTR-Sp1wt") (:end . 73)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 79) (:start . 74)\n  (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "plasmid") (:form . "plasmids") (:end . 93)\n  (:start . 85) (:id . 57))\n ((:tag . "VBG") (:stem . "encode") (:form . "encoding") (:end . 102)\n  (:start . 94) (:id . 58))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 114) (:start . 111)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 120) (:start . 116)\n  (:id . 63))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 125) (:start . 121)\n  (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 128) (:start . 126)\n  (:id . 65))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 135)\n  (:start . 129) (:id . 66))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 142)\n  (:start . 136) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s7.317) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502182@unknown@formal@none@1@S@Total DNA amount was adjusted with pcDNA4.@(((:tag . "JJ") (:stem . "total") (:form . "Total") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "adjust") (:form . "adjusted") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "pcdna4") (:form . "pcDNA4") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s7.318) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502183@unknown@formal@none@1@S@Control siRNA or siRNA targeting wtOGT (10 nM) was cotransfected, and the luciferase activity was measured.@(((:tag . "NNP") (:stem . "Control") (:form . "Control") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "siRNA") (:form . "siRNA") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "siRNA") (:form . "siRNA") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "wtogt") (:form . "wtOGT") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "nM") (:form . "nM") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 50) (:start . 47)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "cotransfecte") (:form . "cotransfected")\n  (:end . 64) (:start . 51) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 56))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 84)\n  (:start . 74) (:id . 57))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 93)\n  (:start . 85) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 106)\n  (:start . 98) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.319) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502184@unknown@formal@none@1@S@The values were adjusted to the total amount of protein and indicate the means ± standard deviations from triplicate determinations.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "adjust") (:form . "adjusted") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "mean") (:form . "means") (:end . 78) (:start . 73)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "±") (:form . "±") (:end . 80) (:start . 79)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 89)\n  (:start . 81) (:id . 57))\n ((:tag . "NNS") (:stem . "deviation") (:form . "deviations") (:end . 100)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "triplicate") (:form . "triplicate") (:end . 116)\n  (:start . 106) (:id . 60))\n ((:tag . "NNS") (:stem . "determination") (:form . "determinations")\n  (:end . 131) (:start . 117) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s7.320) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502185@unknown@formal@none@1@S@The results are presented in terms of percentages of control (Sp1-induced LTR activity).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "percentage") (:form . "percentages") (:end . 49)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "sp1-induced") (:form . "Sp1-induced") (:end . 73)\n  (:start . 62) (:id . 53))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 77) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 86)\n  (:start . 78) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.321) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502186@unknown@formal@none@1@S@Applying these tools to test the effect of Sp1 O-GlcNAcylation on HIV-1 LTR, we showed that the promoter activity (Fig. 8C, bar 4) was strongly reduced after overexpression of wtOGT or resOGT (Fig. 8C, bars 5 and 6).@(((:tag . "VBG") (:stem . "apply") (:form . "Applying") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 62) (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 86) (:start . 80)\n  (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 91) (:start . 87)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 104)\n  (:start . 96) (:id . 60))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 113)\n  (:start . 105) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 119) (:start . 115)\n  (:id . 63))\n ((:tag . "NN") (:stem . "8c") (:form . "8C") (:end . 122) (:start . 120)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 65))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 127) (:start . 124)\n  (:id . 66))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 129) (:start . 128)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 134) (:start . 131)\n  (:id . 69))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 143)\n  (:start . 135) (:id . 70))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 151)\n  (:start . 144) (:id . 71))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 157)\n  (:start . 152) (:id . 72))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 172) (:start . 158) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 175) (:start . 173)\n  (:id . 74))\n ((:tag . "NN") (:stem . "wtogt") (:form . "wtOGT") (:end . 181)\n  (:start . 176) (:id . 75))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 184) (:start . 182)\n  (:id . 76))\n ((:tag . "NN") (:stem . "resogt") (:form . "resOGT") (:end . 191)\n  (:start . 185) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 193) (:start . 192)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 197) (:start . 193)\n  (:id . 79))\n ((:tag . "NN") (:stem . "8c") (:form . "8C") (:end . 200) (:start . 198)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 201) (:start . 200)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 206) (:start . 202)\n  (:id . 82))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 208) (:start . 207)\n  (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 212) (:start . 209)\n  (:id . 84))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 214) (:start . 213)\n  (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 215) (:start . 214)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s7.322) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502187@unknown@formal@none@1@S@Cotransfection of a control siRNA targeting GAPDH had no impact on the HIV-1 LTR activity (Fig. 8C, bars 7 and 8).@(((:tag . "NN") (:stem . "cotransfection") (:form . "Cotransfection")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 49) (:start . 44)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "impact") (:form . "impact") (:end . 63)\n  (:start . 57) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 76) (:start . 71)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "8c") (:form . "8C") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 104) (:start . 100)\n  (:id . 61))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 106) (:start . 105)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.323) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502188@unknown@formal@none@1@S@Knockdown of wtOGT restored the HIV-1 LTR activity (Fig. 8C, bar 9), whereas resOGT escaped silencing and was still able to suppress the promoter activity (Fig. 8C, bar 10).@(((:tag . "NNP") (:stem . "Knockdown") (:form . "Knockdown") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "wtogt") (:form . "wtOGT") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "restore") (:form . "restored") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 50)\n  (:start . 42) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "8c") (:form . "8C") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 57))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 76)\n  (:start . 69) (:id . 58))\n ((:tag . "NN") (:stem . "resogt") (:form . "resOGT") (:end . 83)\n  (:start . 77) (:id . 59))\n ((:tag . "VBD") (:stem . "escape") (:form . "escaped") (:end . 91)\n  (:start . 84) (:id . 60))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 101)\n  (:start . 92) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 109) (:start . 106)\n  (:id . 63))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 115)\n  (:start . 110) (:id . 64))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 120) (:start . 116)\n  (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 123) (:start . 121)\n  (:id . 66))\n ((:tag . "VB") (:stem . "suppress") (:form . "suppress") (:end . 132)\n  (:start . 124) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 68))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 145)\n  (:start . 137) (:id . 69))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 154)\n  (:start . 146) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 160) (:start . 156)\n  (:id . 72))\n ((:tag . "NN") (:stem . "8c") (:form . "8C") (:end . 163) (:start . 161)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 74))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 168) (:start . 165)\n  (:id . 75))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 171) (:start . 169)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s7.324) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502189@unknown@formal@none@1@S@These findings demonstrate that O-GlcNAcylation of Sp1 is required for the inhibition of the HIV-1 LTR promoter by OGT.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 26)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 31) (:start . 27)\n  (:id . 45))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 47) (:start . 32) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 54) (:start . 51)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 66)\n  (:start . 58) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 70) (:start . 67)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 52))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 85)\n  (:start . 75) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 111)\n  (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 114) (:start . 112)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 118) (:start . 115)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s7.325) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502190@unknown@formal@none@1@S@In all previous experiments the O-GlcNAcylation level was increased after infection with HIV-1.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 15)\n  (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 27)\n  (:start . 16) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 47) (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 53) (:start . 48)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 57) (:start . 54)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 67)\n  (:start . 58) (:id . 50))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 73) (:start . 68)\n  (:id . 51))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 83)\n  (:start . 74) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 88) (:start . 84)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 94) (:start . 89)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.326) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502191@unknown@formal@none@1@S@Thus, we aimed to investigate whether increased OGT expression prior to infection may amplify the inhibitory effects on HIV-1 transcription in lymphocytes.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "aim") (:form . "aimed") (:end . 14) (:start . 9)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 29)\n  (:start . 18) (:id . 47))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 37)\n  (:start . 30) (:id . 48))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "ogt") (:form . "OGT") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 62)\n  (:start . 52) (:id . 51))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 68) (:start . 63)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 81)\n  (:start . 72) (:id . 54))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "VB") (:stem . "amplify") (:form . "amplify") (:end . 93)\n  (:start . 86) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 108)\n  (:start . 98) (:id . 58))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 116)\n  (:start . 109) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 119) (:start . 117)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 125)\n  (:start . 120) (:id . 61))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 139) (:start . 126) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 142) (:start . 140)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 154)\n  (:start . 143) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x7.327.1) (:span 82 85)) ((:id . :x7.327.2) (:span 30 37)))\n (:hscopes ((:id . :x7.327.1) (:span 82 154))\n  ((:id . :x7.327.2) (:span 30 154)))\n (:identifiers (:sid . :s7.327) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502192@unknown@formal@none@1@S@Jurkat cells were stably transfected with OGT or, as a control, with d2EGFP.@(((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "stably") (:form . "stably") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 36)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 62)\n  (:start . 55) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "d2EGFP") (:form . "d2EGFP") (:end . 75)\n  (:start . 69) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.328) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502193@unknown@formal@none@1@S@Expression of recombinant OGT in selected clones was confirmed by RT-PCR (Fig. 9A).@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "recombinant") (:form . "recombinant") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "ogt") (:form . "OGT") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 48)\n  (:start . 42) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 62)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 72)\n  (:start . 66) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "9a") (:form . "9A") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.329) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502194@unknown@formal@none@1@S@The stably transfected cells were infected with VSV-G env pseudotyped HIV-1NL4-3LucR-E-, and HIV-1 LTR activity was determined by luciferase assay.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "stably") (:form . "stably") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "infect") (:form . "infected") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "VSV-G") (:form . "VSV-G") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "env") (:form . "env") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "pseudotype") (:form . "pseudotyped") (:end . 69)\n  (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "hiv-1nl4-3lucr-e-") (:form . "HIV-1NL4-3LucR-E-")\n  (:end . 87) (:start . 70) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 98) (:start . 93)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 102) (:start . 99)\n  (:id . 56))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 111)\n  (:start . 103) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 115) (:start . 112)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 126)\n  (:start . 116) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 129) (:start . 127)\n  (:id . 60))\n ((:tag . "NN") (:stem . "luciferase") (:form . "luciferase") (:end . 140)\n  (:start . 130) (:id . 61))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 146)\n  (:start . 141) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.330) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502195@unknown@formal@none@1@S@Of note, HIV-1 LTR activity was 40-fold lower in both OGT-overexpressing Jurkat cell clones than in control cells expressing d2EGFP (Fig. 9B).@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "note") (:form . "note") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 14) (:start . 9)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 27)\n  (:start . 19) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "RB") (:stem . "40-fold") (:form . "40-fold") (:end . 39)\n  (:start . 32) (:id . 49))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "ogt-overexpressing") (:form . "OGT-overexpressing")\n  (:end . 72) (:start . 54) (:id . 53))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 79)\n  (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 91)\n  (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 107)\n  (:start . 100) (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 113)\n  (:start . 108) (:id . 60))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 124)\n  (:start . 114) (:id . 61))\n ((:tag . "NNP") (:stem . "d2EGFP") (:form . "d2EGFP") (:end . 131)\n  (:start . 125) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 137) (:start . 133)\n  (:id . 64))\n ((:tag . "NN") (:stem . "9b") (:form . "9B") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.331) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502196@unknown@formal@none@1@S@These results demonstrate that OGT is a potent inhibitor of HIV-1 LTR activity.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "potent") (:form . "potent") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "inhibitor") (:form . "inhibitor") (:end . 56)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 65) (:start . 60)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s7.332) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502197@unknown@formal@none@1@S@OGT overexpression prior to infection amplifies the inhibitory effect on HIV-1 replication.@(((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 24) (:start . 19)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "VBZ") (:stem . "amplify") (:form . "amplifies") (:end . 47)\n  (:start . 38) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 62)\n  (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 69)\n  (:start . 63) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 78) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 90)\n  (:start . 79) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.333) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502198@unknown@formal@none@1@S@(A) Jurkat cells were stably transfected with plasmids encoding either d2EGFP or OGT.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 10)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 16) (:start . 11)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 21) (:start . 17)\n  (:id . 47))\n ((:tag . "RB") (:stem . "stably") (:form . "stably") (:end . 28)\n  (:start . 22) (:id . 48))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 40)\n  (:start . 29) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "plasmid") (:form . "plasmids") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . "VBG") (:stem . "encode") (:form . "encoding") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 70)\n  (:start . 64) (:id . 53))\n ((:tag . "NNP") (:stem . "d2EGFP") (:form . "d2EGFP") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.334) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502199@unknown@formal@none@1@S@Expression of recombinantly expressed OGT mRNA was confirmed by RT-PCR (upper panel) using specific primers.@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "RB") (:stem . "recombinantly") (:form . "recombinantly")\n  (:end . 27) (:start . 14) (:id . 44))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 37)\n  (:start . 28) (:id . 45))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 41) (:start . 38)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 46) (:start . 42)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 70)\n  (:start . 64) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 77) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 83) (:start . 78)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 90) (:start . 85)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 99)\n  (:start . 91) (:id . 57))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 107)\n  (:start . 100) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.335) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502200@unknown@formal@none@1@S@Amplification of GAPDH served as a loading control (lower panel).@(((:tag . "NNP") (:stem . "Amplification") (:form . "Amplification")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "GAPDH") (:form . "GAPDH") (:end . 22) (:start . 17)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "serve") (:form . "served") (:end . 29)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "loading") (:form . "loading") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s7.336) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502201@unknown@formal@none@1@S@Cellular cDNA was subjected to the amplification reactions in increasing dilutions: undiluted (1), 1:5, and 1:10.@(((:tag . "JJ") (:stem . "cellular") (:form . "Cellular") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "cDNA") (:form . "cDNA") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "subject") (:form . "subjected") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 48) (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "reaction") (:form . "reactions") (:end . 58)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 72)\n  (:start . 62) (:id . 51))\n ((:tag . "NNS") (:stem . "dilution") (:form . "dilutions") (:end . 82)\n  (:start . 73) (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 83) (:start . 82)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "undiluted") (:form . "undiluted") (:end . 93)\n  (:start . 84) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 55))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1:5") (:form . "1:5") (:end . 102) (:start . 99)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 61))\n ((:tag . "CD") (:stem . "1:10") (:form . "1:10") (:end . 112) (:start . 108)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.337) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502202@unknown@formal@none@1@S@Control reactions were carried out in the absence of reverse transcriptase (-RT) with undiluted cDNA template.@(((:tag . "NNP") (:stem . "Control") (:form . "Control") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "reaction") (:form . "reactions") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "transcriptase") (:form . "transcriptase")\n  (:end . 74) (:start . 61) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "-RT") (:form . "-RT") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "undiluted") (:form . "undiluted") (:end . 95)\n  (:start . 86) (:id . 57))\n ((:tag . "NN") (:stem . "cdna") (:form . "cDNA") (:end . 100) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 109)\n  (:start . 101) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s7.338) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502203@unknown@formal@none@1@S@(B) Jurkat cells stably expressing d2EGFP or OGT were infected with VSV-G env pseudotyped HIV-1NL4-3LucR-E-.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Jurkat") (:form . "Jurkat") (:end . 10)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 16) (:start . 11)\n  (:id . 46))\n ((:tag . "RB") (:stem . "stably") (:form . "stably") (:end . 23)\n  (:start . 17) (:id . 47))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 34)\n  (:start . 24) (:id . 48))\n ((:tag . "NNP") (:stem . "d2EGFP") (:form . "d2EGFP") (:end . 41)\n  (:start . 35) (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "infect") (:form . "infected") (:end . 62)\n  (:start . 54) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "VSV-G") (:form . "VSV-G") (:end . 73) (:start . 68)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "env") (:form . "env") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "pseudotype") (:form . "pseudotyped") (:end . 89)\n  (:start . 78) (:id . 57))\n ((:tag . "NN") (:stem . "hiv-1nl4-3lucr-e-") (:form . "HIV-1NL4-3LucR-E-")\n  (:end . 107) (:start . 90) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.339) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502204@unknown@formal@none@1@S@Luciferase activity was measured 48 h after infection.@(((:tag . "NNP") (:stem . "Luciferase") (:form . "Luciferase") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 23) (:start . 20)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s7.340) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502205@unknown@formal@none@1@S@DISCUSSION@(((:tag . "NN") (:stem . "discussion") (:form . "DISCUSSION") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s7.341) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5502206@unknown@formal@none@1@S@Regulation of gene expression by nutrients like glucose and glucosamine is well established (20, 37, 52, 74) and demonstrates that cellular transcription adapts to environmental and metabolic changes.@(((:tag . "NN") (:stem . "regulation") (:form . "Regulation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "nutrient") (:form . "nutrients") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "glucose") (:form . "glucose") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "glucosamine") (:form . "glucosamine") (:end . 71)\n  (:start . 60) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 79) (:start . 75)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "establish") (:form . "established") (:end . 91)\n  (:start . 80) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n  (:id . 55))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 95) (:start . 93)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . "CD") (:stem . "52") (:form . "52") (:end . 103) (:start . 101)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 61))\n ((:tag . "CD") (:stem . "74") (:form . "74") (:end . 107) (:start . 105)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 64))\n ((:tag . "VBZ") (:stem . "demonstrate") (:form . "demonstrates") (:end . 125)\n  (:start . 113) (:id . 65))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 130) (:start . 126)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 139)\n  (:start . 131) (:id . 67))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 153) (:start . 140) (:id . 68))\n ((:tag . "NNS") (:stem . "adapt") (:form . "adapts") (:end . 160)\n  (:start . 154) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 163) (:start . 161)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "environmental") (:form . "environmental")\n  (:end . 177) (:start . 164) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 181) (:start . 178)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "metabolic") (:form . "metabolic") (:end . 191)\n  (:start . 182) (:id . 73))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 199)\n  (:start . 192) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s7.342) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502207@unknown@formal@none@1@S@Viruses critically depend on the host cell metabolism (29).@(((:tag . "NNS") (:stem . "virus") (:form . "Viruses") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "critically") (:form . "critically") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "depend") (:form . "depend") (:end . 25)\n  (:start . 19) (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "metabolism") (:form . "metabolism") (:end . 53)\n  (:start . 43) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s7.343) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502208@unknown@formal@none@1@S@This directed us to investigate the impact of the monosaccharidic metabolite O-GlcNAc on HIV-1 gene expression.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "direct") (:form . "directed") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "impact") (:form . "impact") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "monosaccharidic") (:form . "monosaccharidic")\n  (:end . 65) (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "metabolite") (:form . "metabolite") (:end . 76)\n  (:start . 66) (:id . 52))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 85)\n  (:start . 77) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 94) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 110)\n  (:start . 100) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s7.344) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502209@unknown@formal@none@1@S@We showed that increased O-GlcNAc levels inhibit HIV-1 transcription in human T-cell lines as well as in human primary CD4+ T lymphocytes.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "VBP") (:stem . "inhibit") (:form . "inhibit") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 54) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 68) (:start . 55) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 77) (:start . 72)\n  (:id . 52))\n ((:tag . "NN") (:stem . "t-cell") (:form . "T-cell") (:end . 84)\n  (:start . 78) (:id . 53))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 90) (:start . 85)\n  (:id . 54))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 93) (:start . 91)\n  (:id . 55))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 98) (:start . 94)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 101) (:start . 99)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 110)\n  (:start . 105) (:id . 59))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 118)\n  (:start . 111) (:id . 60))\n ((:tag . "JJ") (:stem . "cd4+") (:form . "CD4+") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 125) (:start . 124)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 137)\n  (:start . 126) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.345) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502210@unknown@formal@none@1@S@This effect appeared to be mediated by the transcription factor Sp1, as supported by several lines of experimental evidence.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 56) (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 63)\n  (:start . 57) (:id . 51))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 81)\n  (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 98) (:start . 93)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 114)\n  (:start . 102) (:id . 60))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 123)\n  (:start . 115) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x7.346.1) (:span 12 20)))\n (:hscopes ((:id . :x7.346.1) (:span 0 123)))\n (:identifiers (:sid . :s7.346) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502211@unknown@formal@none@1@S@First, we demonstrated that O- GlcNAc-mediated inhibition of HIV-1 transcription required the presence of Sp1-binding sites in the HIV-1 LTR promoter.@(((:tag . "RB") (:stem . "first") (:form . "First") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 22)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "o-") (:form . "O-") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "glcnac-mediated") (:form . "GlcNAc-mediated")\n  (:end . 46) (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 66) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 80) (:start . 67) (:id . 52))\n ((:tag . "VBD") (:stem . "require") (:form . "required") (:end . 89)\n  (:start . 81) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 54))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 102)\n  (:start . 94) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 117)\n  (:start . 106) (:id . 57))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 123)\n  (:start . 118) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 126) (:start . 124)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 136)\n  (:start . 131) (:id . 61))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 140) (:start . 137)\n  (:id . 62))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 149)\n  (:start . 141) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.347) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502212@unknown@formal@none@1@S@The Sp1-binding sites are well conserved throughout the lentiviral HIV-1 LTRs (18), and mutation of one or more Sp1-binding sites in the basal HIV-1 LTR promoter leads to a strong delay in replication in human peripheral blood lymphocytes and in T-cell lines (45, 58).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 40)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 51)\n  (:start . 41) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "lentiviral") (:form . "lentiviral") (:end . 66)\n  (:start . 56) (:id . 50))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 72) (:start . 67)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTRs") (:end . 77) (:start . 73)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 53))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 96)\n  (:start . 88) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 59))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 111) (:start . 107)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 123)\n  (:start . 112) (:id . 63))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 129)\n  (:start . 124) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "basal") (:form . "basal") (:end . 142)\n  (:start . 137) (:id . 67))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 148)\n  (:start . 143) (:id . 68))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 152) (:start . 149)\n  (:id . 69))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 161)\n  (:start . 153) (:id . 70))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 167)\n  (:start . 162) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 170) (:start . 168)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 172) (:start . 171)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 179)\n  (:start . 173) (:id . 74))\n ((:tag . "NN") (:stem . "delay") (:form . "delay") (:end . 185)\n  (:start . 180) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 188) (:start . 186)\n  (:id . 76))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 200)\n  (:start . 189) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 203) (:start . 201)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 209)\n  (:start . 204) (:id . 79))\n ((:tag . "JJ") (:stem . "peripheral") (:form . "peripheral") (:end . 220)\n  (:start . 210) (:id . 80))\n ((:tag . "NN") (:stem . "blood") (:form . "blood") (:end . 226)\n  (:start . 221) (:id . 81))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 238)\n  (:start . 227) (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 242) (:start . 239)\n  (:id . 83))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 245) (:start . 243)\n  (:id . 84))\n ((:tag . "NN") (:stem . "t-cell") (:form . "T-cell") (:end . 252)\n  (:start . 246) (:id . 85))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 258)\n  (:start . 253) (:id . 86))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 260) (:start . 259)\n  (:id . 87))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 262) (:start . 260)\n  (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 263) (:start . 262)\n  (:id . 89))\n ((:tag . "CD") (:stem . "58") (:form . "58") (:end . 266) (:start . 264)\n  (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 267) (:start . 266)\n  (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 268) (:start . 267)\n  (:id . 92)))@@@1@51@((:identifiers (:sid . :s7.348) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502213@unknown@formal@none@1@S@This is also reflected in our observations that mutation of the Sp1-binding sites decreases HIV-1 LTR activity in transiently and stably transfected cells.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "reflect") (:form . "reflected") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 42)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 75)\n  (:start . 64) (:id . 53))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "decrease") (:form . "decreases") (:end . 91)\n  (:start . 82) (:id . 55))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 97) (:start . 92)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 101) (:start . 98)\n  (:id . 57))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 110)\n  (:start . 102) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n  (:id . 59))\n ((:tag . "RB") (:stem . "transiently") (:form . "transiently") (:end . 125)\n  (:start . 114) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 61))\n ((:tag . "RB") (:stem . "stably") (:form . "stably") (:end . 136)\n  (:start . 130) (:id . 62))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 148)\n  (:start . 137) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 154)\n  (:start . 149) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s7.349) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502214@unknown@formal@none@1@S@But although Sp1-mutated HIV-1 LTR activity was still measurable and inducible, no significant O-GlcNAc-mediated inhibition of promoter activity was observed.@(((:tag . "CC") (:stem . "but") (:form . "But") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "sp1-mutated") (:form . "Sp1-mutated") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 30) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "measurable") (:form . "measurable") (:end . 64)\n  (:start . 54) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "inducible") (:form . "inducible") (:end . 78)\n  (:start . 69) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 53))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 94)\n  (:start . 83) (:id . 55))\n ((:tag . "JJ") (:stem . "o-glcnac-mediated") (:form . "O-GlcNAc-mediated")\n  (:end . 112) (:start . 95) (:id . 56))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 123)\n  (:start . 113) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 58))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 135)\n  (:start . 127) (:id . 59))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 144)\n  (:start . 136) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 148) (:start . 145)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 157)\n  (:start . 149) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s7.350) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502215@unknown@formal@none@1@S@Second, the presence of the Sp1 protein was crucial for the inhibitory effect of O-GlcNAc on the HIV-1 LTR.@(((:tag . "RB") (:stem . "second") (:form . "Second") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 39)\n  (:start . 32) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 43) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 51)\n  (:start . 44) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 70)\n  (:start . 60) (:id . 54))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 77)\n  (:start . 71) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 89)\n  (:start . 81) (:id . 57))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 102)\n  (:start . 97) (:id . 60))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s7.351) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502216@unknown@formal@none@1@S@Inhibition of Sp1 expression with siRNA completely abolished OGT-mediated inhibition of HIV-1 LTR activity.@(((:tag . "NNP") (:stem . "Inhibition") (:form . "Inhibition") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "siRNA") (:form . "siRNA") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 50)\n  (:start . 40) (:id . 48))\n ((:tag . "VBD") (:stem . "abolish") (:form . "abolished") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . "JJ") (:stem . "ogt-mediated") (:form . "OGT-mediated") (:end . 73)\n  (:start . 61) (:id . 50))\n ((:tag . "NN") (:stem . "inhibition") (:form . "inhibition") (:end . 84)\n  (:start . 74) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 93) (:start . 88)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 97) (:start . 94)\n  (:id . 54))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 106)\n  (:start . 98) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s7.352) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502217@unknown@formal@none@1@S@Interestingly, although Sp1 is implicated in the activation of a large number of genes, depletion of the ubiquitous transcription factor did not induce cytotoxicity.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 59)\n  (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 86) (:start . 81)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "depletion") (:form . "depletion") (:end . 97)\n  (:start . 88) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "ubiquitous") (:form . "ubiquitous") (:end . 115)\n  (:start . 105) (:id . 61))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 129) (:start . 116) (:id . 62))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 136)\n  (:start . 130) (:id . 63))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 140) (:start . 137)\n  (:id . 64))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 144) (:start . 141)\n  (:id . 65))\n ((:tag . "VB") (:stem . "induce") (:form . "induce") (:end . 151)\n  (:start . 145) (:id . 66))\n ((:tag . "NN") (:stem . "cytotoxicity") (:form . "cytotoxicity") (:end . 164)\n  (:start . 152) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s7.353) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502218@unknown@formal@none@1@S@This is in agreement with the observation of Philipsen and coworkers, who disrupted the mouse Sp1 gene and found that Sp1-deficient embryonic stem cells were viable and showed normal growth characteristics (50).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 20)\n  (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 41)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Philipsen") (:form . "Philipsen") (:end . 54)\n  (:start . 45) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "coworker") (:form . "coworkers") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "WP") (:stem . "who") (:form . "who") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "disrupt") (:form . "disrupted") (:end . 83)\n  (:start . 74) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 112)\n  (:start . 107) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 117) (:start . 113)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "sp1-deficient") (:form . "Sp1-deficient")\n  (:end . 131) (:start . 118) (:id . 63))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 141)\n  (:start . 132) (:id . 64))\n ((:tag . "NN") (:stem . "stem") (:form . "stem") (:end . 146) (:start . 142)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 152)\n  (:start . 147) (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 157) (:start . 153)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 164)\n  (:start . 158) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 69))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 175)\n  (:start . 169) (:id . 70))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 182)\n  (:start . 176) (:id . 71))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 189)\n  (:start . 183) (:id . 72))\n ((:tag . "NNS") (:stem . "characteristic") (:form . "characteristics")\n  (:end . 205) (:start . 190) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 207) (:start . 206)\n  (:id . 74))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 209) (:start . 207)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s7.354) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502219@unknown@formal@none@1@S@This might be attributed to the compensation of Sp1-triggered gene transcription by other Sp family members, such as Sp3, which is also ubiquitously expressed and has the potential to activate transcription of certain otherwise Sp1-regulated promoters (70).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "attribute") (:form . "attributed") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "compensation") (:form . "compensation") (:end . 44)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "sp1-triggered") (:form . "Sp1-triggered")\n  (:end . 61) (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 80) (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 83) (:start . 81)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 89) (:start . 84)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sp") (:form . "Sp") (:end . 92) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 99)\n  (:start . 93) (:id . 56))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 107)\n  (:start . 100) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 113) (:start . 109)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Sp3") (:form . "Sp3") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 62))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 127)\n  (:start . 122) (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 130) (:start . 128)\n  (:id . 64))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 135) (:start . 131)\n  (:id . 65))\n ((:tag . "RB") (:stem . "ubiquitously") (:form . "ubiquitously") (:end . 148)\n  (:start . 136) (:id . 66))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 158)\n  (:start . 149) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 166) (:start . 163)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 70))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 180)\n  (:start . 171) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 183) (:start . 181)\n  (:id . 72))\n ((:tag . "VB") (:stem . "activate") (:form . "activate") (:end . 192)\n  (:start . 184) (:id . 73))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 206) (:start . 193) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 209) (:start . 207)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 217)\n  (:start . 210) (:id . 76))\n ((:tag . "JJ") (:stem . "otherwise") (:form . "otherwise") (:end . 227)\n  (:start . 218) (:id . 77))\n ((:tag . "JJ") (:stem . "sp1-regulated") (:form . "Sp1-regulated")\n  (:end . 241) (:start . 228) (:id . 78))\n ((:tag . "NNS") (:stem . "promoter") (:form . "promoters") (:end . 251)\n  (:start . 242) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 253) (:start . 252)\n  (:id . 80))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 255) (:start . 253)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 256) (:start . 255)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x7.355.1) (:span 5 10)))\n (:hscopes ((:id . :x7.355.1) (:span 0 251)))\n (:identifiers (:sid . :s7.355) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502220@unknown@formal@none@1@S@Third, Sp1 was found to be O-GlcNAcylated by OGT, and this decreased its ability to activate the HIV-1 LTR promoter.@(((:tag . "RB") (:stem . "third") (:form . "Third") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 20) (:start . 15)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 26) (:start . 24)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "o-glcnacylate") (:form . "O-GlcNAcylated")\n  (:end . 41) (:start . 27) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 58) (:start . 54)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "decrease") (:form . "decreased") (:end . 68)\n  (:start . 59) (:id . 55))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 80)\n  (:start . 73) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n  (:id . 58))\n ((:tag . "VB") (:stem . "activate") (:form . "activate") (:end . 92)\n  (:start . 84) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 102)\n  (:start . 97) (:id . 61))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 106) (:start . 103)\n  (:id . 62))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 115)\n  (:start . 107) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.356) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502221@unknown@formal@none@1@S@These findings are in accordance with the results of Kudlow and colleagues, who showed that O-GlcNAcylation decreases the capability of Sp1 to activate GC-box-containing promoters (77).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "accordance") (:form . "accordance") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Kudlow") (:form . "Kudlow") (:end . 59)\n  (:start . 53) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "colleague") (:form . "colleagues") (:end . 74)\n  (:start . 64) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "WP") (:stem . "who") (:form . "who") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 86) (:start . 80)\n  (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 91) (:start . 87)\n  (:id . 57))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 107) (:start . 92) (:id . 58))\n ((:tag . "VBZ") (:stem . "decrease") (:form . "decreases") (:end . 117)\n  (:start . 108) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 60))\n ((:tag . "NN") (:stem . "capability") (:form . "capability") (:end . 132)\n  (:start . 122) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 62))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 139) (:start . 136)\n  (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . "VB") (:stem . "activate") (:form . "activate") (:end . 151)\n  (:start . 143) (:id . 65))\n ((:tag . "JJ") (:stem . "gc-box-containing") (:form . "GC-box-containing")\n  (:end . 169) (:start . 152) (:id . 66))\n ((:tag . "NNS") (:stem . "promoter") (:form . "promoters") (:end . 179)\n  (:start . 170) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 181) (:start . 180)\n  (:id . 68))\n ((:tag . "CD") (:stem . "77") (:form . "77") (:end . 183) (:start . 181)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.357) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502222@unknown@formal@none@1@S@But it has to be emphasized that O-GlcNAcylation of Sp1 does not generally inhibit transcription.@(((:tag . "CC") (:stem . "but") (:form . "But") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "emphasize") (:form . "emphasized") (:end . 27)\n  (:start . 17) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 48) (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "RB") (:stem . "generally") (:form . "generally") (:end . 74)\n  (:start . 65) (:id . 54))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 82)\n  (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 96) (:start . 83) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s7.358) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502223@unknown@formal@none@1@S@We have shown here that the human EF1α promoter, which also contains Sp1-binding sites (55, 73, 75), is activated by O-GlcNAcylation of Sp1.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 33) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "ef1α") (:form . "EF1α") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 47)\n  (:start . 39) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 54) (:start . 49)\n  (:id . 52))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 59) (:start . 55)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 68)\n  (:start . 60) (:id . 54))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 80)\n  (:start . 69) (:id . 55))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 86) (:start . 81)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 57))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "CD") (:stem . "73") (:form . "73") (:end . 94) (:start . 92)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 61))\n ((:tag . "CD") (:stem . "75") (:form . "75") (:end . 98) (:start . 96)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 103) (:start . 101)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 113)\n  (:start . 104) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 116) (:start . 114)\n  (:id . 67))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 132) (:start . 117) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 139) (:start . 136)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s7.359) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502224@unknown@formal@none@1@S@Additionally, others have shown that the expression of plasminogen activator inhibitor 1 (14, 19, 20), calmodulin (38), and argininosuccinate synthetase (6, 7) is also increased by Sp1 O-GlcNAcylation.@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 51)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "plasminogen") (:form . "plasminogen") (:end . 66)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "activator") (:form . "activator") (:end . 76)\n  (:start . 67) (:id . 52))\n ((:tag . "NN") (:stem . "inhibitor") (:form . "inhibitor") (:end . 86)\n  (:start . 77) (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 88) (:start . 87)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 100) (:start . 98)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . "NN") (:stem . "calmodulin") (:form . "calmodulin") (:end . 113)\n  (:start . 103) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 64))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 117) (:start . 115)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 68))\n ((:tag . "NN") (:stem . "argininosuccinate") (:form . "argininosuccinate")\n  (:end . 141) (:start . 124) (:id . 69))\n ((:tag . "NN") (:stem . "synthetase") (:form . "synthetase") (:end . 152)\n  (:start . 142) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 71))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 155) (:start . 154)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 73))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 158) (:start . 157)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 75))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 162) (:start . 160)\n  (:id . 76))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 167) (:start . 163)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 177)\n  (:start . 168) (:id . 78))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 180) (:start . 178)\n  (:id . 79))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 184) (:start . 181)\n  (:id . 80))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 200) (:start . 185) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s7.360) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502225@unknown@formal@none@1@S@Thus, O-GlcNAcylation of Sp1 differentially modulates gene expression.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 21) (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "RB") (:stem . "differentially") (:form . "differentially")\n  (:end . 43) (:start . 29) (:id . 47))\n ((:tag . "VBZ") (:stem . "modulate") (:form . "modulates") (:end . 53)\n  (:start . 44) (:id . 48))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 58) (:start . 54)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 69)\n  (:start . 59) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s7.361) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502226@unknown@formal@none@1@S@These differential effects may depend not only on the individual composition of the transcription complexes at different promoters but also on differential Sp1 O-GlcNAcylation patterns in different transcription complexes.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "differential") (:form . "differential") (:end . 18)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 26)\n  (:start . 19) (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "VB") (:stem . "depend") (:form . "depend") (:end . 37)\n  (:start . 31) (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 64)\n  (:start . 54) (:id . 51))\n ((:tag . "NN") (:stem . "composition") (:form . "composition") (:end . 76)\n  (:start . 65) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 97) (:start . 84) (:id . 55))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 107)\n  (:start . 98) (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 110) (:start . 108)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 120)\n  (:start . 111) (:id . 58))\n ((:tag . "NNS") (:stem . "promoter") (:form . "promoters") (:end . 130)\n  (:start . 121) (:id . 59))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 134) (:start . 131)\n  (:id . 60))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 139) (:start . 135)\n  (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 142) (:start . 140)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "differential") (:form . "differential") (:end . 155)\n  (:start . 143) (:id . 63))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 159) (:start . 156)\n  (:id . 64))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 175) (:start . 160) (:id . 65))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 184)\n  (:start . 176) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 187) (:start . 185)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 197)\n  (:start . 188) (:id . 68))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 211) (:start . 198) (:id . 69))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 221)\n  (:start . 212) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x7.362.1) (:span 27 30)))\n (:hscopes ((:id . :x7.362.1) (:span 27 221)))\n (:identifiers (:sid . :s7.362) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502227@unknown@formal@none@1@S@The latter is supported by the fact that transcriptional corepressors recruit OGT to promoters (78), indicating that O-GlcNAcylation is modulated directly at the promoter site.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 56) (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "corepressor") (:form . "corepressors") (:end . 69)\n  (:start . 57) (:id . 51))\n ((:tag . "VBP") (:stem . "recruit") (:form . "recruit") (:end . 77)\n  (:start . 70) (:id . 52))\n ((:tag . "NN") (:stem . "ogt") (:form . "OGT") (:end . 81) (:start . 78)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "promoter") (:form . "promoters") (:end . 94)\n  (:start . 85) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "CD") (:stem . "78") (:form . "78") (:end . 98) (:start . 96)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 111)\n  (:start . 101) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n  (:id . 61))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 132) (:start . 117) (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 135) (:start . 133)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "modulate") (:form . "modulated") (:end . 145)\n  (:start . 136) (:id . 64))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 154)\n  (:start . 146) (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 157) (:start . 155)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 67))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 170)\n  (:start . 162) (:id . 68))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 175) (:start . 171)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x7.363.1) (:span 101 116)))\n (:hscopes ((:id . :x7.363.1) (:span 101 175)))\n (:identifiers (:sid . :s7.363) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502228@unknown@formal@none@1@S@Furthermore, it has been shown that phosphorylation of distinct residues differentially regulates Sp1 activity (5, 10, 11).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 51) (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 72)\n  (:start . 64) (:id . 52))\n ((:tag . "RB") (:stem . "differentially") (:form . "differentially")\n  (:end . 87) (:start . 73) (:id . 53))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "regulates") (:end . 97)\n  (:start . 88) (:id . 54))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 101) (:start . 98)\n  (:id . 55))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 110)\n  (:start . 102) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 57))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 113) (:start . 112)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 59))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s7.364) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502229@unknown@formal@none@1@S@As O-GlcNAcylation appears to have a yin-yang relationship with phosphorylation, the same may apply for O-GlcNAcylation.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 18) (:start . 3) (:id . 43))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 26)\n  (:start . 19) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "yin-yang") (:form . "yin-yang") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 58)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 63) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 79) (:start . 64) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 89) (:start . 85)\n  (:id . 54))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "VB") (:stem . "apply") (:form . "apply") (:end . 99) (:start . 94)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 103) (:start . 100)\n  (:id . 57))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 119) (:start . 104) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x7.365.1) (:span 90 93)) ((:id . :x7.365.2) (:span 19 26)))\n (:hscopes ((:id . :x7.365.1) (:span 90 119)) ((:id . :x7.365.2) (:span 3 79)))\n (:identifiers (:sid . :s7.365) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502230@unknown@formal@none@1@S@Several mechanisms have been suggested for how O-GlcNAcylation of Sp1 inhibits promoter activity.@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "suggest") (:form . "suggested") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 62) (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 78)\n  (:start . 70) (:id . 52))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 87)\n  (:start . 79) (:id . 53))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 96)\n  (:start . 88) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 55)))@@@1@14@((:hcues ((:id . :x7.366.1) (:span 29 38)))\n (:hscopes ((:id . :x7.366.1) (:span 0 96)))\n (:identifiers (:sid . :s7.366) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502231@unknown@formal@none@1@S@For example, O-GlcNAcylation reduces the ability of Sp1 to homomultimerize and to interact with transcriptional coactivator TATA-binding protein-associated factor II 110 (TAFII110) (62, 77).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "O-GlcNAcylation") (:form . "O-GlcNAcylation")\n  (:end . 28) (:start . 13) (:id . 45))\n ((:tag . "VBZ") (:stem . "reduce") (:form . "reduces") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "VB") (:stem . "homomultimerize") (:form . "homomultimerize")\n  (:end . 74) (:start . 59) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "VB") (:stem . "interact") (:form . "interact") (:end . 90)\n  (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 95) (:start . 91)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 111) (:start . 96) (:id . 57))\n ((:tag . "NN") (:stem . "coactivator") (:form . "coactivator") (:end . 123)\n  (:start . 112) (:id . 58))\n ((:tag . "JJ") (:stem . "tata-binding") (:form . "TATA-binding") (:end . 136)\n  (:start . 124) (:id . 59))\n ((:tag . "JJ") (:stem . "protein-associated") (:form . "protein-associated")\n  (:end . 155) (:start . 137) (:id . 60))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 162)\n  (:start . 156) (:id . 61))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 165) (:start . 163)\n  (:id . 62))\n ((:tag . "CD") (:stem . "110") (:form . "110") (:end . 169) (:start . 166)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 171) (:start . 170)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "TAFII110") (:form . "TAFII110") (:end . 179)\n  (:start . 171) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 182) (:start . 181)\n  (:id . 67))\n ((:tag . "CD") (:stem . "62") (:form . "62") (:end . 184) (:start . 182)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 69))\n ((:tag . "CD") (:stem . "77") (:form . "77") (:end . 188) (:start . 186)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s7.367) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502232@unknown@formal@none@1@S@These mechanisms are in accordance with our findings that O-GlcNAcylated Sp1 localizes at the HIV-1 LTR promoter and does not exhibit a decreased DNA-binding activity.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "accordance") (:form . "accordance") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "o-glcnacylated") (:form . "O-GlcNAcylated")\n  (:end . 72) (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 76) (:start . 73)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "localize") (:form . "localizes") (:end . 86)\n  (:start . 77) (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 89) (:start . 87)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 99) (:start . 94)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 103) (:start . 100)\n  (:id . 57))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 112)\n  (:start . 104) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 121) (:start . 117)\n  (:id . 60))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "VB") (:stem . "exhibit") (:form . "exhibit") (:end . 133)\n  (:start . 126) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 135) (:start . 134)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "decrease") (:form . "decreased") (:end . 145)\n  (:start . 136) (:id . 64))\n ((:tag . "JJ") (:stem . "dna-binding") (:form . "DNA-binding") (:end . 157)\n  (:start . 146) (:id . 65))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 166)\n  (:start . 158) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.368) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502233@unknown@formal@none@1@S@Furthermore, O-GlcNAcylated Sp1 seems to act additionally as a repressor of HIV-1 transcription, as the presence of the Sp1-binding sites in the HIV-1 LTR is crucial for the inhibitory effect of OGT.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "o-glcnacylated") (:form . "O-GlcNAcylated")\n  (:end . 27) (:start . 13) (:id . 44))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 31) (:start . 28)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 37) (:start . 32)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "RB") (:stem . "additionally") (:form . "additionally") (:end . 57)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "repressor") (:form . "repressor") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 95) (:start . 82) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 112)\n  (:start . 104) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 131)\n  (:start . 120) (:id . 62))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 137)\n  (:start . 132) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 154) (:start . 151)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 157) (:start . 155)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 165)\n  (:start . 158) (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 169) (:start . 166)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 173) (:start . 170)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 184)\n  (:start . 174) (:id . 72))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 191)\n  (:start . 185) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 194) (:start . 192)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 198) (:start . 195)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x7.369.1) (:span 32 37)))\n (:hscopes ((:id . :x7.369.1) (:span 13 95)))\n (:identifiers (:sid . :s7.369) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502234@unknown@formal@none@1@S@The HIV-1 LTR promoter containing only functional NF-κB-binding sites but mutated Sp1-binding sites (LTR-κB-Sp1mut) was activated by OGT overexpression, indicating that O-GlcNAcylation of NF-κB increases the transcription rate from the LTR-κB-Sp1mut promoter.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 33)\n  (:start . 23) (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 49)\n  (:start . 39) (:id . 48))\n ((:tag . "JJ") (:stem . "nf-κb-binding") (:form . "NF-κB-binding")\n  (:end . 63) (:start . 50) (:id . 49))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 69) (:start . 64)\n  (:id . 50))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 73) (:start . 70)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 81)\n  (:start . 74) (:id . 52))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 93)\n  (:start . 82) (:id . 53))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 99) (:start . 94)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "LTR-κB-Sp1mut") (:form . "LTR-κB-Sp1mut")\n  (:end . 114) (:start . 101) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 119) (:start . 116)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 129)\n  (:start . 120) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 132) (:start . 130)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 136) (:start . 133)\n  (:id . 61))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 151) (:start . 137) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 163)\n  (:start . 153) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 168) (:start . 164)\n  (:id . 65))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 184) (:start . 169) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 193)\n  (:start . 188) (:id . 68))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 203)\n  (:start . 194) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 207) (:start . 204)\n  (:id . 70))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 221) (:start . 208) (:id . 71))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 226) (:start . 222)\n  (:id . 72))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 231) (:start . 227)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 235) (:start . 232)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "LTR-κB-Sp1mut") (:form . "LTR-κB-Sp1mut")\n  (:end . 249) (:start . 236) (:id . 75))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 258)\n  (:start . 250) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 259) (:start . 258)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x7.370.1) (:span 153 168)))\n (:hscopes ((:id . :x7.370.1) (:span 153 258)))\n (:identifiers (:sid . :s7.370) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502235@unknown@formal@none@1@S@Accordingly, O-GlcNAcylation of NF-κB has been described and it was suggested to enhance the nuclear translocation of NF-κB (21).@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 28) (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 37) (:start . 32)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 56)\n  (:start . 47) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "suggest") (:form . "suggested") (:end . 77)\n  (:start . 68) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "VB") (:stem . "enhance") (:form . "enhance") (:end . 88)\n  (:start . 81) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 100)\n  (:start . 93) (:id . 57))\n ((:tag . "NN") (:stem . "translocation") (:form . "translocation")\n  (:end . 114) (:start . 101) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 123)\n  (:start . 118) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 127) (:start . 125)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x7.371.1) (:span 68 77)))\n (:hscopes ((:id . :x7.371.1) (:span 68 123)))\n (:identifiers (:sid . :s7.371) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502236@unknown@formal@none@1@S@However, the transcription of the wild-type HIV-1 LTR (LTR-κB-Sp1wt) containing both NF-κB- and Sp1-binding sites was inhibited by O-GlcNAcylation of Sp1.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 26) (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "LTR-κB-Sp1wt") (:form . "LTR-κB-Sp1wt") (:end . 67)\n  (:start . 55) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 79)\n  (:start . 69) (:id . 54))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "nf-κb-") (:form . "NF-κB-") (:end . 91)\n  (:start . 85) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 107)\n  (:start . 96) (:id . 58))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 113)\n  (:start . 108) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 117) (:start . 114)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "inhibit") (:form . "inhibited") (:end . 127)\n  (:start . 118) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 146) (:start . 131) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 153) (:start . 150)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s7.372) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502237@unknown@formal@none@1@S@This indicates that O-GlcNAcylation of Sp1 inhibits the activity of the HIV-1 LTR in a dominant manner.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 35) (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 77) (:start . 72)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 86) (:start . 85)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 95)\n  (:start . 87) (:id . 57))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 102)\n  (:start . 96) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x7.373.1) (:span 5 19)))\n (:hscopes ((:id . :x7.373.1) (:span 5 102)))\n (:identifiers (:sid . :s7.373) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502238@unknown@formal@none@1@S@Unlike the NF-κB-binding sites, the Sp1-binding sites are well conserved throughout primate lentiviral LTRs (18, 79), suggesting a conserved regulation of Sp1-mediated gene transcription for lentiviral LTRs, which is probably dominant over NF-κB regulation.@(((:tag . "IN") (:stem . "unlike") (:form . "Unlike") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "nf-κb-binding") (:form . "NF-κB-binding")\n  (:end . 24) (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 30) (:start . 25)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "sp1-binding") (:form . "Sp1-binding") (:end . 47)\n  (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 83)\n  (:start . 73) (:id . 53))\n ((:tag . "JJ") (:stem . "primate") (:form . "primate") (:end . 91)\n  (:start . 84) (:id . 54))\n ((:tag . "JJ") (:stem . "lentiviral") (:form . "lentiviral") (:end . 102)\n  (:start . 92) (:id . 55))\n ((:tag . "NNS") (:stem . "ltr") (:form . "LTRs") (:end . 107) (:start . 103)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 57))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . "CD") (:stem . "79") (:form . "79") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 128)\n  (:start . 118) (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 140)\n  (:start . 131) (:id . 65))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 151)\n  (:start . 141) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "sp1-mediated") (:form . "Sp1-mediated") (:end . 167)\n  (:start . 155) (:id . 68))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 172) (:start . 168)\n  (:id . 69))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 186) (:start . 173) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 190) (:start . 187)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "lentiviral") (:form . "lentiviral") (:end . 201)\n  (:start . 191) (:id . 72))\n ((:tag . "NNS") (:stem . "ltr") (:form . "LTRs") (:end . 206) (:start . 202)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 207) (:start . 206)\n  (:id . 74))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 213)\n  (:start . 208) (:id . 75))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 216) (:start . 214)\n  (:id . 76))\n ((:tag . "RB") (:stem . "probably") (:form . "probably") (:end . 225)\n  (:start . 217) (:id . 77))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 234)\n  (:start . 226) (:id . 78))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 239) (:start . 235)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 245)\n  (:start . 240) (:id . 80))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 256)\n  (:start . 246) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x7.374.1) (:span 217 225))\n  ((:id . :x7.374.2) (:span 118 128)))\n (:hscopes ((:id . :x7.374.1) (:span 217 256))\n  ((:id . :x7.374.2) (:span 118 256)))\n (:identifiers (:sid . :s7.374) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502239@unknown@formal@none@1@S@Furthermore, the dominant effect of Sp1 over NF-κB might be attributed to the synergistic mode of action of both transcription factors on the HIV-1 LTR (59, 60).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "NF-κB") (:form . "NF-κB") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "attribute") (:form . "attributed") (:end . 70)\n  (:start . 60) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "synergistic") (:form . "synergistic") (:end . 89)\n  (:start . 78) (:id . 56))\n ((:tag . "NN") (:stem . "mode") (:form . "mode") (:end . 94) (:start . 90)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "NN") (:stem . "action") (:form . "action") (:end . 104)\n  (:start . 98) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 60))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 112) (:start . 108)\n  (:id . 61))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 126) (:start . 113) (:id . 62))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 134)\n  (:start . 127) (:id . 63))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 147)\n  (:start . 142) (:id . 66))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 151) (:start . 148)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . "CD") (:stem . "59") (:form . "59") (:end . 155) (:start . 153)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 70))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 159) (:start . 157)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x7.375.1) (:span 51 56)))\n (:hscopes ((:id . :x7.375.1) (:span 13 151)))\n (:identifiers (:sid . :s7.375) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502240@unknown@formal@none@1@S@A potential molecular mechanism for the dominant repressive effect of O-GlcNAcylated Sp1 on the HIV-1 LTR relies on the ability of Sp1 to recruit corepressors to the promoter.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 11)\n  (:start . 2) (:id . 43))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . "JJ") (:stem . "repressive") (:form . "repressive") (:end . 59)\n  (:start . 49) (:id . 49))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 66)\n  (:start . 60) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "o-glcnacylated") (:form . "O-GlcNAcylated")\n  (:end . 84) (:start . 70) (:id . 52))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 88) (:start . 85)\n  (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 91) (:start . 89)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 101)\n  (:start . 96) (:id . 56))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 105) (:start . 102)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "rely") (:form . "relies") (:end . 112)\n  (:start . 106) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 115) (:start . 113)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 127)\n  (:start . 120) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . "VB") (:stem . "recruit") (:form . "recruit") (:end . 145)\n  (:start . 138) (:id . 65))\n ((:tag . "NNS") (:stem . "corepressor") (:form . "corepressors") (:end . 158)\n  (:start . 146) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 161) (:start . 159)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 68))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 174)\n  (:start . 166) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x7.376.1) (:span 2 11)))\n (:hscopes ((:id . :x7.376.1) (:span 2 105)))\n (:identifiers (:sid . :s7.376) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502241@unknown@formal@none@1@S@It has been reported that Sp1 can act as an anchor site for a repressor complex consisting of histone deacetylases and mSin3a (82).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 43) (:start . 41)\n  (:id . 51))\n ((:tag . "NN") (:stem . "anchor") (:form . "anchor") (:end . 50)\n  (:start . 44) (:id . 52))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 55))\n ((:tag . "NN") (:stem . "repressor") (:form . "repressor") (:end . 71)\n  (:start . 62) (:id . 56))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 79)\n  (:start . 72) (:id . 57))\n ((:tag . "VBG") (:stem . "consist") (:form . "consisting") (:end . 90)\n  (:start . 80) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "NN") (:stem . "histone") (:form . "histone") (:end . 101)\n  (:start . 94) (:id . 60))\n ((:tag . "NNS") (:stem . "deacetylas") (:form . "deacetylases") (:end . 114)\n  (:start . 102) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 62))\n ((:tag . "NN") (:stem . "msin3a") (:form . "mSin3a") (:end . 125)\n  (:start . 119) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 64))\n ((:tag . "CD") (:stem . "82") (:form . "82") (:end . 129) (:start . 127)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s7.377) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502242@unknown@formal@none@1@S@Intriguingly, Sp1 has also been detected in a DNA-protein complex with c-Myc and histone deacetylase 1 at the HIV-1 LTR, and it has been shown that this complex is involved in the establishment of proviral latency (33).@(((:tag . "RB") (:stem . "intriguingly") (:form . "Intriguingly") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "dna-protein") (:form . "DNA-protein") (:end . 57)\n  (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 70) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "c-myc") (:form . "c-Myc") (:end . 76) (:start . 71)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "histone") (:form . "histone") (:end . 88)\n  (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "deacetylase") (:form . "deacetylase") (:end . 100)\n  (:start . 89) (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 105) (:start . 103)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 115)\n  (:start . 110) (:id . 61))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 119) (:start . 116)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 64))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 127) (:start . 125)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 131) (:start . 128)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 136) (:start . 132)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 142)\n  (:start . 137) (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 147) (:start . 143)\n  (:id . 69))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 152) (:start . 148)\n  (:id . 70))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 160)\n  (:start . 153) (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 163) (:start . 161)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 172)\n  (:start . 164) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 175) (:start . 173)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 75))\n ((:tag . "NN") (:stem . "establishment") (:form . "establishment")\n  (:end . 193) (:start . 180) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 196) (:start . 194)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "proviral") (:form . "proviral") (:end . 205)\n  (:start . 197) (:id . 78))\n ((:tag . "NN") (:stem . "latency") (:form . "latency") (:end . 213)\n  (:start . 206) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 215) (:start . 214)\n  (:id . 80))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 217) (:start . 215)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 218) (:start . 217)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s7.378) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502243@unknown@formal@none@1@S@Thus, O-GlcNAcylation of Sp1 might quickly put initiated viral replication into a state of latency.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 21) (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sp1") (:form . "Sp1") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "RB") (:stem . "quickly") (:form . "quickly") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . "VB") (:stem . "put") (:form . "put") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "initiate") (:form . "initiated") (:end . 56)\n  (:start . 47) (:id . 50))\n ((:tag . "JJ") (:stem . "viral") (:form . "viral") (:end . 62) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 74)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 79) (:start . 75)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 81) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 87) (:start . 82)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "NN") (:stem . "latency") (:form . "latency") (:end . 98)\n  (:start . 91) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x7.379.1) (:span 29 34)))\n (:hscopes ((:id . :x7.379.1) (:span 29 98)))\n (:identifiers (:sid . :s7.379) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502244@unknown@formal@none@1@S@Most importantly, increased O-GlcNAcylation of Sp1 prior to HIV-1 infection might efficiently prevent the onset of viral replication.@(((:tag . "RBS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "importantly") (:form . "importantly") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 43) (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 56) (:start . 51)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "infection") (:form . "infection") (:end . 75)\n  (:start . 66) (:id . 52))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 81) (:start . 76)\n  (:id . 53))\n ((:tag . "RB") (:stem . "efficiently") (:form . "efficiently") (:end . 93)\n  (:start . 82) (:id . 54))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 101)\n  (:start . 94) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 56))\n ((:tag . "NN") (:stem . "onset") (:form . "onset") (:end . 111)\n  (:start . 106) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "viral") (:form . "viral") (:end . 120)\n  (:start . 115) (:id . 59))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 132)\n  (:start . 121) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x7.380.1) (:span 76 81)))\n (:hscopes ((:id . :x7.380.1) (:span 76 132)))\n (:identifiers (:sid . :s7.380) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502245@unknown@formal@none@1@S@This is supported by the fact that stable overexpression of OGT strongly inhibited replication of HIV-1 in de novo-infected lymphocytes.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "stable") (:form . "stable") (:end . 41)\n  (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 56) (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "OGT") (:form . "OGT") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . "VBD") (:stem . "inhibit") (:form . "inhibited") (:end . 82)\n  (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 94)\n  (:start . 83) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 103)\n  (:start . 98) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . "FW") (:stem . "de") (:form . "de") (:end . 109) (:start . 107)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "novo-infected") (:form . "novo-infected")\n  (:end . 123) (:start . 110) (:id . 60))\n ((:tag . "NNS") (:stem . "lymphocyte") (:form . "lymphocytes") (:end . 135)\n  (:start . 124) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s7.381) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502246@unknown@formal@none@1@S@Altogether, these results suggest that O-GlcNAcylated Sp1 efficiently inhibits gene expression from the HIV-1 LTR and may be involved in the regulation of the viral life cycle.@(((:tag . "RB") (:stem . "altogether") (:form . "Altogether") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "o-glcnacylated") (:form . "O-GlcNAcylated")\n  (:end . 53) (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 57) (:start . 54)\n  (:id . 49))\n ((:tag . "RB") (:stem . "efficiently") (:form . "efficiently") (:end . 69)\n  (:start . 58) (:id . 50))\n ((:tag . "VBZ") (:stem . "inhibit") (:form . "inhibits") (:end . 78)\n  (:start . 70) (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 83) (:start . 79)\n  (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 94)\n  (:start . 84) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 99) (:start . 95)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 109)\n  (:start . 104) (:id . 56))\n ((:tag . "NNP") (:stem . "LTR") (:form . "LTR") (:end . 113) (:start . 110)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 58))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 121) (:start . 118)\n  (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 124) (:start . 122)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 133)\n  (:start . 125) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 63))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 151)\n  (:start . 141) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "viral") (:form . "viral") (:end . 164)\n  (:start . 159) (:id . 67))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 169) (:start . 165)\n  (:id . 68))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 175)\n  (:start . 170) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x7.382.1) (:span 118 121)) ((:id . :x7.382.2) (:span 26 33)))\n (:hscopes ((:id . :x7.382.1) (:span 118 175))\n  ((:id . :x7.382.2) (:span 26 175)))\n (:identifiers (:sid . :s7.382) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502247@unknown@formal@none@1@S@Many reports have evaluated the effect of highly active antiretroviral therapy (HAART) on glucose metabolism (15, 17, 49) and the appearance of diabetes as a consequence of HAART (40, 51).@(((:tag . "JJ") (:stem . "many") (:form . "Many") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "evaluate") (:form . "evaluated") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 48)\n  (:start . 42) (:id . 49))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "JJ") (:stem . "antiretroviral") (:form . "antiretroviral")\n  (:end . 70) (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "therapy") (:form . "therapy") (:end . 78)\n  (:start . 71) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "HAART") (:form . "HAART") (:end . 85) (:start . 80)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "glucose") (:form . "glucose") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . "NN") (:stem . "metabolism") (:form . "metabolism") (:end . 108)\n  (:start . 98) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 59))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 61))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 116) (:start . 114)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . "CD") (:stem . "49") (:form . "49") (:end . 120) (:start . 118)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 121) (:start . 120)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 67))\n ((:tag . "NN") (:stem . "appearance") (:form . "appearance") (:end . 140)\n  (:start . 130) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "diabete") (:form . "diabetes") (:end . 152)\n  (:start . 144) (:id . 70))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 155) (:start . 153)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 157) (:start . 156)\n  (:id . 72))\n ((:tag . "NN") (:stem . "consequence") (:form . "consequence") (:end . 169)\n  (:start . 158) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 172) (:start . 170)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "HAART") (:form . "HAART") (:end . 178)\n  (:start . 173) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 180) (:start . 179)\n  (:id . 76))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 182) (:start . 180)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 78))\n ((:tag . "CD") (:stem . "51") (:form . "51") (:end . 186) (:start . 184)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s7.383) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502248@unknown@formal@none@1@S@But up to now, no studies have investigated the effect of glucose metabolism on HIV-1 replication.@(((:tag . "CC") (:stem . "but") (:form . "But") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "up") (:form . "up") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 17) (:start . 15)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 25)\n  (:start . 18) (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 30) (:start . 26)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "investigate") (:form . "investigated") (:end . 43)\n  (:start . 31) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "glucose") (:form . "glucose") (:end . 65)\n  (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "metabolism") (:form . "metabolism") (:end . 76)\n  (:start . 66) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 85) (:start . 80)\n  (:id . 57))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 97)\n  (:start . 86) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s7.384) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502249@unknown@formal@none@1@S@Our results indicate that the O-GlcNAc level, and thus the glucose metabolism, may influence the life cycle of HIV-1.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "O-GlcNAc") (:form . "O-GlcNAc") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "glucose") (:form . "glucose") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "metabolism") (:form . "metabolism") (:end . 77)\n  (:start . 67) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "VB") (:stem . "influence") (:form . "influence") (:end . 92)\n  (:start . 83) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 101) (:start . 97)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 107)\n  (:start . 102) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "HIV-1") (:form . "HIV-1") (:end . 116)\n  (:start . 111) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x7.385.1) (:span 79 82)) ((:id . :x7.385.2) (:span 12 25)))\n (:hscopes ((:id . :x7.385.1) (:span 79 116))\n  ((:id . :x7.385.2) (:span 12 116)))\n (:identifiers (:sid . :s7.385) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502250@unknown@formal@none@1@S@Accordingly, inducers of Sp1 O-GlcNAcylation such as GlcN and 2-deoxyglucose, which are approved in clinical treatment of osteoarthritis and human genital herpes infections, respectively (3, 61), may support HAART.@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "inducer") (:form . "inducers") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sp1") (:form . "Sp1") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "o-glcnacylation") (:form . "O-GlcNAcylation")\n  (:end . 44) (:start . 29) (:id . 47))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "GlcN") (:form . "GlcN") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "2-deoxyglucose") (:form . "2-deoxyglucose")\n  (:end . 76) (:start . 62) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 83) (:start . 78)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "approve") (:form . "approved") (:end . 96)\n  (:start . 88) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "clinical") (:form . "clinical") (:end . 108)\n  (:start . 100) (:id . 58))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 118)\n  (:start . 109) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 60))\n ((:tag . "NN") (:stem . "osteoarthritis") (:form . "osteoarthritis")\n  (:end . 136) (:start . 122) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 146)\n  (:start . 141) (:id . 63))\n ((:tag . "JJ") (:stem . "genital") (:form . "genital") (:end . 154)\n  (:start . 147) (:id . 64))\n ((:tag . "NN") (:stem . "herpes") (:form . "herpes") (:end . 161)\n  (:start . 155) (:id . 65))\n ((:tag . "NNS") (:stem . "infection") (:form . "infections") (:end . 172)\n  (:start . 162) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 67))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 186)\n  (:start . 174) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 188) (:start . 187)\n  (:id . 69))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 189) (:start . 188)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n  (:id . 71))\n ((:tag . "CD") (:stem . "61") (:form . "61") (:end . 193) (:start . 191)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n  (:id . 74))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 199) (:start . 196)\n  (:id . 75))\n ((:tag . "VB") (:stem . "support") (:form . "support") (:end . 207)\n  (:start . 200) (:id . 76))\n ((:tag . "NNP") (:stem . "HAART") (:form . "HAART") (:end . 213)\n  (:start . 208) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x7.386.1) (:span 196 199)))\n (:hscopes ((:id . :x7.386.1) (:span 196 213)))\n (:identifiers (:sid . :s7.386) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502251@unknown@formal@none@1@S@The establishment of a metabolic treatment may supplement the repertoire of antiretroviral therapies against AIDS.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "establishment") (:form . "establishment")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "metabolic") (:form . "metabolic") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "VB") (:stem . "supplement") (:form . "supplement") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "NN") (:stem . "repertoire") (:form . "repertoire") (:end . 72)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "antiretroviral") (:form . "antiretroviral")\n  (:end . 90) (:start . 76) (:id . 53))\n ((:tag . "NNS") (:stem . "therapy") (:form . "therapies") (:end . 100)\n  (:start . 91) (:id . 54))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 108)\n  (:start . 101) (:id . 55))\n ((:tag . "NNP") (:stem . "AIDS") (:form . "AIDS") (:end . 113) (:start . 109)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x7.387.1) (:span 43 46)))\n (:hscopes ((:id . :x7.387.1) (:span 43 113)))\n (:identifiers (:sid . :s7.387) (:did . :pmc2663287) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502252@unknown@formal@none@1@S@Inactivation of Drosophila Huntingtin affects long-term adult functioning and the pathogenesis of a Huntington’s disease model@(((:tag . "NN") (:stem . "inactivation") (:form . "Inactivation") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 26)\n  (:start . 16) (:id . 44))\n ((:tag . "NNP") (:stem . "Huntingtin") (:form . "Huntingtin") (:end . 37)\n  (:start . 27) (:id . 45))\n ((:tag . "VBZ") (:stem . "affect") (:form . "affects") (:end . 45)\n  (:start . 38) (:id . 46))\n ((:tag . "JJ") (:stem . "long-term") (:form . "long-term") (:end . 55)\n  (:start . 46) (:id . 47))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 61) (:start . 56)\n  (:id . 48))\n ((:tag . "NN") (:stem . "functioning") (:form . "functioning") (:end . 73)\n  (:start . 62) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 51))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 94)\n  (:start . 82) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Huntington") (:form . "Huntington") (:end . 110)\n  (:start . 100) (:id . 55))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 112) (:start . 111)\n  (:id . 56))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 120)\n  (:start . 113) (:id . 57))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 126)\n  (:start . 121) (:id . 58)))@@@1@17@((:identifiers (:sid . :s8.1) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5502253@unknown@formal@none@1@S@SUMMARY@(((:tag . "NN") (:stem . "summary") (:form . "SUMMARY") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s8.2) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5502254@unknown@formal@none@1@S@A polyglutamine expansion in the huntingtin (HTT) gene causes neurodegeneration in Huntington’s disease (HD), but the in vivo function of the native protein (Htt) is largely unknown.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "polyglutamine") (:form . "polyglutamine")\n  (:end . 15) (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "huntingtin") (:form . "huntingtin") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "HTT") (:form . "HTT") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "neurodegeneration") (:form . "neurodegeneration")\n  (:end . 79) (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Huntington") (:form . "Huntington") (:end . 93)\n  (:start . 83) (:id . 55))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 103)\n  (:start . 96) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 113) (:start . 110)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 63))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n  (:id . 64))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 125) (:start . 121)\n  (:id . 65))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 134)\n  (:start . 126) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 148)\n  (:start . 142) (:id . 69))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 156)\n  (:start . 149) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 158) (:start . 157)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 161) (:start . 158)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 73))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 165) (:start . 163)\n  (:id . 74))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 173)\n  (:start . 166) (:id . 75))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 181)\n  (:start . 174) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x8.3.1) (:span 174 181)))\n (:hscopes ((:id . :x8.3.1) (:span 114 181)))\n (:identifiers (:sid . :s8.3) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502255@unknown@formal@none@1@S@Numerous biochemical and in vitro studies have suggested a role for Htt in neuronal development, synaptic function and axonal trafficking.@(((:tag . "JJ") (:stem . "numerous") (:form . "Numerous") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "biochemical") (:form . "biochemical") (:end . 20)\n  (:start . 9) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 44))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "suggest") (:form . "suggested") (:end . 56)\n  (:start . 47) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 63) (:start . 59)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 83)\n  (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 95)\n  (:start . 84) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 105)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 114)\n  (:start . 106) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 125)\n  (:start . 119) (:id . 61))\n ((:tag . "NN") (:stem . "trafficking") (:form . "trafficking") (:end . 137)\n  (:start . 126) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x8.4.1) (:span 47 56)))\n (:hscopes ((:id . :x8.4.1) (:span 47 137)))\n (:identifiers (:sid . :s8.4) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502256@unknown@formal@none@1@S@To test these models, we generated a null mutant in the putative Drosophila HTT homolog (htt, hereafter referred to asdhtt) and, surprisingly, found that dhtt mutant animals are viable with no obvious developmental defects.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 34)\n  (:start . 25) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 48)\n  (:start . 42) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 64)\n  (:start . 56) (:id . 54))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 75)\n  (:start . 65) (:id . 55))\n ((:tag . "NNP") (:stem . "HTT") (:form . "HTT") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 87)\n  (:start . 80) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 58))\n ((:tag . "NN") (:stem . "htt") (:form . "htt") (:end . 92) (:start . 89)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . "RB") (:stem . "hereafter") (:form . "hereafter") (:end . 103)\n  (:start . 94) (:id . 61))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 112)\n  (:start . 104) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n  (:id . 63))\n ((:tag . "VB") (:stem . "asdhtt") (:form . "asdhtt") (:end . 122)\n  (:start . 116) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 67))\n ((:tag . "RB") (:stem . "surprisingly") (:form . "surprisingly") (:end . 141)\n  (:start . 129) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 69))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 148)\n  (:start . 143) (:id . 70))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 153) (:start . 149)\n  (:id . 71))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 158) (:start . 154)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 165)\n  (:start . 159) (:id . 73))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 173)\n  (:start . 166) (:id . 74))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 177) (:start . 174)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 184)\n  (:start . 178) (:id . 76))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 189) (:start . 185)\n  (:id . 77))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 192) (:start . 190)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 200)\n  (:start . 193) (:id . 79))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 214) (:start . 201) (:id . 80))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 222)\n  (:start . 215) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 223) (:start . 222)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s8.5) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502257@unknown@formal@none@1@S@Instead, dhtt is required for maintaining the mobility and long-term survival of adult animals, and for modulating axonal terminal complexity in the adult brain.@(((:tag . "RB") (:stem . "instead") (:form . "Instead") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "maintain") (:form . "maintaining") (:end . 41)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "long-term") (:form . "long-term") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 86) (:start . 81)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 94)\n  (:start . 87) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 103) (:start . 100)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "modulate") (:form . "modulating") (:end . 114)\n  (:start . 104) (:id . 60))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 121)\n  (:start . 115) (:id . 61))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 130)\n  (:start . 122) (:id . 62))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 141)\n  (:start . 131) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 154)\n  (:start . 149) (:id . 66))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 160)\n  (:start . 155) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.6) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502258@unknown@formal@none@1@S@Furthermore, removing endogenous dhtt significantly accelerates the neurodegenerative phenotype associated with a Drosophila model of polyglutamine Htt toxicity (HD-Q93), providing in vivo evidence that disrupting the normal function of Htt might contribute to HD pathogenesis.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "remove") (:form . "removing") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 32)\n  (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 51) (:start . 38) (:id . 47))\n ((:tag . "VBZ") (:stem . "accelerate") (:form . "accelerates") (:end . 63)\n  (:start . 52) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "neurodegenerative") (:form . "neurodegenerative")\n  (:end . 85) (:start . 68) (:id . 50))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 95)\n  (:start . 86) (:id . 51))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 106)\n  (:start . 96) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 111) (:start . 107)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 113) (:start . 112)\n  (:id . 54))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 124)\n  (:start . 114) (:id . 55))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 130)\n  (:start . 125) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 57))\n ((:tag . "NN") (:stem . "polyglutamine") (:form . "polyglutamine")\n  (:end . 147) (:start . 134) (:id . 58))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 151) (:start . 148)\n  (:id . 59))\n ((:tag . "NN") (:stem . "toxicity") (:form . "toxicity") (:end . 160)\n  (:start . 152) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 168)\n  (:start . 162) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 170) (:start . 169)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "provide") (:form . "providing") (:end . 180)\n  (:start . 171) (:id . 65))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 183) (:start . 181)\n  (:id . 66))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 188) (:start . 184)\n  (:id . 67))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 197)\n  (:start . 189) (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 202) (:start . 198)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "disrupt") (:form . "disrupting") (:end . 213)\n  (:start . 203) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 217) (:start . 214)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 224)\n  (:start . 218) (:id . 72))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 233)\n  (:start . 225) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 236) (:start . 234)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 240) (:start . 237)\n  (:id . 75))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 246)\n  (:start . 241) (:id . 76))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 257)\n  (:start . 247) (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 260) (:start . 258)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 263) (:start . 261)\n  (:id . 79))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 276)\n  (:start . 264) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 277) (:start . 276)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x8.7.1) (:span 241 246)))\n (:hscopes ((:id . :x8.7.1) (:span 241 276)))\n (:identifiers (:sid . :s8.7) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502259@unknown@formal@none@1@S@INTRODUCTION@(((:tag . "NN") (:stem . "introduction") (:form . "INTRODUCTION") (:end . 12)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s8.8) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5502260@unknown@formal@none@1@S@Huntington’s disease (HD) is an autosomal dominant, progressive neurodegenerative disorder characterized clinically by deteriorating choreic movements, psychiatric disturbances and cognitive deficits (Gusella and MacDonald, 1995; Martin and Gusella, 1986; Vonsattel et al., 1985).@(((:tag . "NNP") (:stem . "Huntington") (:form . "Huntington") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 31) (:start . 29)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "autosomal") (:form . "autosomal") (:end . 41)\n  (:start . 32) (:id . 50))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "progressive") (:form . "progressive") (:end . 63)\n  (:start . 52) (:id . 53))\n ((:tag . "JJ") (:stem . "neurodegenerative") (:form . "neurodegenerative")\n  (:end . 81) (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "disorder") (:form . "disorder") (:end . 90)\n  (:start . 82) (:id . 55))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n  (:end . 104) (:start . 91) (:id . 56))\n ((:tag . "RB") (:stem . "clinically") (:form . "clinically") (:end . 115)\n  (:start . 105) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 118) (:start . 116)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "deteriorate") (:form . "deteriorating")\n  (:end . 132) (:start . 119) (:id . 59))\n ((:tag . "JJ") (:stem . "choreic") (:form . "choreic") (:end . 140)\n  (:start . 133) (:id . 60))\n ((:tag . "NNS") (:stem . "movement") (:form . "movements") (:end . 150)\n  (:start . 141) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "psychiatric") (:form . "psychiatric") (:end . 163)\n  (:start . 152) (:id . 63))\n ((:tag . "NNS") (:stem . "disturbance") (:form . "disturbances") (:end . 176)\n  (:start . 164) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 180) (:start . 177)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "cognitive") (:form . "cognitive") (:end . 190)\n  (:start . 181) (:id . 66))\n ((:tag . "NNS") (:stem . "deficit") (:form . "deficits") (:end . 199)\n  (:start . 191) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 201) (:start . 200)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Gusella") (:form . "Gusella") (:end . 208)\n  (:start . 201) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 212) (:start . 209)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "MacDonald") (:form . "MacDonald") (:end . 222)\n  (:start . 213) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 223) (:start . 222)\n  (:id . 72))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 228) (:start . 224)\n  (:id . 73))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 229) (:start . 228)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Martin") (:form . "Martin") (:end . 236)\n  (:start . 230) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 240) (:start . 237)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Gusella") (:form . "Gusella") (:end . 248)\n  (:start . 241) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 249) (:start . 248)\n  (:id . 78))\n ((:tag . "CD") (:stem . "1986") (:form . "1986") (:end . 254) (:start . 250)\n  (:id . 79))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 255) (:start . 254)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Vonsattel") (:form . "Vonsattel") (:end . 265)\n  (:start . 256) (:id . 81))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 268) (:start . 266)\n  (:id . 82))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 272) (:start . 269)\n  (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 273) (:start . 272)\n  (:id . 84))\n ((:tag . "CD") (:stem . "1985") (:form . "1985") (:end . 278) (:start . 274)\n  (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 279) (:start . 278)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 280) (:start . 279)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s8.9) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502261@unknown@formal@none@1@S@HD is caused by an abnormal expansion of a polyglutamine (polyQ) tract at the N-terminus of a large cytoplasmic protein, huntingtin (Htt) (The Huntington’s Disease Collaborative Research Group, 1993).@(((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 12) (:start . 6)\n  (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 27)\n  (:start . 19) (:id . 47))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "polyglutamine") (:form . "polyglutamine")\n  (:end . 56) (:start . 43) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "polyq") (:form . "polyQ") (:end . 63) (:start . 58)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . "NN") (:stem . "tract") (:form . "tract") (:end . 70) (:start . 65)\n  (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "N-terminus") (:form . "N-terminus") (:end . 88)\n  (:start . 78) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 99) (:start . 94)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 111)\n  (:start . 100) (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 119)\n  (:start . 112) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 64))\n ((:tag . "NN") (:stem . "huntingtin") (:form . "huntingtin") (:end . 131)\n  (:start . 121) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 136) (:start . 133)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 142) (:start . 139)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Huntington") (:form . "Huntington") (:end . 153)\n  (:start . 143) (:id . 71))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 155) (:start . 154)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Disease") (:form . "Disease") (:end . 163)\n  (:start . 156) (:id . 73))\n ((:tag . "NNP") (:stem . "Collaborative") (:form . "Collaborative")\n  (:end . 177) (:start . 164) (:id . 74))\n ((:tag . "NNP") (:stem . "Research") (:form . "Research") (:end . 186)\n  (:start . 178) (:id . 75))\n ((:tag . "NNP") (:stem . "Group") (:form . "Group") (:end . 192)\n  (:start . 187) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 193) (:start . 192)\n  (:id . 77))\n ((:tag . "CD") (:stem . "1993") (:form . "1993") (:end . 198) (:start . 194)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s8.10) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502262@unknown@formal@none@1@S@The polyQ tract contains between 6 and 35 repeats in the wild-type Htt protein, whereas it is expanded to beyond 36 repeats in HD (The Huntington’s Disease Collaborative Research Group, 1993).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "polyq") (:form . "polyQ") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "tract") (:form . "tract") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 49)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 78)\n  (:start . 71) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 87)\n  (:start . 80) (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "expand") (:form . "expanded") (:end . 102)\n  (:start . 94) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "IN") (:stem . "beyond") (:form . "beyond") (:end . 112)\n  (:start . 106) (:id . 62))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 115) (:start . 113)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 123)\n  (:start . 116) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 126) (:start . 124)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 129) (:start . 127)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 134) (:start . 131)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Huntington") (:form . "Huntington") (:end . 145)\n  (:start . 135) (:id . 69))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 147) (:start . 146)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Disease") (:form . "Disease") (:end . 155)\n  (:start . 148) (:id . 71))\n ((:tag . "NNP") (:stem . "Collaborative") (:form . "Collaborative")\n  (:end . 169) (:start . 156) (:id . 72))\n ((:tag . "NNP") (:stem . "Research") (:form . "Research") (:end . 178)\n  (:start . 170) (:id . 73))\n ((:tag . "NNP") (:stem . "Group") (:form . "Group") (:end . 184)\n  (:start . 179) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 75))\n ((:tag . "CD") (:stem . "1993") (:form . "1993") (:end . 190) (:start . 186)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 191) (:start . 190)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s8.11) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502263@unknown@formal@none@1@S@Numerous studies have demonstrated that mutant Htt containing an expanded polyQ tract is toxic to neurons (Cattaneo et al., 2001; Gusella and MacDonald, 2000).@(((:tag . "JJ") (:stem . "numerous") (:form . "Numerous") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "demonstrate") (:form . "demonstrated") (:end . 34)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 46)\n  (:start . 40) (:id . 47))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 61)\n  (:start . 51) (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "expand") (:form . "expanded") (:end . 73)\n  (:start . 65) (:id . 51))\n ((:tag . "NN") (:stem . "polyq") (:form . "polyQ") (:end . 79) (:start . 74)\n  (:id . 52))\n ((:tag . "NN") (:stem . "tract") (:form . "tract") (:end . 85) (:start . 80)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "toxic") (:form . "toxic") (:end . 94) (:start . 89)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 105)\n  (:start . 98) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Cattaneo") (:form . "Cattaneo") (:end . 115)\n  (:start . 107) (:id . 59))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 118) (:start . 116)\n  (:id . 60))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 122) (:start . 119)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 62))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 128) (:start . 124)\n  (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 129) (:start . 128)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Gusella") (:form . "Gusella") (:end . 137)\n  (:start . 130) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "MacDonald") (:form . "MacDonald") (:end . 151)\n  (:start . 142) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 68))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 157) (:start . 153)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s8.12) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502264@unknown@formal@none@1@S@PolyQ expansion is also linked to at least eight other neurodegenerative disorders, collectively referred to as polyQ diseases (Riley and Orr, 2006; Zoghbi and Orr, 2000).@(((:tag . "NNP") (:stem . "PolyQ") (:form . "PolyQ") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "link") (:form . "linked") (:end . 30) (:start . 24)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "CD") (:stem . "eight") (:form . "eight") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "neurodegenerative") (:form . "neurodegenerative")\n  (:end . 72) (:start . 55) (:id . 52))\n ((:tag . "NNS") (:stem . "disorder") (:form . "disorders") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "RB") (:stem . "collectively") (:form . "collectively") (:end . 96)\n  (:start . 84) (:id . 55))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 105)\n  (:start . 97) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . "NN") (:stem . "polyq") (:form . "polyQ") (:end . 117)\n  (:start . 112) (:id . 59))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 126)\n  (:start . 118) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Riley") (:form . "Riley") (:end . 133)\n  (:start . 128) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Orr") (:form . "Orr") (:end . 141) (:start . 138)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 65))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 147) (:start . 143)\n  (:id . 66))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 148) (:start . 147)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Zoghbi") (:form . "Zoghbi") (:end . 155)\n  (:start . 149) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Orr") (:form . "Orr") (:end . 163) (:start . 160)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 71))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 169) (:start . 165)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.13) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502265@unknown@formal@none@1@S@Although Htt is ubiquitously expressed in the brain, HD mainly affects medium-sized spiny neurons in the striatum and to a lesser extent cortical pyramidal neurons that project to the striatum, suggesting that other cellular factors also contribute to pathogenesis (Cattaneo et al., 2001; Vonsattel and DiFiglia, 1998).@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "ubiquitously") (:form . "ubiquitously") (:end . 28)\n  (:start . 16) (:id . 45))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . 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5502266@unknown@formal@none@1@S@Recent studies indicate that an alteration of wild-type Htt function might contribute to this specificity and to subsequent disease progression (Cattaneo et al., 2001).@(((:tag . "JJ") (:stem . "recent") (:form . "Recent") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "alteration") (:form . "alteration") (:end . 42)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 55)\n  (:start . 46) (:id . 49))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 85)\n  (:start . 75) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 93) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 105)\n  (:start . 94) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 123)\n  (:start . 113) (:id . 59))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 131)\n  (:start . 124) (:id . 60))\n ((:tag . "NN") (:stem . "progression") (:form . "progression") (:end . 143)\n  (:start . 132) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Cattaneo") (:form . "Cattaneo") (:end . 153)\n  (:start . 145) (:id . 63))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 156) (:start . 154)\n  (:id . 64))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 160) (:start . 157)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 66))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 166) (:start . 162)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x8.15.1) (:span 69 74)) ((:id . :x8.15.2) (:span 15 28)))\n (:hscopes ((:id . :x8.15.1) (:span 69 143)) ((:id . :x8.15.2) (:span 15 143)))\n (:identifiers (:sid . :s8.15) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502267@unknown@formal@none@1@S@For example, mutant Htt can sequester wild-type Htt into insoluble aggregates, thereby exerting a dominant negative effect (Huang et al., 1998; Kazantsev et al., 1999; Narain et al., 1999; Preisinger et al., 1999; Wheeler et al., 2000).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "VB") (:stem . "sequester") (:form . "sequester") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "JJ") (:stem . "wild-type") (:form . 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"negative") (:end . 115)\n  (:start . 107) (:id . 59))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 122)\n  (:start . 116) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Huang") (:form . "Huang") (:end . 129)\n  (:start . 124) (:id . 62))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 136) (:start . 133)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 65))\n ((:tag . "CD") (:stem . "1998") (:form . "1998") (:end . 142) (:start . 138)\n  (:id . 66))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Kazantsev") (:form . "Kazantsev") (:end . 153)\n  (:start . 144) (:id . 68))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 156) (:start . 154)\n  (:id . 69))\n ((:tag . 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"Preisinger") (:end . 199)\n  (:start . 189) (:id . 80))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 202) (:start . 200)\n  (:id . 81))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 206) (:start . 203)\n  (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 207) (:start . 206)\n  (:id . 83))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 212) (:start . 208)\n  (:id . 84))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 213) (:start . 212)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "Wheeler") (:form . "Wheeler") (:end . 221)\n  (:start . 214) (:id . 86))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 224) (:start . 222)\n  (:id . 87))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 228) (:start . 225)\n  (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 229) (:start . 228)\n  (:id . 89))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 234) (:start . 230)\n  (:id . 90))\n ((:tag . ")") (:stem . 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5502268@unknown@formal@none@1@S@In addition, wild-type Htt can suppress the cell death induced by mutant polyQ-expanded Htt in vitro (Leavitt et al., 2001; Van Raamsdonk et al., 2005).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "VB") (:stem . "suppress") (:form . "suppress") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "induce") (:form . "induced") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 72)\n  (:start . 66) (:id . 54))\n ((:tag . "JJ") (:stem . "polyq-expanded") (:form . "polyQ-expanded")\n  (:end . 87) (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "htt") (:form . "Htt") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 100) (:start . 95)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Leavitt") (:form . "Leavitt") (:end . 109)\n  (:start . 102) (:id . 60))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 122) (:start . 118)\n  (:id . 64))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 123) (:start . 122)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Van") (:form . "Van") (:end . 127) (:start . 124)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Raamsdonk") (:form . "Raamsdonk") (:end . 137)\n  (:start . 128) (:id . 67))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 140) (:start . 138)\n  (:id . 68))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 144) (:start . 141)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 70))\n ((:tag . "CD") (:stem . "2005") (:form . "2005") (:end . 150) (:start . 146)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s8.17) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502269@unknown@formal@none@1@S@Furthermore, wild-type Htt is proposed to have a neuroprotective role as expression of Htt can protect cultured striatal neurons from stress- and toxin-mediated cell death (Rigamonti et al., 2000).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "neuroprotective") (:form . "neuroprotective")\n  (:end . 64) (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 69) (:start . 65)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 83)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 94) (:start . 91)\n  (:id . 57))\n ((:tag . "VB") (:stem . "protect") (:form . "protect") (:end . 102)\n  (:start . 95) (:id . 58))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 111)\n  (:start . 103) (:id . 59))\n ((:tag . "JJ") (:stem . "striatal") (:form . "striatal") (:end . 120)\n  (:start . 112) (:id . 60))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 128)\n  (:start . 121) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 133) (:start . 129)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "stress-") (:form . "stress-") (:end . 141)\n  (:start . 134) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "toxin-mediated") (:form . "toxin-mediated")\n  (:end . 160) (:start . 146) (:id . 65))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 165) (:start . 161)\n  (:id . 66))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 171)\n  (:start . 166) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 173) (:start . 172)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Rigamonti") (:form . "Rigamonti") (:end . 182)\n  (:start . 173) (:id . 69))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 185) (:start . 183)\n  (:id . 70))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 189) (:start . 186)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n  (:id . 72))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 195) (:start . 191)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 196) (:start . 195)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x8.18.1) (:span 30 38)))\n (:hscopes ((:id . :x8.18.1) (:span 13 69)))\n (:identifiers (:sid . :s8.18) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502270@unknown@formal@none@1@S@Since its identification, the normal function of Htt has been subject to extensive investigation (Cattaneo et al., 2001; Harjes and Wanker, 2003).@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 24) (:start . 10) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "subject") (:form . "subject") (:end . 69)\n  (:start . 62) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 82)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "investigation") (:form . "investigation")\n  (:end . 96) (:start . 83) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Cattaneo") (:form . "Cattaneo") (:end . 106)\n  (:start . 98) (:id . 58))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 109) (:start . 107)\n  (:id . 59))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 113) (:start . 110)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 119) (:start . 115)\n  (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Harjes") (:form . "Harjes") (:end . 127)\n  (:start . 121) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Wanker") (:form . "Wanker") (:end . 138)\n  (:start . 132) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 67))\n ((:tag . "CD") (:stem . "2003") (:form . "2003") (:end . 144) (:start . 140)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.19) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502271@unknown@formal@none@1@S@The murine Htt homolog (also known as Hdh) is essential during early mouse development, as Htt-null mice die during gastrulation at embryonic day 7.5 (Duyao et al., 1995; Nasir et al., 1995; Zeitlin et al., 1995).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "murine") (:form . "murine") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 34) (:start . 29)\n  (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Hdh") (:form . "Hdh") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 45) (:start . 43)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 55)\n  (:start . 46) (:id . 53))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 62)\n  (:start . 56) (:id . 54))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 68) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 74) (:start . 69)\n  (:id . 56))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 86)\n  (:start . 75) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "htt-null") (:form . "Htt-null") (:end . 99)\n  (:start . 91) (:id . 60))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 104)\n  (:start . 100) (:id . 61))\n ((:tag . "VBP") (:stem . "die") (:form . "die") (:end . 108) (:start . 105)\n  (:id . 62))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 115)\n  (:start . 109) (:id . 63))\n ((:tag . "NN") (:stem . "gastrulation") (:form . "gastrulation") (:end . 128)\n  (:start . 116) (:id . 64))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 131) (:start . 129)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 141)\n  (:start . 132) (:id . 66))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 145) (:start . 142)\n  (:id . 67))\n ((:tag . "CD") (:stem . "7.5") (:form . "7.5") (:end . 149) (:start . 146)\n  (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Duyao") (:form . "Duyao") (:end . 156)\n  (:start . 151) (:id . 70))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 159) (:start . 157)\n  (:id . 71))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 163) (:start . 160)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 73))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 169) (:start . 165)\n  (:id . 74))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 170) (:start . 169)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Nasir") (:form . "Nasir") (:end . 176)\n  (:start . 171) (:id . 76))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 179) (:start . 177)\n  (:id . 77))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 183) (:start . 180)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 79))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 189) (:start . 185)\n  (:id . 80))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 190) (:start . 189)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Zeitlin") (:form . "Zeitlin") (:end . 198)\n  (:start . 191) (:id . 82))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 201) (:start . 199)\n  (:id . 83))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 205) (:start . 202)\n  (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 206) (:start . 205)\n  (:id . 85))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 211) (:start . 207)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 212) (:start . 211)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s8.20) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502272@unknown@formal@none@1@S@Chimeric analysis demonstrated that the early embryonic lethality is the result of a crucial role of Hdh in extraembryonic membranes, as this lethality can be rescued by providing wild-type Hdh function in extraembryonic tissue (Dragatsis et al., 1998).@(((:tag . "JJ") (:stem . "chimeric") (:form . "Chimeric") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 30)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 45) (:start . 40)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 55)\n  (:start . 46) (:id . 48))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 65)\n  (:start . 56) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 68) (:start . 66)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 79)\n  (:start . 73) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 92)\n  (:start . 85) (:id . 55))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Hdh") (:form . "Hdh") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "extraembryonic") (:form . "extraembryonic")\n  (:end . 122) (:start . 108) (:id . 60))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 132)\n  (:start . 123) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 136) (:start . 134)\n  (:id . 63))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 141) (:start . 137)\n  (:id . 64))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 151)\n  (:start . 142) (:id . 65))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 155) (:start . 152)\n  (:id . 66))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 158) (:start . 156)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 166)\n  (:start . 159) (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 169) (:start . 167)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "provide") (:form . "providing") (:end . 179)\n  (:start . 170) (:id . 70))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 189)\n  (:start . 180) (:id . 71))\n ((:tag . "NN") (:stem . "hdh") (:form . "Hdh") (:end . 193) (:start . 190)\n  (:id . 72))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 202)\n  (:start . 194) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 205) (:start . 203)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "extraembryonic") (:form . "extraembryonic")\n  (:end . 220) (:start . 206) (:id . 75))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 227)\n  (:start . 221) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 229) (:start . 228)\n  (:id . 77))\n ((:tag . "NN") (:stem . "dragatsis") (:form . "Dragatsis") (:end . 238)\n  (:start . 229) (:id . 78))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 241) (:start . 239)\n  (:id . 79))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 245) (:start . 242)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 246) (:start . 245)\n  (:id . 81))\n ((:tag . "CD") (:stem . "1998") (:form . "1998") (:end . 251) (:start . 247)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 252) (:start . 251)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 253) (:start . 252)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x8.21.1) (:span 152 155)))\n (:hscopes ((:id . :x8.21.1) (:span 137 227)))\n (:identifiers (:sid . :s8.21) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502273@unknown@formal@none@1@S@Conditional knockout of Hdh in the mouse forebrain at postnatal or late embryonic stages causes a progressive neurodegenerative phenotype, lending support to the hypothesis that depletion of normal Htt activity during disease progression contributes to HD pathogenesis (Dragatsis et al., 2000).@(((:tag . "JJ") (:stem . "conditional") (:form . "Conditional") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "knockout") (:form . "knockout") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Hdh") (:form . "Hdh") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . 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"pathogenesis") (:form . "pathogenesis") (:end . 268)\n  (:start . 256) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 270) (:start . 269)\n  (:id . 80))\n ((:tag . "NN") (:stem . "dragatsis") (:form . "Dragatsis") (:end . 279)\n  (:start . 270) (:id . 81))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 282) (:start . 280)\n  (:id . 82))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 286) (:start . 283)\n  (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 287) (:start . 286)\n  (:id . 84))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 292) (:start . 288)\n  (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 293) (:start . 292)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 294) (:start . 293)\n  (:id . 87)))@@@1@46@((:hcues ((:id . :x8.22.1) (:span 162 172)))\n (:hscopes ((:id . :x8.22.1) (:span 162 268)))\n (:identifiers (:sid . :s8.22) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502274@unknown@formal@none@1@S@A more recent study in zebrafish, which used morpholino oligos to transiently knockdown endogenous Htt, suggests that Htt has a role in normal blood function and iron utilization (Lumsden et al., 2007).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "zebrafish") (:form . "zebrafish") (:end . 32)\n  (:start . 23) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 39) (:start . 34)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "morpholino") (:form . "morpholino") (:end . 55)\n  (:start . 45) (:id . 51))\n ((:tag . "NNS") (:stem . "oligo") (:form . "oligos") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "RB") (:stem . "transiently") (:form . "transiently") (:end . 77)\n  (:start . 66) (:id . 54))\n ((:tag . "JJ") (:stem . "knockdown") (:form . "knockdown") (:end . 87)\n  (:start . 78) (:id . 55))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 98)\n  (:start . 88) (:id . 56))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 112)\n  (:start . 104) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 117) (:start . 113)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 121) (:start . 118)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 125) (:start . 122)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 127) (:start . 126)\n  (:id . 63))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 132) (:start . 128)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 142)\n  (:start . 136) (:id . 66))\n ((:tag . "NN") (:stem . "blood") (:form . "blood") (:end . 148)\n  (:start . 143) (:id . 67))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 157)\n  (:start . 149) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 69))\n ((:tag . "NN") (:stem . "iron") (:form . "iron") (:end . 166) (:start . 162)\n  (:id . 70))\n ((:tag . "NN") (:stem . "utilization") (:form . "utilization") (:end . 178)\n  (:start . 167) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 180) (:start . 179)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Lumsden") (:form . "Lumsden") (:end . 187)\n  (:start . 180) (:id . 73))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 190) (:start . 188)\n  (:id . 74))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 194) (:start . 191)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n  (:id . 76))\n ((:tag . "CD") (:stem . "2007") (:form . "2007") (:end . 200) (:start . 196)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 201) (:start . 200)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x8.23.1) (:span 104 112)))\n (:hscopes ((:id . :x8.23.1) (:span 104 178)))\n (:identifiers (:sid . :s8.23) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502275@unknown@formal@none@1@S@Currently, little is known about the normal biological function of wild-type Htt (Cattaneo et al., 2005).@(((:tag . "RB") (:stem . "currently") (:form . "Currently") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "little") (:form . "little") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 76)\n  (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "htt") (:form . "Htt") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Cattaneo") (:form . "Cattaneo") (:end . 90)\n  (:start . 82) (:id . 56))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "CD") (:stem . "2005") (:form . "2005") (:end . 103) (:start . 99)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.24) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502276@unknown@formal@none@1@S@Htt encodes a large cytoplasmic protein of 350 kDa.@(((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "CD") (:stem . "350") (:form . "350") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "kda") (:form . "kDa") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 51) (:start . 50)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s8.25) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502277@unknown@formal@none@1@S@Structural analysis of Htt proteins identified the presence of many HEAT (huntingtin, elongation factor 3, the A subunit of protein phosphatase 2A and TOR1) repeats, which are approximately 40-amino acid (a.a.) long structural motifs, composed of two anti-parallel helices, of unknown function (Andrade and Bork, 1995).@(((:tag . "JJ") (:stem . "structural") (:form . "Structural") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 46)\n  (:start . 36) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 59)\n  (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "huntingtin") (:form . "huntingtin") (:end . 84)\n  (:start . 74) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "elongation") (:form . "elongation") (:end . 96)\n  (:start . 86) (:id . 56))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 103)\n  (:start . 97) (:id . 57))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "NN") (:stem . "subunit") (:form . "subunit") (:end . 120)\n  (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 63))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 131)\n  (:start . 124) (:id . 64))\n ((:tag . "NN") (:stem . "phosphatase") (:form . "phosphatase") (:end . 143)\n  (:start . 132) (:id . 65))\n ((:tag . "NN") (:stem . "2a") (:form . "2A") (:end . 146) (:start . 144)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 67))\n ((:tag . "NN") (:stem . "tor1") (:form . "TOR1") (:end . 155) (:start . 151)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 164)\n  (:start . 157) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 71))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 171)\n  (:start . 166) (:id . 72))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 175) (:start . 172)\n  (:id . 73))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 189) (:start . 176) (:id . 74))\n ((:tag . "JJ") (:stem . "40-amino") (:form . "40-amino") (:end . 198)\n  (:start . 190) (:id . 75))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 203) (:start . 199)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 205) (:start . 204)\n  (:id . 77))\n ((:tag . "NN") (:stem . "a.a.") (:form . "a.a.") (:end . 209) (:start . 205)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 215) (:start . 211)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 226)\n  (:start . 216) (:id . 81))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 233)\n  (:start . 227) (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 234) (:start . 233)\n  (:id . 83))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 243)\n  (:start . 235) (:id . 84))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 246) (:start . 244)\n  (:id . 85))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 250) (:start . 247)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "anti-parallel") (:form . "anti-parallel")\n  (:end . 264) (:start . 251) (:id . 87))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 272)\n  (:start . 265) (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 273) (:start . 272)\n  (:id . 89))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 276) (:start . 274)\n  (:id . 90))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 284)\n  (:start . 277) (:id . 91))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 293)\n  (:start . 285) (:id . 92))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 295) (:start . 294)\n  (:id . 93))\n ((:tag . "NNP") (:stem . "Andrade") (:form . "Andrade") (:end . 302)\n  (:start . 295) (:id . 94))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 306) (:start . 303)\n  (:id . 95))\n ((:tag . "NNP") (:stem . "Bork") (:form . "Bork") (:end . 311) (:start . 307)\n  (:id . 96))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 312) (:start . 311)\n  (:id . 97))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 317) (:start . 313)\n  (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 318) (:start . 317)\n  (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 319) (:start . 318)\n  (:id . 100)))@@@1@59@((:identifiers (:sid . :s8.26) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502278@unknown@formal@none@1@S@No other domains have been identified in Htt to suggest a biological function for the protein.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "VB") (:stem . "suggest") (:form . "suggest") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 68)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 77)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 93)\n  (:start . 86) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x8.27.1) (:span 48 55)))\n (:hscopes ((:id . :x8.27.1) (:span 48 93)))\n (:identifiers (:sid . :s8.27) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502279@unknown@formal@none@1@S@Functional studies in mammalian systems, mainly from protein interaction assays, have associated Htt with diverse cellular processes including: endocytosis; modulation of synapse structure and synaptic transmission; transcriptional regulation, especially of the brain-derived neurotrophic factor (BDNF) which is essential for the survival of the striatal neurons affected in HD; axonal transport of BDNF and vesicles; and apoptosis (Cattaneo et al., 2001; Cattaneo et al., 2005; Harjes and Wanker, 2003; Zuccato et al., 2001; Zuccato and Cattaneo, 2007).@(((:tag . "JJ") (:stem . "functional") (:form . "Functional") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 18)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . 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5502280@unknown@formal@none@1@S@Importantly, only a few of these proposed functions of Htt have been directly tested in vivo owing to the early embryonic lethality associated with Htt-null mutant mice.@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 63) (:start . 59)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 77)\n  (:start . 69) (:id . 55))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 84) (:start . 78)\n  (:id . 56))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "owe") (:form . "owing") (:end . 98) (:start . 93)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 111)\n  (:start . 106) (:id . 62))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 121)\n  (:start . 112) (:id . 63))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 131)\n  (:start . 122) (:id . 64))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 142)\n  (:start . 132) (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 147) (:start . 143)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "htt-null") (:form . "Htt-null") (:end . 156)\n  (:start . 148) (:id . 67))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 163)\n  (:start . 157) (:id . 68))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 168)\n  (:start . 164) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.29) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502281@unknown@formal@none@1@S@In an extensive search for Htt homologs in other species, Li et al. (Li et al., 1999) identified a single HTT homolog in Drosophila (htt, hereafter referred to as dhtt).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 15)\n  (:start . 6) (:id . 44))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Li") (:form . "Li") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 56))\n ((:tag . "FW") (:stem . "li") (:form . "Li") (:end . 71) (:start . 69)\n  (:id . 57))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 74) (:start . 72)\n  (:id . 58))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 78) (:start . 75)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 84) (:start . 80)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 96)\n  (:start . 86) (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 98) (:start . 97)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 105)\n  (:start . 99) (:id . 65))\n ((:tag . "NN") (:stem . "htt") (:form . "HTT") (:end . 109) (:start . 106)\n  (:id . 66))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 117)\n  (:start . 110) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 131)\n  (:start . 121) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 70))\n ((:tag . "NN") (:stem . "htt") (:form . "htt") (:end . 136) (:start . 133)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 72))\n ((:tag . "RB") (:stem . "hereafter") (:form . "hereafter") (:end . 147)\n  (:start . 138) (:id . 73))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 156)\n  (:start . 148) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 159) (:start . 157)\n  (:id . 75))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 162) (:start . 160)\n  (:id . 76))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 167) (:start . 163)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 168) (:start . 167)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s8.30) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502282@unknown@formal@none@1@S@By sequence comparison, the homologous regions between Drosophila and human Htt proteins are mainly located within five discrete areas, including three relatively large continuous regions and two small segments, that cover about one-third of the total protein length (supplementary material Fig. S1A).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "region") (:form . 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"of") (:end . 241) (:start . 239)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 245) (:start . 242)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 251)\n  (:start . 246) (:id . 80))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 259)\n  (:start . 252) (:id . 81))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 266)\n  (:start . 260) (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 268) (:start . 267)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 281) (:start . 268) (:id . 84))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 290)\n  (:start . 282) (:id . 85))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 295) (:start . 291)\n  (:id . 86))\n ((:tag . "NNP") (:stem . "S1A") (:form . "S1A") (:end . 299) (:start . 296)\n  (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 300) (:start . 299)\n  (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 301) (:start . 300)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s8.31) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502283@unknown@formal@none@1@S@At the amino acid level, these homologous regions, which are comprised of about 1200 a.a. residues in Drosophila Htt (dHtt), share around 24% identity and 49% similarity (Li et al., 1999).@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 47))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 30) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 41)\n  (:start . 31) (:id . 49))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 49)\n  (:start . 42) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "comprise") (:form . "comprised") (:end . 70)\n  (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "RB") (:stem . "about") (:form . "about") (:end . 79) (:start . 74)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1200") (:form . "1200") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . "NN") (:stem . "a.a.") (:form . "a.a.") (:end . 89) (:start . 85)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 98)\n  (:start . 90) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 101) (:start . 99)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 112)\n  (:start . 102) (:id . 61))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 122) (:start . 118)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "share") (:form . "share") (:end . 130)\n  (:start . 125) (:id . 67))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 137)\n  (:start . 131) (:id . 68))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 140) (:start . 138)\n  (:id . 69))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 141) (:start . 140)\n  (:id . 70))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 150)\n  (:start . 142) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 72))\n ((:tag . "CD") (:stem . "49") (:form . "49") (:end . 157) (:start . 155)\n  (:id . 73))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 158) (:start . 157)\n  (:id . 74))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 169)\n  (:start . 159) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 171) (:start . 170)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Li") (:form . "Li") (:end . 173) (:start . 171)\n  (:id . 77))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 176) (:start . 174)\n  (:id . 78))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 180) (:start . 177)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 181) (:start . 180)\n  (:id . 80))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 186) (:start . 182)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.32) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502284@unknown@formal@none@1@S@In addition to the sequence similarity, other shared features support the proposal that the Drosophila gene identified in the study by Li et al. is indeed the fly homolog of human Htt (Li et al., 1999).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "shared") (:form . "shared") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 61)\n  (:start . 53) (:id . 51))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 69)\n  (:start . 62) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "proposal") (:form . "proposal") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 102)\n  (:start . 92) (:id . 57))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 107) (:start . 103)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 118)\n  (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 131)\n  (:start . 126) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 134) (:start . 132)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Li") (:form . "Li") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 144) (:start . 141)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 147) (:start . 145)\n  (:id . 67))\n ((:tag . "RB") (:stem . "indeed") (:form . "indeed") (:end . 154)\n  (:start . 148) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "fly") (:form . "fly") (:end . 162) (:start . 159)\n  (:id . 70))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 170)\n  (:start . 163) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 179)\n  (:start . 174) (:id . 73))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 183) (:start . 180)\n  (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Li") (:form . "Li") (:end . 187) (:start . 185)\n  (:id . 76))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 190) (:start . 188)\n  (:id . 77))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 194) (:start . 191)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n  (:id . 79))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 200) (:start . 196)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 201) (:start . 200)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x8.33.1) (:span 74 82)))\n (:hscopes ((:id . :x8.33.1) (:span 74 183)))\n (:identifiers (:sid . :s8.33) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502285@unknown@formal@none@1@S@For example, in terms of the protein size, both the Drosophila and human Htt proteins are unusually large and contain 3583 and 3144 a.a. residues, respectively (Li et al., 1999).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 21) (:start . 16)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 36)\n  (:start . 29) (:id . 49))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 51))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 47) (:start . 43)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 62)\n  (:start . 52) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 72) (:start . 67)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 76) (:start . 73)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 85)\n  (:start . 77) (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 89) (:start . 86)\n  (:id . 59))\n ((:tag . "RB") (:stem . "unusually") (:form . "unusually") (:end . 99)\n  (:start . 90) (:id . 60))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 105)\n  (:start . 100) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 117)\n  (:start . 110) (:id . 63))\n ((:tag . "CD") (:stem . "3583") (:form . "3583") (:end . 122) (:start . 118)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 65))\n ((:tag . "CD") (:stem . "3144") (:form . "3144") (:end . 131) (:start . 127)\n  (:id . 66))\n ((:tag . "NN") (:stem . "a.a.") (:form . "a.a.") (:end . 136) (:start . 132)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 145)\n  (:start . 137) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 69))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 159)\n  (:start . 147) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 161) (:start . 160)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Li") (:form . "Li") (:end . 163) (:start . 161)\n  (:id . 72))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 166) (:start . 164)\n  (:id . 73))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 170) (:start . 167)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 75))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 176) (:start . 172)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 177) (:start . 176)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s8.34) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502286@unknown@formal@none@1@S@In addition, the regions with a relatively high level of conservation are not only clustered in large continuous stretches, but are also located in the same order and distributed over the entire length of the proteins.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 42)\n  (:start . 32) (:id . 49))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 69)\n  (:start . 57) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 82) (:start . 78)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "cluster") (:form . "clustered") (:end . 92)\n  (:start . 83) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "continuous") (:form . "continuous") (:end . 112)\n  (:start . 102) (:id . 60))\n ((:tag . "NNS") (:stem . "stretch") (:form . "stretches") (:end . 122)\n  (:start . 113) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 62))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 131) (:start . 128)\n  (:id . 64))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 136) (:start . 132)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "locate") (:form . "located") (:end . 144)\n  (:start . 137) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 147) (:start . 145)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 156) (:start . 152)\n  (:id . 69))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 162)\n  (:start . 157) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "distribute") (:form . "distributed") (:end . 178)\n  (:start . 167) (:id . 72))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 183) (:start . 179)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 187) (:start . 184)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 194)\n  (:start . 188) (:id . 75))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 201)\n  (:start . 195) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 204) (:start . 202)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 208) (:start . 205)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 217)\n  (:start . 209) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s8.35) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502287@unknown@formal@none@1@S@Moreover, dhtt and mammalian HD genes share similar patterns of gene expression (Li et al., 1999) (Fig. 1).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "share") (:form . "share") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 51)\n  (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 60)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 79)\n  (:start . 69) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Li") (:form . "Li") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 96) (:start . 92)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 103) (:start . 99)\n  (:id . 63))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 105) (:start . 104)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s8.36) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502288@unknown@formal@none@1@S@Interestingly, although an HTT homolog exists in Drosophila, no HTT-like gene has been found in other less complex eukaryote species such as C. elegans or the yeast S. cerevisiae (Li et al., 1999).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "HTT") (:form . "HTT") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "VBZ") (:stem . "exist") (:form . "exists") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 59)\n  (:start . 49) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 51))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "htt-like") (:form . "HTT-like") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 114)\n  (:start . 107) (:id . 61))\n ((:tag . "JJ") (:stem . "eukaryote") (:form . "eukaryote") (:end . 124)\n  (:start . 115) (:id . 62))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 132)\n  (:start . 125) (:id . 63))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 137) (:start . 133)\n  (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 143) (:start . 141)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 151)\n  (:start . 144) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 154) (:start . 152)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n  (:id . 69))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 164)\n  (:start . 159) (:id . 70))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 167) (:start . 165)\n  (:id . 71))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 178)\n  (:start . 168) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 180) (:start . 179)\n  (:id . 73))\n ((:tag . "FW") (:stem . "li") (:form . "Li") (:end . 182) (:start . 180)\n  (:id . 74))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 185) (:start . 183)\n  (:id . 75))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 189) (:start . 186)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n  (:id . 77))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 195) (:start . 191)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 196) (:start . 195)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s8.37) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502289@unknown@formal@none@1@S@Ubiquitous expression of dhtt in Drosophila.@(((:tag . "JJ") (:stem . "ubiquitous") (:form . "Ubiquitous") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 44) (:start . 43)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s8.38) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502290@unknown@formal@none@1@S@(A–F) dhtt is widely expressed at a low level during Drosophila development, as revealed by whole-mount in situ hybridization.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–F") (:form . "A–F") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 10) (:start . 6)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 46))\n ((:tag . "RB") (:stem . "widely") (:form . "widely") (:end . 20)\n  (:start . 14) (:id . 47))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 30)\n  (:start . 21) (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 35) (:start . 34)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 39) (:start . 36)\n  (:id . 51))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 45) (:start . 40)\n  (:id . 52))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 52)\n  (:start . 46) (:id . 53))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 63)\n  (:start . 53) (:id . 54))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 75)\n  (:start . 64) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "reveal") (:form . "revealed") (:end . 88)\n  (:start . 80) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "whole-mount") (:form . "whole-mount") (:end . 103)\n  (:start . 92) (:id . 60))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . "FW") (:stem . "situ") (:form . "situ") (:end . 111) (:start . 107)\n  (:id . 62))\n ((:tag . "NN") (:stem . "hybridization") (:form . "hybridization")\n  (:end . 125) (:start . 112) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.39) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502291@unknown@formal@none@1@S@(A,B) Stage 15 Drosophila embryos stained with digoxigenin (DIG)-labeled dhtt antisense probes revealed the low-level and ubiquitous expression of the dhtt transcript (A); control embryos at the corresponding stage, which were stained with dhtt sense probes, showed only minimal background signals (B).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A,B") (:form . "A,B") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Stage") (:form . "Stage") (:end . 11) (:start . 6)\n  (:id . 45))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 14) (:start . 12)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 25)\n  (:start . 15) (:id . 47))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "digoxigenin") (:form . "digoxigenin") (:end . 58)\n  (:start . 47) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "DIG)-labeled") (:form . "DIG)-labeled") (:end . 72)\n  (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "antisense") (:form . "antisense") (:end . 87)\n  (:start . 78) (:id . 55))\n ((:tag . "NNS") (:stem . "probe") (:form . "probes") (:end . 94)\n  (:start . 88) (:id . 56))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 103)\n  (:start . 95) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "low-level") (:form . 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")") (:end . 170) (:start . 169)\n  (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 171) (:start . 170)\n  (:id . 70))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 179)\n  (:start . 172) (:id . 71))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 187)\n  (:start . 180) (:id . 72))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 190) (:start . 188)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 194) (:start . 191)\n  (:id . 74))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 208)\n  (:start . 195) (:id . 75))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 214)\n  (:start . 209) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 215) (:start . 214)\n  (:id . 77))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 221)\n  (:start . 216) (:id . 78))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 226) (:start . 222)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 234)\n  (:start . 227) (:id . 80))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 239) (:start . 235)\n  (:id . 81))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 244) (:start . 240)\n  (:id . 82))\n ((:tag . "NN") (:stem . "sense") (:form . "sense") (:end . 250)\n  (:start . 245) (:id . 83))\n ((:tag . "NNS") (:stem . "probe") (:form . "probes") (:end . 257)\n  (:start . 251) (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 258) (:start . 257)\n  (:id . 85))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 265)\n  (:start . 259) (:id . 86))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 270) (:start . 266)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "minimal") (:form . "minimal") (:end . 278)\n  (:start . 271) (:id . 88))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 289)\n  (:start . 279) (:id . 89))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 297)\n  (:start . 290) (:id . 90))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 299) (:start . 298)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 300) (:start . 299)\n  (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 301) (:start . 300)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 302) (:start . 301)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s8.40) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502292@unknown@formal@none@1@S@All embryos are lateral views, anterior to the left and dorsal side up.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "view") (:form . "views") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "left") (:form . "left") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 62)\n  (:start . 56) (:id . 53))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.41) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502293@unknown@formal@none@1@S@(C–F) Third instar larval tissues hybridized with dhtt antisense probes.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C–F") (:form . "C–F") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "third") (:form . "Third") (:end . 11) (:start . 6)\n  (:id . 45))\n ((:tag . "IN") (:stem . "instar") (:form . "instar") (:end . 18)\n  (:start . 12) (:id . 46))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 25)\n  (:start . 19) (:id . 47))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "VBN") (:stem . "hybridize") (:form . "hybridized") (:end . 44)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "antisense") (:form . "antisense") (:end . 64)\n  (:start . 55) (:id . 52))\n ((:tag . "NNS") (:stem . "probe") (:form . "probes") (:end . 71)\n  (:start . 65) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s8.42) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502294@unknown@formal@none@1@S@Low-level and ubiquitous dhtt expression was observed in the brain (C), wing and leg (D) and eye imaginal discs (E).@(((:tag . "JJ") (:stem . "low-level") (:form . "Low-level") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "ubiquitous") (:form . "ubiquitous") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 53)\n  (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 66) (:start . 61)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "wing") (:form . "wing") (:end . 76) (:start . 72)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "NN") (:stem . "leg") (:form . "leg") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 87) (:start . 86)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 62))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 96) (:start . 93)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "imaginal") (:form . "imaginal") (:end . 105)\n  (:start . 97) (:id . 64))\n ((:tag . "NNS") (:stem . "disc") (:form . "discs") (:end . 111)\n  (:start . 106) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 114) (:start . 113)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s8.43) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502295@unknown@formal@none@1@S@(F) A negative in situ control – an eye imaginal disc from a dhtt deletion mutant stained in parallel – showed only minimal background signals.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 5) (:start . 4)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 14)\n  (:start . 6) (:id . 46))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 47))\n ((:tag . "FW") (:stem . "situ") (:form . "situ") (:end . 22) (:start . 18)\n  (:id . 48))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 30)\n  (:start . 23) (:id . 49))\n ((:tag . "VBD") (:stem . "–") (:form . "–") (:end . 32) (:start . 31)\n  (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 35) (:start . 33)\n  (:id . 51))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 39) (:start . 36)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "imaginal") (:form . "imaginal") (:end . 48)\n  (:start . 40) (:id . 53))\n ((:tag . "NN") (:stem . "disc") (:form . "disc") (:end . 53) (:start . 49)\n  (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 58) (:start . 54)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 65) (:start . 61)\n  (:id . 57))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 74)\n  (:start . 66) (:id . 58))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 81)\n  (:start . 75) (:id . 59))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 89)\n  (:start . 82) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "parallel") (:form . "parallel") (:end . 101)\n  (:start . 93) (:id . 62))\n ((:tag . "NN") (:stem . "–") (:form . "–") (:end . 103) (:start . 102)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 110)\n  (:start . 104) (:id . 64))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 115) (:start . 111)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "minimal") (:form . "minimal") (:end . 123)\n  (:start . 116) (:id . 66))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 134)\n  (:start . 124) (:id . 67))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 142)\n  (:start . 135) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s8.44) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502296@unknown@formal@none@1@S@(G–K) The dHtt protein predominantly localizes to the cytoplasm.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "G–K") (:form . "G–K") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 9) (:start . 6)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 14) (:start . 10)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 22)\n  (:start . 15) (:id . 47))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 36) (:start . 23) (:id . 48))\n ((:tag . "VBZ") (:stem . "localize") (:form . "localizes") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cytoplasm") (:form . "cytoplasm") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s8.45) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502297@unknown@formal@none@1@S@(G,H) In transfected Drosophila S2 cells, ectopically expressed dHtt protein (green) was found predominantly in the cytoplasm; it was also found on cellular protrusions, but was mostly excluded from the nucleus.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "G,H") (:form . "G,H") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "In") (:end . 8) (:start . 6)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 20)\n  (:start . 9) (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 31)\n  (:start . 21) (:id . 47))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "RB") (:stem . "ectopically") (:form . "ectopically") (:end . 53)\n  (:start . 42) (:id . 51))\n ((:tag . "VBD") (:stem . "express") (:form . "expressed") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 76)\n  (:start . 69) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 83) (:start . 78)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 88) (:start . 85)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 94) (:start . 89)\n  (:id . 59))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 108) (:start . 95) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 62))\n ((:tag . "NN") (:stem . "cytoplasm") (:form . "cytoplasm") (:end . 125)\n  (:start . 116) (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 126) (:start . 125)\n  (:id . 64))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 129) (:start . 127)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 138) (:start . 134)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 144)\n  (:start . 139) (:id . 68))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 147) (:start . 145)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 156)\n  (:start . 148) (:id . 70))\n ((:tag . "NNS") (:stem . "protrusion") (:form . "protrusions") (:end . 168)\n  (:start . 157) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 72))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 173) (:start . 170)\n  (:id . 73))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 177) (:start . 174)\n  (:id . 74))\n ((:tag . "RB") (:stem . "mostly") (:form . "mostly") (:end . 184)\n  (:start . 178) (:id . 75))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 193)\n  (:start . 185) (:id . 76))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 198) (:start . 194)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 202) (:start . 199)\n  (:id . 78))\n ((:tag . "NN") (:stem . "nucleus") (:form . "nucleus") (:end . 210)\n  (:start . 203) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s8.46) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502298@unknown@formal@none@1@S@(G) Overlaying images of the S2 cells co-stained with phalloidin (red), which detects F–actin, and the DNA dye DAPI (blue) reveal the overall cell morphology and the cell nuclei, respectively.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "overlaying") (:form . "Overlaying") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 21)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 31) (:start . 29)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 37) (:start . 32)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "co-staine") (:form . "co-stained") (:end . 48)\n  (:start . 38) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "NN") (:stem . "phalloidin") (:form . "phalloidin") (:end . 64)\n  (:start . 54) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 77) (:start . 72)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "detect") (:form . "detects") (:end . 85)\n  (:start . 78) (:id . 59))\n ((:tag . "NNP") (:stem . "F–actin") (:form . "F–actin") (:end . 93)\n  (:start . 86) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 106) (:start . 103)\n  (:id . 64))\n ((:tag . "NN") (:stem . "dye") (:form . "dye") (:end . 110) (:start . 107)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "DAPI") (:form . "DAPI") (:end . 115) (:start . 111)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 67))\n ((:tag . "NN") (:stem . "blue") (:form . "blue") (:end . 121) (:start . 117)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 69))\n ((:tag . "VBP") (:stem . "reveal") (:form . "reveal") (:end . 129)\n  (:start . 123) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 141)\n  (:start . 134) (:id . 72))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 146) (:start . 142)\n  (:id . 73))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 157)\n  (:start . 147) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 76))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 170) (:start . 166)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 177)\n  (:start . 171) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 178) (:start . 177)\n  (:id . 79))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 191)\n  (:start . 179) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s8.47) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502299@unknown@formal@none@1@S@(I–K) Cytoplasmic localization of the dHtt protein (green) ectopically expressed in Drosophila third instar larval imaginal disc tissues.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "I–K") (:form . "I–K") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "Cytoplasmic") (:end . 17)\n  (:start . 6) (:id . 45))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 30)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 50)\n  (:start . 43) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 57) (:start . 52)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "RB") (:stem . "ectopically") (:form . "ectopically") (:end . 70)\n  (:start . 59) (:id . 54))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 80)\n  (:start . 71) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 94)\n  (:start . 84) (:id . 57))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 100) (:start . 95)\n  (:id . 58))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 107)\n  (:start . 101) (:id . 59))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 114)\n  (:start . 108) (:id . 60))\n ((:tag . "JJ") (:stem . "imaginal") (:form . "imaginal") (:end . 123)\n  (:start . 115) (:id . 61))\n ((:tag . "NN") (:stem . "disc") (:form . "disc") (:end . 128) (:start . 124)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 136)\n  (:start . 129) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.48) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502300@unknown@formal@none@1@S@(I) The anti-dHtt antibody can recognize overexpressed dHtt in the patched expression domain driven by patched-Gal4 and shows the characteristic striped dHtt expression pattern in the middle of the wing and leg imaginal discs.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "LS") (:stem . "i") (:form . "I") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "anti-dhtt") (:form . "anti-dHtt") (:end . 17)\n  (:start . 8) (:id . 46))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 26)\n  (:start . 18) (:id . 47))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "VB") (:stem . "recognize") (:form . "recognize") (:end . 40)\n  (:start . 31) (:id . 49))\n ((:tag . "JJ") (:stem . "overexpressed") (:form . "overexpressed")\n  (:end . 54) (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "patch") (:form . "patched") (:end . 74)\n  (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 85)\n  (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 92)\n  (:start . 86) (:id . 56))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 99)\n  (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 102) (:start . 100)\n  (:id . 58))\n ((:tag . "NN") (:stem . "patched-gal4") (:form . "patched-Gal4") (:end . 115)\n  (:start . 103) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 125)\n  (:start . 120) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 144) (:start . 130) (:id . 63))\n ((:tag . "VBN") (:stem . "strip") (:form . "striped") (:end . 152)\n  (:start . 145) (:id . 64))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 157) (:start . 153)\n  (:id . 65))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 168)\n  (:start . 158) (:id . 66))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 176)\n  (:start . 169) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 179) (:start . 177)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n  (:id . 69))\n ((:tag . "NN") (:stem . "middle") (:form . "middle") (:end . 190)\n  (:start . 184) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 193) (:start . 191)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n  (:id . 72))\n ((:tag . "NN") (:stem . "wing") (:form . "wing") (:end . 202) (:start . 198)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 206) (:start . 203)\n  (:id . 74))\n ((:tag . "NN") (:stem . "leg") (:form . "leg") (:end . 210) (:start . 207)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "imaginal") (:form . "imaginal") (:end . 219)\n  (:start . 211) (:id . 76))\n ((:tag . "NNS") (:stem . "disc") (:form . "discs") (:end . 225)\n  (:start . 220) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s8.49) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502301@unknown@formal@none@1@S@Genotype: patched-Gal4/+>UAS-dhtt/+.@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotype") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "CD") (:stem . "patched-Gal4/+>UAS-dhtt/+")\n  (:form . "patched-Gal4/+>UAS-dhtt/+") (:end . 35) (:start . 10) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 36) (:start . 35)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s8.50) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502302@unknown@formal@none@1@S@(J,K) High-magnification view of an eye imaginal disc with ectopically expressed dHtt protein [green (J)], which shows a mainly cytoplasmic localization.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "J,K") (:form . "J,K") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "high-magnification") (:form . "High-magnification")\n  (:end . 24) (:start . 6) (:id . 45))\n ((:tag . "NN") (:stem . "view") (:form . "view") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "imaginal") (:form . "imaginal") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "disc") (:form . "disc") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "RB") (:stem . "ectopically") (:form . "ectopically") (:end . 70)\n  (:start . 59) (:id . 53))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 80)\n  (:start . 71) (:id . 54))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 93)\n  (:start . 86) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 100) (:start . 95)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 105) (:start . 104)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 63))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 112)\n  (:start . 107) (:id . 64))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 118)\n  (:start . 113) (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 120) (:start . 119)\n  (:id . 66))\n ((:tag . "RB") (:stem . "mainly") (:form . "mainly") (:end . 127)\n  (:start . 121) (:id . 67))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 139)\n  (:start . 128) (:id . 68))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 152)\n  (:start . 140) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.51) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502303@unknown@formal@none@1@S@(K) Overlaying images of the same eye disc region co-stained with DAPI (red) to reveal the cell nuclei.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "K") (:form . "K") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "overlaying") (:form . "Overlaying") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 21)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 33) (:start . 29)\n  (:id . 49))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 37) (:start . 34)\n  (:id . 50))\n ((:tag . "NN") (:stem . "disc") (:form . "disc") (:end . 42) (:start . 38)\n  (:id . 51))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 49)\n  (:start . 43) (:id . 52))\n ((:tag . "VBN") (:stem . "co-staine") (:form . "co-stained") (:end . 60)\n  (:start . 50) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "DAPI") (:form . "DAPI") (:end . 70) (:start . 66)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 75) (:start . 72)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n  (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 79) (:start . 77)\n  (:id . 59))\n ((:tag . "VB") (:stem . "reveal") (:form . "reveal") (:end . 86)\n  (:start . 80) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 61))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 95) (:start . 91)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 102)\n  (:start . 96) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.52) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502304@unknown@formal@none@1@S@Genotype: GMR-Gal4/+>UAS-dhtt/+.@(((:tag . "NNP") (:stem . "Genotype") (:form . "Genotype") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "CD") (:stem . "GMR-Gal4/+>UAS-dhtt/+")\n  (:form . "GMR-Gal4/+>UAS-dhtt/+") (:end . 31) (:start . 10) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 32) (:start . 31)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s8.53) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502305@unknown@formal@none@1@S@The identification of a Drosophila Htt homolog provides a unique opportunity to evaluate the role of Htt in this well-established genetic model system.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 64)\n  (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "opportunity") (:form . "opportunity") (:end . 76)\n  (:start . 65) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 88)\n  (:start . 80) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 112) (:start . 108)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "well-established") (:form . "well-established")\n  (:end . 129) (:start . 113) (:id . 61))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 137)\n  (:start . 130) (:id . 62))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 143)\n  (:start . 138) (:id . 63))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 150)\n  (:start . 144) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s8.54) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502306@unknown@formal@none@1@S@Several cellular processes implicated in Htt function, including axonal transport and synapse formation, have been well-characterized in Drosophila, allowing an in vivo evaluation of their relationship with Htt.@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 26)\n  (:start . 17) (:id . 44))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 37)\n  (:start . 27) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 53)\n  (:start . 45) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 64)\n  (:start . 55) (:id . 50))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 71)\n  (:start . 65) (:id . 51))\n ((:tag . "NN") (:stem . "transport") (:form . "transport") (:end . 81)\n  (:start . 72) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 53))\n ((:tag . "NN") (:stem . "synapse") (:form . "synapse") (:end . 93)\n  (:start . 86) (:id . 54))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 103)\n  (:start . 94) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 109) (:start . 105)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 114) (:start . 110)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "well-characterize") (:form . "well-characterized")\n  (:end . 133) (:start . 115) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 147)\n  (:start . 137) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "allow") (:form . "allowing") (:end . 157)\n  (:start . 149) (:id . 63))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 160) (:start . 158)\n  (:id . 64))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 163) (:start . 161)\n  (:id . 65))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 168) (:start . 164)\n  (:id . 66))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 179)\n  (:start . 169) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 182) (:start . 180)\n  (:id . 68))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 188)\n  (:start . 183) (:id . 69))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 201)\n  (:start . 189) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 206) (:start . 202)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 210) (:start . 207)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s8.55) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502307@unknown@formal@none@1@S@Further, as fly models of HD have been well-established, this model allows an in vivo examination of the function of endogenous Htt in HD pathogenesis (Marsh and Thompson, 2006; Steffan et al., 2001).@(((:tag . "RB") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "fly") (:form . "fly") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 22)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 33) (:start . 29)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 38) (:start . 34)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "well-established") (:form . "well-established")\n  (:end . 55) (:start . 39) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 74)\n  (:start . 68) (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 85) (:start . 81)\n  (:id . 58))\n ((:tag . "NN") (:stem . "examination") (:form . "examination") (:end . 97)\n  (:start . 86) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 61))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 113)\n  (:start . 105) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 127)\n  (:start . 117) (:id . 64))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 131) (:start . 128)\n  (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 137) (:start . 135)\n  (:id . 67))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 150)\n  (:start . 138) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 152) (:start . 151)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Marsh") (:form . "Marsh") (:end . 157)\n  (:start . 152) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Thompson") (:form . "Thompson") (:end . 170)\n  (:start . 162) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 73))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 176) (:start . 172)\n  (:id . 74))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 177) (:start . 176)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Steffan") (:form . "Steffan") (:end . 185)\n  (:start . 178) (:id . 76))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 188) (:start . 186)\n  (:id . 77))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 192) (:start . 189)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 193) (:start . 192)\n  (:id . 79))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 198) (:start . 194)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s8.56) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502308@unknown@formal@none@1@S@In this study, we report the isolation of a dhtt mutant and describe its phenotype.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "report") (:form . "report") (:end . 24)\n  (:start . 18) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . "isolation") (:form . "isolation") (:end . 38)\n  (:start . 29) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 48) (:start . 44)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 55)\n  (:start . 49) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 68)\n  (:start . 60) (:id . 55))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 82)\n  (:start . 73) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s8.57) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502309@unknown@formal@none@1@S@Further, we examine how the removal of endogenous dhtt affects several cellular processes that have previously been implicated with Htt, and test how the loss of endogenous dhtt affects the pathogenesis associated with an established Drosophila model of polyQ toxicity (HD-Q93).@(((:tag . "RB") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "examine") (:form . "examine") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "removal") (:form . "removal") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 49)\n  (:start . 39) (:id . 50))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "affect") (:form . "affects") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 79)\n  (:start . 71) (:id . 54))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 89)\n  (:start . 80) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 99) (:start . 95)\n  (:id . 57))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 110)\n  (:start . 100) (:id . 58))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 126)\n  (:start . 116) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 131) (:start . 127)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 135) (:start . 132)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 64))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 145) (:start . 141)\n  (:id . 65))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 149) (:start . 146)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 67))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 158) (:start . 154)\n  (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 161) (:start . 159)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 172)\n  (:start . 162) (:id . 70))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 177) (:start . 173)\n  (:id . 71))\n ((:tag . "VBZ") (:stem . "affect") (:form . "affects") (:end . 185)\n  (:start . 178) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 189) (:start . 186)\n  (:id . 73))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 202)\n  (:start . 190) (:id . 74))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 213)\n  (:start . 203) (:id . 75))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 218) (:start . 214)\n  (:id . 76))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 221) (:start . 219)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "establish") (:form . "established") (:end . 233)\n  (:start . 222) (:id . 78))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 244)\n  (:start . 234) (:id . 79))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 250)\n  (:start . 245) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 253) (:start . 251)\n  (:id . 81))\n ((:tag . "NN") (:stem . "polyq") (:form . "polyQ") (:end . 259)\n  (:start . 254) (:id . 82))\n ((:tag . "NN") (:stem . "toxicity") (:form . "toxicity") (:end . 268)\n  (:start . 260) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 270) (:start . 269)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 276)\n  (:start . 270) (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 277) (:start . 276)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 278) (:start . 277)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s8.58) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502310@unknown@formal@none@1@S@RESULTS@(((:tag . "NNS") (:stem . "results") (:form . "RESULTS") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s8.59) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5502311@unknown@formal@none@1@S@HEAT repeats in dHtt@(((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 20) (:start . 16)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s8.60) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502312@unknown@formal@none@1@S@Considering the limited sequence homology between mammalian and fly Htt, it is important to examine the extent of the structural similarity between these proteins.@(((:tag . "VBG") (:stem . "consider") (:form . "Considering") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "NN") (:stem . "homology") (:form . "homology") (:end . 41)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 49)\n  (:start . 42) (:id . 47))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 59)\n  (:start . 50) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "fly") (:form . "fly") (:end . 67) (:start . 64)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 71) (:start . 68)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 88)\n  (:start . 79) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 99)\n  (:start . 92) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 110)\n  (:start . 104) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 128)\n  (:start . 118) (:id . 62))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 139)\n  (:start . 129) (:id . 63))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 147)\n  (:start . 140) (:id . 64))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 153)\n  (:start . 148) (:id . 65))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 162)\n  (:start . 154) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s8.61) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502313@unknown@formal@none@1@S@In the Htt family proteins, the HEAT repeat is the only identifiable structural motif (Andrade and Bork, 1995; Cattaneo et al., 2005).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 17)\n  (:start . 11) (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 36) (:start . 32)\n  (:id . 49))\n ((:tag . "NN") (:stem . "repeat") (:form . "repeat") (:end . 43)\n  (:start . 37) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 46) (:start . 44)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 52))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "identifiable") (:form . "identifiable") (:end . 68)\n  (:start . 56) (:id . 54))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 79)\n  (:start . 69) (:id . 55))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Andrade") (:form . "Andrade") (:end . 94)\n  (:start . 87) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Bork") (:form . "Bork") (:end . 103) (:start . 99)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 61))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 109) (:start . 105)\n  (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 110) (:start . 109)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Cattaneo") (:form . "Cattaneo") (:end . 119)\n  (:start . 111) (:id . 64))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 122) (:start . 120)\n  (:id . 65))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 126) (:start . 123)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 67))\n ((:tag . "CD") (:stem . "2005") (:form . "2005") (:end . 132) (:start . 128)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.62) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502314@unknown@formal@none@1@S@A previous phylogenetic study identified 16 HEAT repeats in human Htt and, notably, 14 of these 16 repeats were also found in insect Htt proteins including dHtt (Tartari et al., 2008).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 23)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 29) (:start . 24)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 56)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . "RB") (:stem . "notably") (:form . "notably") (:end . 82)\n  (:start . 75) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 95) (:start . 90)\n  (:id . 59))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 98) (:start . 96)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 106)\n  (:start . 99) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 111) (:start . 107)\n  (:id . 62))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 116) (:start . 112)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 122)\n  (:start . 117) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 125) (:start . 123)\n  (:id . 65))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 132)\n  (:start . 126) (:id . 66))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 136) (:start . 133)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 145)\n  (:start . 137) (:id . 68))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 155)\n  (:start . 146) (:id . 69))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 160) (:start . 156)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Tartari") (:form . "Tartari") (:end . 169)\n  (:start . 162) (:id . 72))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 172) (:start . 170)\n  (:id . 73))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 176) (:start . 173)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 75))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 182) (:start . 178)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s8.63) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502315@unknown@formal@none@1@S@A less stringent structural analysis predicted up to 40 HEAT repeats (including the AAA, ADB and IMB subgroups) in human Htt (see Methods).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "stringent") (:form . "stringent") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 36)\n  (:start . 28) (:id . 46))\n ((:tag . "VBD") (:stem . "predict") (:form . "predicted") (:end . 46)\n  (:start . 37) (:id . 47))\n ((:tag . "RB") (:stem . "up") (:form . "up") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 79)\n  (:start . 70) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AAA") (:form . "AAA") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "ADB") (:form . "ADB") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "IMB") (:form . "IMB") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "subgroup") (:form . "subgroups") (:end . 110)\n  (:start . 101) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 120)\n  (:start . 115) (:id . 64))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 124) (:start . 121)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 66))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 129) (:start . 126)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 137)\n  (:start . 130) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.64) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502316@unknown@formal@none@1@S@Interestingly, using the same parameter, 38 HEAT repeats could be identified in dHtt (see supplementary material Fig. S1 for details of the predicted HEAT repeats).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "parameter") (:form . "parameter") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 76)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 103) (:start . 90) (:id . 59))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 112)\n  (:start . 104) (:id . 60))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 117) (:start . 113)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 120) (:start . 118)\n  (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 124) (:start . 121)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 132)\n  (:start . 125) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 149)\n  (:start . 140) (:id . 67))\n ((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 154) (:start . 150)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 162)\n  (:start . 155) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 163) (:start . 162)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s8.65) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502317@unknown@formal@none@1@S@Further, these HEAT repeats span the entire length of each protein and have a similar distribution, clustering in four groups at the N-, middle- and C-terminal regions, which have a large overlap with their segments of homologous sequences (supplementary material Fig. S1B).@(((:tag . "RB") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "VBP") (:stem . "span") (:form . "span") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 75) (:start . 71)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 85)\n  (:start . 78) (:id . 57))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 98)\n  (:start . 86) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "cluster") (:form . "clustering") (:end . 110)\n  (:start . 100) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 118) (:start . 114)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 125)\n  (:start . 119) (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 128) (:start . 126)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 65))\n ((:tag . "NN") (:stem . "n-") (:form . "N-") (:end . 135) (:start . 133)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 67))\n ((:tag . "NN") (:stem . "middle-") (:form . "middle-") (:end . 144)\n  (:start . 137) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 159)\n  (:start . 149) (:id . 70))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 167)\n  (:start . 160) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 72))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 174)\n  (:start . 169) (:id . 73))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 179) (:start . 175)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 181) (:start . 180)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 187)\n  (:start . 182) (:id . 76))\n ((:tag . "NN") (:stem . "overlap") (:form . "overlap") (:end . 195)\n  (:start . 188) (:id . 77))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 200) (:start . 196)\n  (:id . 78))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 206)\n  (:start . 201) (:id . 79))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 215)\n  (:start . 207) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 218) (:start . 216)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 229)\n  (:start . 219) (:id . 82))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 239)\n  (:start . 230) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 241) (:start . 240)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 254) (:start . 241) (:id . 85))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 263)\n  (:start . 255) (:id . 86))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 268) (:start . 264)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "S1B") (:form . "S1B") (:end . 272) (:start . 269)\n  (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 273) (:start . 272)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 274) (:start . 273)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s8.66) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502318@unknown@formal@none@1@S@Although further studies are needed to elucidate the structure of the Htt proteins, this rather remarkable similarity raises the possibility of a conserved secondary structure among Htt family proteins and that both human and Drosophila Htt proteins are composed largely of repeated HEAT motifs.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "need") (:form . "needed") (:end . 35) (:start . 29)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "VB") (:stem . "elucidate") (:form . "elucidate") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 62)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 95)\n  (:start . 89) (:id . 57))\n ((:tag . "JJ") (:stem . "remarkable") (:form . "remarkable") (:end . 106)\n  (:start . 96) (:id . 58))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 117)\n  (:start . 107) (:id . 59))\n ((:tag . "VBZ") (:stem . "raise") (:form . "raises") (:end . 124)\n  (:start . 118) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n  (:id . 61))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 140)\n  (:start . 129) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 145) (:start . 144)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 155)\n  (:start . 146) (:id . 65))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 165)\n  (:start . 156) (:id . 66))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 175)\n  (:start . 166) (:id . 67))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 181)\n  (:start . 176) (:id . 68))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 185) (:start . 182)\n  (:id . 69))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 192)\n  (:start . 186) (:id . 70))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 201)\n  (:start . 193) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 205) (:start . 202)\n  (:id . 72))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 210) (:start . 206)\n  (:id . 73))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 215) (:start . 211)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 221)\n  (:start . 216) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 225) (:start . 222)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 236)\n  (:start . 226) (:id . 77))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 240) (:start . 237)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 249)\n  (:start . 241) (:id . 79))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 253) (:start . 250)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "compose") (:form . "composed") (:end . 262)\n  (:start . 254) (:id . 81))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 270)\n  (:start . 263) (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 273) (:start . 271)\n  (:id . 83))\n ((:tag . "VBN") (:stem . "repeat") (:form . "repeated") (:end . 282)\n  (:start . 274) (:id . 84))\n ((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 287) (:start . 283)\n  (:id . 85))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 294)\n  (:start . 288) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 295) (:start . 294)\n  (:id . 87)))@@@1@46@((:hcues ((:id . :x8.67.1) (:span 118 140)))\n (:hscopes ((:id . :x8.67.1) (:span 118 294)))\n (:identifiers (:sid . :s8.67) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502319@unknown@formal@none@1@S@Ubiquitous expression of dhtt in Drosophila@(((:tag . "JJ") (:stem . "ubiquitous") (:form . "Ubiquitous") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 43)\n  (:start . 33) (:id . 47)))@@@1@6@((:identifiers (:sid . :s8.68) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502320@unknown@formal@none@1@S@Previous analysis has shown that dhtt is widely expressed during all developmental stages from embryos to adults (Li et al., 1999).@(((:tag . "JJ") (:stem . "previous") (:form . "Previous") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "RB") (:stem . "widely") (:form . "widely") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 64)\n  (:start . 58) (:id . 51))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 82) (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 89)\n  (:start . 83) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 102)\n  (:start . 95) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 112)\n  (:start . 106) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Li") (:form . "Li") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 123) (:start . 120)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 129) (:start . 125)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s8.69) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502321@unknown@formal@none@1@S@We confirmed the expression of the dhtt transcript in adults using reverse transcription (RT)-PCR (data not shown) (Fig. 5C).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "transcript") (:form . "transcript") (:end . 50)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 74)\n  (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 88) (:start . 75) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "RT)-PCR") (:form . "RT)-PCR") (:end . 97)\n  (:start . 90) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 103) (:start . 99)\n  (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 113)\n  (:start . 108) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 120) (:start . 116)\n  (:id . 63))\n ((:tag . "NN") (:stem . "5c") (:form . "5C") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s8.70) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502322@unknown@formal@none@1@S@To examine the tissue-specific dhtt expression, we performed whole-mount RNA in situ hybridization.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "tissue-specific") (:form . "tissue-specific")\n  (:end . 30) (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 46)\n  (:start . 36) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "perform") (:form . "performed") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . "JJ") (:stem . "whole-mount") (:form . "whole-mount") (:end . 72)\n  (:start . 61) (:id . 51))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 76) (:start . 73)\n  (:id . 52))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "FW") (:stem . "situ") (:form . "situ") (:end . 84) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "hybridization") (:form . "hybridization")\n  (:end . 98) (:start . 85) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.71) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502323@unknown@formal@none@1@S@Staining with two DIG-labeled antisense probes, targeting different regions of dhtt, revealed similar ubiquitous dhtt expression at different stages of fly embryogenesis and in larval tissues (Fig. 1A–F and data not shown), whereas a positive control performed in parallel gave rise to robust in situ signals (supplementary material Fig. S2).@(((:tag . "VBG") (:stem . "stain") (:form . "Staining") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "dig-labeled") (:form . "DIG-labeled") (:end . 29)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "antisense") (:form . "antisense") (:end . 39)\n  (:start . 30) (:id . 46))\n ((:tag . "NNS") (:stem . "probe") (:form . "probes") (:end . 46)\n  (:start . 40) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 67)\n  (:start . 58) (:id . 50))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 75)\n  (:start . 68) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 52))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 83) (:start . 79)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 93)\n  (:start . 85) (:id . 55))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 101)\n  (:start . 94) (:id . 56))\n ((:tag . "JJ") (:stem . "ubiquitous") (:form . "ubiquitous") (:end . 112)\n  (:start . 102) (:id . 57))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 117) (:start . 113)\n  (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 128)\n  (:start . 118) (:id . 59))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 131) (:start . 129)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 141)\n  (:start . 132) (:id . 61))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 148)\n  (:start . 142) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 63))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 155) (:start . 152)\n  (:id . 64))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 169) (:start . 156) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 173) (:start . 170)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 176) (:start . 174)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 183)\n  (:start . 177) (:id . 68))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 191)\n  (:start . 184) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 193) (:start . 192)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 197) (:start . 193)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "1A–F") (:form . "1A–F") (:end . 202) (:start . 198)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 206) (:start . 203)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 211)\n  (:start . 207) (:id . 74))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 215) (:start . 212)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 221)\n  (:start . 216) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 222) (:start . 221)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 223) (:start . 222)\n  (:id . 78))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 231)\n  (:start . 224) (:id . 79))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 233) (:start . 232)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 242)\n  (:start . 234) (:id . 81))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 250)\n  (:start . 243) (:id . 82))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 260)\n  (:start . 251) (:id . 83))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 263) (:start . 261)\n  (:id . 84))\n ((:tag . "NN") (:stem . "parallel") (:form . "parallel") (:end . 272)\n  (:start . 264) (:id . 85))\n ((:tag . "VBD") (:stem . "give") (:form . "gave") (:end . 277) (:start . 273)\n  (:id . 86))\n ((:tag . "NN") (:stem . "rise") (:form . "rise") (:end . 282) (:start . 278)\n  (:id . 87))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 285) (:start . 283)\n  (:id . 88))\n ((:tag . "JJ") (:stem . "robust") (:form . 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5502324@unknown@formal@none@1@S@Importantly, of the two negative controls included in the assay, one using sense dhtt RNA probes on wild-type samples (Fig. 1B) and the other using the same set of antisense dhtt RNA probes against tissues from a dhtt deletion mutant that had been generated subsequently (Fig. 1F), both produced much weaker background signals.@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "control") (:form . 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"other") (:end . 141)\n  (:start . 136) (:id . 69))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 147) (:start . 142)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 156) (:start . 152)\n  (:id . 72))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 160) (:start . 157)\n  (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "antisense") (:form . "antisense") (:end . 173)\n  (:start . 164) (:id . 75))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 178) (:start . 174)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 182) (:start . 179)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "probe") (:form . "probes") (:end . 189)\n  (:start . 183) (:id . 78))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 197)\n  (:start . 190) (:id . 79))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 205)\n  (:start . 198) (:id . 80))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 210) (:start . 206)\n  (:id . 81))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 212) (:start . 211)\n  (:id . 82))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 217) (:start . 213)\n  (:id . 83))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 226)\n  (:start . 218) (:id . 84))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 233)\n  (:start . 227) (:id . 85))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 238) (:start . 234)\n  (:id . 86))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 242) (:start . 239)\n  (:id . 87))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 247) (:start . 243)\n  (:id . 88))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 257)\n  (:start . 248) (:id . 89))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 270)\n  (:start . 258) (:id . 90))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 272) (:start . 271)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 276) (:start . 272)\n  (:id . 92))\n ((:tag . "NN") (:stem . "1f") (:form . "1F") (:end . 279) (:start . 277)\n  (:id . 93))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 280) (:start . 279)\n  (:id . 94))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 281) (:start . 280)\n  (:id . 95))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 286) (:start . 282)\n  (:id . 96))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 295)\n  (:start . 287) (:id . 97))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 300) (:start . 296)\n  (:id . 98))\n ((:tag . "JJR") (:stem . "weak") (:form . "weaker") (:end . 307)\n  (:start . 301) (:id . 99))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 318)\n  (:start . 308) (:id . 100))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 326)\n  (:start . 319) (:id . 101))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 327) (:start . 326)\n  (:id . 102)))@@@1@61@((:identifiers (:sid . :s8.73) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502325@unknown@formal@none@1@S@Together, these data indicate that dhtt is widely expressed at low levels during all stages of Drosophila development.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "RB") (:stem . "widely") (:form . "widely") (:end . 49)\n  (:start . 43) (:id . 50))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 59)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 80)\n  (:start . 74) (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 91)\n  (:start . 85) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 105)\n  (:start . 95) (:id . 59))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 117)\n  (:start . 106) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x8.74.1) (:span 21 34)))\n (:hscopes ((:id . :x8.74.1) (:span 21 117)))\n (:identifiers (:sid . :s8.74) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502326@unknown@formal@none@1@S@Compromised mobility and viability of aging dhtt-ko mutants.@(((:tag . "VBN") (:stem . "compromise") (:form . "Compromised") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 44))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "age") (:form . "aging") (:end . 43) (:start . 38)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 59)\n  (:start . 52) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s8.75) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502327@unknown@formal@none@1@S@(A) Spontaneous locomotion assay.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "spontaneous") (:form . "Spontaneous") (:end . 15)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "locomotion") (:form . "locomotion") (:end . 26)\n  (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 33) (:start . 32)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s8.76) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502328@unknown@formal@none@1@S@dhtt-ko mutants show normal mobility at day 15 but older animals show significantly reduced mobility.@(((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 27)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 36)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "old") (:form . "older") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 83) (:start . 70) (:id . 54))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 91)\n  (:start . 84) (:id . 55))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 100)\n  (:start . 92) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.77) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502329@unknown@formal@none@1@S@(B) Age-dependent survival rate of adult animals.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "age-dependent") (:form . "Age-dependent")\n  (:end . 17) (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s8.78) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502330@unknown@formal@none@1@S@dhtt-ko mutants have a reduced life span.@(((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "span") (:form . "span") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 41) (:start . 40)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s8.79) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502331@unknown@formal@none@1@S@Both the mobility and viability defects in dhtt-ko mutants were rescued by the presence of a dhtt genomic minigene construct (‘dhtt-ko Rescue’).@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 58)\n  (:start . 51) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 63) (:start . 59)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 87)\n  (:start . 79) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 92) (:start . 91)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 97) (:start . 93)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 105)\n  (:start . 98) (:id . 59))\n ((:tag . "NN") (:stem . "minigene") (:form . "minigene") (:end . 114)\n  (:start . 106) (:id . 60))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 124)\n  (:start . 115) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 62))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 127) (:start . 126)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 134)\n  (:start . 127) (:id . 64))\n ((:tag . "NN") (:stem . "Rescue") (:form . "Rescue") (:end . 141)\n  (:start . 135) (:id . 65))\n ((:tag . "''") (:stem . "’") (:form . "’") (:end . 142) (:start . 141)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.80) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502332@unknown@formal@none@1@S@Flies were collected from at least three different batches.@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "batch") (:form . "batches") (:end . 58)\n  (:start . 51) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s8.81) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502333@unknown@formal@none@1@S@The total number of flies counted for viability quantification were: wild type, n=659; dhtt-ko, n =1573; dhtt-ko Rescue, n=804; elav-Gal4/+; dhtt-ko, n=550.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "count") (:form . "counted") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "quantification") (:form . "quantification")\n  (:end . 62) (:start . 48) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . "NN") (:stem . "n=659") (:form . "n=659") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 94)\n  (:start . 87) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 97) (:start . 96)\n  (:id . 60))\n ((:tag . "NN") (:stem . "=1573") (:form . "=1573") (:end . 103) (:start . 98)\n  (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 112)\n  (:start . 105) (:id . 63))\n ((:tag . "NN") (:stem . "rescue") (:form . "Rescue") (:end . 119)\n  (:start . 113) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 65))\n ((:tag . "NN") (:stem . "n=804") (:form . "n=804") (:end . 126)\n  (:start . 121) (:id . 66))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 127) (:start . 126)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "elav-gal4/+") (:form . "elav-Gal4/+") (:end . 139)\n  (:start . 128) (:id . 68))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 140) (:start . 139)\n  (:id . 69))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 148)\n  (:start . 141) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 71))\n ((:tag . "NN") (:stem . "n=550") (:form . "n=550") (:end . 155)\n  (:start . 150) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s8.82) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502334@unknown@formal@none@1@S@The difference between wild-type and dhtt-ko flies is statistically significant, P=0.0001, Student’s t-test.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 50) (:start . 45)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n  (:end . 67) (:start . 54) (:id . 50))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 79)\n  (:start . 68) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "P=0.0001") (:form . "P=0.0001") (:end . 89)\n  (:start . 81) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 98)\n  (:start . 91) (:id . 55))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 100) (:start . 99)\n  (:id . 56))\n ((:tag . "NN") (:stem . "t-test") (:form . "t-test") (:end . 107)\n  (:start . 101) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s8.83) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502335@unknown@formal@none@1@S@The difference between wild-type and dhtt-ko Rescue flies is not statistically significant, P=0.36.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "NN") (:stem . "rescue") (:form . "Rescue") (:end . 51)\n  (:start . 45) (:id . 48))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 57) (:start . 52)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n  (:end . 78) (:start . 65) (:id . 52))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 90)\n  (:start . 79) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "P=0.36") (:form . "P=0.36") (:end . 98)\n  (:start . 92) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.84) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502336@unknown@formal@none@1@S@The difference between wild-type and elav-Gal4/+; dhtt-ko flies is statistically significant, P<0.00001.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "elav-gal4/+") (:form . "elav-Gal4/+") (:end . 48)\n  (:start . 37) (:id . 47))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 49) (:start . 48)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 63) (:start . 58)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n  (:end . 80) (:start . 67) (:id . 52))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 92)\n  (:start . 81) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "P<0.00001") (:form . "P<0.00001") (:end . 103)\n  (:start . 94) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.85) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502337@unknown@formal@none@1@S@The data in (A,B) are presented as the means±s.e.m.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "A,B") (:form . "A,B") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 31)\n  (:start . 22) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 34) (:start . 32)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 51))\n ((:tag . "NN") (:stem . "means±s.e.m") (:form . "means±s.e.m") (:end . 50)\n  (:start . 39) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 51) (:start . 50)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s8.86) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502338@unknown@formal@none@1@S@(C) RT-PCR analysis confirmed that expression of endogenous dhtt was lost in dhtt-ko mutants (lane 3) but was restored by the presence of the dhtt genomic minigene rescue construct (lane 4), similar to that in wild-type controls (lane 2).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 10)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 19)\n  (:start . 11) (:id . 46))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 29)\n  (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 45)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 59)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 68) (:start . 65)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "lose") (:form . "lost") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 84)\n  (:start . 77) (:id . 56))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 61))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 105) (:start . 102)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 109) (:start . 106)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "restore") (:form . "restored") (:end . 118)\n  (:start . 110) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 121) (:start . 119)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 66))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 134)\n  (:start . 126) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 69))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 146) (:start . 142)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 154)\n  (:start . 147) (:id . 71))\n ((:tag . "NN") (:stem . "minigene") (:form . "minigene") (:end . 163)\n  (:start . 155) (:id . 72))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 170)\n  (:start . 164) (:id . 73))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 180)\n  (:start . 171) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 182) (:start . 181)\n  (:id . 75))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 186) (:start . 182)\n  (:id . 76))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 188) (:start . 187)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 198)\n  (:start . 191) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 201) (:start . 199)\n  (:id . 81))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 206) (:start . 202)\n  (:id . 82))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 209) (:start . 207)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 219)\n  (:start . 210) (:id . 84))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 228)\n  (:start . 220) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 230) (:start . 229)\n  (:id . 86))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 234) (:start . 230)\n  (:id . 87))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 236) (:start . 235)\n  (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 237) (:start . 236)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s8.87) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502339@unknown@formal@none@1@S@RT-PCR was performed on total RNA samples extracted from adult animals of each of the indicated genotypes.@(((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 62) (:start . 57)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 70)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "indicated") (:form . "indicated") (:end . 95)\n  (:start . 86) (:id . 57))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 105)\n  (:start . 96) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s8.88) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502340@unknown@formal@none@1@S@Primers for RT-PCR were located in adjacent exons in the control rp49 gene (the group of four wells on the left) or in neighboring exons at the N-terminal (targeting exons 5 and 6, dhtt-N), middle (targeting exons 13 and 15, dhtt-M) and C-terminal (targeting exons 23 and 24, dhtt-C) regions of the dhtt gene (see Methods).@(((:tag . "NNS") (:stem . "primer") (:form . "Primers") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "adjacent") (:form . "adjacent") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "rp49") (:form . "rp49") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 85) (:start . 80)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 93) (:start . 89)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "well") (:form . "wells") (:end . 99) (:start . 94)\n  (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 102) (:start . 100)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 62))\n ((:tag . "NN") (:stem . "left") (:form . "left") (:end . 111) (:start . 107)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 115) (:start . 113)\n  (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 118) (:start . 116)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "neighbor") (:form . "neighboring") (:end . 130)\n  (:start . 119) (:id . 67))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 136)\n  (:start . 131) (:id . 68))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 139) (:start . 137)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 154)\n  (:start . 144) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 165)\n  (:start . 156) (:id . 73))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 171)\n  (:start . 166) (:id . 74))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 173) (:start . 172)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 177) (:start . 174)\n  (:id . 76))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 179) (:start . 178)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "dhtt-N") (:form . "dhtt-N") (:end . 187)\n  (:start . 181) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "middle") (:form . "middle") (:end . 196)\n  (:start . 190) (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 198) (:start . 197)\n  (:id . 83))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 207)\n  (:start . 198) (:id . 84))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 213)\n  (:start . 208) (:id . 85))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 216) (:start . 214)\n  (:id . 86))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 220) (:start . 217)\n  (:id . 87))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 223) (:start . 221)\n  (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 224) (:start . 223)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "dhtt-M") (:form . "dhtt-M") (:end . 231)\n  (:start . 225) (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 232) (:start . 231)\n  (:id . 91))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 236) (:start . 233)\n  (:id . 92))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 247)\n  (:start . 237) (:id . 93))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 249) (:start . 248)\n  (:id . 94))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 258)\n  (:start . 249) (:id . 95))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 264)\n  (:start . 259) (:id . 96))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 267) (:start . 265)\n  (:id . 97))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 271) (:start . 268)\n  (:id . 98))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 274) (:start . 272)\n  (:id . 99))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 275) (:start . 274)\n  (:id . 100))\n ((:tag . "NN") (:stem . "dhtt-c") (:form . "dhtt-C") (:end . 282)\n  (:start . 276) (:id . 101))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 283) (:start . 282)\n  (:id . 102))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 291)\n  (:start . 284) (:id . 103))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 294) (:start . 292)\n  (:id . 104))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 298) (:start . 295)\n  (:id . 105))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 303) (:start . 299)\n  (:id . 106))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 308) (:start . 304)\n  (:id . 107))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 310) (:start . 309)\n  (:id . 108))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 313) (:start . 310)\n  (:id . 109))\n ((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 321)\n  (:start . 314) (:id . 110))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 322) (:start . 321)\n  (:id . 111))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 323) (:start . 322)\n  (:id . 112)))@@@1@71@((:identifiers (:sid . :s8.89) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502341@unknown@formal@none@1@S@The lane 1s are controls of PCR products from a wild-type genomic DNA template using these primer pairs, which are longer than the RT-PCR products generated by the same pair of primers owing to the spliced-out introns, thus confirming that RT-PCR products were indeed amplified from transcribed RNA templates.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "lane") (:form . "lane") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "1") (:form . "1s") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . 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"by") (:end . 159) (:start . 157)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 168) (:start . 164)\n  (:id . 71))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 173) (:start . 169)\n  (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 184)\n  (:start . 177) (:id . 74))\n ((:tag . "VBG") (:stem . "owe") (:form . "owing") (:end . 190) (:start . 185)\n  (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 193) (:start . 191)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "spliced-out") (:form . "spliced-out") (:end . 209)\n  (:start . 198) (:id . 78))\n ((:tag . "NNS") (:stem . "intron") (:form . "introns") (:end . 217)\n  (:start . 210) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 218) (:start . 217)\n  (:id . 80))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 223) (:start . 219)\n  (:id . 81))\n ((:tag . "VBG") (:stem . "confirm") (:form . "confirming") (:end . 234)\n  (:start . 224) (:id . 82))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 239) (:start . 235)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 246)\n  (:start . 240) (:id . 84))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 255)\n  (:start . 247) (:id . 85))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 260) (:start . 256)\n  (:id . 86))\n ((:tag . "RB") (:stem . "indeed") (:form . "indeed") (:end . 267)\n  (:start . 261) (:id . 87))\n ((:tag . "VBN") (:stem . "amplify") (:form . "amplified") (:end . 277)\n  (:start . 268) (:id . 88))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 282) (:start . 278)\n  (:id . 89))\n ((:tag . "VBN") (:stem . "transcribe") (:form . "transcribed") (:end . 294)\n  (:start . 283) (:id . 90))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 298) (:start . 295)\n  (:id . 91))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 308)\n  (:start . 299) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 309) (:start . 308)\n  (:id . 93)))@@@1@52@((:identifiers (:sid . :s8.90) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502342@unknown@formal@none@1@S@w1118: wild-type control.@(((:tag . "LS") (:stem . "w1118") (:form . "w1118") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 25) (:start . 24)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s8.91) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502343@unknown@formal@none@1@S@dHtt is a cytoplasmic protein@(((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 9) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 21)\n  (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 29)\n  (:start . 22) (:id . 46)))@@@1@5@((:identifiers (:sid . :s8.92) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502344@unknown@formal@none@1@S@Mammalian Htt proteins are largely cytoplasmic with a widespread expression pattern (DiFiglia et al., 1995; Gutekunst et al., 1995; Sharp et al., 1995).@(((:tag . "JJ") (:stem . "mammalian") (:form . "Mammalian") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 46)\n  (:start . 35) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "widespread") (:form . "widespread") (:end . 64)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 75)\n  (:start . 65) (:id . 51))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 83)\n  (:start . 76) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "DiFiglia") (:form . "DiFiglia") (:end . 93)\n  (:start . 85) (:id . 54))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 96) (:start . 94)\n  (:id . 55))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 100) (:start . 97)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 106) (:start . 102)\n  (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 107) (:start . 106)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Gutekunst") (:form . "Gutekunst") (:end . 117)\n  (:start . 108) (:id . 60))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 120) (:start . 118)\n  (:id . 61))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 124) (:start . 121)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 63))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 130) (:start . 126)\n  (:id . 64))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 131) (:start . 130)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Sharp") (:form . "Sharp") (:end . 137)\n  (:start . 132) (:id . 66))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 140) (:start . 138)\n  (:id . 67))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 144) (:start . 141)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 69))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 150) (:start . 146)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s8.93) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502345@unknown@formal@none@1@S@To determine the expression and subcellular localization of the endogenous dHtt protein, we developed an affinity-purified polyclonal antibody against dHtt.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "subcellular") (:form . "subcellular") (:end . 43)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 56)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 74)\n  (:start . 64) (:id . 51))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 79) (:start . 75)\n  (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 87)\n  (:start . 80) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "develop") (:form . "developed") (:end . 101)\n  (:start . 92) (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 104) (:start . 102)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "affinity-purified") (:form . "affinity-purified")\n  (:end . 122) (:start . 105) (:id . 58))\n ((:tag . "JJ") (:stem . "polyclonal") (:form . "polyclonal") (:end . 133)\n  (:start . 123) (:id . 59))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 142)\n  (:start . 134) (:id . 60))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 150)\n  (:start . 143) (:id . 61))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 155) (:start . 151)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s8.94) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502346@unknown@formal@none@1@S@The specificity of this antibody was confirmed by its ability to recognize ectopically expressed dHtt protein in transfected Drosophila S2 cells (Fig. 1G,H) and larval tissues (Fig. 1I–K).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "VB") (:stem . "recognize") (:form . "recognize") (:end . 74)\n  (:start . 65) (:id . 53))\n ((:tag . "RB") (:stem . "ectopically") (:form . "ectopically") (:end . 86)\n  (:start . 75) (:id . 54))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 96)\n  (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 101) (:start . 97)\n  (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 109)\n  (:start . 102) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 124)\n  (:start . 113) (:id . 59))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 135)\n  (:start . 125) (:id . 60))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 138) (:start . 136)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 144)\n  (:start . 139) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 150) (:start . 146)\n  (:id . 64))\n ((:tag . "CD") (:stem . "1G,H") (:form . "1G,H") (:end . 155) (:start . 151)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 167)\n  (:start . 161) (:id . 68))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 175)\n  (:start . 168) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 181) (:start . 177)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "1I–K") (:form . "1I–K") (:end . 186) (:start . 182)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.95) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502347@unknown@formal@none@1@S@When the dHtt protein was ectopically expressed from a UAS-dhtt transgene by using a patched-Gal4 driver, our anti-dHtt antibody could easily detect the striped pattern of dHtt expression in the middle of imaginal discs, which is the characteristic domain of Patched expression (Fig. 1I).@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "RB") (:stem . "ectopically") (:form . "ectopically") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "uas-dhtt") (:form . "UAS-dhtt") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 73)\n  (:start . 64) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 82) (:start . 77)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "patched-gal4") (:form . "patched-Gal4") (:end . 97)\n  (:start . 85) (:id . 56))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 104)\n  (:start . 98) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "anti-dhtt") (:form . "anti-dHtt") (:end . 119)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 128)\n  (:start . 120) (:id . 61))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 134)\n  (:start . 129) (:id . 62))\n ((:tag . "RB") (:stem . "easily") (:form . "easily") (:end . 141)\n  (:start . 135) (:id . 63))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 148)\n  (:start . 142) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "strip") (:form . "striped") (:end . 160)\n  (:start . 153) (:id . 66))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 168)\n  (:start . 161) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 68))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 176) (:start . 172)\n  (:id . 69))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 187)\n  (:start . 177) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 190) (:start . 188)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 194) (:start . 191)\n  (:id . 72))\n ((:tag . "NN") (:stem . "middle") (:form . "middle") (:end . 201)\n  (:start . 195) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 204) (:start . 202)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "imaginal") (:form . "imaginal") (:end . 213)\n  (:start . 205) (:id . 75))\n ((:tag . "NNS") (:stem . "disc") (:form . "discs") (:end . 219)\n  (:start . 214) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 220) (:start . 219)\n  (:id . 77))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 226)\n  (:start . 221) (:id . 78))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 229) (:start . 227)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 233) (:start . 230)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 248) (:start . 234) (:id . 81))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 255)\n  (:start . 249) (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 258) (:start . 256)\n  (:id . 83))\n ((:tag . "VBN") (:stem . "patch") (:form . "Patched") (:end . 266)\n  (:start . 259) (:id . 84))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 277)\n  (:start . 267) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 279) (:start . 278)\n  (:id . 86))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 283) (:start . 279)\n  (:id . 87))\n ((:tag . "NN") (:stem . "1i") (:form . "1I") (:end . 286) (:start . 284)\n  (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 287) (:start . 286)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 288) (:start . 287)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s8.96) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502348@unknown@formal@none@1@S@In wild-type animals, use of the anti-dHtt antibody resulted in low-level ubiquitous staining in embryos, larval and adult tissues, with no specific pattern of protein expression (data not shown).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "anti-dhtt") (:form . "anti-dHtt") (:end . 42)\n  (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 51)\n  (:start . 43) (:id . 50))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 60)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "low-level") (:form . "low-level") (:end . 73)\n  (:start . 64) (:id . 53))\n ((:tag . "JJ") (:stem . "ubiquitous") (:form . "ubiquitous") (:end . 84)\n  (:start . 74) (:id . 54))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 93)\n  (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 104)\n  (:start . 97) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 112)\n  (:start . 106) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 122)\n  (:start . 117) (:id . 61))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 130)\n  (:start . 123) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 136) (:start . 132)\n  (:id . 64))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 139) (:start . 137)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 148)\n  (:start . 140) (:id . 66))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 156)\n  (:start . 149) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 159) (:start . 157)\n  (:id . 68))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 167)\n  (:start . 160) (:id . 69))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 178)\n  (:start . 168) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 180) (:start . 179)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 184)\n  (:start . 180) (:id . 72))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 188) (:start . 185)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 194)\n  (:start . 189) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.97) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502349@unknown@formal@none@1@S@At the subcellular level, ectopically expressed dHtt was found predominantly in the cytoplasm in transfected S2 cells and in larval tissues (Fig. 1G–K and data not shown), suggesting that dHtt, similar to its human counterpart, is mainly a cytoplasmic protein.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "subcellular") (:form . "subcellular") (:end . 18)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "RB") (:stem . "ectopically") (:form . "ectopically") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 62) (:start . 57)\n  (:id . 51))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 76) (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cytoplasm") (:form . "cytoplasm") (:end . 93)\n  (:start . 84) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 108)\n  (:start . 97) (:id . 57))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 117)\n  (:start . 112) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 124) (:start . 122)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 131)\n  (:start . 125) (:id . 62))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 139)\n  (:start . 132) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 145) (:start . 141)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "1G–K") (:form . "1G–K") (:end . 150) (:start . 146)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 159)\n  (:start . 155) (:id . 68))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 163) (:start . 160)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 169)\n  (:start . 164) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 182)\n  (:start . 172) (:id . 73))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 187) (:start . 183)\n  (:id . 74))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 192) (:start . 188)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 193) (:start . 192)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 201)\n  (:start . 194) (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 204) (:start . 202)\n  (:id . 78))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 208) (:start . 205)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 214)\n  (:start . 209) (:id . 80))\n ((:tag . "NN") (:stem . "counterpart") (:form . "counterpart") (:end . 226)\n  (:start . 215) (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 227) (:start . 226)\n  (:id . 82))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 230) (:start . 228)\n  (:id . 83))\n ((:tag . "RB") (:stem . "mainly") (:form . "mainly") (:end . 237)\n  (:start . 231) (:id . 84))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 239) (:start . 238)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "cytoplasmic") (:form . "cytoplasmic") (:end . 251)\n  (:start . 240) (:id . 86))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 259)\n  (:start . 252) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 260) (:start . 259)\n  (:id . 88)))@@@1@47@((:hcues ((:id . :x8.98.1) (:span 172 182)))\n (:hscopes ((:id . :x8.98.1) (:span 172 259)))\n (:identifiers (:sid . :s8.98) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502350@unknown@formal@none@1@S@Creating a dhtt deletion@(((:tag . "VBG") (:stem . "create") (:form . "Creating") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 24)\n  (:start . 16) (:id . 45)))@@@1@4@((:identifiers (:sid . :s8.99) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502351@unknown@formal@none@1@S@Similar to human Htt, dhtt encodes an unusually large protein of 3583 a.a. residues.@(((:tag . "JJ") (:stem . "similar") (:form . "Similar") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 34)\n  (:start . 27) (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "RB") (:stem . "unusually") (:form . "unusually") (:end . 47)\n  (:start . 38) (:id . 50))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "CD") (:stem . "3583") (:form . "3583") (:end . 69) (:start . 65)\n  (:id . 54))\n ((:tag . "NN") (:stem . "a.a.") (:form . "a.a.") (:end . 74) (:start . 70)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 83)\n  (:start . 75) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.100) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502352@unknown@formal@none@1@S@The cDNA for the dhtt gene is 11,579 base pairs (bp) long and is derived from 29 exons in a 38 kb transcribed genomic region at cytological interval 98E2 (Li et al., 1999) (Fig. 2A,C).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cdna") (:form . "cDNA") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "CD") (:stem . "11,579") (:form . "11,579") (:end . 36)\n  (:start . 30) (:id . 49))\n ((:tag . "NN") (:stem . "base") (:form . "base") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 47) (:start . 42)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . "NN") (:stem . "bp") (:form . "bp") (:end . 51) (:start . 49)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 54))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 57) (:start . 53)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 64) (:start . 62)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 72)\n  (:start . 65) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 77) (:start . 73)\n  (:id . 59))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 80) (:start . 78)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 86) (:start . 81)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 91) (:start . 90)\n  (:id . 63))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 94) (:start . 92)\n  (:id . 64))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 97) (:start . 95)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "transcribe") (:form . "transcribed") (:end . 109)\n  (:start . 98) (:id . 66))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 117)\n  (:start . 110) (:id . 67))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 124)\n  (:start . 118) (:id . 68))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 127) (:start . 125)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "cytological") (:form . "cytological") (:end . 139)\n  (:start . 128) (:id . 70))\n ((:tag . "NN") (:stem . "interval") (:form . "interval") (:end . 148)\n  (:start . 140) (:id . 71))\n ((:tag . "NN") (:stem . "98e2") (:form . "98E2") (:end . 153) (:start . 149)\n  (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Li") (:form . "Li") (:end . 157) (:start . 155)\n  (:id . 74))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 160) (:start . 158)\n  (:id . 75))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 164) (:start . 161)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 77))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 170) (:start . 166)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 171) (:start . 170)\n  (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 173) (:start . 172)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 177) (:start . 173)\n  (:id . 81))\n ((:tag . "CD") (:stem . "2A,C") (:form . "2A,C") (:end . 182) (:start . 178)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s8.101) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502353@unknown@formal@none@1@S@No null mutations in dhtt have been isolated previously.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 55)\n  (:start . 45) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s8.102) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502354@unknown@formal@none@1@S@To generate a null mutant for dHtt, we selected two FRT-bearing insertion lines surrounding dhtt: p-element d08071, which is inserted at the 5' end of the neighboring CG9990 gene, and piggyBac insertion f05417, which is located inside the intron between dhtt exon 27 and exon 28 near the 3' end of the gene (Fig. 2A).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "null") (:form . "null") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 47)\n  (:start . 39) (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "frt-bearing") (:form . "FRT-bearing") (:end . 63)\n  (:start . 52) (:id . 53))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 73)\n  (:start . 64) (:id . 54))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 79) (:start . 74)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "surround") (:form . "surrounding") (:end . 91)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "p-element") (:form . "p-element") (:end . 107)\n  (:start . 98) (:id . 59))\n ((:tag . "NN") (:stem . "d08071") (:form . "d08071") (:end . 114)\n  (:start . 108) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 121)\n  (:start . 116) (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 133)\n  (:start . 125) (:id . 64))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 136) (:start . 134)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 66))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 142) (:start . 141)\n  (:id . 67))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 143) (:start . 142)\n  (:id . 68))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 147) (:start . 144)\n  (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "neighbor") (:form . "neighboring") (:end . 166)\n  (:start . 155) (:id . 72))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 173)\n  (:start . 167) (:id . 73))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 178) (:start . 174)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 179) (:start . 178)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 183) (:start . 180)\n  (:id . 76))\n ((:tag . "NN") (:stem . "piggybac") (:form . "piggyBac") (:end . 192)\n  (:start . 184) (:id . 77))\n ((:tag . "NN") (:stem . "insertion") (:form . "insertion") (:end . 202)\n  (:start . 193) (:id . 78))\n ((:tag . "NN") (:stem . "f05417") (:form . "f05417") (:end . 209)\n  (:start . 203) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 210) (:start . 209)\n  (:id . 80))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 216)\n  (:start . 211) (:id . 81))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 219) (:start . 217)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 227)\n  (:start . 220) (:id . 83))\n ((:tag . "IN") (:stem . "inside") (:form . "inside") (:end . 234)\n  (:start . 228) (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 238) (:start . 235)\n  (:id . 85))\n ((:tag . "NN") (:stem . "intron") (:form . "intron") (:end . 245)\n  (:start . 239) (:id . 86))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 253)\n  (:start . 246) (:id . 87))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 258) (:start . 254)\n  (:id . 88))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 263) (:start . 259)\n  (:id . 89))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 266) (:start . 264)\n  (:id . 90))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 270) (:start . 267)\n  (:id . 91))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 275) (:start . 271)\n  (:id . 92))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 278) (:start . 276)\n  (:id . 93))\n ((:tag . "IN") (:stem . "near") (:form . "near") (:end . 283) (:start . 279)\n  (:id . 94))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 287) (:start . 284)\n  (:id . 95))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 289) (:start . 288)\n  (:id . 96))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 290) (:start . 289)\n  (:id . 97))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 294) (:start . 291)\n  (:id . 98))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 297) (:start . 295)\n  (:id . 99))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 301) (:start . 298)\n  (:id . 100))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 306) (:start . 302)\n  (:id . 101))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 308) (:start . 307)\n  (:id . 102))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 312) (:start . 308)\n  (:id . 103))\n ((:tag . "NN") (:stem . "2a") (:form . "2A") (:end . 315) (:start . 313)\n  (:id . 104))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 316) (:start . 315)\n  (:id . 105))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 317) (:start . 316)\n  (:id . 106)))@@@1@65@((:identifiers (:sid . :s8.103) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502355@unknown@formal@none@1@S@Using flipase (FLP)–FRT-mediated recombination (Parks et al., 2004), we generated a precise deletion of 55 kb between the two insertions (see Methods).@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "flipase") (:form . "flipase") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "FLP)–FRT-mediated") (:form . "FLP)–FRT-mediated")\n  (:end . 32) (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "recombination") (:form . "recombination")\n  (:end . 46) (:start . 33) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Park") (:form . "Parks") (:end . 53) (:start . 48)\n  (:id . 48))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 56) (:start . 54)\n  (:id . 49))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 51))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 81)\n  (:start . 72) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "precise") (:form . "precise") (:end . 91)\n  (:start . 84) (:id . 58))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 100)\n  (:start . 92) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 60))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 117)\n  (:start . 110) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 64))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 125) (:start . 122)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "insertion") (:form . "insertions") (:end . 136)\n  (:start . 126) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 67))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 141) (:start . 138)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 149)\n  (:start . 142) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 150) (:start . 149)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s8.104) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502356@unknown@formal@none@1@S@This deletion allele, termed Df(98E2), removed most of the CG9990 gene and 34 kb of the 38 kb genomic-coding region for dhtt, with only the last two exons of the dhtt gene remaining (Fig. 2A–C).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "term") (:form . "termed") (:end . 28) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "remove") (:form . "removed") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 65)\n  (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 59))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 90) (:start . 88)\n  (:id . 60))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 93) (:start . 91)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "genomic-coding") (:form . "genomic-coding")\n  (:end . 108) (:start . 94) (:id . 62))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 115)\n  (:start . 109) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 119) (:start . 116)\n  (:id . 64))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 124) (:start . 120)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 130) (:start . 126)\n  (:id . 67))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 135) (:start . 131)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 144) (:start . 140)\n  (:id . 70))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 148) (:start . 145)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 154)\n  (:start . 149) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 157) (:start . 155)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 74))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 166) (:start . 162)\n  (:id . 75))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 171) (:start . 167)\n  (:id . 76))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 181)\n  (:start . 172) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 183) (:start . 182)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 187) (:start . 183)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "2A–C") (:form . "2A–C") (:end . 192) (:start . 188)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 193) (:start . 192)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s8.105) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502357@unknown@formal@none@1@S@The deletion was confirmed by inverse PCR from extracted genomic DNA and by DNA sequencing (data not shown).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "inverse") (:form . "inverse") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "pcr") (:form . "PCR") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 56)\n  (:start . 47) (:id . 50))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 64)\n  (:start . 57) (:id . 51))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 90)\n  (:start . 80) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 96) (:start . 92)\n  (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 100) (:start . 97)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.106) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502358@unknown@formal@none@1@S@Genomic organization of the dhtt locus and the dhtt-ko deletion.@(((:tag . "JJ") (:stem . "genomic") (:form . "Genomic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 20)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "locus") (:form . "locus") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s8.107) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502359@unknown@formal@none@1@S@(A) The genomic structure of cytological region 98E2.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 15)\n  (:start . 8) (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 25)\n  (:start . 16) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "cytological") (:form . "cytological") (:end . 40)\n  (:start . 29) (:id . 49))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 47)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "98e2") (:form . "98E2") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s8.108) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502360@unknown@formal@none@1@S@The scale bar on top indicates the gene size (in base pairs).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "top") (:form . "top") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 30)\n  (:start . 21) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 52))\n ((:tag . "NN") (:stem . "base") (:form . "base") (:end . 53) (:start . 49)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 59) (:start . 54)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.109) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502361@unknown@formal@none@1@S@The position and transcriptional direction of dhtt and nearby genes (open boxes) is shown; introns (dashed lines) and exons (colored filled boxes) are labeled, as well as the FRT insertions (triangles) used for generating the Df(98E2) deficiency.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 32) (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "direction") (:form . "direction") (:end . 42)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 50) (:start . 46)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "nearby") (:form . "nearby") (:end . 61)\n  (:start . 55) (:id . 50))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 67) (:start . 62)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "open") (:form . "open") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "box") (:form . "boxes") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 89) (:start . 84)\n  (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "intron") (:form . "introns") (:end . 98)\n  (:start . 91) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "dash") (:form . "dashed") (:end . 106)\n  (:start . 100) (:id . 61))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 112)\n  (:start . 107) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 123)\n  (:start . 118) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "color") (:form . "colored") (:end . 132)\n  (:start . 125) (:id . 67))\n ((:tag . "VBN") (:stem . "fill") (:form . "filled") (:end . 139)\n  (:start . 133) (:id . 68))\n ((:tag . "NNS") (:stem . "box") (:form . "boxes") (:end . 145) (:start . 140)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 70))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 150) (:start . 147)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 158)\n  (:start . 151) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n  (:id . 73))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 162) (:start . 160)\n  (:id . 74))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 167) (:start . 163)\n  (:id . 75))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 170) (:start . 168)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 174) (:start . 171)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "FRT") (:form . "FRT") (:end . 178) (:start . 175)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "insertion") (:form . "insertions") (:end . 189)\n  (:start . 179) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 191) (:start . 190)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "triangle") (:form . "triangles") (:end . 200)\n  (:start . 191) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 201) (:start . 200)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 206) (:start . 202)\n  (:id . 83))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 210) (:start . 207)\n  (:id . 84))\n ((:tag . "VBG") (:stem . "generate") (:form . "generating") (:end . 221)\n  (:start . 211) (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 225) (:start . 222)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 234)\n  (:start . 226) (:id . 87))\n ((:tag . "NN") (:stem . "deficiency") (:form . "deficiency") (:end . 245)\n  (:start . 235) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s8.110) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502362@unknown@formal@none@1@S@(B) dhtt-ko was generated by an FRT-mediated precise deletion [Df(98E2)] of a 55 kb genomic region covering most of CG9990 and dhtt.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 25)\n  (:start . 16) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 31) (:start . 29)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "frt-mediated") (:form . "FRT-mediated") (:end . 44)\n  (:start . 32) (:id . 50))\n ((:tag . "JJ") (:stem . "precise") (:form . "precise") (:end . 52)\n  (:start . 45) (:id . 51))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 61)\n  (:start . 53) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 71)\n  (:start . 63) (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n  (:id . 57))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 80) (:start . 78)\n  (:id . 58))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 83) (:start . 81)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 91)\n  (:start . 84) (:id . 60))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 98)\n  (:start . 92) (:id . 61))\n ((:tag . "VBG") (:stem . "cover") (:form . "covering") (:end . 107)\n  (:start . 99) (:id . 62))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 112) (:start . 108)\n  (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 64))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 122)\n  (:start . 116) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 66))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 131) (:start . 127)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.111) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502363@unknown@formal@none@1@S@A genomic transgene covering the entirety of CG9990 (open box) was reintroduced as a transgenic construct in the Df(98E2) background.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "VBG") (:stem . "cover") (:form . "covering") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "entirety") (:form . "entirety") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "CG9990") (:form . "CG9990") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "open") (:form . "open") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "box") (:form . "box") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "reintroduce") (:form . "reintroduced") (:end . 79)\n  (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 95)\n  (:start . 85) (:id . 58))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 105)\n  (:start . 96) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 121)\n  (:start . 113) (:id . 62))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 132)\n  (:start . 122) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.112) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502364@unknown@formal@none@1@S@(C) Detailed genomic structure of the dhtt gene.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "VBD") (:stem . "detail") (:form . "Detailed") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 20)\n  (:start . 13) (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 30)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 48) (:start . 47)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s8.113) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502365@unknown@formal@none@1@S@The scale bar, with predicted BamHI fragments, is drawn at the top.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 29)\n  (:start . 20) (:id . 47))\n ((:tag . "NNP") (:stem . "BamHI") (:form . "BamHI") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 45)\n  (:start . 36) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "draw") (:form . "drawn") (:end . 55) (:start . 50)\n  (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "top") (:form . "top") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.114) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502366@unknown@formal@none@1@S@The exons of the dhtt gene are depicted as red arrows and squares, whereas introns are highlighted as red dashed lines, both are drawn to scale.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "depict") (:form . "depicted") (:end . 39)\n  (:start . 31) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 53)\n  (:start . 47) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "square") (:form . "squares") (:end . 65)\n  (:start . 58) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 74)\n  (:start . 67) (:id . 56))\n ((:tag . "NNS") (:stem . "intron") (:form . "introns") (:end . 82)\n  (:start . 75) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 98)\n  (:start . 87) (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 101) (:start . 99)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 105) (:start . 102)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "dashed") (:form . "dashed") (:end . 112)\n  (:start . 106) (:id . 62))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 118)\n  (:start . 113) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 64))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 124) (:start . 120)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 128) (:start . 125)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "draw") (:form . "drawn") (:end . 134)\n  (:start . 129) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 137) (:start . 135)\n  (:id . 68))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 143)\n  (:start . 138) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.115) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502367@unknown@formal@none@1@S@(D) The dhtt-ko removes all but the last two of the 29 exons in dhtt, as verified by Southern blotting using BamHI digestion of genomic DNA.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 15)\n  (:start . 8) (:id . 46))\n ((:tag . "VBZ") (:stem . "remove") (:form . "removes") (:end . 23)\n  (:start . 16) (:id . 47))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 27) (:start . 24)\n  (:id . 48))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 31) (:start . 28)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 40) (:start . 36)\n  (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 44) (:start . 41)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 54))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 54) (:start . 52)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 60) (:start . 55)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 68) (:start . 64)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 72) (:start . 70)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 81)\n  (:start . 73) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 84) (:start . 82)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "southern") (:form . "Southern") (:end . 93)\n  (:start . 85) (:id . 63))\n ((:tag . "NN") (:stem . "blotting") (:form . "blotting") (:end . 102)\n  (:start . 94) (:id . 64))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 108) (:start . 103)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "BamHI") (:form . "BamHI") (:end . 114)\n  (:start . 109) (:id . 66))\n ((:tag . "NN") (:stem . "digestion") (:form . "digestion") (:end . 124)\n  (:start . 115) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 135)\n  (:start . 128) (:id . 69))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 139) (:start . 136)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s8.116) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502368@unknown@formal@none@1@S@DNA extracted from control and dhtt-ko adult animals was hybridized with a DNA probe targeting all exons of dhtt (see Methods).@(((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "hybridize") (:form . "hybridized") (:end . 67)\n  (:start . 57) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 74) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "probe") (:form . "probe") (:end . 84) (:start . 79)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 104) (:start . 99)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 112) (:start . 108)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 125)\n  (:start . 118) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s8.117) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502369@unknown@formal@none@1@S@The two BamHI fragments (1.95 kb and 1.59 kb) that contain the last two remaining exons in dhtt-ko mutants are highlighted in (C).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "BamHI") (:form . "BamHI") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "CD") (:stem . "1.95") (:form . "1.95") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "CD") (:stem . "1.59") (:form . "1.59") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 50) (:start . 46)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 58)\n  (:start . 51) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 67) (:start . 63)\n  (:id . 56))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 71) (:start . 68)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 81)\n  (:start . 72) (:id . 58))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 87) (:start . 82)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 98)\n  (:start . 91) (:id . 61))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 106)\n  (:start . 99) (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 122)\n  (:start . 111) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 125) (:start . 123)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 128) (:start . 127)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s8.118) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502370@unknown@formal@none@1@S@Drosophila containing the Df(98E2) deletion, which removes both CG9990 and dhtt, are homozygous lethal at the embryonic stage.@(((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 34)\n  (:start . 26) (:id . 45))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 43)\n  (:start . 35) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 50) (:start . 45)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "remove") (:form . "removes") (:end . 58)\n  (:start . 51) (:id . 49))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 63) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 70)\n  (:start . 64) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 52))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 79) (:start . 75)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 95)\n  (:start . 85) (:id . 56))\n ((:tag . "NN") (:stem . "lethal") (:form . "lethal") (:end . 102)\n  (:start . 96) (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 119)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 125)\n  (:start . 120) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.119) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502371@unknown@formal@none@1@S@CG9990 encodes a previously uncharacterized protein belonging to the ABC transporter superfamily (Dean et al., 2001).@(((:tag . "NNP") (:stem . "CG9990") (:form . "CG9990") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "uncharacterized") (:form . "uncharacterized")\n  (:end . 43) (:start . 28) (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 51)\n  (:start . 44) (:id . 47))\n ((:tag . "VBG") (:stem . "belong") (:form . "belonging") (:end . 61)\n  (:start . 52) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "ABC") (:form . "ABC") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "transporter") (:form . "transporter") (:end . 84)\n  (:start . 73) (:id . 52))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 96)\n  (:start . 85) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Dean") (:form . "Dean") (:end . 102) (:start . 98)\n  (:id . 55))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 105) (:start . 103)\n  (:id . 56))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 109) (:start . 106)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 58))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s8.120) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502372@unknown@formal@none@1@S@To separate the mutant phenotype of dhtt from CG9990, we generated transgenic flies carrying a CG9990 genomic rescue transgene in the Df(98E2) background (see Methods).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "separate") (:form . "separate") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 77)\n  (:start . 67) (:id . 54))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 101)\n  (:start . 95) (:id . 58))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 109)\n  (:start . 102) (:id . 59))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 116)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 126)\n  (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 142)\n  (:start . 134) (:id . 64))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 153)\n  (:start . 143) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 66))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 158) (:start . 155)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 166)\n  (:start . 159) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.121) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502373@unknown@formal@none@1@S@These lines, referred to as dhtt-ko (dhtt-knockout only), carry both the CG9990 rescue transgene and the Df(98E2) deletion, and thus are mutant only for dhtt (Fig. 2B–D).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dhtt-knockout") (:form . "dhtt-knockout")\n  (:end . 50) (:start . 37) (:id . 50))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "carry") (:form . "carry") (:end . 63) (:start . 58)\n  (:id . 54))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 79)\n  (:start . 73) (:id . 57))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 86)\n  (:start . 80) (:id . 58))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 96)\n  (:start . 87) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 113)\n  (:start . 105) (:id . 62))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 122)\n  (:start . 114) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 65))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 132) (:start . 128)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 136) (:start . 133)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 143)\n  (:start . 137) (:id . 68))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 148) (:start . 144)\n  (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 152) (:start . 149)\n  (:id . 70))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 157) (:start . 153)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 163) (:start . 159)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "2B–D") (:form . "2B–D") (:end . 168) (:start . 164)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.122) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502374@unknown@formal@none@1@S@dhtt is dispensable for Drosophila development@(((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "dispensable") (:form . "dispensable") (:end . 19)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 46)\n  (:start . 35) (:id . 47)))@@@1@6@((:identifiers (:sid . :s8.123) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502375@unknown@formal@none@1@S@The dhtt-ko allele removes 27 of the 29 exons of dhtt (Fig. 2).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "remove") (:form . "removes") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 59) (:start . 55)\n  (:id . 54))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 61) (:start . 60)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.124) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502376@unknown@formal@none@1@S@Since Htt homozygous knockout mice die during early embryogenesis (Duyao et al., 1995; Nasir et al., 1995; Zeitlin et al., 1995), we expected that loss of dhtt in the fly would be associated with prominent developmental defects.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "knockout") (:form . "knockout") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "die") (:form . "die") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 51) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 65) (:start . 52) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Duyao") (:form . "Duyao") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Nasir") (:form . "Nasir") (:end . 92) (:start . 87)\n  (:id . 58))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 99) (:start . 96)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 61))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 105) (:start . 101)\n  (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 106) (:start . 105)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Zeitlin") (:form . "Zeitlin") (:end . 114)\n  (:start . 107) (:id . 64))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 117) (:start . 115)\n  (:id . 65))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 121) (:start . 118)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 67))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 127) (:start . 123)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 70))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 132) (:start . 130)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "expect") (:form . "expected") (:end . 141)\n  (:start . 133) (:id . 72))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 146) (:start . 142)\n  (:id . 73))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 151) (:start . 147)\n  (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n  (:id . 75))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 159) (:start . 155)\n  (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 162) (:start . 160)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 78))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 170) (:start . 167)\n  (:id . 79))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 176)\n  (:start . 171) (:id . 80))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 179) (:start . 177)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 190)\n  (:start . 180) (:id . 82))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 195) (:start . 191)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "prominent") (:form . "prominent") (:end . 205)\n  (:start . 196) (:id . 84))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 219) (:start . 206) (:id . 85))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 227)\n  (:start . 220) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n  (:id . 87)))@@@1@46@((:hcues ((:id . :x8.125.1) (:span 171 176)))\n (:hscopes ((:id . :x8.125.1) (:span 147 227)))\n (:identifiers (:sid . :s8.125) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502377@unknown@formal@none@1@S@However, dhtt-ko flies are homozygous viable, demonstrating that the lethality observed following the Df(98E2) deletion is caused by loss of CG9990.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating") (:end . 59)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 97)\n  (:start . 88) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 110)\n  (:start . 102) (:id . 57))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 119)\n  (:start . 111) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 122) (:start . 120)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 129)\n  (:start . 123) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 132) (:start . 130)\n  (:id . 61))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 137) (:start . 133)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "CG9990") (:form . "CG9990") (:end . 147)\n  (:start . 141) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s8.126) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502378@unknown@formal@none@1@S@To verify that the dhtt gene is indeed deleted in dhtt-ko flies, we extracted genomic DNA from homozygous dhtt-ko adults and performed a Southern blot analysis.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "verify") (:form . "verify") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "RB") (:stem . "indeed") (:form . "indeed") (:end . 38)\n  (:start . 32) (:id . 49))\n ((:tag . "VBN") (:stem . "delete") (:form . "deleted") (:end . 46)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 63) (:start . 58)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 67) (:start . 65)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "extract") (:form . "extracted") (:end . 77)\n  (:start . 68) (:id . 56))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 85)\n  (:start . 78) (:id . 57))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 94) (:start . 90)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 105)\n  (:start . 95) (:id . 60))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 113)\n  (:start . 106) (:id . 61))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 120)\n  (:start . 114) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "perform") (:form . "performed") (:end . 134)\n  (:start . 125) (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 136) (:start . 135)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "southern") (:form . "Southern") (:end . 145)\n  (:start . 137) (:id . 66))\n ((:tag . "NN") (:stem . "blot") (:form . "blot") (:end . 150) (:start . 146)\n  (:id . 67))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 159)\n  (:start . 151) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s8.127) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502379@unknown@formal@none@1@S@As shown in Fig. 2D, all genomic DNA containing the dhtt gene was removed in dhtt-ko flies except for the final two 3' exons.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 24) (:start . 21)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 32)\n  (:start . 25) (:id . 49))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 36) (:start . 33)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 47)\n  (:start . 37) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 56) (:start . 52)\n  (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 65) (:start . 62)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "remove") (:form . "removed") (:end . 73)\n  (:start . 66) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 84)\n  (:start . 77) (:id . 58))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 90) (:start . 85)\n  (:id . 59))\n ((:tag . "IN") (:stem . "except") (:form . "except") (:end . 97)\n  (:start . 91) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 101) (:start . 98)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 111)\n  (:start . 106) (:id . 63))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 115) (:start . 112)\n  (:id . 64))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 117) (:start . 116)\n  (:id . 65))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 118) (:start . 117)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 124)\n  (:start . 119) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.128) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502380@unknown@formal@none@1@S@Further analyses demonstrated that homozygous dhtt-ko flies develop at a similar rate to wild-type flies and give rise to fertile adults with no discernible morphological abnormalities.@(((:tag . "JJ") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 29)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 45)\n  (:start . 35) (:id . 46))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 53)\n  (:start . 46) (:id . 47))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 59) (:start . 54)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "develop") (:form . "develop") (:end . 67)\n  (:start . 60) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 70) (:start . 68)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 80)\n  (:start . 73) (:id . 52))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 85) (:start . 81)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 98)\n  (:start . 89) (:id . 55))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 104) (:start . 99)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "give") (:form . "give") (:end . 113) (:start . 109)\n  (:id . 58))\n ((:tag . "NN") (:stem . "rise") (:form . "rise") (:end . 118) (:start . 114)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 121) (:start . 119)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "fertile") (:form . "fertile") (:end . 129)\n  (:start . 122) (:id . 61))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 136)\n  (:start . 130) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 141) (:start . 137)\n  (:id . 63))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "discernible") (:form . "discernible") (:end . 156)\n  (:start . 145) (:id . 65))\n ((:tag . "JJ") (:stem . "morphological") (:form . "morphological")\n  (:end . 170) (:start . 157) (:id . 66))\n ((:tag . "NNS") (:stem . "abnormality") (:form . "abnormalities")\n  (:end . 184) (:start . 171) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.129) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502381@unknown@formal@none@1@S@The progeny derived from homozygous dhtt-ko flies did not show a reduction in viability or display other obvious developmental defects, suggesting that maternally contributed dhtt has no significant effect on animal development or function.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "progeny") (:form . "progeny") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 49) (:start . 44)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "VB") (:stem . "show") (:form . "show") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 74)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 87)\n  (:start . 78) (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 98)\n  (:start . 91) (:id . 57))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 104) (:start . 99)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 112)\n  (:start . 105) (:id . 59))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 126) (:start . 113) (:id . 60))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 134)\n  (:start . 127) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 146)\n  (:start . 136) (:id . 63))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 151) (:start . 147)\n  (:id . 64))\n ((:tag . "RB") (:stem . "maternally") (:form . "maternally") (:end . 162)\n  (:start . 152) (:id . 65))\n ((:tag . "VBN") (:stem . "contribute") (:form . "contributed") (:end . 174)\n  (:start . 163) (:id . 66))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 179) (:start . 175)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 183) (:start . 180)\n  (:id . 68))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 186) (:start . 184)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 198)\n  (:start . 187) (:id . 70))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 205)\n  (:start . 199) (:id . 71))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 208) (:start . 206)\n  (:id . 72))\n ((:tag . "NN") (:stem . "animal") (:form . "animal") (:end . 215)\n  (:start . 209) (:id . 73))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 227)\n  (:start . 216) (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 230) (:start . 228)\n  (:id . 75))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 239)\n  (:start . 231) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 240) (:start . 239)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x8.130.1) (:span 136 146)))\n (:hscopes ((:id . :x8.130.1) (:span 136 239)))\n (:identifiers (:sid . :s8.130) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502382@unknown@formal@none@1@S@To determine whether developmental defects are present in dhtt-ko animals, we characterized dhtt-ko mutants using a variety of cellular and neuronal markers.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 34) (:start . 21) (:id . 45))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 42)\n  (:start . 35) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 46) (:start . 43)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 54)\n  (:start . 47) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 65)\n  (:start . 58) (:id . 50))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 73)\n  (:start . 66) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "characterize") (:form . "characterized")\n  (:end . 91) (:start . 78) (:id . 54))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 99)\n  (:start . 92) (:id . 55))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 107)\n  (:start . 100) (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 113) (:start . 108)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n  (:id . 58))\n ((:tag . "NN") (:stem . "variety") (:form . "variety") (:end . 123)\n  (:start . 116) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 135)\n  (:start . 127) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 148)\n  (:start . 140) (:id . 63))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 156)\n  (:start . 149) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x8.131.1) (:span 13 20)))\n (:hscopes ((:id . :x8.131.1) (:span 13 73)))\n (:identifiers (:sid . :s8.131) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502383@unknown@formal@none@1@S@These studies failed to reveal any obvious developmental abnormalities during embryogenesis, or during larval and adult stages (Fig. 3 and data not shown).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 20) (:start . 14)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "VB") (:stem . "reveal") (:form . "reveal") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 56) (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "abnormality") (:form . "abnormalities") (:end . 70)\n  (:start . 57) (:id . 50))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 77)\n  (:start . 71) (:id . 51))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 91) (:start . 78) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 95) (:start . 93)\n  (:id . 54))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 102)\n  (:start . 96) (:id . 55))\n ((:tag . "NN") (:stem . "larval") (:form . "larval") (:end . 109)\n  (:start . 103) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 119)\n  (:start . 114) (:id . 58))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 126)\n  (:start . 120) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 132) (:start . 128)\n  (:id . 61))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 134) (:start . 133)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 143)\n  (:start . 139) (:id . 64))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 147) (:start . 144)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 153)\n  (:start . 148) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.132) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502384@unknown@formal@none@1@S@In particular, the embryonic central nervous system (CNS) (Fig. 3A) and muscles, and the larval muscles, CNS, eye and other imaginal discs all appeared normal (Fig. 3B and data not shown).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "CNS") (:form . "CNS") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 63) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "3a") (:form . "3A") (:end . 66) (:start . 64)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "muscle") (:form . "muscles") (:end . 79)\n  (:start . 72) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 95)\n  (:start . 89) (:id . 62))\n ((:tag . "NNS") (:stem . "muscle") (:form . "muscles") (:end . 103)\n  (:start . 96) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "CNS") (:form . "CNS") (:end . 108) (:start . 105)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 66))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 113) (:start . 110)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 123)\n  (:start . 118) (:id . 69))\n ((:tag . "JJ") (:stem . "imaginal") (:form . "imaginal") (:end . 132)\n  (:start . 124) (:id . 70))\n ((:tag . "NNS") (:stem . "disc") (:form . "discs") (:end . 138)\n  (:start . 133) (:id . 71))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 142) (:start . 139)\n  (:id . 72))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 151)\n  (:start . 143) (:id . 73))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 158)\n  (:start . 152) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 164) (:start . 160)\n  (:id . 76))\n ((:tag . "NN") (:stem . "3b") (:form . "3B") (:end . 167) (:start . 165)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 176)\n  (:start . 172) (:id . 79))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 180) (:start . 177)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 186)\n  (:start . 181) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.133) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502385@unknown@formal@none@1@S@Further, in aged adults (40-day-old flies), the external eye morphology was normal and the eight neuronal photoreceptor cells in each ommatidium were clearly present, together with their accessory cells (Fig. 3C,D).@(((:tag . "RB") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "40-day-old") (:form . "40-day-old") (:end . 35)\n  (:start . 25) (:id . 48))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "external") (:form . "external") (:end . 56)\n  (:start . 48) (:id . 53))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 71)\n  (:start . 61) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 82)\n  (:start . 76) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 59))\n ((:tag . "CD") (:stem . "eight") (:form . "eight") (:end . 96) (:start . 91)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 105)\n  (:start . 97) (:id . 61))\n ((:tag . "NN") (:stem . "photoreceptor") (:form . "photoreceptor")\n  (:end . 119) (:start . 106) (:id . 62))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 125)\n  (:start . 120) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 64))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 133) (:start . 129)\n  (:id . 65))\n ((:tag . "NN") (:stem . "ommatidium") (:form . "ommatidium") (:end . 144)\n  (:start . 134) (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 149) (:start . 145)\n  (:id . 67))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 157)\n  (:start . 150) (:id . 68))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 165)\n  (:start . 158) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 70))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 175)\n  (:start . 167) (:id . 71))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 180) (:start . 176)\n  (:id . 72))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 186)\n  (:start . 181) (:id . 73))\n ((:tag . "JJ") (:stem . "accessory") (:form . "accessory") (:end . 196)\n  (:start . 187) (:id . 74))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 202)\n  (:start . 197) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 204) (:start . 203)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 208) (:start . 204)\n  (:id . 77))\n ((:tag . "CD") (:stem . "3C,D") (:form . "3C,D") (:end . 213) (:start . 209)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s8.134) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502386@unknown@formal@none@1@S@We note that our finding is different from a recent study that examined dhtt function using RNA interference (RNAi), which implicated a role for dhtt in axonal transport and eye integrity (Gunawardena et al., 2003).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "note") (:form . "note") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 51)\n  (:start . 45) (:id . 51))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 57) (:start . 52)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 71)\n  (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 85)\n  (:start . 77) (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 91) (:start . 86)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "NN") (:stem . "interference") (:form . "interference") (:end . 108)\n  (:start . 96) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 114) (:start . 110)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 63))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 122)\n  (:start . 117) (:id . 64))\n ((:tag . "VBD") (:stem . "implicate") (:form . "implicated") (:end . 133)\n  (:start . 123) (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 135) (:start . 134)\n  (:id . 66))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 140) (:start . 136)\n  (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 144) (:start . 141)\n  (:id . 68))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 149) (:start . 145)\n  (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 152) (:start . 150)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 159)\n  (:start . 153) (:id . 71))\n ((:tag . "NN") (:stem . "transport") (:form . "transport") (:end . 169)\n  (:start . 160) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 173) (:start . 170)\n  (:id . 73))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 177) (:start . 174)\n  (:id . 74))\n ((:tag . "NN") (:stem . "integrity") (:form . "integrity") (:end . 187)\n  (:start . 178) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Gunawardena") (:form . "Gunawardena") (:end . 200)\n  (:start . 189) (:id . 77))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 203) (:start . 201)\n  (:id . 78))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 207) (:start . 204)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 208) (:start . 207)\n  (:id . 80))\n ((:tag . "CD") (:stem . "2003") (:form . "2003") (:end . 213) (:start . 209)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.135) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502387@unknown@formal@none@1@S@The exact nature of this phenotype discrepancy is not clear.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "exact") (:form . "exact") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "nature") (:form . "nature") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "discrepancy") (:form . "discrepancy") (:end . 46)\n  (:start . 35) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 52)))@@@1@11@((:hcues ((:id . :x8.136.1) (:span 50 59)))\n (:hscopes ((:id . :x8.136.1) (:span 0 59)))\n (:identifiers (:sid . :s8.136) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502388@unknown@formal@none@1@S@Given the experiment was carried out at 29°C, it is possible that the observed RNAi phenotypes were the result of cellular toxicity caused by the high-level expression of Gal4 (Gunawardena et al., 2003).@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "RB") (:stem . "out") (:form . "out") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "29°c") (:form . "29°C") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 60)\n  (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 78)\n  (:start . 70) (:id . 56))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 94)\n  (:start . 84) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 99) (:start . 95)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 110)\n  (:start . 104) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 122)\n  (:start . 114) (:id . 63))\n ((:tag . "NN") (:stem . "toxicity") (:form . "toxicity") (:end . 131)\n  (:start . 123) (:id . 64))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 138)\n  (:start . 132) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 141) (:start . 139)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "high-level") (:form . "high-level") (:end . 156)\n  (:start . 146) (:id . 68))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 167)\n  (:start . 157) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 170) (:start . 168)\n  (:id . 70))\n ((:tag . "NN") (:stem . "gal4") (:form . "Gal4") (:end . 175) (:start . 171)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Gunawardena") (:form . "Gunawardena") (:end . 188)\n  (:start . 177) (:id . 73))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 191) (:start . 189)\n  (:id . 74))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 195) (:start . 192)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n  (:id . 76))\n ((:tag . "CD") (:stem . "2003") (:form . "2003") (:end . 201) (:start . 197)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 202) (:start . 201)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x8.137.1) (:span 52 60)))\n (:hscopes ((:id . :x8.137.1) (:span 52 175)))\n (:identifiers (:sid . :s8.137) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502389@unknown@formal@none@1@S@The more severe phenotypes might also be the result of the non-specific RNAi off-target effects caused by the knockdown of unrelated genes (Kulkarni et al., 2006).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "non-specific") (:form . "non-specific") (:end . 71)\n  (:start . 59) (:id . 53))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "off-target") (:form . "off-target") (:end . 87)\n  (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 95)\n  (:start . 88) (:id . 56))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 102)\n  (:start . 96) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 119)\n  (:start . 110) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "unrelated") (:form . "unrelated") (:end . 132)\n  (:start . 123) (:id . 62))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 138)\n  (:start . 133) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Kulkarni") (:form . "Kulkarni") (:end . 148)\n  (:start . 140) (:id . 65))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 151) (:start . 149)\n  (:id . 66))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 155) (:start . 152)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 68))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 161) (:start . 157)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x8.138.1) (:span 27 32)))\n (:hscopes ((:id . :x8.138.1) (:span 27 138)))\n (:identifiers (:sid . :s8.138) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502390@unknown@formal@none@1@S@Nevertheless, our results suggest that dhtt is dispensable for normal Drosophila development.@(((:tag . "RB") (:stem . "nevertheless") (:form . "Nevertheless") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dispensable") (:form . "dispensable") (:end . 58)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 69)\n  (:start . 63) (:id . 52))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 80)\n  (:start . 70) (:id . 53))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 92)\n  (:start . 81) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 55)))@@@1@14@((:hcues ((:id . :x8.139.1) (:span 26 33)))\n (:hscopes ((:id . :x8.139.1) (:span 26 92)))\n (:identifiers (:sid . :s8.139) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502391@unknown@formal@none@1@S@This result is in contrast to the essential role of Htt in mouse (Duyao et al., 1995; Nasir et al., 1995; Zeitlin et al., 1995).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 64) (:start . 59)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Duyao") (:form . "Duyao") (:end . 71) (:start . 66)\n  (:id . 56))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 74) (:start . 72)\n  (:id . 57))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 78) (:start . 75)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 84) (:start . 80)\n  (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 85) (:start . 84)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Nasir") (:form . "Nasir") (:end . 91) (:start . 86)\n  (:id . 62))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 94) (:start . 92)\n  (:id . 63))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 98) (:start . 95)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 65))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 104) (:start . 100)\n  (:id . 66))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 105) (:start . 104)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Zeitlin") (:form . "Zeitlin") (:end . 113)\n  (:start . 106) (:id . 68))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 116) (:start . 114)\n  (:id . 69))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 120) (:start . 117)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 71))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 126) (:start . 122)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 127) (:start . 126)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.140) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502392@unknown@formal@none@1@S@These phenotypic differences are probably the result of differences in mouse and fly embryogenesis, as the early lethality of Htt-null mice is due to the function of Hdh in extraembryonic membranes, for which there are no equivalents in Drosophila (Dragatsis et al., 1998) (see Discussion).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "phenotypic") (:form . "phenotypic") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 28)\n  (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n  (:id . 45))\n ((:tag . "RB") (:stem . "probably") (:form . "probably") (:end . 41)\n  (:start . 33) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 47))\n ((:tag . "NN") (:stem . "result") (:form . 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5502393@unknown@formal@none@1@S@dhtt is dispensable for Drosophila development.@(((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "dispensable") (:form . "dispensable") (:end . 19)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 46)\n  (:start . 35) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s8.142) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502394@unknown@formal@none@1@S@(A) Normal development of the CNS during embryogenesis in dhtt-ko flies (A3,A4) compared with wild-type controls (A1,A2), as revealed by anti-Armadillo staining.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "normal") (:form . "Normal") (:end . 10) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 22)\n  (:start . 11) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cns") (:form . "CNS") (:end . 33) (:start . 30)\n  (:id . 49))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 40)\n  (:start . 34) (:id . 50))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 54) (:start . 41) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 65)\n  (:start . 58) (:id . 53))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "A3,A4") (:form . "A3,A4") (:end . 78) (:start . 73)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 79) (:start . 78)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 88)\n  (:start . 80) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 93) (:start . 89)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 103)\n  (:start . 94) (:id . 60))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 112)\n  (:start . 104) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "A1,A2") (:form . "A1,A2") (:end . 119)\n  (:start . 114) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 124) (:start . 122)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "reveal") (:form . "revealed") (:end . 133)\n  (:start . 125) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 136) (:start . 134)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "anti-armadillo") (:form . "anti-Armadillo")\n  (:end . 151) (:start . 137) (:id . 69))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 160)\n  (:start . 152) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s8.143) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502395@unknown@formal@none@1@S@(A2,A4) Enlarged views of the ventral nerve cord in wild-type (A2) and dhtt-ko (A4) embryos show its regular ladder-like structure.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A2,A4") (:form . "A2,A4") (:end . 6) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 7) (:start . 6) (:id . 44))\n ((:tag . "VBD") (:stem . "enlarge") (:form . "Enlarged") (:end . 16)\n  (:start . 8) (:id . 45))\n ((:tag . "NNS") (:stem . "view") (:form . "views") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 37)\n  (:start . 30) (:id . 49))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 43) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cord") (:form . "cord") (:end . 48) (:start . 44)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 61)\n  (:start . 52) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "a2") (:form . "A2") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 78)\n  (:start . 71) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n  (:id . 59))\n ((:tag . "NN") (:stem . "a4") (:form . "A4") (:end . 82) (:start . 80)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 91)\n  (:start . 84) (:id . 62))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 96) (:start . 92)\n  (:id . 63))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 100) (:start . 97)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 108)\n  (:start . 101) (:id . 65))\n ((:tag . "JJ") (:stem . "ladder-like") (:form . "ladder-like") (:end . 120)\n  (:start . 109) (:id . 66))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 130)\n  (:start . 121) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.144) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502396@unknown@formal@none@1@S@(B) Differentiation and patterning of the eye during the third instar larval stage in dhtt-ko flies (B3,B4) is indistinguishable from wild-type controls (B1,B2), as revealed by anti-Elav staining (red) (B2,B4) to label differentiated neurons and phalloidin staining for F-actin (green) (B1,B3) to reveal the overall cytoskeleton organization.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Differentiation") (:form . "Differentiation")\n  (:end . 19) (:start . 4) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "patterning") (:form . "patterning") (:end . 34)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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"JJ") (:stem . "overall") (:form . "overall") (:end . 315)\n  (:start . 308) (:id . 101))\n ((:tag . "NN") (:stem . "cytoskeleton") (:form . "cytoskeleton") (:end . 328)\n  (:start . 316) (:id . 102))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 341)\n  (:start . 329) (:id . 103))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 342) (:start . 341)\n  (:id . 104)))@@@1@63@((:identifiers (:sid . :s8.145) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502397@unknown@formal@none@1@S@(C,D) Eye images of 40-day-old dhtt-ko mutants.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C,D") (:form . "C,D") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Eye") (:form . "Eye") (:end . 9) (:start . 6)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 16)\n  (:start . 10) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "40-day-old") (:form . "40-day-old") (:end . 30)\n  (:start . 20) (:id . 48))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 38)\n  (:start . 31) (:id . 49))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 46)\n  (:start . 39) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s8.146) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502398@unknown@formal@none@1@S@Both the overall external eye morphology (C) and the internal organization of neuronal photoreceptors (D) are normal, even in the 40-day-old dhtt-ko adults.@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "JJ") (:stem . "external") (:form . "external") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 61)\n  (:start . 53) (:id . 53))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 74)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . "NNS") (:stem . "photoreceptor") (:form . "photoreceptors")\n  (:end . 101) (:start . 87) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 109) (:start . 106)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 116)\n  (:start . 110) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 122) (:start . 118)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 125) (:start . 123)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "40-day-old") (:form . "40-day-old") (:end . 140)\n  (:start . 130) (:id . 67))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 148)\n  (:start . 141) (:id . 68))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 155)\n  (:start . 149) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.147) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502399@unknown@formal@none@1@S@(E–I) Synaptic development is normal in dhtt mutants.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "LS") (:stem . "e–i") (:form . "E–I") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "Synaptic") (:end . 14)\n  (:start . 6) (:id . 45))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 26)\n  (:start . 15) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 52)\n  (:start . 45) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s8.148) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502400@unknown@formal@none@1@S@Low (E1,E5) and high (E2–E4,E6–E8,F1–F8) magnification confocal images of glutamatergic NMJs in the abdominal segment A3 of third instar muscles 6 and 7.@(((:tag . "JJ") (:stem . "low") (:form . "Low") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "E1,E5") (:form . "E1,E5") (:end . 10) (:start . 5)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 15) (:start . 12)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 20) (:start . 16)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 48))\n ((:tag . "NN") (:stem . "E2–E4,E6–E8,F1–F8") (:form . "E2–E4,E6–E8,F1–F8")\n  (:end . 39) (:start . 22) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "NN") (:stem . "magnification") (:form . "magnification")\n  (:end . 54) (:start . 41) (:id . 51))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 70)\n  (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "glutamatergic") (:form . "glutamatergic")\n  (:end . 87) (:start . 74) (:id . 55))\n ((:tag . "NNS") (:stem . "nmj") (:form . "NMJs") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "abdominal") (:form . "abdominal") (:end . 109)\n  (:start . 100) (:id . 59))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 117)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "a3") (:form . "A3") (:end . 120) (:start . 118)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 129)\n  (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 136)\n  (:start . 130) (:id . 64))\n ((:tag . "NNS") (:stem . "muscle") (:form . "muscles") (:end . 144)\n  (:start . 137) (:id . 65))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 146) (:start . 145)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 67))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 152) (:start . 151)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s8.149) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502401@unknown@formal@none@1@S@(E) NMJs are double-labeled with the neuronal membrane marker anti-HRP (red) and anti-Dlg (green), which reveal the well-defined presynaptic and postsynaptic NMJ structures in wild-type (E1–E4) and dhtt-ko mutants (E5–E8).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "nmj") (:form . "NMJs") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 12) (:start . 9)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "double-labeled") (:form . "double-labeled")\n  (:end . 27) (:start . 13) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 45)\n  (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "anti-hrp") (:form . "anti-HRP") (:end . 70)\n  (:start . 62) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "anti-dlg") (:form . "anti-Dlg") (:end . 89)\n  (:start . 81) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 96) (:start . 91)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 62))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 104)\n  (:start . 99) (:id . 63))\n ((:tag . "VBP") (:stem . "reveal") (:form . "reveal") (:end . 111)\n  (:start . 105) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "well-defined") (:form . "well-defined") (:end . 128)\n  (:start . 116) (:id . 66))\n ((:tag . "JJ") (:stem . "presynaptic") (:form . "presynaptic") (:end . 140)\n  (:start . 129) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 157)\n  (:start . 145) (:id . 69))\n ((:tag . "NNP") (:stem . "NMJ") (:form . "NMJ") (:end . 161) (:start . 158)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 172)\n  (:start . 162) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 175) (:start . 173)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 185)\n  (:start . 176) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 187) (:start . 186)\n  (:id . 74))\n ((:tag . "NN") (:stem . "e1–e4") (:form . "E1–E4") (:end . 192)\n  (:start . 187) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 193) (:start . 192)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 197) (:start . 194)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 205)\n  (:start . 198) (:id . 78))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 213)\n  (:start . 206) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 215) (:start . 214)\n  (:id . 80))\n ((:tag . "NN") (:stem . "e5–e8") (:form . "E5–E8") (:end . 220)\n  (:start . 215) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.150) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502402@unknown@formal@none@1@S@(E2–E4,E6–E8) Magnified views of the areas highlighted in (E1,E5).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E2–E4,E6–E8") (:form . "E2–E4,E6–E8") (:end . 12)\n  (:start . 1) (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "magnified") (:form . "Magnified") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "NNS") (:stem . "view") (:form . "views") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 54)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "E1,E5") (:form . "E1,E5") (:end . 64) (:start . 59)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s8.151) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502403@unknown@formal@none@1@S@(F) NMJs are labeled with anti-HRP (white) (F1,F5), the periactive zone marker anti-FasII (green) (F2,F6) and the active zone marker nc82 (red) (F3,F7), revealing the normal periactive zone and active zone organization in wild-type (F1–F4) and dhtt-ko flies (F5–F8).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "nmj") (:form . "NMJs") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 12) (:start . 9)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 20)\n  (:start . 13) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "anti-hrp") (:form . "anti-HRP") (:end . 34)\n  (:start . 26) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 41) (:start . 36)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "F1,F5") (:form . "F1,F5") (:end . 49) (:start . 44)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "periactive") (:form . "periactive") (:end . 66)\n  (:start . 56) (:id . 58))\n ((:tag . "NN") (:stem . "zone") (:form . "zone") (:end . 71) (:start . 67)\n  (:id . 59))\n ((:tag . "NN") (:stem . "marker") (:form . 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"zone") (:form . "zone") (:end . 125) (:start . 121)\n  (:id . 71))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 132)\n  (:start . 126) (:id . 72))\n ((:tag . "NN") (:stem . "nc82") (:form . "nc82") (:end . 137) (:start . 133)\n  (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 74))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 142) (:start . 139)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "F3,F7") (:form . "F3,F7") (:end . 150)\n  (:start . 145) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 80))\n ((:tag . "VBG") (:stem . "reveal") (:form . "revealing") (:end . 162)\n  (:start . 153) (:id . 81))\n ((:tag . 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"(") (:form . "(") (:end . 233) (:start . 232)\n  (:id . 92))\n ((:tag . "NN") (:stem . "f1–f4") (:form . "F1–F4") (:end . 238)\n  (:start . 233) (:id . 93))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 239) (:start . 238)\n  (:id . 94))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 243) (:start . 240)\n  (:id . 95))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 251)\n  (:start . 244) (:id . 96))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 257) (:start . 252)\n  (:id . 97))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 259) (:start . 258)\n  (:id . 98))\n ((:tag . "NN") (:stem . "f5–f8") (:form . "F5–F8") (:end . 264)\n  (:start . 259) (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 265) (:start . 264)\n  (:id . 100))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 266) (:start . 265)\n  (:id . 101)))@@@1@60@((:identifiers (:sid . :s8.152) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502404@unknown@formal@none@1@S@(F4,F8) Overlayed images of (F1–F3,F5–F7), respectively.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "F4,F8") (:form . "F4,F8") (:end . 6) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 7) (:start . 6) (:id . 44))\n ((:tag . "VBD") (:stem . "overlay") (:form . "Overlayed") (:end . 17)\n  (:start . 8) (:id . 45))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "F1–F3,F5–F7") (:form . "F1–F3,F5–F7") (:end . 40)\n  (:start . 29) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 51))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 55)\n  (:start . 43) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s8.153) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502405@unknown@formal@none@1@S@WT: w1118 wild-type control.@(((:tag . "NNP") (:stem . "WT") (:form . "WT") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 3) (:start . 2) (:id . 43))\n ((:tag . "CD") (:stem . "w1118") (:form . "w1118") (:end . 9) (:start . 4)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 19)\n  (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 28) (:start . 27)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s8.154) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502406@unknown@formal@none@1@S@Bar, 5 µm (in all panels).@(((:tag . "NNP") (:stem . "Bar") (:form . "Bar") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 6) (:start . 5)\n  (:id . 44))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 9) (:start . 7)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 11) (:start . 10)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 47))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 17) (:start . 14)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 24)\n  (:start . 18) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 26) (:start . 25)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s8.155) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502407@unknown@formal@none@1@S@(G–I) Quantitative analysis of NMJs in muscle 6 and 7 of the abdominal segment A3 for wild-type control (WT, blue) and dhtt-ko mutant (red) flies.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "LS") (:stem . "g–i") (:form . "G–I") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "Quantitative") (:end . 18)\n  (:start . 6) (:id . 45))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "nmj") (:form . "NMJs") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "muscle") (:form . "muscle") (:end . 45)\n  (:start . 39) (:id . 50))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 47) (:start . 46)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 53) (:start . 52)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "abdominal") (:form . "abdominal") (:end . 70)\n  (:start . 61) (:id . 56))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 78)\n  (:start . 71) (:id . 57))\n ((:tag . "NN") (:stem . "a3") (:form . "A3") (:end . 81) (:start . 79)\n  (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 85) (:start . 82)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 95)\n  (:start . 86) (:id . 60))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 103)\n  (:start . 96) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "WT") (:form . "WT") (:end . 107) (:start . 105)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 113) (:start . 109)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 67))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 126)\n  (:start . 119) (:id . 68))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 133)\n  (:start . 127) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 138) (:start . 135)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 145) (:start . 140)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.156) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502408@unknown@formal@none@1@S@(G) Average number of type 1b boutons: WT control=34.5±1.6 (n=24), dhtt-ko mutants=33.5±2.4 (n=21); the difference is statistically insignificant, P=0.72 (Student’s t-test).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 18)\n  (:start . 12) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 26) (:start . 22)\n  (:id . 48))\n ((:tag . "NN") (:stem . "1b") (:form . "1b") (:end . 29) (:start . 27)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "bouton") (:form . "boutons") (:end . 37)\n  (:start . 30) (:id . 50))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 38) (:start . 37)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "wt") (:form . "WT") (:end . 41) (:start . 39)\n  (:id . 52))\n ((:tag . "NN") (:stem . "control=34.5±1.6") (:form . "control=34.5±1.6")\n  (:end . 58) (:start . 42) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "n=24") (:form . "n=24") (:end . 64) (:start . 60)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 65) (:start . 64)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 74)\n  (:start . 67) (:id . 58))\n ((:tag . "NN") (:stem . "mutants=33.5±2.4") (:form . "mutants=33.5±2.4")\n  (:end . 91) (:start . 75) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . "NN") (:stem . "n=21") (:form . "n=21") (:end . 97) (:start . 93)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 99) (:start . 98)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 64))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 114)\n  (:start . 104) (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 117) (:start . 115)\n  (:id . 66))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n  (:end . 131) (:start . 118) (:id . 67))\n ((:tag . "JJ") (:stem . "insignificant") (:form . "insignificant")\n  (:end . 145) (:start . 132) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "P=0.72") (:form . "P=0.72") (:end . 153)\n  (:start . 147) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 162)\n  (:start . 155) (:id . 72))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 164) (:start . 163)\n  (:id . 73))\n ((:tag . "NN") (:stem . "t-test") (:form . "t-test") (:end . 171)\n  (:start . 165) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.157) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502409@unknown@formal@none@1@S@(H) Average number of total boutons: WT control=63.1±1.8 (n=24), dhtt-ko mutants=62.3±2.0 (n=21); P=0.76-@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 18)\n  (:start . 12) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 27) (:start . 22)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "bouton") (:form . "boutons") (:end . 35)\n  (:start . 28) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "wt") (:form . "WT") (:end . 39) (:start . 37)\n  (:id . 51))\n ((:tag . "NN") (:stem . "control=63.1±1.8") (:form . "control=63.1±1.8")\n  (:end . 56) (:start . 40) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "n=24") (:form . "n=24") (:end . 62) (:start . 58)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 72)\n  (:start . 65) (:id . 57))\n ((:tag . "NN") (:stem . "mutants=62.3±2.0") (:form . "mutants=62.3±2.0")\n  (:end . 89) (:start . 73) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "NN") (:stem . "n=21") (:form . "n=21") (:end . 95) (:start . 91)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 97) (:start . 96)\n  (:id . 62))\n ((:tag . "NN") (:stem . "p=0.76-") (:form . "P=0.76-") (:end . 105)\n  (:start . 98) (:id . 63)))@@@1@22@((:identifiers (:sid . :s8.158) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502410@unknown@formal@none@1@S@(I) Total number of branches: WT control=18.0±0.6 (n=28), dhtt-ko mutants=17.4±0.6 (n=34); P=0.52.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "i") (:form . "I") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "total") (:form . "Total") (:end . 9) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 16)\n  (:start . 10) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "branch") (:form . "branches") (:end . 28)\n  (:start . 20) (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 29) (:start . 28)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "wt") (:form . "WT") (:end . 32) (:start . 30)\n  (:id . 50))\n ((:tag . "NN") (:stem . "control=18.0±0.6") (:form . "control=18.0±0.6")\n  (:end . 49) (:start . 33) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "n=28") (:form . "n=28") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 56) (:start . 55)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 65)\n  (:start . 58) (:id . 56))\n ((:tag . "NN") (:stem . "mutants=17.4±0.6") (:form . "mutants=17.4±0.6")\n  (:end . 82) (:start . 66) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 58))\n ((:tag . "NN") (:stem . "n=34") (:form . "n=34") (:end . 88) (:start . 84)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 90) (:start . 89)\n  (:id . 61))\n ((:tag . "NN") (:stem . "p=0.52") (:form . "P=0.52") (:end . 97)\n  (:start . 91) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s8.159) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502411@unknown@formal@none@1@S@The data in (G–I) are presented as the means±s.e.m.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "G–I") (:form . "G–I") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 31)\n  (:start . 22) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 34) (:start . 32)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 51))\n ((:tag . "NN") (:stem . "means±s.e.m") (:form . "means±s.e.m") (:end . 50)\n  (:start . 39) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 51) (:start . 50)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s8.160) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502412@unknown@formal@none@1@S@(standard error of the mean).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 9)\n  (:start . 1) (:id . 43))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mean") (:form . "mean") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s8.161) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502413@unknown@formal@none@1@S@Normal synapse organization in dhtt-ko@(((:tag . "JJ") (:stem . "normal") (:form . "Normal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "synapse") (:form . "synapse") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 27)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 38)\n  (:start . 31) (:id . 46)))@@@1@5@((:identifiers (:sid . :s8.162) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502414@unknown@formal@none@1@S@Htt has been reported to interact with a diverse group of proteins whose functions have been directly or indirectly linked to synapse organization and synaptic activity (Harjes and Wanker, 2003), including proteins that regulate cytoskeleton dynamics and clathrin-mediated endocytosis [e.g. HIP1 (Sla2p), HIP12, PACSIN/syndapin 1 and endophilin 3] (Chopra et al., 2000; Higgins and McMahon, 2002; Kalchman et al., 1997; Modregger et al., 2002; Seki et al., 1998; Singaraja et al., 2002; Sittler et al., 1998; Wanker et al., 1997); axonal vesicle transport (e.g. HAP1) (Engelender et al., 1997; Gunawardena et al., 2003); and dendritic morphogenesis and synaptic plasticity (e.g. the postsynaptic density protein DLG4/PSD95 and the adaptor proteins GRB2 and TRIP10/CIP4) (Holbert et al., 2003; Liu et al., 1997; Sun et al., 2001).@(((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . 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5502415@unknown@formal@none@1@S@To test whether dhtt plays a role in synapse organization, we examined the formation of glutamatergic neuromuscular junctions (NMJs) in third instar larvae, a well-characterized system for studying synapse formation and function in Drosophila (Budnik and Gramates, 1999).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "play") (:form . "plays") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "synapse") (:form . "synapse") (:end . 44)\n  (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 57)\n  (:start . 45) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 70)\n  (:start . 62) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 84)\n  (:start . 75) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "glutamatergic") (:form . "glutamatergic")\n  (:end . 101) (:start . 88) (:id . 58))\n ((:tag . "JJ") (:stem . "neuromuscular") (:form . "neuromuscular")\n  (:end . 115) (:start . 102) (:id . 59))\n ((:tag . "NNS") (:stem . "junction") (:form . "junctions") (:end . 125)\n  (:start . 116) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "NMJ") (:form . "NMJs") (:end . 131) (:start . 127)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 141)\n  (:start . 136) (:id . 65))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 148)\n  (:start . 142) (:id . 66))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 155)\n  (:start . 149) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 158) (:start . 157)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "well-characterized") (:form . "well-characterized")\n  (:end . 177) (:start . 159) (:id . 70))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 184)\n  (:start . 178) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 188) (:start . 185)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "study") (:form . "studying") (:end . 197)\n  (:start . 189) (:id . 73))\n ((:tag . "NN") (:stem . "synapse") (:form . "synapse") (:end . 205)\n  (:start . 198) (:id . 74))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 215)\n  (:start . 206) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 219) (:start . 216)\n  (:id . 76))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 228)\n  (:start . 220) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 231) (:start . 229)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 242)\n  (:start . 232) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 244) (:start . 243)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Budnik") (:form . "Budnik") (:end . 250)\n  (:start . 244) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 254) (:start . 251)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Gramates") (:form . "Gramates") (:end . 263)\n  (:start . 255) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 264) (:start . 263)\n  (:id . 84))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 269) (:start . 265)\n  (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 270) (:start . 269)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 271) (:start . 270)\n  (:id . 87)))@@@1@46@((:hcues ((:id . :x8.164.1) (:span 8 15)))\n (:hscopes ((:id . :x8.164.1) (:span 8 57)))\n (:identifiers (:sid . :s8.164) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502416@unknown@formal@none@1@S@Examination with a panel of synapse markers showed that axonal pathfinding, muscle innervation and overall synapse structure are normal in dhtt mutants (Fig. 3 and data not shown).@(((:tag . "NNP") (:stem . "Examination") (:form . "Examination") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 16) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "NN") (:stem . "panel") (:form . "panel") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "synapse") (:form . "synapse") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 50) (:start . 44)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "pathfinding") (:form . "pathfinding") (:end . 74)\n  (:start . 63) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "NN") (:stem . "muscle") (:form . "muscle") (:end . 82)\n  (:start . 76) (:id . 54))\n ((:tag . "NN") (:stem . "innervation") (:form . "innervation") (:end . 94)\n  (:start . 83) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 106)\n  (:start . 99) (:id . 57))\n ((:tag . "NN") (:stem . "synapse") (:form . "synapse") (:end . 114)\n  (:start . 107) (:id . 58))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 124)\n  (:start . 115) (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 128) (:start . 125)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 135)\n  (:start . 129) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 138) (:start . 136)\n  (:id . 62))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 143) (:start . 139)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 151)\n  (:start . 144) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 157) (:start . 153)\n  (:id . 66))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 159) (:start . 158)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 163) (:start . 160)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 168)\n  (:start . 164) (:id . 69))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 172) (:start . 169)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 178)\n  (:start . 173) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s8.165) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502417@unknown@formal@none@1@S@Double-labeling with the axonal membrane marker anti-HRP and the postsynaptic density marker anti-Dlg (the Drosophila PSD95 homolog) revealed well-organized presynaptic and postsynaptic structures (Fig. 3E1–E8), as well as an enrichment of synaptic vesicles at the synapses, with no obvious synapse retraction phenotype (data not shown).@(((:tag . "JJ") (:stem . "double-labeling") (:form . "Double-labeling")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 20) (:start . 16)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 31)\n  (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 40)\n  (:start . 32) (:id . 46))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 47)\n  (:start . 41) (:id . 47))\n ((:tag . "NN") (:stem . 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5502418@unknown@formal@none@1@S@Moreover, dhtt mutants showed normal organization of the presynaptic microtubule (MT) cytoskeleton, with the presence of stable MT bundles traversing the center of NMJ branches and a dynamically reorganized MT network at distal boutons (data not shown).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 29) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 49)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "presynaptic") (:form . "presynaptic") (:end . 68)\n  (:start . 57) (:id . 51))\n ((:tag . "NN") (:stem . "microtubule") (:form . "microtubule") (:end . 80)\n  (:start . 69) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "MT") (:form . "MT") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cytoskeleton") (:form . "cytoskeleton") (:end . 98)\n  (:start . 86) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 104) (:start . 100)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 117)\n  (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "stable") (:form . "stable") (:end . 127)\n  (:start . 121) (:id . 62))\n ((:tag . "NNP") (:stem . "MT") (:form . "MT") (:end . 130) (:start . 128)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "bundle") (:form . "bundles") (:end . 138)\n  (:start . 131) (:id . 64))\n ((:tag . "VBG") (:stem . "traverse") (:form . "traversing") (:end . 149)\n  (:start . 139) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 66))\n ((:tag . "NN") (:stem . "center") (:form . "center") (:end . 160)\n  (:start . 154) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "NMJ") (:form . "NMJ") (:end . 167) (:start . 164)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "branch") (:form . "branches") (:end . 176)\n  (:start . 168) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 180) (:start . 177)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 182) (:start . 181)\n  (:id . 72))\n ((:tag . "RB") (:stem . "dynamically") (:form . "dynamically") (:end . 194)\n  (:start . 183) (:id . 73))\n ((:tag . "VBN") (:stem . "reorganize") (:form . "reorganized") (:end . 206)\n  (:start . 195) (:id . 74))\n ((:tag . "NN") (:stem . "mt") (:form . "MT") (:end . 209) (:start . 207)\n  (:id . 75))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 217)\n  (:start . 210) (:id . 76))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 220) (:start . 218)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "distal") (:form . "distal") (:end . 227)\n  (:start . 221) (:id . 78))\n ((:tag . "NNS") (:stem . "bouton") (:form . "boutons") (:end . 235)\n  (:start . 228) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 237) (:start . 236)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 241)\n  (:start . 237) (:id . 81))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 245) (:start . 242)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 251)\n  (:start . 246) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 252) (:start . 251)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 253) (:start . 252)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s8.167) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502419@unknown@formal@none@1@S@Quantification of NMJ bouton number and axonal branching did not reveal a significant difference between wild-type controls and dhtt mutants (Fig. 3G–I).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "NMJ") (:form . "NMJ") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "bouton") (:form . "bouton") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 35)\n  (:start . 29) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 46)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "branching") (:form . "branching") (:end . 56)\n  (:start . 47) (:id . 49))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "VB") (:stem . "reveal") (:form . "reveal") (:end . 71)\n  (:start . 65) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 85)\n  (:start . 74) (:id . 54))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 96)\n  (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 104)\n  (:start . 97) (:id . 56))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 114)\n  (:start . 105) (:id . 57))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 123)\n  (:start . 115) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 59))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 132) (:start . 128)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 140)\n  (:start . 133) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 146) (:start . 142)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "3G–I") (:form . "3G–I") (:end . 151) (:start . 147)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s8.168) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502420@unknown@formal@none@1@S@Finally, dhtt mutants displayed the stereotypical complementary pattern of active zones surrounded by the honeycomb-like organization of periactive zones, and examination of multiple synaptic proteins such as nc82 (an active zone marker) and fasciclin II (FasII, a periactive zones marker) showed normal synaptic localization (Fig. 3F1–F8).@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "stereotypical") (:form . 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5502421@unknown@formal@none@1@S@As a control, we also examined synapse organization in CG9990 transgenic animals, which displayed similar well-organized NMJ structures (supplementary material Fig. S3 and data not shown).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 21) (:start . 17)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 30)\n  (:start . 22) (:id . 48))\n ((:tag . "NN") (:stem . "synapse") (:form . "synapse") (:end . 38)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 51)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "CG9990") (:form . "CG9990") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 72)\n  (:start . 62) (:id . 53))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 80)\n  (:start . 73) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 87) (:start . 82)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 97)\n  (:start . 88) (:id . 57))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 105)\n  (:start . 98) (:id . 58))\n ((:tag . "JJ") (:stem . "well-organized") (:form . "well-organized")\n  (:end . 120) (:start . 106) (:id . 59))\n ((:tag . "NNP") (:stem . "NMJ") (:form . "NMJ") (:end . 124) (:start . 121)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 135)\n  (:start . 125) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 150) (:start . 137) (:id . 63))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 159)\n  (:start . 151) (:id . 64))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 164) (:start . 160)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 167) (:start . 165)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 176)\n  (:start . 172) (:id . 68))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 180) (:start . 177)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 186)\n  (:start . 181) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s8.170) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502422@unknown@formal@none@1@S@Together, these results suggest that dhtt is not essential for synapse formation and organization at NMJs.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "synapse") (:form . "synapse") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 80)\n  (:start . 71) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 97)\n  (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "NMJ") (:form . "NMJs") (:end . 105) (:start . 101)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x8.171.1) (:span 24 31)))\n (:hscopes ((:id . :x8.171.1) (:span 24 105)))\n (:identifiers (:sid . :s8.171) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502423@unknown@formal@none@1@S@dhtt is not essential for axonal transport@(((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 32)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "transport") (:form . "transport") (:end . 42)\n  (:start . 33) (:id . 48)))@@@1@7@((:identifiers (:sid . :s8.172) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502424@unknown@formal@none@1@S@Htt has also been proposed to regulate axonal vesicle transport because one of its binding partners, HAP1, interacts directly with p150Glued, which is an essential subunit of the dynactin complex involved in regulating dynein-mediated retrograde axonal transport (Engelender et al., 1997; Gunawardena et al., 2003; Harjes and Wanker, 2003).@(((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "VB") (:stem . "regulate") (:form . 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5502425@unknown@formal@none@1@S@In Drosophila, individuals that are defective for essential components of the axonal transport machinery often display characteristic mobility phenotypes, such as tail flipping during larva crawling, and progressive lethargy and paralysis (Gindhart et al., 1998; Gunawardena and Goldstein, 2001; Martin et al., 1999).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "individual") (:form . "individuals") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "defective") (:form . 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5502426@unknown@formal@none@1@S@Such mutant animals also develop an axonal swelling phenotype, owing to the abnormal accumulation of synaptic vesicles along axons, and fail to properly deliver and localize synaptic components to the termini (Gindhart et al., 1998; Gunawardena and Goldstein, 2001; Martin et al., 1999).@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "develop") (:form . "develop") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . 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5502427@unknown@formal@none@1@S@dhtt mutants showed normal crawling behavior during larval stages.@(((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 19) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "VBG") (:stem . "crawl") (:form . "crawling") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "behavior") (:form . "behavior") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 51)\n  (:start . 45) (:id . 48))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 58)\n  (:start . 52) (:id . 49))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 65)\n  (:start . 59) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s8.176) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502428@unknown@formal@none@1@S@Furthermore, the distributions of the synaptic vesicle markers anti-synaptotagmin (Syt) and anti-cysteine string protein (CSP) were normal, revealing no obvious accumulation or axonal swellings (Fig. 4 and data not shown).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 30) (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "vesicle") (:form . "vesicle") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 62)\n  (:start . 55) (:id . 50))\n ((:tag . "JJ") (:stem . "anti-synaptotagmin") (:form . "anti-synaptotagmin")\n  (:end . 81) (:start . 63) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Syt") (:form . "Syt") (:end . 86) (:start . 83)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "anti-cysteine") (:form . "anti-cysteine")\n  (:end . 105) (:start . 92) (:id . 56))\n ((:tag . "NN") (:stem . "string") (:form . "string") (:end . 112)\n  (:start . 106) (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 120)\n  (:start . 113) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "CSP") (:form . "CSP") (:end . 125) (:start . 122)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 131) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 138)\n  (:start . 132) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "reveal") (:form . "revealing") (:end . 149)\n  (:start . 140) (:id . 65))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 152) (:start . 150)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 160)\n  (:start . 153) (:id . 67))\n ((:tag . "NN") (:stem . "accumulation") (:form . "accumulation") (:end . 173)\n  (:start . 161) (:id . 68))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 176) (:start . 174)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 183)\n  (:start . 177) (:id . 70))\n ((:tag . "NNS") (:stem . "swelling") (:form . "swellings") (:end . 193)\n  (:start . 184) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 195) (:start . 194)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 199) (:start . 195)\n  (:id . 73))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 201) (:start . 200)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 205) (:start . 202)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 210)\n  (:start . 206) (:id . 76))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 214) (:start . 211)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 220)\n  (:start . 215) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s8.177) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502429@unknown@formal@none@1@S@Further, immunostaining with other synaptic components, including synapsin (a reserved vesicle pool marker), FasII (a periactive zone marker) and Dlg, demonstrated that synaptic components were properly delivered to synapses (Fig. 3E–F and data not shown).@(((:tag . "RB") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "immunostaining") (:form . "immunostaining")\n  (:end . 23) (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 54)\n  (:start . 44) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 65)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "synapsin") (:form . "synapsin") (:end . 74)\n  (:start . 66) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "reserve") (:form . "reserved") (:end . 86)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "vesicle") (:form . "vesicle") (:end . 94)\n  (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "pool") (:form . "pool") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 106)\n  (:start . 100) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "FasII") (:form . "FasII") (:end . 114)\n  (:start . 109) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 117) (:start . 116)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "periactive") (:form . "periactive") (:end . 128)\n  (:start . 118) (:id . 63))\n ((:tag . "NN") (:stem . "zone") (:form . "zone") (:end . 133) (:start . 129)\n  (:id . 64))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 140)\n  (:start . 134) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Dlg") (:form . "Dlg") (:end . 149) (:start . 146)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 69))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 163)\n  (:start . 151) (:id . 70))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 168) (:start . 164)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 177)\n  (:start . 169) (:id . 72))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 188)\n  (:start . 178) (:id . 73))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 193) (:start . 189)\n  (:id . 74))\n ((:tag . "RB") (:stem . "properly") (:form . "properly") (:end . 202)\n  (:start . 194) (:id . 75))\n ((:tag . "VBN") (:stem . "deliver") (:form . "delivered") (:end . 212)\n  (:start . 203) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 215) (:start . 213)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "synapsis") (:form . "synapses") (:end . 224)\n  (:start . 216) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 226) (:start . 225)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 230) (:start . 226)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "3E–F") (:form . "3E–F") (:end . 235) (:start . 231)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 239) (:start . 236)\n  (:id . 82))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 244)\n  (:start . 240) (:id . 83))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 248) (:start . 245)\n  (:id . 84))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 254)\n  (:start . 249) (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 255) (:start . 254)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 256) (:start . 255)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s8.178) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502430@unknown@formal@none@1@S@Similarly, examination of CG9990 transgenic animals failed to reveal discernible larval mobility or axonal transport defects (supplementary material Fig. S3).@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "examination") (:form . "examination") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "CG9990") (:form . "CG9990") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 58) (:start . 52)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "VB") (:stem . "reveal") (:form . "reveal") (:end . 68)\n  (:start . 62) (:id . 51))\n ((:tag . "JJ") (:stem . "discernible") (:form . "discernible") (:end . 80)\n  (:start . 69) (:id . 52))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 87)\n  (:start . 81) (:id . 53))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 96)\n  (:start . 88) (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 99) (:start . 97)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 106)\n  (:start . 100) (:id . 56))\n ((:tag . "NN") (:stem . "transport") (:form . "transport") (:end . 116)\n  (:start . 107) (:id . 57))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 124)\n  (:start . 117) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 139) (:start . 126) (:id . 60))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 148)\n  (:start . 140) (:id . 61))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 153) (:start . 149)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 156) (:start . 154)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s8.179) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502431@unknown@formal@none@1@S@Together, these results suggest that dhtt does not play an essential role in axonal transport.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 68)\n  (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 83)\n  (:start . 77) (:id . 56))\n ((:tag . "NN") (:stem . "transport") (:form . "transport") (:end . 93)\n  (:start . 84) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x8.180.1) (:span 24 31)))\n (:hscopes ((:id . :x8.180.1) (:span 24 93)))\n (:identifiers (:sid . :s8.180) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502432@unknown@formal@none@1@S@Normal axonal transport in dhtt-ko mutants.@(((:tag . "JJ") (:stem . "normal") (:form . "Normal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 13) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "transport") (:form . "transport") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 42)\n  (:start . 35) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s8.181) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502433@unknown@formal@none@1@S@Confocal images of wild-type control (A–C) and dhtt-ko (D–F) NMJs and neighboring axons (white arrows) of the larval peripheral nervous system (anti-HRP, red).@(((:tag . "JJ") (:stem . "confocal") (:form . "Confocal") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "A–C") (:form . "A–C") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "D–F") (:form . "D–F") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "nmj") (:form . "NMJs") (:end . 65) (:start . 61)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "neighbor") (:form . "neighboring") (:end . 81)\n  (:start . 70) (:id . 57))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 87) (:start . 82)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 94) (:start . 89)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 101)\n  (:start . 95) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 116)\n  (:start . 110) (:id . 65))\n ((:tag . "JJ") (:stem . "peripheral") (:form . "peripheral") (:end . 127)\n  (:start . 117) (:id . 66))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 135)\n  (:start . 128) (:id . 67))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 142)\n  (:start . 136) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 144) (:start . 143)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "anti-hrp") (:form . "anti-HRP") (:end . 152)\n  (:start . 144) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 157) (:start . 154)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.182) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502434@unknown@formal@none@1@S@Synaptic vesicles (green, anti-Syt) are properly delivered to NMJs and show no obvious accumulation in the axons of dhtt-komutants (D–F), similar to the wild-type controls (A–C).@(((:tag . "JJ") (:stem . "synaptic") (:form . "Synaptic") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "vesicle") (:form . "vesicles") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 19) (:start . 18)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "anti-syt") (:form . "anti-Syt") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 35) (:start . 34)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "RB") (:stem . "properly") (:form . "properly") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "VBN") (:stem . "deliver") (:form . "delivered") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "nmj") (:form . "NMJs") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "VB") (:stem . "show") (:form . "show") (:end . 75) (:start . 71)\n  (:id . 55))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 86)\n  (:start . 79) (:id . 57))\n ((:tag . "NN") (:stem . "accumulation") (:form . "accumulation") (:end . 99)\n  (:start . 87) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 112)\n  (:start . 107) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "dhtt-komutant") (:form . "dhtt-komutants")\n  (:end . 130) (:start . 116) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 132) (:start . 131)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "D–F") (:form . "D–F") (:end . 135) (:start . 132)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 145)\n  (:start . 138) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 162)\n  (:start . 153) (:id . 71))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 171)\n  (:start . 163) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 173) (:start . 172)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "A–C") (:form . "A–C") (:end . 176) (:start . 173)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 177) (:start . 176)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.183) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502435@unknown@formal@none@1@S@Signals for Syt were overexposed in (B,C,E,F) in order to reveal any possible abnormal accumulations of synaptic vesicles within axons (white arrows).@(((:tag . "NNS") (:stem . "signal") (:form . "Signals") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Syt") (:form . "Syt") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "overexpose") (:form . "overexposed") (:end . 32)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "B,C,E,F") (:form . "B,C,E,F") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 54) (:start . 49)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "VB") (:stem . "reveal") (:form . "reveal") (:end . 64)\n  (:start . 58) (:id . 54))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 77)\n  (:start . 69) (:id . 56))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 86)\n  (:start . 78) (:id . 57))\n ((:tag . "NNS") (:stem . "accumulation") (:form . "accumulations")\n  (:end . 100) (:start . 87) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 112)\n  (:start . 104) (:id . 60))\n ((:tag . "NNS") (:stem . "vesicle") (:form . "vesicles") (:end . 121)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 128)\n  (:start . 122) (:id . 62))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 134)\n  (:start . 129) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 141)\n  (:start . 136) (:id . 65))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 148)\n  (:start . 142) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.184) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502436@unknown@formal@none@1@S@(C,F) Overlayed images of double staining with anti-HRP and anti-Syt.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C,F") (:form . "C,F") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "VBD") (:stem . "overlay") (:form . "Overlayed") (:end . 15)\n  (:start . 6) (:id . 45))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 22)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 32)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "anti-hrp") (:form . "anti-HRP") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "anti-syt") (:form . "anti-Syt") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s8.185) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502437@unknown@formal@none@1@S@WT: w1118 wild-type control.@(((:tag . "NNP") (:stem . "WT") (:form . "WT") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 3) (:start . 2) (:id . 43))\n ((:tag . "CD") (:stem . "w1118") (:form . "w1118") (:end . 9) (:start . 4)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 19)\n  (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 28) (:start . 27)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s8.186) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502438@unknown@formal@none@1@S@Bars, 10 µm.@(((:tag . "NNS") (:stem . "bar") (:form . "Bars") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 11) (:start . 9)\n  (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 12) (:start . 11)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s8.187) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502439@unknown@formal@none@1@S@dhtt is crucial for aged adults@(((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 31)\n  (:start . 25) (:id . 47)))@@@1@6@((:identifiers (:sid . :s8.188) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502440@unknown@formal@none@1@S@We next investigated whether dhtt might function in adult animals.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "next") (:form . "next") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "investigate") (:form . "investigated") (:end . 20)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 65)\n  (:start . 58) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 52)))@@@1@11@((:hcues ((:id . :x8.189.1) (:span 34 39)) ((:id . :x8.189.2) (:span 21 28)))\n (:hscopes ((:id . :x8.189.1) (:span 34 65)) ((:id . :x8.189.2) (:span 21 65)))\n (:identifiers (:sid . :s8.189) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502441@unknown@formal@none@1@S@We examined whether newly emerged dhtt adults were hypersensitive to stress tests including prolonged heat and cold exposure, vortexing and feeding with the oxidative stress compound paraquat.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "RB") (:stem . "newly") (:form . "newly") (:end . 25) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "emerge") (:form . "emerged") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "hypersensitive") (:form . "hypersensitive")\n  (:end . 65) (:start . 51) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "NN") (:stem . "stress") (:form . "stress") (:end . 75)\n  (:start . 69) (:id . 52))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 81) (:start . 76)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 91)\n  (:start . 82) (:id . 54))\n ((:tag . "VBN") (:stem . "prolong") (:form . "prolonged") (:end . 101)\n  (:start . 92) (:id . 55))\n ((:tag . "NN") (:stem . "heat") (:form . "heat") (:end . 106) (:start . 102)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "cold") (:form . "cold") (:end . 115) (:start . 111)\n  (:id . 58))\n ((:tag . "NN") (:stem . "exposure") (:form . "exposure") (:end . 124)\n  (:start . 116) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 60))\n ((:tag . "NN") (:stem . "vortexing") (:form . "vortexing") (:end . 135)\n  (:start . 126) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . "NN") (:stem . "feeding") (:form . "feeding") (:end . 147)\n  (:start . 140) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 152) (:start . 148)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "oxidative") (:form . "oxidative") (:end . 166)\n  (:start . 157) (:id . 66))\n ((:tag . "NN") (:stem . "stress") (:form . "stress") (:end . 173)\n  (:start . 167) (:id . 67))\n ((:tag . "NN") (:stem . "compound") (:form . "compound") (:end . 182)\n  (:start . 174) (:id . 68))\n ((:tag . "NN") (:stem . "paraquat") (:form . "paraquat") (:end . 191)\n  (:start . 183) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x8.190.1) (:span 12 19)))\n (:hscopes ((:id . :x8.190.1) (:span 12 191)))\n (:identifiers (:sid . :s8.190) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502442@unknown@formal@none@1@S@In these tests, dhtt mutants showed similar responses to wild-type controls (data not shown).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 28)\n  (:start . 21) (:id . 47))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 35) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 66)\n  (:start . 57) (:id . 52))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 75)\n  (:start . 67) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 91) (:start . 86)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s8.191) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502443@unknown@formal@none@1@S@Thus, unlike flies that are mutated for Parkinson’s disease genes such as parkin and pink1, which are sensitive to multiple stress challenges (Clark et al., 2006; Greene et al., 2003; Park et al., 2006), loss of dhtt does not render young adult animals more vulnerable to environmental stresses.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "unlike") (:form . "unlike") (:end . 12) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Parkinson") (:form . "Parkinson") (:end . 49)\n  (:start . 40) (:id . 50))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "disease") (:form . "disease") (:end . 59)\n  (:start . 52) (:id . 52))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "parkin") (:form . "parkin") (:end . 80)\n  (:start . 74) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "pink1") (:form . "pink1") (:end . 90) (:start . 85)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 97) (:start . 92)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 101) (:start . 98)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "sensitive") (:form . "sensitive") (:end . 111)\n  (:start . 102) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 114) (:start . 112)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 123)\n  (:start . 115) (:id . 64))\n ((:tag . "NN") (:stem . "stress") (:form . "stress") (:end . 130)\n  (:start . 124) (:id . 65))\n ((:tag . "NNS") (:stem . "challenge") (:form . "challenges") (:end . 141)\n  (:start . 131) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Clark") (:form . "Clark") (:end . 148)\n  (:start . 143) (:id . 68))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 151) (:start . 149)\n  (:id . 69))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 155) (:start . 152)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 71))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 161) (:start . 157)\n  (:id . 72))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 162) (:start . 161)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Greene") (:form . "Greene") (:end . 169)\n  (:start . 163) (:id . 74))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 172) (:start . 170)\n  (:id . 75))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 176) (:start . 173)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 77))\n ((:tag . "CD") (:stem . "2003") (:form . "2003") (:end . 182) (:start . 178)\n  (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 183) (:start . 182)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Park") (:form . "Park") (:end . 188) (:start . 184)\n  (:id . 80))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 191) (:start . 189)\n  (:id . 81))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 195) (:start . 192)\n  (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n  (:id . 83))\n ((:tag . "CD") (:stem . "2006") (:form . "2006") (:end . 201) (:start . 197)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 202) (:start . 201)\n  (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 203) (:start . 202)\n  (:id . 86))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 208) (:start . 204)\n  (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 211) (:start . 209)\n  (:id . 88))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 216) (:start . 212)\n  (:id . 89))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 221) (:start . 217)\n  (:id . 90))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 225) (:start . 222)\n  (:id . 91))\n ((:tag . "VB") (:stem . "render") (:form . "render") (:end . 232)\n  (:start . 226) (:id . 92))\n ((:tag . "JJ") (:stem . "young") (:form . "young") (:end . 238)\n  (:start . 233) (:id . 93))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 244)\n  (:start . 239) (:id . 94))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 252)\n  (:start . 245) (:id . 95))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 257) (:start . 253)\n  (:id . 96))\n ((:tag . "JJ") (:stem . "vulnerable") (:form . "vulnerable") (:end . 268)\n  (:start . 258) (:id . 97))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 271) (:start . 269)\n  (:id . 98))\n ((:tag . "JJ") (:stem . "environmental") (:form . "environmental")\n  (:end . 285) (:start . 272) (:id . 99))\n ((:tag . "NNS") (:stem . "stress") (:form . "stresses") (:end . 294)\n  (:start . 286) (:id . 100))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 295) (:start . 294)\n  (:id . 101)))@@@1@60@((:identifiers (:sid . :s8.192) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502444@unknown@formal@none@1@S@Next, we followed the activity and viability of dhtt animals throughout the adult life cycle.@(((:tag . "RB") (:stem . "next") (:form . "Next") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "follow") (:form . "followed") (:end . 17)\n  (:start . 9) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 44)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 60)\n  (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 71)\n  (:start . 61) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 81) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s8.193) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502445@unknown@formal@none@1@S@Although no discernible difference in the activity and survival rate was observed between dhtt-ko and wild-type young adults, we observed striking defects in older adult dhtt-ko flies.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "discernible") (:form . "discernible") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 34)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 63)\n  (:start . 55) (:id . 50))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 81)\n  (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 89)\n  (:start . 82) (:id . 54))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 97)\n  (:start . 90) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 111)\n  (:start . 102) (:id . 57))\n ((:tag . "JJ") (:stem . "young") (:form . "young") (:end . 117)\n  (:start . 112) (:id . 58))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 124)\n  (:start . 118) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 128) (:start . 126)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 137)\n  (:start . 129) (:id . 62))\n ((:tag . "JJ") (:stem . "striking") (:form . "striking") (:end . 146)\n  (:start . 138) (:id . 63))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 154)\n  (:start . 147) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 157) (:start . 155)\n  (:id . 65))\n ((:tag . "JJR") (:stem . "old") (:form . "older") (:end . 163) (:start . 158)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 169)\n  (:start . 164) (:id . 67))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 177)\n  (:start . 170) (:id . 68))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 183) (:start . 178)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.194) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502446@unknown@formal@none@1@S@dhtt-ko animals showed similar spontaneous locomotion to that of wild-type controls at day 15 and earlier (Fig. 5A; supplementary material Movie 1).@(((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 22) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "JJ") (:stem . "spontaneous") (:form . "spontaneous") (:end . 42)\n  (:start . 31) (:id . 46))\n ((:tag . "NN") (:stem . "locomotion") (:form . "locomotion") (:end . 53)\n  (:start . 43) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 48))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 74)\n  (:start . 65) (:id . 51))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 83)\n  (:start . 75) (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 86) (:start . 84)\n  (:id . 53))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 90) (:start . 87)\n  (:id . 54))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 93) (:start . 91)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 56))\n ((:tag . "JJR") (:stem . "early") (:form . "earlier") (:end . 105)\n  (:start . 98) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 111) (:start . 107)\n  (:id . 59))\n ((:tag . "NN") (:stem . "5a") (:form . "5A") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 129) (:start . 116) (:id . 62))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 138)\n  (:start . 130) (:id . 63))\n ((:tag . "NNP") (:stem . "Movie") (:form . "Movie") (:end . 144)\n  (:start . 139) (:id . 64))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 146) (:start . 145)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s8.195) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502447@unknown@formal@none@1@S@However, as flies aged, dhtt-ko mutants displayed a rapidly declining mobility, which was evident by day 25.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 31)\n  (:start . 24) (:id . 48))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 39)\n  (:start . 32) (:id . 49))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 49)\n  (:start . 40) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 59)\n  (:start . 52) (:id . 52))\n ((:tag . "VBG") (:stem . "decline") (:form . "declining") (:end . 69)\n  (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "evident") (:form . "evident") (:end . 97)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 107) (:start . 105)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.196) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502448@unknown@formal@none@1@S@By day 40, almost all dhtt mutants showed severely compromised mobility (Fig. 5A; supplementary material Movie 2) and their viability declined quickly.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 45))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 17)\n  (:start . 11) (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 26) (:start . 22)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 34)\n  (:start . 27) (:id . 49))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 41) (:start . 35)\n  (:id . 50))\n ((:tag . "RB") (:stem . "severely") (:form . "severely") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . "VBN") (:stem . "compromise") (:form . "compromised") (:end . 62)\n  (:start . 51) (:id . 52))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 71)\n  (:start . 63) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "5a") (:form . "5A") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 95) (:start . 82) (:id . 58))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 104)\n  (:start . 96) (:id . 59))\n ((:tag . "NNP") (:stem . "Movie") (:form . "Movie") (:end . 110)\n  (:start . 105) (:id . 60))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 63))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 123)\n  (:start . 118) (:id . 64))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 133)\n  (:start . 124) (:id . 65))\n ((:tag . "VBD") (:stem . "decline") (:form . "declined") (:end . 142)\n  (:start . 134) (:id . 66))\n ((:tag . "RB") (:stem . "quickly") (:form . "quickly") (:end . 150)\n  (:start . 143) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.197) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502449@unknown@formal@none@1@S@Whereas, on average, half of the wild-type controls died around day 59 but could live for up to 90 days, half of the dhtt-ko flies died around day 43 and almost all by day 50 (Fig. 5B).@(((:tag . "IN") (:stem . "whereas") (:form . "Whereas") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "half") (:form . "half") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 42)\n  (:start . 33) (:id . 50))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 51)\n  (:start . 43) (:id . 51))\n ((:tag . "VBD") (:stem . "die") (:form . "died") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 63)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "CD") (:stem . "59") (:form . "59") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 74) (:start . 71)\n  (:id . 56))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 80) (:start . 75)\n  (:id . 57))\n ((:tag . "VB") (:stem . "live") (:form . "live") (:end . 85) (:start . 81)\n  (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 89) (:start . 86)\n  (:id . 59))\n ((:tag . "RB") (:stem . "up") (:form . "up") (:end . 92) (:start . 90)\n  (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 61))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 98) (:start . 96)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 103) (:start . 99)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 64))\n ((:tag . "NN") (:stem . "half") (:form . "half") (:end . 109) (:start . 105)\n  (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 124)\n  (:start . 117) (:id . 68))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 130) (:start . 125)\n  (:id . 69))\n ((:tag . "VBD") (:stem . "die") (:form . "died") (:end . 135) (:start . 131)\n  (:id . 70))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 142)\n  (:start . 136) (:id . 71))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 146) (:start . 143)\n  (:id . 72))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 149) (:start . 147)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 153) (:start . 150)\n  (:id . 74))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 160)\n  (:start . 154) (:id . 75))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 164) (:start . 161)\n  (:id . 76))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 167) (:start . 165)\n  (:id . 77))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 171) (:start . 168)\n  (:id . 78))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 174) (:start . 172)\n  (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 180) (:start . 176)\n  (:id . 81))\n ((:tag . "NN") (:stem . "5b") (:form . "5B") (:end . 183) (:start . 181)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s8.198) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502450@unknown@formal@none@1@S@To verify that the late-onset mobility and viability defects were because of loss of dhtt, we constructed a dhtt minigene that expressed full-length dhtt under the control of its endogenous regulatory region (see Methods).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "verify") (:form . "verify") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "late-onset") (:form . "late-onset") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 52)\n  (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 73)\n  (:start . 66) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 81) (:start . 77)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "construct") (:form . "constructed") (:end . 105)\n  (:start . 94) (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 112) (:start . 108)\n  (:id . 61))\n ((:tag . "NN") (:stem . "minigene") (:form . "minigene") (:end . 121)\n  (:start . 113) (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 126) (:start . 122)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "express") (:form . "expressed") (:end . 136)\n  (:start . 127) (:id . 64))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 148)\n  (:start . 137) (:id . 65))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 153) (:start . 149)\n  (:id . 66))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 159)\n  (:start . 154) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 68))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 171)\n  (:start . 164) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 174) (:start . 172)\n  (:id . 70))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 178) (:start . 175)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 189)\n  (:start . 179) (:id . 72))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 200)\n  (:start . 190) (:id . 73))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 207)\n  (:start . 201) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 209) (:start . 208)\n  (:id . 75))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 212) (:start . 209)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 220)\n  (:start . 213) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s8.199) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502451@unknown@formal@none@1@S@In the presence of this mini-dhtt transgene, the expression of the dhtt gene was restored in dhtt-ko mutants, as confirmed by RT-PCR (Fig. 5C)@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 15)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mini-dhtt") (:form . "mini-dhtt") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 59)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "restore") (:form . "restored") (:end . 89)\n  (:start . 81) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 100)\n  (:start . 93) (:id . 59))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 108)\n  (:start . 101) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 122)\n  (:start . 113) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 125) (:start . 123)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 132)\n  (:start . 126) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 138) (:start . 134)\n  (:id . 67))\n ((:tag . "NN") (:stem . "5c") (:form . "5C") (:end . 141) (:start . 139)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s8.200) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502452@unknown@formal@none@1@S@Both the late-onset mobility and viability phenotypes observed in dhtt-ko mutants were rescued by the dhtt transgene (Fig. 5A,B; supplementary material Movie 3).@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "late-onset") (:form . "late-onset") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 53)\n  (:start . 43) (:id . 48))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 62)\n  (:start . 54) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 73)\n  (:start . 66) (:id . 51))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 81)\n  (:start . 74) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 86) (:start . 82)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 94)\n  (:start . 87) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 97) (:start . 95)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 106) (:start . 102)\n  (:id . 57))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 116)\n  (:start . 107) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 122) (:start . 118)\n  (:id . 60))\n ((:tag . "CD") (:stem . "5A,B") (:form . "5A,B") (:end . 127) (:start . 123)\n  (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 128) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 142) (:start . 129) (:id . 63))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 151)\n  (:start . 143) (:id . 64))\n ((:tag . "NNP") (:stem . "Movie") (:form . "Movie") (:end . 157)\n  (:start . 152) (:id . 65))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 159) (:start . 158)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.201) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5502454@unknown@formal@none@1@S@Thus, although dhtt is not essential for normal Drosophila development, its function is important in maintaining the long-term mobility and survival of adult animals.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 14)\n  (:start . 6) (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 36)\n  (:start . 27) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 47)\n  (:start . 41) (:id . 50))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 58)\n  (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 70)\n  (:start . 59) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 84)\n  (:start . 76) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 97)\n  (:start . 88) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "maintain") (:form . "maintaining") (:end . 112)\n  (:start . 101) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "long-term") (:form . "long-term") (:end . 126)\n  (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 135)\n  (:start . 127) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 63))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 148)\n  (:start . 140) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 157)\n  (:start . 152) (:id . 66))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 165)\n  (:start . 158) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.203) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502455@unknown@formal@none@1@S@dhtt-ko is dispensable for normal neurotransmission@(((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "dispensable") (:form . "dispensable") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "neurotransmission") (:form . "neurotransmission")\n  (:end . 51) (:start . 34) (:id . 47)))@@@1@6@((:identifiers (:sid . :s8.204) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502456@unknown@formal@none@1@S@The observed mobility and viability phenotype could be because of an underlying neurotransmission defect in dhtt mutants as several proposed Htt functions, such as axonal vesicle transport and clathrin-mediated endocytosis in neurons, are essential for the delivery and recycling of synaptic vesicles at nerve terminals to ensure effective neurotransmission (Cattaneo et al., 2001; Eaton et al., 2002; Harjes and Wanker, 2003; Hinshaw, 2000; Slepnev and De Camilli, 2000).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . 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"De") (:end . 456) (:start . 454)\n  (:id . 118))\n ((:tag . "NNP") (:stem . "Camilli") (:form . "Camilli") (:end . 464)\n  (:start . 457) (:id . 119))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 465) (:start . 464)\n  (:id . 120))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 470) (:start . 466)\n  (:id . 121))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 471) (:start . 470)\n  (:id . 122))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 472) (:start . 471)\n  (:id . 123)))@@@1@82@((:hcues ((:id . :x8.205.1) (:span 46 51)))\n (:hscopes ((:id . :x8.205.1) (:span 0 357)))\n (:identifiers (:sid . :s8.205) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502457@unknown@formal@none@1@S@To test the neuronal communication in dhtt mutants, we measured synaptic physiology at the well-characterized third instar larval NMJ.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "communication") (:form . "communication")\n  (:end . 34) (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "measure") (:form . "measured") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . "NN") (:stem . "physiology") (:form . "physiology") (:end . 83)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "well-characterized") (:form . "well-characterized")\n  (:end . 109) (:start . 91) (:id . 57))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 115)\n  (:start . 110) (:id . 58))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 122)\n  (:start . 116) (:id . 59))\n ((:tag . "NN") (:stem . "larval") (:form . "larval") (:end . 129)\n  (:start . 123) (:id . 60))\n ((:tag . "NNP") (:stem . "NMJ") (:form . "NMJ") (:end . 133) (:start . 130)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.206) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502458@unknown@formal@none@1@S@We quantified the amplitude of evoked excitatory junctional potentials (EJPs), resting membrane potential and paired-pulse facilitation (PPF) (Fig. 6A–D and data not shown).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "quantify") (:form . "quantified") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "amplitude") (:form . "amplitude") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "evoke") (:form . "evoked") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "JJ") (:stem . "excitatory") (:form . "excitatory") (:end . 48)\n  (:start . 38) (:id . 48))\n ((:tag . "JJ") (:stem . "junctional") (:form . "junctional") (:end . 59)\n  (:start . 49) (:id . 49))\n ((:tag . "NNS") (:stem . "potential") (:form . "potentials") (:end . 70)\n  (:start . 60) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "EJP") (:form . "EJPs") (:end . 76) (:start . 72)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "rest") (:form . "resting") (:end . 86)\n  (:start . 79) (:id . 55))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 95)\n  (:start . 87) (:id . 56))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 105)\n  (:start . 96) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 58))\n ((:tag . "NN") (:stem . "paired-pulse") (:form . "paired-pulse") (:end . 122)\n  (:start . 110) (:id . 59))\n ((:tag . "NN") (:stem . "facilitation") (:form . "facilitation") (:end . 135)\n  (:start . 123) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "PPF") (:form . "PPF") (:end . 140) (:start . 137)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 147) (:start . 143)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "6A–D") (:form . "6A–D") (:end . 152) (:start . 148)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 161)\n  (:start . 157) (:id . 68))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 165) (:start . 162)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 171)\n  (:start . 166) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s8.207) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502459@unknown@formal@none@1@S@In adult animals, we recorded electroretinogram (ERG) responses in the eye and quantified DLM (dorsal longitudinal flight muscle) bursting activity in the giant fiber flight circuit (Fig. 6E and data not shown).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "record") (:form . "recorded") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "NN") (:stem . "electroretinogram") (:form . "electroretinogram")\n  (:end . 47) (:start . 30) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "ERG") (:form . "ERG") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "quantify") (:form . "quantified") (:end . 89)\n  (:start . 79) (:id . 57))\n ((:tag . "NNP") (:stem . "DLM") (:form . "DLM") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 101)\n  (:start . 95) (:id . 60))\n ((:tag . "JJ") (:stem . "longitudinal") (:form . "longitudinal") (:end . 114)\n  (:start . 102) (:id . 61))\n ((:tag . "NN") (:stem . "flight") (:form . "flight") (:end . 121)\n  (:start . 115) (:id . 62))\n ((:tag . "NN") (:stem . "muscle") (:form . "muscle") (:end . 128)\n  (:start . 122) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 64))\n ((:tag . "NN") (:stem . "bursting") (:form . "bursting") (:end . 138)\n  (:start . 130) (:id . 65))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 147)\n  (:start . 139) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "giant") (:form . "giant") (:end . 160)\n  (:start . 155) (:id . 69))\n ((:tag . "NN") (:stem . "fiber") (:form . "fiber") (:end . 166)\n  (:start . 161) (:id . 70))\n ((:tag . "NN") (:stem . "flight") (:form . "flight") (:end . 173)\n  (:start . 167) (:id . 71))\n ((:tag . "NN") (:stem . "circuit") (:form . "circuit") (:end . 181)\n  (:start . 174) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 183) (:start . 182)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 187) (:start . 183)\n  (:id . 74))\n ((:tag . "NN") (:stem . "6e") (:form . "6E") (:end . 190) (:start . 188)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 199)\n  (:start . 195) (:id . 77))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 203) (:start . 200)\n  (:id . 78))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 209)\n  (:start . 204) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s8.208) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502460@unknown@formal@none@1@S@Following exhaustive analysis, we found no significant defect in either synaptic transmission or short-term plasticity in dhtt mutants.@(((:tag . "VBG") (:stem . "follow") (:form . "Following") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "exhaustive") (:form . "exhaustive") (:end . 20)\n  (:start . 10) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 29)\n  (:start . 21) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 54)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "defect") (:form . "defect") (:end . 61)\n  (:start . 55) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 71)\n  (:start . 65) (:id . 52))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 80)\n  (:start . 72) (:id . 53))\n ((:tag . "NN") (:stem . "transmission") (:form . "transmission") (:end . 93)\n  (:start . 81) (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 96) (:start . 94)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "short-term") (:form . "short-term") (:end . 107)\n  (:start . 97) (:id . 56))\n ((:tag . "NN") (:stem . "plasticity") (:form . "plasticity") (:end . 118)\n  (:start . 108) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 58))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 126) (:start . 122)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 134)\n  (:start . 127) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s8.209) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502461@unknown@formal@none@1@S@Together, these data suggest that dhtt is not essential for neurotransmission.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 55)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "NN") (:stem . "neurotransmission") (:form . "neurotransmission")\n  (:end . 77) (:start . 60) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 54)))@@@1@13@((:hcues ((:id . :x8.210.1) (:span 21 28)))\n (:hscopes ((:id . :x8.210.1) (:span 21 77)))\n (:identifiers (:sid . :s8.210) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502462@unknown@formal@none@1@S@Normal synaptic transmission in dhtt-ko mutants.@(((:tag . "JJ") (:stem . "normal") (:form . "Normal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 15)\n  (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "transmission") (:form . "transmission") (:end . 28)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 39)\n  (:start . 32) (:id . 46))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 47)\n  (:start . 40) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 48) (:start . 47)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s8.211) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502463@unknown@formal@none@1@S@(A–F) Electrophysiological analyses of dhtt mutants (see Methods).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–F") (:form . "A–F") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "electrophysiological")\n  (:form . "Electrophysiological") (:end . 26) (:start . 6) (:id . 45))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s8.212) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502464@unknown@formal@none@1@S@(A) Voltage traces of evoked EJPs recorded from muscle fiber 6 in dhtt mutant or control third instar larvae.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "voltage") (:form . "Voltage") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "trace") (:form . "traces") (:end . 18)\n  (:start . 12) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "evoke") (:form . "evoked") (:end . 28)\n  (:start . 22) (:id . 48))\n ((:tag . "NNS") (:stem . "ejp") (:form . "EJPs") (:end . 33) (:start . 29)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "record") (:form . "recorded") (:end . 42)\n  (:start . 34) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "muscle") (:form . "muscle") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . "NN") (:stem . "fiber") (:form . "fiber") (:end . 60) (:start . 55)\n  (:id . 53))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 70) (:start . 66)\n  (:id . 56))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 77)\n  (:start . 71) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 80) (:start . 78)\n  (:id . 58))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 88)\n  (:start . 81) (:id . 59))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 94) (:start . 89)\n  (:id . 60))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 101)\n  (:start . 95) (:id . 61))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 108)\n  (:start . 102) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s8.213) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502465@unknown@formal@none@1@S@(B) Measurements of evoked EJP amplitude.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "measurement") (:form . "Measurements") (:end . 16)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "evoke") (:form . "evoked") (:end . 26)\n  (:start . 20) (:id . 47))\n ((:tag . "NNP") (:stem . "EJP") (:form . "EJP") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "amplitude") (:form . "amplitude") (:end . 40)\n  (:start . 31) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 41) (:start . 40)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s8.214) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502466@unknown@formal@none@1@S@The dhtt-ko mutants exhibited no significant difference in synaptic vesicle release following stimulation (P=0.18, Student’s t-test).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "exhibit") (:form . "exhibited") (:end . 29)\n  (:start . 20) (:id . 45))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 44)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 55)\n  (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 67)\n  (:start . 59) (:id . 50))\n ((:tag . "NN") (:stem . "vesicle") (:form . "vesicle") (:end . 75)\n  (:start . 68) (:id . 51))\n ((:tag . "NN") (:stem . "release") (:form . "release") (:end . 83)\n  (:start . 76) (:id . 52))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 93)\n  (:start . 84) (:id . 53))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 105)\n  (:start . 94) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 55))\n ((:tag . "NN") (:stem . "p=0.18") (:form . "P=0.18") (:end . 113)\n  (:start . 107) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 122)\n  (:start . 115) (:id . 58))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 124) (:start . 123)\n  (:id . 59))\n ((:tag . "NN") (:stem . "t-test") (:form . "t-test") (:end . 131)\n  (:start . 125) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.215) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502467@unknown@formal@none@1@S@Resting membrane potential was unchanged in animals lacking dhtt.@(((:tag . "VBG") (:stem . "rest") (:form . "Resting") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 26)\n  (:start . 17) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "unchanged") (:form . "unchanged") (:end . 40)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "VBG") (:stem . "lack") (:form . "lacking") (:end . 59)\n  (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 64) (:start . 60)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s8.216) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502468@unknown@formal@none@1@S@(C) Voltage traces and (D) quantification of PPF in control and dhtt mutant third instar larvae.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "voltage") (:form . "Voltage") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "trace") (:form . "traces") (:end . 18)\n  (:start . 12) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 25) (:start . 24)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 26) (:start . 25)\n  (:id . 50))\n ((:tag . "NN") (:stem . "quantification") (:form . "quantification")\n  (:end . 41) (:start . 27) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "PPF") (:form . "PPF") (:end . 48) (:start . 45)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 54))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 59)\n  (:start . 52) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 68) (:start . 64)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 75)\n  (:start . 69) (:id . 58))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 81) (:start . 76)\n  (:id . 59))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 88)\n  (:start . 82) (:id . 60))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 95)\n  (:start . 89) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.217) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502469@unknown@formal@none@1@S@No change in the amplitude of PPF was observed in dhtt mutants, indicating that short-term plasticity is intact.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "change") (:form . "change") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "amplitude") (:form . "amplitude") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PPF") (:form . "PPF") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 54) (:start . 50)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 62)\n  (:start . 55) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 74)\n  (:start . 64) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 79) (:start . 75)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "short-term") (:form . "short-term") (:end . 90)\n  (:start . 80) (:id . 57))\n ((:tag . "NN") (:stem . "plasticity") (:form . "plasticity") (:end . 101)\n  (:start . 91) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 104) (:start . 102)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "intact") (:form . "intact") (:end . 111)\n  (:start . 105) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x8.218.1) (:span 64 79)))\n (:hscopes ((:id . :x8.218.1) (:span 64 111)))\n (:identifiers (:sid . :s8.218) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502470@unknown@formal@none@1@S@(E) ERGs recorded from controls and dhtt-ko mutants aged 40–45 days or from dhtt-ko mutants aged 1–3 days at 20°C (top graphs) or at 37°C (bottom graphs); heat pulses were given at regular intervals.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "ERG") (:form . "ERGs") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "record") (:form . "recorded") (:end . 17)\n  (:start . 9) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 22) (:start . 18)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 31)\n  (:start . 23) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 43)\n  (:start . 36) (:id . 50))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 51)\n  (:start . 44) (:id . 51))\n ((:tag . "VBN") (:stem . "age") (:form . "aged") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "CD") (:stem . "40–45") (:form . "40–45") (:end . 62) (:start . 57)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 83)\n  (:start . 76) (:id . 57))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 91)\n  (:start . 84) (:id . 58))\n ((:tag . "VBN") (:stem . "age") (:form . "aged") (:end . 96) (:start . 92)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1–3") (:form . "1–3") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 105) (:start . 101)\n  (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 108) (:start . 106)\n  (:id . 62))\n ((:tag . "NN") (:stem . "20°c") (:form . "20°C") (:end . 113) (:start . 109)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 118) (:start . 115)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "graph") (:form . "graphs") (:end . 125)\n  (:start . 119) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 129) (:start . 127)\n  (:id . 68))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 132) (:start . 130)\n  (:id . 69))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 137) (:start . 133)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "bottom") (:form . "bottom") (:end . 145)\n  (:start . 139) (:id . 72))\n ((:tag . "NNS") (:stem . "graph") (:form . "graphs") (:end . 152)\n  (:start . 146) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 74))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 154) (:start . 153)\n  (:id . 75))\n ((:tag . "NN") (:stem . "heat") (:form . "heat") (:end . 159) (:start . 155)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "pulse") (:form . "pulses") (:end . 166)\n  (:start . 160) (:id . 77))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 171) (:start . 167)\n  (:id . 78))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 177)\n  (:start . 172) (:id . 79))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 180) (:start . 178)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 188)\n  (:start . 181) (:id . 81))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 198)\n  (:start . 189) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.219) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502471@unknown@formal@none@1@S@The black bar below the trace indicates the test light pulses.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "trace") (:form . "trace") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 39)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "light") (:form . "light") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "pulse") (:form . "pulses") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s8.220) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502472@unknown@formal@none@1@S@(F) Percentage of adult animals aged 40–45 days with a loss of phototransduction at 37°C.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "percentage") (:form . "Percentage") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 23) (:start . 18)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 31)\n  (:start . 24) (:id . 48))\n ((:tag . "VBN") (:stem . "age") (:form . "aged") (:end . 36) (:start . 32)\n  (:id . 49))\n ((:tag . "CD") (:stem . "40–45") (:form . "40–45") (:end . 42) (:start . 37)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 52) (:start . 48)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 59) (:start . 55)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 55))\n ((:tag . "NN") (:stem . "phototransduction") (:form . "phototransduction")\n  (:end . 80) (:start . 63) (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 88) (:start . 84)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s8.221) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502473@unknown@formal@none@1@S@dhtt-ko mutants showed a more severe temperature-induced loss of phototransduction than control flies, suggesting that photoreceptors in aged dhtt-ko mutants were stress-sensitive compared with the controls.@(((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 22) (:start . 16)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "JJ") (:stem . "temperature-induced")\n  (:form . "temperature-induced") (:end . 56) (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 61) (:start . 57)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "NN") (:stem . "phototransduction") (:form . "phototransduction")\n  (:end . 82) (:start . 65) (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 87) (:start . 83)\n  (:id . 52))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 95)\n  (:start . 88) (:id . 53))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 101) (:start . 96)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 113)\n  (:start . 103) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 118) (:start . 114)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "photoreceptor") (:form . "photoreceptors")\n  (:end . 133) (:start . 119) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 141) (:start . 137)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 149)\n  (:start . 142) (:id . 61))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 157)\n  (:start . 150) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 162) (:start . 158)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "stress-sensitive") (:form . "stress-sensitive")\n  (:end . 179) (:start . 163) (:id . 64))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 188)\n  (:start . 180) (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 193) (:start . 189)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 206)\n  (:start . 198) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x8.222.1) (:span 103 113)))\n (:hscopes ((:id . :x8.222.1) (:span 103 206)))\n (:identifiers (:sid . :s8.222) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502474@unknown@formal@none@1@S@The dhtt-ko Rescue animals were used as controls in the above electrophysiological analyses to ensure a consistent genetic background (A–F).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "rescue") (:form . "Rescue") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 61) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "electrophysiological")\n  (:form . "electrophysiological") (:end . 82) (:start . 62) (:id . 53))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 91)\n  (:start . 83) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 55))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 101)\n  (:start . 95) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 103) (:start . 102)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 114)\n  (:start . 104) (:id . 58))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 122)\n  (:start . 115) (:id . 59))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 133)\n  (:start . 123) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "A–F") (:form . "A–F") (:end . 138) (:start . 135)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.223) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502475@unknown@formal@none@1@S@The data in (B) and (D) are presented as the means±s.e.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 15) (:start . 14)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 21) (:start . 20)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 22) (:start . 21)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 23) (:start . 22)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 37)\n  (:start . 28) (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 40) (:start . 38)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 55))\n ((:tag . "NN") (:stem . "means±s.e") (:form . "means±s.e") (:end . 54)\n  (:start . 45) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.224) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502476@unknown@formal@none@1@S@To investigate whether the observed mobility and viability phenotypes in aged dhtt mutants are correlated with neuronal communication defects, we screened for electrophysiological phenotypes in animals aged 40–45 days, when behavioral motor abnormalities are prominent.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 58)\n  (:start . 49) (:id . 49))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 69)\n  (:start . 59) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 77) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 82) (:start . 78)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 90)\n  (:start . 83) (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 94) (:start . 91)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "correlate") (:form . "correlated") (:end . 105)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 110) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 119)\n  (:start . 111) (:id . 58))\n ((:tag . "NN") (:stem . "communication") (:form . "communication")\n  (:end . 133) (:start . 120) (:id . 59))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 141)\n  (:start . 134) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 61))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 145) (:start . 143)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "screen") (:form . "screened") (:end . 154)\n  (:start . 146) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 158) (:start . 155)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "electrophysiological")\n  (:form . "electrophysiological") (:end . 179) (:start . 159) (:id . 65))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 190)\n  (:start . 180) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 193) (:start . 191)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 201)\n  (:start . 194) (:id . 68))\n ((:tag . "VBN") (:stem . "age") (:form . "aged") (:end . 206) (:start . 202)\n  (:id . 69))\n ((:tag . "CD") (:stem . "40–45") (:form . "40–45") (:end . 212)\n  (:start . 207) (:id . 70))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 217) (:start . 213)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 218) (:start . 217)\n  (:id . 72))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 223) (:start . 219)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "behavioral") (:form . "behavioral") (:end . 234)\n  (:start . 224) (:id . 74))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 240)\n  (:start . 235) (:id . 75))\n ((:tag . "NNS") (:stem . "abnormality") (:form . "abnormalities")\n  (:end . 254) (:start . 241) (:id . 76))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 258) (:start . 255)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "prominent") (:form . "prominent") (:end . 268)\n  (:start . 259) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 269) (:start . 268)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x8.225.1) (:span 15 22)))\n (:hscopes ((:id . :x8.225.1) (:span 15 141)))\n (:identifiers (:sid . :s8.225) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502477@unknown@formal@none@1@S@Aged dhtt mutant adults did not display abnormal seizure activity in extracellular recordings from DLM flight muscles in the giant fiber escape pathway, as has been observed in temperature-sensitive Drosophila mutants that have altered synaptic transmission (Guan et al., 2005).@(((:tag . "VBN") (:stem . "age") (:form . "Aged") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "VB") (:stem . "display") (:form . "display") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "seizure") (:form . "seizure") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 65)\n  (:start . 57) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 82) (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "recording") (:form . "recordings") (:end . 93)\n  (:start . 83) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 98) (:start . 94)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "DLM") (:form . "DLM") (:end . 102) (:start . 99)\n  (:id . 56))\n ((:tag . "NN") (:stem . "flight") (:form . "flight") (:end . 109)\n  (:start . 103) (:id . 57))\n ((:tag . "NNS") (:stem . "muscle") (:form . "muscles") (:end . 117)\n  (:start . 110) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "giant") (:form . "giant") (:end . 130)\n  (:start . 125) (:id . 61))\n ((:tag . "NN") (:stem . "fiber") (:form . "fiber") (:end . 136)\n  (:start . 131) (:id . 62))\n ((:tag . "NN") (:stem . "escape") (:form . "escape") (:end . 143)\n  (:start . 137) (:id . 63))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 151)\n  (:start . 144) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 155) (:start . 153)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 159) (:start . 156)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 164) (:start . 160)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 173)\n  (:start . 165) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 176) (:start . 174)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "temperature-sensitive")\n  (:form . "temperature-sensitive") (:end . 198) (:start . 177) (:id . 71))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 209)\n  (:start . 199) (:id . 72))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 217)\n  (:start . 210) (:id . 73))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 222) (:start . 218)\n  (:id . 74))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 227) (:start . 223)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "alter") (:form . "altered") (:end . 235)\n  (:start . 228) (:id . 76))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 244)\n  (:start . 236) (:id . 77))\n ((:tag . "NN") (:stem . "transmission") (:form . "transmission") (:end . 257)\n  (:start . 245) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 259) (:start . 258)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Guan") (:form . "Guan") (:end . 263) (:start . 259)\n  (:id . 80))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 266) (:start . 264)\n  (:id . 81))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 270) (:start . 267)\n  (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 271) (:start . 270)\n  (:id . 83))\n ((:tag . "CD") (:stem . "2005") (:form . "2005") (:end . 276) (:start . 272)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 277) (:start . 276)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 278) (:start . 277)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s8.226) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502478@unknown@formal@none@1@S@Aged mutants also showed normal visual transduction and synaptic transmission in the visual system at room temperature (Fig. 6E and data not shown), consistent with the observation that dhtt does not play a crucial role in neurotransmission.@(((:tag . "JJ") (:stem . "aged") (:form . "Aged") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 24) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "visual") (:form . "visual") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "transduction") (:form . "transduction") (:end . 51)\n  (:start . 39) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "transmission") (:form . "transmission") (:end . 77)\n  (:start . 65) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "visual") (:form . "visual") (:end . 91)\n  (:start . 85) (:id . 54))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 98)\n  (:start . 92) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 101) (:start . 99)\n  (:id . 56))\n ((:tag . "NN") (:stem . "room") (:form . "room") (:end . 106) (:start . 102)\n  (:id . 57))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 118)\n  (:start . 107) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 120) (:start . 119)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 124) (:start . 120)\n  (:id . 60))\n ((:tag . "NN") (:stem . "6e") (:form . "6E") (:end . 127) (:start . 125)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 136)\n  (:start . 132) (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 140) (:start . 137)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 146)\n  (:start . 141) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 159)\n  (:start . 149) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 164) (:start . 160)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 70))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 180)\n  (:start . 169) (:id . 71))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 185) (:start . 181)\n  (:id . 72))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 190) (:start . 186)\n  (:id . 73))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 195) (:start . 191)\n  (:id . 74))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 199) (:start . 196)\n  (:id . 75))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 204) (:start . 200)\n  (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 206) (:start . 205)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 214)\n  (:start . 207) (:id . 78))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 219) (:start . 215)\n  (:id . 79))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 222) (:start . 220)\n  (:id . 80))\n ((:tag . "NN") (:stem . "neurotransmission") (:form . "neurotransmission")\n  (:end . 240) (:start . 223) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 241) (:start . 240)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s8.227) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502479@unknown@formal@none@1@S@Previous studies have shown that mutations affecting synaptic function often manifest a more prominent phenotype under temperature-induced stress (Atkinson et al., 1991; Coyle et al., 2004).@(((:tag . "JJ") (:stem . "previous") (:form . "Previous") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "VBG") (:stem . "affect") (:form . "affecting") (:end . 52)\n  (:start . 43) (:id . 48))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 61)\n  (:start . 53) (:id . 49))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 70)\n  (:start . 62) (:id . 50))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 76) (:start . 71)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "manifest") (:form . "manifest") (:end . 85)\n  (:start . 77) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 87) (:start . 86)\n  (:id . 53))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 92) (:start . 88)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "prominent") (:form . "prominent") (:end . 102)\n  (:start . 93) (:id . 55))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 112)\n  (:start . 103) (:id . 56))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 118)\n  (:start . 113) (:id . 57))\n ((:tag . "JJ") (:stem . "temperature-induced")\n  (:form . "temperature-induced") (:end . 138) (:start . 119) (:id . 58))\n ((:tag . "NN") (:stem . "stress") (:form . "stress") (:end . 145)\n  (:start . 139) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Atkinson") (:form . "Atkinson") (:end . 155)\n  (:start . 147) (:id . 61))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 158) (:start . 156)\n  (:id . 62))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 162) (:start . 159)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 64))\n ((:tag . "CD") (:stem . "1991") (:form . "1991") (:end . 168) (:start . 164)\n  (:id . 65))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 169) (:start . 168)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Coyle") (:form . "Coyle") (:end . 175)\n  (:start . 170) (:id . 67))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 178) (:start . 176)\n  (:id . 68))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 182) (:start . 179)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 70))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 188) (:start . 184)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s8.228) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502480@unknown@formal@none@1@S@To assess whether phototransduction can be maintained under an elevated temperature in dhtt mutants, we performed ERG recordings at 37°C.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "phototransduction") (:form . "phototransduction")\n  (:end . 35) (:start . 18) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 39) (:start . 36)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "maintain") (:form . "maintained") (:end . 53)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 59) (:start . 54)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "elevated") (:form . "elevated") (:end . 71)\n  (:start . 63) (:id . 51))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 83)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 53))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 91) (:start . 87)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 99)\n  (:start . 92) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "perform") (:form . "performed") (:end . 113)\n  (:start . 104) (:id . 58))\n ((:tag . "NN") (:stem . "erg") (:form . "ERG") (:end . 117) (:start . 114)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "recording") (:form . "recordings") (:end . 128)\n  (:start . 118) (:id . 60))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 131) (:start . 129)\n  (:id . 61))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 136) (:start . 132)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x8.229.1) (:span 36 39)) ((:id . :x8.229.2) (:span 10 17)))\n (:hscopes ((:id . :x8.229.1) (:span 18 99)) ((:id . :x8.229.2) (:span 10 99)))\n (:identifiers (:sid . :s8.229) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502481@unknown@formal@none@1@S@Although dhtt mutants aged 1–3 days displayed normal ERGs at both 20°C and 37°C, aged dhtt mutants displayed abnormal sensitivity to 37°C, with over 60% of aged mutants losing light-induced phototransduction and the on/off transients at 37°C compared with only 20% of control aged adults (Fig. 6E,F), indicating an important role of dhtt in maintaining phototransduction under temperature-induced stress.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "VBN") (:stem . "age") (:form . "aged") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "CD") (:stem . "1–3") (:form . "1–3") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "day") (:form . 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"dhtt") (:form . "dhtt") (:end . 90) (:start . 86)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 98)\n  (:start . 91) (:id . 59))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 108)\n  (:start . 99) (:id . 60))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 117)\n  (:start . 109) (:id . 61))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 129)\n  (:start . 118) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 137) (:start . 133)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 143) (:start . 139)\n  (:id . 66))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 148) (:start . 144)\n  (:id . 67))\n ((:tag . "CD") (:stem . "60") (:form . 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"on/off") (:end . 222)\n  (:start . 216) (:id . 78))\n ((:tag . "NNS") (:stem . "transient") (:form . "transients") (:end . 233)\n  (:start . 223) (:id . 79))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 236) (:start . 234)\n  (:id . 80))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 241) (:start . 237)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 250)\n  (:start . 242) (:id . 82))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 255) (:start . 251)\n  (:id . 83))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 260) (:start . 256)\n  (:id . 84))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 263) (:start . 261)\n  (:id . 85))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 264) (:start . 263)\n  (:id . 86))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 267) (:start . 265)\n  (:id . 87))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 275)\n  (:start . 268) (:id . 88))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 280) (:start . 276)\n  (:id . 89))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 287)\n  (:start . 281) (:id . 90))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 289) (:start . 288)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 293) (:start . 289)\n  (:id . 92))\n ((:tag . "CD") (:stem . "6E,F") (:form . "6E,F") (:end . 298) (:start . 294)\n  (:id . 93))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 299) (:start . 298)\n  (:id . 94))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 300) (:start . 299)\n  (:id . 95))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 311)\n  (:start . 301) (:id . 96))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 314) (:start . 312)\n  (:id . 97))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 324)\n  (:start . 315) (:id . 98))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 329) (:start . 325)\n  (:id . 99))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 332) (:start . 330)\n  (:id . 100))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 337) (:start . 333)\n  (:id . 101))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 340) (:start . 338)\n  (:id . 102))\n ((:tag . "VBG") (:stem . "maintain") (:form . "maintaining") (:end . 352)\n  (:start . 341) (:id . 103))\n ((:tag . "NN") (:stem . "phototransduction") (:form . "phototransduction")\n  (:end . 370) (:start . 353) (:id . 104))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 376)\n  (:start . 371) (:id . 105))\n ((:tag . "JJ") (:stem . "temperature-induced")\n  (:form . "temperature-induced") (:end . 396) (:start . 377) (:id . 106))\n ((:tag . "NN") (:stem . "stress") (:form . "stress") (:end . 403)\n  (:start . 397) (:id . 107))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 404) (:start . 403)\n  (:id . 108)))@@@1@67@((:hcues ((:id . :x8.230.1) (:span 301 311)))\n (:hscopes ((:id . :x8.230.1) (:span 301 403)))\n (:identifiers (:sid . :s8.230) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502482@unknown@formal@none@1@S@Given that aged dhtt mutant adults did not show additional motor defects when placed at 37°C, we hypothesize that the loss of photoreceptor depolarization found in ERG recordings reflects temperature-sensitive defects in the phototransduction cycle, rather than in synaptic transmission.@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "VB") (:stem . "show") (:form . "show") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 58)\n  (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 64) (:start . 59)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "place") (:form . "placed") (:end . 84)\n  (:start . 78) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 92) (:start . 88)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "hypothesize") (:form . "hypothesize") (:end . 108)\n  (:start . 97) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 122) (:start . 118)\n  (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 64))\n ((:tag . "NN") (:stem . "photoreceptor") (:form . "photoreceptor")\n  (:end . 139) (:start . 126) (:id . 65))\n ((:tag . "NN") (:stem . "depolarization") (:form . "depolarization")\n  (:end . 154) (:start . 140) (:id . 66))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 160)\n  (:start . 155) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 163) (:start . 161)\n  (:id . 68))\n ((:tag . "NN") (:stem . "erg") (:form . "ERG") (:end . 167) (:start . 164)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "recording") (:form . "recordings") (:end . 178)\n  (:start . 168) (:id . 70))\n ((:tag . "VBZ") (:stem . "reflect") (:form . "reflects") (:end . 187)\n  (:start . 179) (:id . 71))\n ((:tag . "JJ") (:stem . "temperature-sensitive")\n  (:form . "temperature-sensitive") (:end . 209) (:start . 188) (:id . 72))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 217)\n  (:start . 210) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 220) (:start . 218)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 224) (:start . 221)\n  (:id . 75))\n ((:tag . "NN") (:stem . "phototransduction") (:form . "phototransduction")\n  (:end . 242) (:start . 225) (:id . 76))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 248)\n  (:start . 243) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 249) (:start . 248)\n  (:id . 78))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 256)\n  (:start . 250) (:id . 79))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 261) (:start . 257)\n  (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 264) (:start . 262)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 273)\n  (:start . 265) (:id . 82))\n ((:tag . "NN") (:stem . "transmission") (:form . "transmission") (:end . 286)\n  (:start . 274) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 287) (:start . 286)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x8.231.1) (:span 97 108)))\n (:hscopes ((:id . :x8.231.1) (:span 97 286)))\n (:identifiers (:sid . :s8.231) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502483@unknown@formal@none@1@S@These results suggest that aged dhtt mutants are more sensitive to stress than young dhtt animals or aged controls.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "sensitive") (:form . "sensitive") (:end . 63)\n  (:start . 54) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "stress") (:form . "stress") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "young") (:form . "young") (:end . 84) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 114)\n  (:start . 106) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x8.232.1) (:span 14 21)))\n (:hscopes ((:id . :x8.232.1) (:span 14 114)))\n (:identifiers (:sid . :s8.232) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502484@unknown@formal@none@1@S@Reduced axon terminal complexity in dhtt-ko brains@(((:tag . "VBN") (:stem . "reduce") (:form . "Reduced") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 32)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 50)\n  (:start . 44) (:id . 48)))@@@1@7@((:identifiers (:sid . :s8.233) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502485@unknown@formal@none@1@S@To further test for dhtt function in the adult brain, we examined dhtt brain morphology using a series of cellular markers.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 52) (:start . 47)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 65)\n  (:start . 57) (:id . 54))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 70) (:start . 66)\n  (:id . 55))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 76) (:start . 71)\n  (:id . 56))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 87)\n  (:start . 77) (:id . 57))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 93) (:start . 88)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 102)\n  (:start . 96) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 114)\n  (:start . 106) (:id . 62))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 122)\n  (:start . 115) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.234) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502486@unknown@formal@none@1@S@The overall patterning and gross morphology of dhtt-ko brains appeared normal, as shown by staining with antibodies such as the glial cell marker anti-Repo, the pan-neuronal marker anti-Elav and the synaptic vesicle marker anti-CSP (data not shown).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "patterning") (:form . "patterning") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "gross") (:form . "gross") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 61)\n  (:start . 55) (:id . 50))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 70)\n  (:start . 62) (:id . 51))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 77)\n  (:start . 71) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 87) (:start . 82)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "stain") (:form . "staining") (:end . 99)\n  (:start . 91) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 104) (:start . 100)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 115)\n  (:start . 105) (:id . 59))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 120) (:start . 116)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 123) (:start . 121)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 133)\n  (:start . 128) (:id . 63))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 138) (:start . 134)\n  (:id . 64))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 145)\n  (:start . 139) (:id . 65))\n ((:tag . "JJ") (:stem . "anti-repo") (:form . "anti-Repo") (:end . 155)\n  (:start . 146) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 160) (:start . 157)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "pan-neuronal") (:form . "pan-neuronal") (:end . 173)\n  (:start . 161) (:id . 69))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 180)\n  (:start . 174) (:id . 70))\n ((:tag . "NN") (:stem . "anti-elav") (:form . "anti-Elav") (:end . 190)\n  (:start . 181) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 198) (:start . 195)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 207)\n  (:start . 199) (:id . 74))\n ((:tag . "NN") (:stem . "vesicle") (:form . "vesicle") (:end . 215)\n  (:start . 208) (:id . 75))\n ((:tag . "NN") (:stem . "marker") (:form . "marker") (:end . 222)\n  (:start . 216) (:id . 76))\n ((:tag . "JJ") (:stem . "anti-csp") (:form . "anti-CSP") (:end . 231)\n  (:start . 223) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 233) (:start . 232)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 237)\n  (:start . 233) (:id . 79))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 241) (:start . 238)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 247)\n  (:start . 242) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 248) (:start . 247)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 249) (:start . 248)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.235) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502487@unknown@formal@none@1@S@In addition, within the ventral nerve cord, the neuropile was similarly enriched with synaptic vesicles.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cord") (:form . "cord") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 57)\n  (:start . 48) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "RB") (:stem . "similarly") (:form . "similarly") (:end . 71)\n  (:start . 62) (:id . 54))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 80)\n  (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 94)\n  (:start . 86) (:id . 57))\n ((:tag . "NNS") (:stem . "vesicle") (:form . "vesicles") (:end . 103)\n  (:start . 95) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s8.236) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502488@unknown@formal@none@1@S@Further, the overall axonal morphology of dhtt-ko mutants appeared normal with no clear axonal blebbing or defasciculation phenotypes (data not shown).@(((:tag . "RB") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 66)\n  (:start . 58) (:id . 51))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 73)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 78) (:start . 74)\n  (:id . 53))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 87) (:start . 82)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 94)\n  (:start . 88) (:id . 56))\n ((:tag . "NN") (:stem . "blebbing") (:form . "blebbing") (:end . 103)\n  (:start . 95) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "defasciculation") (:form . "defasciculation")\n  (:end . 122) (:start . 107) (:id . 59))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 133)\n  (:start . 123) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 139)\n  (:start . 135) (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 143) (:start . 140)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 149)\n  (:start . 144) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 150) (:start . 149)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s8.237) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502489@unknown@formal@none@1@S@Interestingly, examination of the mushroom bodies (MBs), which are involved in learning and memory in flies, by anti-FasII staining revealed that the signal intensity was weaker in dhtt mutants than in wild-type controls, despite appearing morphologically normal (Fig. 7J,M).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "examination") (:form . "examination") (:end . 26)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mushroom") (:form . "mushroom") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 49) (:start . 43)\n  (:id . 48))\n ((:tag . 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(:end . 275) (:start . 274)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s8.238) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502490@unknown@formal@none@1@S@Quantification of MB size and FasII staining signals revealed that, although there was a slight reduction in the average size of MBs in dhtt-ko mutants compared with wild-type controls (Fig. 7P) (average area covered by each MB: wild type=13,352±156 µm2, dhtt-ko mutant=11,927±310 µm2; P=0.0003), the average signal intensity of FasII signals in the MBs of dhtt-ko mutants was decreased by ~50% (Fig. 7Q) (relative signal intensity of MBs: wild type=100±5.8/µm2, dhtt-ko mutant=47.7±6.1/µm2; P<0.0001; total number of MBs quantified: wild-type control, n=13; dhtt-ko mutants, n=10).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "size") (:form . 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5502493@unknown@formal@none@1@S@In the same brain, A307-positive neurons and their axonal projections are revealed by using a membrane-bound mCD8-eGFP reporter (green) (B).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "a307-positive") (:form . "A307-positive")\n  (:end . 32) (:start . 19) (:id . 47))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 50)\n  (:start . 45) (:id . 50))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 57)\n  (:start . 51) (:id . 51))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 69)\n  (:start . 58) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "reveal") (:form . "revealed") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 91) (:start . 86)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "membrane-bound") (:form . "membrane-bound")\n  (:end . 108) (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "mcd8-egfp") (:form . "mCD8-eGFP") (:end . 118)\n  (:start . 109) (:id . 59))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 127)\n  (:start . 119) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 61))\n ((:tag . "NN") (:stem . "green") (:form . "green") (:end . 134)\n  (:start . 129) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 135) (:start . 134)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s8.242) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502494@unknown@formal@none@1@S@(C) An overlay of images (A) and (B) showing the relative positions of MBs and A307-positive neurons in the brain.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "An") (:end . 6) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "overlay") (:form . "overlay") (:end . 14)\n  (:start . 7) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 24)\n  (:start . 18) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 27) (:start . 26)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 28) (:start . 27)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 34) (:start . 33)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 35) (:start . 34)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 36) (:start . 35)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 44)\n  (:start . 37) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 57)\n  (:start . 49) (:id . 58))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 67)\n  (:start . 58) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "mb") (:form . "MBs") (:end . 74) (:start . 71)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "a307-positive") (:form . "A307-positive")\n  (:end . 92) (:start . 79) (:id . 63))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 100)\n  (:start . 93) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 66))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 113)\n  (:start . 108) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.243) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502495@unknown@formal@none@1@S@A307-positive neurons with prominent axonal projections are highlighted [white arrows in (C)].@(((:tag . "JJ") (:stem . "a307-positive") (:form . "A307-positive")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 21)\n  (:start . 14) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "prominent") (:form . "prominent") (:end . 36)\n  (:start . 27) (:id . 45))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 43)\n  (:start . 37) (:id . 46))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 55)\n  (:start . 44) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 59) (:start . 56)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 71)\n  (:start . 60) (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 73) (:start . 72)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 78) (:start . 73)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 85)\n  (:start . 79) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 91) (:start . 90)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s8.244) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502496@unknown@formal@none@1@S@The white dashed lines delineate the region magnified in the following pictures (D–O).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "dashed") (:form . "dashed") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "delineate") (:form . "delineate") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "VBN") (:stem . "magnify") (:form . "magnified") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 70)\n  (:start . 61) (:id . 52))\n ((:tag . "NNS") (:stem . "picture") (:form . "pictures") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "D–O") (:form . "D–O") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.245) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502497@unknown@formal@none@1@S@(D–I) Axonal projection patterns and axon terminal structures of A307-positive neurons in 40-day-old wild-type (D–F) and dhtt-ko mutant (G–I) brains.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "LS") (:stem . "d–i") (:form . "D–I") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "axonal") (:form . "Axonal") (:end . 12) (:start . 6)\n  (:id . 45))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 23)\n  (:start . 13) (:id . 46))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 50)\n  (:start . 42) (:id . 50))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 61)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "a307-positive") (:form . "A307-positive")\n  (:end . 78) (:start . 65) (:id . 53))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 86)\n  (:start . 79) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "40-day-old") (:form . "40-day-old") (:end . 100)\n  (:start . 90) (:id . 56))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 110)\n  (:start . 101) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "D–F") (:form . "D–F") (:end . 115) (:start . 112)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 128)\n  (:start . 121) (:id . 62))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 135)\n  (:start . 129) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "G–I") (:form . "G–I") (:end . 140) (:start . 137)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 148)\n  (:start . 142) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.246) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502498@unknown@formal@none@1@S@For clear visualization, the posterior (D,G) and anterior (E,H) of the brains are projected separately.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "visualization") (:form . "visualization")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "D,G") (:form . "D,G") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 57)\n  (:start . 49) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "E,H") (:form . "E,H") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 77)\n  (:start . 71) (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 81) (:start . 78)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "project") (:form . "projected") (:end . 91)\n  (:start . 82) (:id . 60))\n ((:tag . "RB") (:stem . "separately") (:form . "separately") (:end . 102)\n  (:start . 92) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.247) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502499@unknown@formal@none@1@S@(D,G) A307-positive neurons have a similar axonal projection pattern (white arrows) in dhtt-ko mutant (G) and control brains (D).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D,G") (:form . "D,G") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "a307-positive") (:form . "A307-positive")\n  (:end . 19) (:start . 6) (:id . 45))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 49)\n  (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 60)\n  (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 75) (:start . 70)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 82)\n  (:start . 76) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 94)\n  (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 101)\n  (:start . 95) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 104) (:start . 103)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 63))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 117)\n  (:start . 110) (:id . 64))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 124)\n  (:start . 118) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 127) (:start . 126)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s8.248) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502500@unknown@formal@none@1@S@(E,H) Anterior views of the same brain regions showing the axon terminal structure.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E,H") (:form . "E,H") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "anterior") (:form . "Anterior") (:end . 14)\n  (:start . 6) (:id . 45))\n ((:tag . "NNS") (:stem . "view") (:form . "views") (:end . 20) (:start . 15)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 32) (:start . 28)\n  (:id . 49))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 38) (:start . 33)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 46)\n  (:start . 39) (:id . 51))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 54)\n  (:start . 47) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 63) (:start . 59)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 72)\n  (:start . 64) (:id . 55))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 82)\n  (:start . 73) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.249) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502501@unknown@formal@none@1@S@The white dashed lines border one axon terminus in each brain, which are further magnified in (F) and (I), respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "dashed") (:form . "dashed") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "border") (:form . "border") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "terminus") (:form . "terminus") (:end . 47)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 61) (:start . 56)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 80)\n  (:start . 73) (:id . 56))\n ((:tag . "VBN") (:stem . "magnify") (:form . "magnified") (:end . 90)\n  (:start . 81) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 63))\n ((:tag . "NN") (:stem . "i") (:form . "I") (:end . 104) (:start . 103)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 66))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 119)\n  (:start . 107) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.250) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502502@unknown@formal@none@1@S@Notice the significant reduction in branching and varicosities at the axonal termini of the dhtt-ko mutant (H,I).@(((:tag . "VB") (:stem . "notice") (:form . "Notice") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "branching") (:form . "branching") (:end . 45)\n  (:start . 36) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "varicosity") (:form . "varicosities") (:end . 62)\n  (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 76)\n  (:start . 70) (:id . 52))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 84)\n  (:start . 77) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 99)\n  (:start . 92) (:id . 56))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 106)\n  (:start . 100) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "H,I") (:form . "H,I") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s8.251) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502503@unknown@formal@none@1@S@(J–O) The MBs (J,M) and axonal termini of A307-labeled neurons (K,N) in another pair of 40-day-old wild-type (J–L) and dhtt-ko mutant (M–O) brains.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "J–O") (:form . "J–O") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 9) (:start . 6)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "MB") (:form . "MBs") (:end . 13) (:start . 10)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "J,M") (:form . "J,M") (:end . 18) (:start . 15)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 19) (:start . 18)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 30)\n  (:start . 24) (:id . 51))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 38)\n  (:start . 31) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "a307-labeled") (:form . "A307-labeled") (:end . 54)\n  (:start . 42) (:id . 54))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 62)\n  (:start . 55) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "K,N") (:form . "K,N") (:end . 67) (:start . 64)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n  (:id . 59))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 79)\n  (:start . 72) (:id . 60))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 84) (:start . 80)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "40-day-old") (:form . "40-day-old") (:end . 98)\n  (:start . 88) (:id . 63))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 108)\n  (:start . 99) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "J–L") (:form . "J–L") (:end . 113) (:start . 110)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 68))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 126)\n  (:start . 119) (:id . 69))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 133)\n  (:start . 127) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "M–O") (:form . "M–O") (:end . 138) (:start . 135)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 146)\n  (:start . 140) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s8.252) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502504@unknown@formal@none@1@S@(M) The overall morphology of the MBs is normal but the signal intensity is weaker in the dhtt-ko mutant.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 15)\n  (:start . 8) (:id . 46))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 26)\n  (:start . 16) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "MB") (:form . "MBs") (:end . 37) (:start . 34)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 47)\n  (:start . 41) (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 51) (:start . 48)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 54))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 62)\n  (:start . 56) (:id . 55))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 72)\n  (:start . 63) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 75) (:start . 73)\n  (:id . 57))\n ((:tag . "JJR") (:stem . "weak") (:form . "weaker") (:end . 82) (:start . 76)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 97)\n  (:start . 90) (:id . 61))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 104)\n  (:start . 98) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s8.253) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502505@unknown@formal@none@1@S@The white dashed lines border one axon terminus in each brain.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "dashed") (:form . "dashed") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "border") (:form . "border") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "terminus") (:form . "terminus") (:end . 47)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 61) (:start . 56)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s8.254) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502506@unknown@formal@none@1@S@Note the reduced complexity of axonal termini in the dhtt-ko mutant.@(((:tag . "VB") (:stem . "note") (:form . "Note") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 67)\n  (:start . 61) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s8.255) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502507@unknown@formal@none@1@S@The top of each image is the dorsal end of the brain.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "top") (:form . "top") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "image") (:form . "image") (:end . 21) (:start . 16)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 35)\n  (:start . 29) (:id . 49))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 52))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 52) (:start . 47)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s8.256) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502508@unknown@formal@none@1@S@WT=w1118 wild-type control.@(((:tag . "CD") (:stem . "wt=w1118") (:form . "WT=w1118") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 26)\n  (:start . 19) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 27) (:start . 26)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s8.257) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502509@unknown@formal@none@1@S@Bars, 10 µm (F,I) and 30 µm (all other panels).@(((:tag . "NNS") (:stem . "bar") (:form . "Bars") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "µm") (:form . "µm") (:end . 11) (:start . 9)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "F,I") (:form . "F,I") (:end . 16) (:start . 13)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 17) (:start . 16)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 49))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 24) (:start . 22)\n  (:id . 50))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 27) (:start . 25)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 29) (:start . 28)\n  (:id . 52))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 32) (:start . 29)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 38) (:start . 33)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 45)\n  (:start . 39) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.258) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502510@unknown@formal@none@1@S@(P,Q) Quantification of the average area covered by each MB (P) and the relative signal intensity of MBs (Q) between wild-type controls (WT, blue) and dhtt-ko mutants (red), as revealed by anti-FasII staining.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "P,Q") (:form . "P,Q") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Quantification") (:form . "Quantification")\n  (:end . 20) (:start . 6) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "p") (:form . "P") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 80)\n  (:start . 72) (:id . 59))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 87)\n  (:start . 81) (:id . 60))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 97)\n  (:start . 88) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "MB") (:form . "MBs") (:end . 104) (:start . 101)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Q") (:form . "Q") (:end . 107) (:start . 106)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 66))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 116)\n  (:start . 109) (:id . 67))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 126)\n  (:start . 117) (:id . 68))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 135)\n  (:start . 127) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "WT") (:form . "WT") (:end . 139) (:start . 137)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 145) (:start . 141)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 158)\n  (:start . 151) (:id . 76))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 166)\n  (:start . 159) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 168) (:start . 167)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 171) (:start . 168)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 81))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 176) (:start . 174)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "reveal") (:form . "revealed") (:end . 185)\n  (:start . 177) (:id . 83))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 188) (:start . 186)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "anti-fasii") (:form . "anti-FasII") (:end . 199)\n  (:start . 189) (:id . 85))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 208)\n  (:start . 200) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s8.259) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502511@unknown@formal@none@1@S@When calculating the relative signal intensity of MBs, the value for the average signal intensity from the wild-type controls was set as 100, (s.e.m.=5.8); the relative signal intensity of the dhtt-ko mutants=47.7±6.1; P<0.0001. (R)@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "calculate") (:form . "calculating") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 36)\n  (:start . 30) (:id . 46))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 46)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "MB") (:form . "MBs") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 64) (:start . 59)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 80)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 87)\n  (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 97)\n  (:start . 88) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 102) (:start . 98)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 116)\n  (:start . 107) (:id . 60))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 125)\n  (:start . 117) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 133) (:start . 130)\n  (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 136) (:start . 134)\n  (:id . 64))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 140) (:start . 137)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . "NN") (:stem . "s.e.m.=5.8") (:form . "s.e.m.=5.8") (:end . 153)\n  (:start . 143) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 155) (:start . 154)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 168)\n  (:start . 160) (:id . 72))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 175)\n  (:start . 169) (:id . 73))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 185)\n  (:start . 176) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 188) (:start . 186)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 192) (:start . 189)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 200)\n  (:start . 193) (:id . 77))\n ((:tag . "NN") (:stem . "mutants=47.7±6.1") (:form . "mutants=47.7±6.1")\n  (:end . 217) (:start . 201) (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 218) (:start . 217)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "P<0.0001.") (:form . "P<0.0001.") (:end . 228)\n  (:start . 219) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 230) (:start . 229)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "R") (:form . "R") (:end . 231) (:start . 230)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 232) (:start . 231)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.260) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502512@unknown@formal@none@1@S@Quantification of the average total area covered by each A307-positive axonal terminus.@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "a307-positive") (:form . "A307-positive")\n  (:end . 70) (:start . 57) (:id . 51))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 77)\n  (:start . 71) (:id . 52))\n ((:tag . "NN") (:stem . "terminus") (:form . "terminus") (:end . 86)\n  (:start . 78) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s8.261) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502513@unknown@formal@none@1@S@The genotypes of each fly line tested are indicated under each chart.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 37) (:start . 31)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "chart") (:form . "chart") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s8.262) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502514@unknown@formal@none@1@S@WT=w1118 wild-type control.@(((:tag . "CD") (:stem . "wt=w1118") (:form . "WT=w1118") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 26)\n  (:start . 19) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 27) (:start . 26)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s8.263) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502515@unknown@formal@none@1@S@The data in (P–R) are presented as the means±s.e.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "P–R") (:form . "P–R") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 31)\n  (:start . 22) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 34) (:start . 32)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 51))\n ((:tag . "NN") (:stem . "means±s.e") (:form . "means±s.e") (:end . 48)\n  (:start . 39) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s8.264) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502516@unknown@formal@none@1@S@To examine the effect of dhtt loss-of-function on the detailed structure of individual neurons in the brain, we used the A307-Gal4 line, which labels the pair of giant fiber (GF) neurons and a small number of other neurons of unknown identity in the adult brain, to examine axonal projection patterns and the fine axonal terminal structure of individual neurons (Phelan et al., 1996) (Fig. 7).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . 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(:end . 376) (:start . 373)\n  (:id . 109))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 377) (:start . 376)\n  (:id . 110))\n ((:tag . "CD") (:stem . "1996") (:form . "1996") (:end . 382) (:start . 378)\n  (:id . 111))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 383) (:start . 382)\n  (:id . 112))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 385) (:start . 384)\n  (:id . 113))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 389) (:start . 385)\n  (:id . 114))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 391) (:start . 390)\n  (:id . 115))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 392) (:start . 391)\n  (:id . 116))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 393) (:start . 392)\n  (:id . 117)))@@@1@76@((:identifiers (:sid . :s8.265) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502517@unknown@formal@none@1@S@Among the A307-Gal4 labeled neurons, one pair, located at the dorsal-lateral edge of the brain, projects a prominent axon tract along the dorsal-posterior surface to the dorsal-central region of the brain, forming extensive dendritic connections (Fig. 7B–D; supplementary material Fig. S4).@(((:tag . "IN") (:stem . "among") (:form . "Among") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "a307-gal4") (:form . "A307-Gal4") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . 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5502518@unknown@formal@none@1@S@These neurons further extend their projections anteriorly, establishing a complex axon terminal structure with extensive varicosities and fine branches above the antennal lobe region of the brain (Fig. 7E,F,K; supplementary material Fig. S4).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "VBP") (:stem . "extend") (:form . "extend") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 34)\n  (:start . 29) (:id . 46))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 46)\n  (:start . 35) (:id . 47))\n ((:tag . "RB") (:stem . "anteriorly") (:form . "anteriorly") (:end . 57)\n  (:start . 47) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "establish") (:form . "establishing") (:end . 71)\n  (:start . 59) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 81)\n  (:start . 74) (:id . 52))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 86) (:start . 82)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 95)\n  (:start . 87) (:id . 54))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 105)\n  (:start . 96) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 110) (:start . 106)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 120)\n  (:start . 111) (:id . 57))\n ((:tag . "NNS") (:stem . "varicosity") (:form . "varicosities") (:end . 133)\n  (:start . 121) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "fine") (:form . "fine") (:end . 142) (:start . 138)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "branch") (:form . "branches") (:end . 151)\n  (:start . 143) (:id . 61))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 157)\n  (:start . 152) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "antennal") (:form . "antennal") (:end . 170)\n  (:start . 162) (:id . 64))\n ((:tag . "NN") (:stem . "lobe") (:form . "lobe") (:end . 175) (:start . 171)\n  (:id . 65))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 182)\n  (:start . 176) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 185) (:start . 183)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 189) (:start . 186)\n  (:id . 68))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 195)\n  (:start . 190) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 197) (:start . 196)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 201) (:start . 197)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "7E,F,K") (:form . "7E,F,K") (:end . 208)\n  (:start . 202) (:id . 72))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 209) (:start . 208)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 223) (:start . 210) (:id . 74))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 232)\n  (:start . 224) (:id . 75))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 237) (:start . 233)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 240) (:start . 238)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 241) (:start . 240)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 242) (:start . 241)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s8.267) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502519@unknown@formal@none@1@S@In dhtt-ko mutants, the axonal projections of A307-positive neurons follow the same path and their axons terminate at similar locations to those in wild-type flies; this is consistent with the observation that dhtt does not affect axonal integrity or pathfinding (Fig. 7G,H).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 42)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "a307-positive") (:form . "A307-positive")\n  (:end . 59) (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 67)\n  (:start . 60) (:id . 51))\n ((:tag . "VBP") (:stem . "follow") (:form . "follow") (:end . 74)\n  (:start . 68) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 98)\n  (:start . 93) (:id . 57))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 104) (:start . 99)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 114)\n  (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 125)\n  (:start . 118) (:id . 61))\n ((:tag . "NNS") (:stem . "location") (:form . "locations") (:end . 135)\n  (:start . 126) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 138) (:start . 136)\n  (:id . 63))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 144)\n  (:start . 139) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 147) (:start . 145)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 157)\n  (:start . 148) (:id . 66))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 163) (:start . 158)\n  (:id . 67))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 164) (:start . 163)\n  (:id . 68))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 169) (:start . 165)\n  (:id . 69))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 172) (:start . 170)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 183)\n  (:start . 173) (:id . 71))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 188) (:start . 184)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 192) (:start . 189)\n  (:id . 73))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 204)\n  (:start . 193) (:id . 74))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 209) (:start . 205)\n  (:id . 75))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 214) (:start . 210)\n  (:id . 76))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 219) (:start . 215)\n  (:id . 77))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 223) (:start . 220)\n  (:id . 78))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 230)\n  (:start . 224) (:id . 79))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 237)\n  (:start . 231) (:id . 80))\n ((:tag . "NN") (:stem . "integrity") (:form . "integrity") (:end . 247)\n  (:start . 238) (:id . 81))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 250) (:start . 248)\n  (:id . 82))\n ((:tag . "NN") (:stem . "pathfinding") (:form . "pathfinding") (:end . 262)\n  (:start . 251) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 264) (:start . 263)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 268) (:start . 264)\n  (:id . 85))\n ((:tag . "CD") (:stem . "7G,H") (:form . "7G,H") (:end . 273) (:start . 269)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 274) (:start . 273)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 275) (:start . 274)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s8.268) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502520@unknown@formal@none@1@S@Interestingly, axonal termini from both wild-type and dhtt-ko flies show a similar age-dependent maturation process, whereas axonal termini in young adult brains are mainly composed of a network of variable thin branches with no clearly recognizable synaptic boutons (supplementary material Fig. S4C,F) (3-day-old flies).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "wild-type") (:form . 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5502521@unknown@formal@none@1@S@Mature boutons develop as the animals age, with many prominent boutons being easily identifiable in the brains of 40-day-old flies (Fig. 7F,I; compare with supplementary material Fig. S4C,F).@(((:tag . "JJ") (:stem . "mature") (:form . "Mature") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "bouton") (:form . "boutons") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "VBP") (:stem . "develop") (:form . "develop") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "age") (:form . "age") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "prominent") (:form . "prominent") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "NNS") (:stem . "bouton") (:form . "boutons") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 76) (:start . 71)\n  (:id . 54))\n ((:tag . "RB") (:stem . "easily") (:form . "easily") (:end . 83)\n  (:start . 77) (:id . 55))\n ((:tag . "JJ") (:stem . "identifiable") (:form . "identifiable") (:end . 96)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 110)\n  (:start . 104) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "40-day-old") (:form . "40-day-old") (:end . 124)\n  (:start . 114) (:id . 61))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 130) (:start . 125)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 132) (:start . 131)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 136) (:start . 132)\n  (:id . 64))\n ((:tag . "CD") (:stem . "7F,I") (:form . "7F,I") (:end . 141) (:start . 137)\n  (:id . 65))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 142) (:start . 141)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "compare") (:form . "compare") (:end . 150)\n  (:start . 143) (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 155) (:start . 151)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 169) (:start . 156) (:id . 69))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 178)\n  (:start . 170) (:id . 70))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 183) (:start . 179)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "S4C,F") (:form . "S4C,F") (:end . 189)\n  (:start . 184) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.270) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502522@unknown@formal@none@1@S@Owing to the significant variation in their structure and the lack of recognizable boutons, it is difficult to directly quantify and compare the size of these axonal termini in young adults.@(((:tag . "VBG") (:stem . "owe") (:form . "Owing") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "variation") (:form . "variation") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 43)\n  (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "recognizable") (:form . "recognizable") (:end . 82)\n  (:start . 70) (:id . 54))\n ((:tag . "NNS") (:stem . "bouton") (:form . "boutons") (:end . 90)\n  (:start . 83) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 107)\n  (:start . 98) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 119)\n  (:start . 111) (:id . 61))\n ((:tag . "VB") (:stem . "quantify") (:form . "quantify") (:end . 128)\n  (:start . 120) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 63))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 140)\n  (:start . 133) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 65))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 149) (:start . 145)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n  (:id . 67))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 158)\n  (:start . 153) (:id . 68))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 165)\n  (:start . 159) (:id . 69))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 173)\n  (:start . 166) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 176) (:start . 174)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "young") (:form . "young") (:end . 182)\n  (:start . 177) (:id . 72))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 189)\n  (:start . 183) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.271) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502523@unknown@formal@none@1@S@However, in aged dhtt-ko mutants, it is apparent that the axonal termini contain a significantly reduced number of varicosities and branches (Fig. 7H,I,N).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "apparent") (:form . "apparent") (:end . 48)\n  (:start . 40) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 64)\n  (:start . 58) (:id . 54))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 72)\n  (:start . 65) (:id . 55))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 80)\n  (:start . 73) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 96) (:start . 83) (:id . 58))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 104)\n  (:start . 97) (:id . 59))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 111)\n  (:start . 105) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "varicosity") (:form . "varicosities") (:end . 127)\n  (:start . 115) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "branch") (:form . "branches") (:end . 140)\n  (:start . 132) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 146) (:start . 142)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "7H,I,N") (:form . "7H,I,N") (:end . 153)\n  (:start . 147) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x8.272.1) (:span 40 48)))\n (:hscopes ((:id . :x8.272.1) (:span 40 140)))\n (:identifiers (:sid . :s8.272) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502524@unknown@formal@none@1@S@Quantification of the total area covered by each axonal terminus revealed that the A307-positive axonal termini in 40-day-old dhtt-ko mutants cover about half of the area compared with controls (Fig. 7R) (average area covered by each axonal terminus: wild-type control=168.7±8.0 µm2, dhtt-ko mutant=86.1±7.2 µm2; P<0.0001; total number of A307-positive axonal termini quantified: wild-type control, n=18; dhtt-ko mutants, n=17).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "cover") (:form . 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5502525@unknown@formal@none@1@S@To rule out the possibility that this reduced complexity was because of the accelerated aging process or a secondary effect associated with the reduced mobility of dhtt-ko mutants, we examined the axonal termini of the A307-positive neurons in 83-day-old wild-type flies, as animals at this age are near the end of their life span and have severely reduced mobility.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "rule") (:form . "rule") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 27)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . 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"dhtt-ko") (:end . 171)\n  (:start . 164) (:id . 68))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 179)\n  (:start . 172) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n  (:id . 70))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 183) (:start . 181)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 192)\n  (:start . 184) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 203)\n  (:start . 197) (:id . 74))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 211)\n  (:start . 204) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 214) (:start . 212)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 218) (:start . 215)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "a307-positive") (:form . "A307-positive")\n  (:end . 232) (:start . 219) (:id . 78))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 240)\n  (:start . 233) (:id . 79))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 243) (:start . 241)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "83-day-old") (:form . "83-day-old") (:end . 254)\n  (:start . 244) (:id . 81))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 264)\n  (:start . 255) (:id . 82))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 270) (:start . 265)\n  (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 271) (:start . 270)\n  (:id . 84))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 274) (:start . 272)\n  (:id . 85))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 282)\n  (:start . 275) (:id . 86))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 285) (:start . 283)\n  (:id . 87))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 290) (:start . 286)\n  (:id . 88))\n ((:tag . "NN") (:stem . "age") (:form . "age") (:end . 294) (:start . 291)\n  (:id . 89))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 298) (:start . 295)\n  (:id . 90))\n ((:tag . "IN") (:stem . "near") (:form . "near") (:end . 303) (:start . 299)\n  (:id . 91))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 307) (:start . 304)\n  (:id . 92))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 311) (:start . 308)\n  (:id . 93))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 314) (:start . 312)\n  (:id . 94))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 320)\n  (:start . 315) (:id . 95))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 325) (:start . 321)\n  (:id . 96))\n ((:tag . "NN") (:stem . "span") (:form . "span") (:end . 330) (:start . 326)\n  (:id . 97))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 334) (:start . 331)\n  (:id . 98))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 339) (:start . 335)\n  (:id . 99))\n ((:tag . "RB") (:stem . "severely") (:form . "severely") (:end . 348)\n  (:start . 340) (:id . 100))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 356)\n  (:start . 349) (:id . 101))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 365)\n  (:start . 357) (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 366) (:start . 365)\n  (:id . 103)))@@@1@62@((:hcues ((:id . :x8.274.1) (:span 102 104)) ((:id . :x8.274.2) (:span 16 27)))\n (:hscopes ((:id . :x8.274.1) (:span 72 179))\n  ((:id . :x8.274.2) (:span 16 179)))\n (:identifiers (:sid . :s8.274) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502526@unknown@formal@none@1@S@The structure of the axonal termini in these flies is similar to that of 40-day-old flies and shows no obvious reduction in terminal complexity (supplementary material Fig. S5).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 69) (:start . 65)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "40-day-old") (:form . "40-day-old") (:end . 83)\n  (:start . 73) (:id . 56))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 89) (:start . 84)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 99) (:start . 94)\n  (:id . 59))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 110)\n  (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 120)\n  (:start . 111) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 132)\n  (:start . 124) (:id . 64))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 143)\n  (:start . 133) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 158) (:start . 145) (:id . 67))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 167)\n  (:start . 159) (:id . 68))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 172) (:start . 168)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 175) (:start . 173)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s8.275) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502527@unknown@formal@none@1@S@Using the membrane-bound mCD8-eGFP reporter driven by the GF-specific A307-Gal4 line, we further analyzed the axonal projection and terminal morphology of the GF neurons in dhtt-ko mutants.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "membrane-bound") (:form . "membrane-bound")\n  (:end . 24) (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "mcd8-egfp") (:form . "mCD8-eGFP") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 43)\n  (:start . 35) (:id . 46))\n ((:tag . "VBN") (:stem . "drive") (:form . "driven") (:end . 50)\n  (:start . 44) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 53) (:start . 51)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "gf-specific") (:form . "GF-specific") (:end . 69)\n  (:start . 58) (:id . 50))\n ((:tag . "NN") (:stem . "a307-gal4") (:form . "A307-Gal4") (:end . 79)\n  (:start . 70) (:id . 51))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 84) (:start . 80)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 96)\n  (:start . 89) (:id . 55))\n ((:tag . "VBD") (:stem . "analyze") (:form . "analyzed") (:end . 105)\n  (:start . 97) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 116)\n  (:start . 110) (:id . 58))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 127)\n  (:start . 117) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 140)\n  (:start . 132) (:id . 61))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 151)\n  (:start . 141) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "GF") (:form . "GF") (:end . 161) (:start . 159)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 169)\n  (:start . 162) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 172) (:start . 170)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 180)\n  (:start . 173) (:id . 68))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 188)\n  (:start . 181) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.276) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502528@unknown@formal@none@1@S@The GF neurons are a pair of large interneurons located in the central brain and project their prominent axons, which are unbranched, to the mesothoracic neuromere (T2) in the ventral nerve cord, where they bend laterally and synapse with other interneurons and motor neurons (Phelan et al., 1996).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "GF") (:form . "GF") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . 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5502529@unknown@formal@none@1@S@In both young (3-day-old) and aged (40-day-old) dhtt-ko mutants, GF neurons project normally to the T2 neuromere and form the characteristic terminal bends, resembling those observed in wild-type controls (supplementary material Fig. S6).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "young") (:form . "young") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "3-day-old") (:form . "3-day-old") (:end . 24)\n  (:start . 15) (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 34) (:start . 30)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "40-day-old") (:form . "40-day-old") (:end . 46)\n  (:start . 36) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 55)\n  (:start . 48) (:id . 53))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 63)\n  (:start . 56) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "GF") (:form . "GF") (:end . 67) (:start . 65)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 75)\n  (:start . 68) (:id . 57))\n ((:tag . "VBP") (:stem . "project") (:form . "project") (:end . 83)\n  (:start . 76) (:id . 58))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 92)\n  (:start . 84) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 61))\n ((:tag . "NN") (:stem . "t2") (:form . "T2") (:end . 102) (:start . 100)\n  (:id . 62))\n ((:tag . "NN") (:stem . "neuromere") (:form . "neuromere") (:end . 112)\n  (:start . 103) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 64))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 121) (:start . 117)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 140) (:start . 126) (:id . 67))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 149)\n  (:start . 141) (:id . 68))\n ((:tag . "NNS") (:stem . "bend") (:form . "bends") (:end . 155)\n  (:start . 150) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "resemble") (:form . "resembling") (:end . 167)\n  (:start . 157) (:id . 71))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 173)\n  (:start . 168) (:id . 72))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 182)\n  (:start . 174) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 185) (:start . 183)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 195)\n  (:start . 186) (:id . 75))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 204)\n  (:start . 196) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 206) (:start . 205)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 219) (:start . 206) (:id . 78))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 228)\n  (:start . 220) (:id . 79))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 233) (:start . 229)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "S6") (:form . "S6") (:end . 236) (:start . 234)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 237) (:start . 236)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.278) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502530@unknown@formal@none@1@S@In 3-day-old animals, the signal intensity of the mCD8-eGFP reporter at the GF axonal termini was similar between dhtt-ko mutants and wild-type controls (supplementary material Fig. S6B,C) (total number of 3-day-old GF axonal termini examined: wild-type control, n=10; dhtt-ko mutants, n=12).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "3-day-old") (:form . "3-day-old") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 32)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 42)\n  (:start . 33) (:id . 48))\n ((:tag . 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5502532@unknown@formal@none@1@S@The exact nature behind such a difference remains to be clarified, but might represent subtle alterations in axonal transport of membrane proteins in aged neurons.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "exact") (:form . "exact") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "nature") (:form . "nature") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "behind") (:form . "behind") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 41)\n  (:start . 31) (:id . 48))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "clarify") (:form . "clarified") (:end . 65)\n  (:start . 56) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . "VB") (:stem . "represent") (:form . "represent") (:end . 86)\n  (:start . 77) (:id . 56))\n ((:tag . "JJ") (:stem . "subtle") (:form . "subtle") (:end . 93)\n  (:start . 87) (:id . 57))\n ((:tag . "NNS") (:stem . "alteration") (:form . "alterations") (:end . 105)\n  (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 115)\n  (:start . 109) (:id . 60))\n ((:tag . "NN") (:stem . "transport") (:form . "transport") (:end . 125)\n  (:start . 116) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 137)\n  (:start . 129) (:id . 63))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 146)\n  (:start . 138) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "aged") (:form . "aged") (:end . 154) (:start . 150)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 162)\n  (:start . 155) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x8.281.1) (:span 71 76)))\n (:hscopes ((:id . :x8.281.1) (:span 71 162)))\n (:identifiers (:sid . :s8.281) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502533@unknown@formal@none@1@S@Nevertheless, these results suggest that dhtt does not affect axonal pathfinding and overall brain organization, but has a functional role in regulating the complexity of axonal termini in the adult brain.@(((:tag . "RB") (:stem . "nevertheless") (:form . "Nevertheless") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 61)\n  (:start . 55) (:id . 51))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "pathfinding") (:form . "pathfinding") (:end . 80)\n  (:start . 69) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 92)\n  (:start . 85) (:id . 55))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 111)\n  (:start . 99) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 58))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 116) (:start . 113)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 120) (:start . 117)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 122) (:start . 121)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 133)\n  (:start . 123) (:id . 62))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 138) (:start . 134)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "regulate") (:form . "regulating") (:end . 152)\n  (:start . 142) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 66))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 167)\n  (:start . 157) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 170) (:start . 168)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 177)\n  (:start . 171) (:id . 69))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 185)\n  (:start . 178) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 188) (:start . 186)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 192) (:start . 189)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 198)\n  (:start . 193) (:id . 73))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 204)\n  (:start . 199) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x8.282.1) (:span 28 35)))\n (:hscopes ((:id . :x8.282.1) (:span 28 204)))\n (:identifiers (:sid . :s8.282) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502534@unknown@formal@none@1@S@Loss of dhtt enhances the pathogenesis of HD flies@(((:tag . "NN") (:stem . "loss") (:form . "Loss") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "enhance") (:form . "enhances") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 38)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 50) (:start . 45)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s8.283) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502535@unknown@formal@none@1@S@Earlier studies in cell culture and Htt mutant mice have shown that wild-type Htt has a protective role for CNS neurons (Dragatsis et al., 2000; O’Kusky et al., 1999; Rigamonti et al., 2000; Van Raamsdonk et al., 2005).@(((:tag . "JJR") (:stem . "early") (:form . "Earlier") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 77)\n  (:start . 68) (:id . 54))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "protective") (:form . "protective") (:end . 98)\n  (:start . 88) (:id . 58))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 103) (:start . 99)\n  (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 107) (:start . 104)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "CNS") (:form . "CNS") (:end . 111) (:start . 108)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 119)\n  (:start . 112) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Dragatsis") (:form . "Dragatsis") (:end . 130)\n  (:start . 121) (:id . 64))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 133) (:start . 131)\n  (:id . 65))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 137) (:start . 134)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 67))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 143) (:start . 139)\n  (:id . 68))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 144) (:start . 143)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "O’Kusky") (:form . "O’Kusky") (:end . 152)\n  (:start . 145) (:id . 70))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 155) (:start . 153)\n  (:id . 71))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 159) (:start . 156)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 73))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 165) (:start . 161)\n  (:id . 74))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 166) (:start . 165)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Rigamonti") (:form . "Rigamonti") (:end . 176)\n  (:start . 167) (:id . 76))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 179) (:start . 177)\n  (:id . 77))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 183) (:start . 180)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 79))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 189) (:start . 185)\n  (:id . 80))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 190) (:start . 189)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Van") (:form . "Van") (:end . 194) (:start . 191)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Raamsdonk") (:form . "Raamsdonk") (:end . 204)\n  (:start . 195) (:id . 83))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 207) (:start . 205)\n  (:id . 84))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 211) (:start . 208)\n  (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 212) (:start . 211)\n  (:id . 86))\n ((:tag . "CD") (:stem . "2005") (:form . "2005") (:end . 217) (:start . 213)\n  (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 218) (:start . 217)\n  (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s8.284) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502536@unknown@formal@none@1@S@Further, existing evidence suggests that normal Htt activity can be inactivated by mechanisms such as abnormal sequestration into insoluble aggregates (Huang et al., 1998; Kazantsev et al., 1999; Narain et al., 1999; Preisinger et al., 1999; Wheeler et al., 2000).@(((:tag . "RB") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 47)\n  (:start . 41) (:id . 48))\n ((:tag . "NNP") (:stem . "Htt") (:form . 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5502537@unknown@formal@none@1@S@These and other observations have lead to the hypothesis that the perturbation of endogenous Htt function, such as by late-onset inactivation of endogenous Htt, contributes to HD pathogenesis (Cattaneo et al., 2001).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 28)\n  (:start . 16) (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "lead") (:form . "lead") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "perturbation") (:form . "perturbation") (:end . 78)\n  (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 92)\n  (:start . 82) (:id . 55))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 105)\n  (:start . 97) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 111) (:start . 107)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 117) (:start . 115)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "late-onset") (:form . "late-onset") (:end . 128)\n  (:start . 118) (:id . 62))\n ((:tag . "NN") (:stem . "inactivation") (:form . "inactivation") (:end . 141)\n  (:start . 129) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 155)\n  (:start . 145) (:id . 65))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 159) (:start . 156)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "contribute") (:form . "contributes") (:end . 172)\n  (:start . 161) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 175) (:start . 173)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 178) (:start . 176)\n  (:id . 70))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 191)\n  (:start . 179) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 193) (:start . 192)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Cattaneo") (:form . "Cattaneo") (:end . 201)\n  (:start . 193) (:id . 73))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 204) (:start . 202)\n  (:id . 74))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 208) (:start . 205)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 209) (:start . 208)\n  (:id . 76))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 214) (:start . 210)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 215) (:start . 214)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x8.286.1) (:span 46 56)))\n (:hscopes ((:id . :x8.286.1) (:span 46 191)))\n (:identifiers (:sid . :s8.286) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502538@unknown@formal@none@1@S@Attempts to test this directly in mouse Hdh mutants have been complicated by the crucial role of Hdh in early mouse embryogenesis and in the later stages of brain development (Auerbach et al., 2001; Dragatsis et al., 2000; Duyao et al., 1995; Leavitt et al., 2001; Nasir et al., 1995; Van Raamsdonk et al., 2005; White et al., 1997; Zeitlin et al., 1995).@(((:tag . "NNS") (:stem . "attempt") (:form . "Attempts") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mouse") (:form . 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5502539@unknown@formal@none@1@S@However, we have a unique opportunity to examine this in Drosophila because dhtt is not essential for fly embryogenesis and dhtt mutants appear to behave normally at young ages, with only a mild axon terminal defect in the brain.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 25)\n  (:start . 19) (:id . 47))\n ((:tag . "NN") (:stem . "opportunity") (:form . "opportunity") (:end . 37)\n  (:start . 26) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 67)\n  (:start . 57) (:id . 53))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 75)\n  (:start . 68) (:id . 54))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 97)\n  (:start . 88) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "fly") (:form . "fly") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 119) (:start . 106) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 62))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 128) (:start . 124)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 136)\n  (:start . 129) (:id . 64))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 143)\n  (:start . 137) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 146) (:start . 144)\n  (:id . 66))\n ((:tag . "VB") (:stem . "behave") (:form . "behave") (:end . 153)\n  (:start . 147) (:id . 67))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 162)\n  (:start . 154) (:id . 68))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 165) (:start . 163)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "young") (:form . "young") (:end . 171)\n  (:start . 166) (:id . 70))\n ((:tag . "NNS") (:stem . "age") (:form . "ages") (:end . 176) (:start . 172)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 72))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 182) (:start . 178)\n  (:id . 73))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 187) (:start . 183)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 189) (:start . 188)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "mild") (:form . "mild") (:end . 194) (:start . 190)\n  (:id . 76))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 199) (:start . 195)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 208)\n  (:start . 200) (:id . 78))\n ((:tag . "NN") (:stem . "defect") (:form . "defect") (:end . 215)\n  (:start . 209) (:id . 79))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 218) (:start . 216)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 222) (:start . 219)\n  (:id . 81))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 228)\n  (:start . 223) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x8.288.1) (:span 137 143)))\n (:hscopes ((:id . :x8.288.1) (:span 124 228)))\n (:identifiers (:sid . :s8.288) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502540@unknown@formal@none@1@S@We used a well-established fly HD model for polyQ toxicity (HD-Q93), in which the human HTT exon 1, with 93 glutamine repeats, is expressed in all neuronal tissues (genotype: elav-Gal4/+; UAS-Httexon1-Q93/+) (Steffan et al., 2001).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 9) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "well-established") (:form . "well-established")\n  (:end . 26) (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "polyq") (:form . "polyQ") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "toxicity") (:form . "toxicity") (:end . 58)\n  (:start . 50) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 77) (:start . 72)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 87) (:start . 82)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "HTT") (:form . "HTT") (:end . 91) (:start . 88)\n  (:id . 60))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 96) (:start . 92)\n  (:id . 61))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 98) (:start . 97)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 104) (:start . 100)\n  (:id . 64))\n ((:tag . "CD") (:stem . "93") (:form . "93") (:end . 107) (:start . 105)\n  (:id . 65))\n ((:tag . "NN") (:stem . "glutamine") (:form . "glutamine") (:end . 117)\n  (:start . 108) (:id . 66))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 125)\n  (:start . 118) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 129) (:start . 127)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 139)\n  (:start . 130) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 142) (:start . 140)\n  (:id . 71))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 146) (:start . 143)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 155)\n  (:start . 147) (:id . 73))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 163)\n  (:start . 156) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 165) (:start . 164)\n  (:id . 75))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 173)\n  (:start . 165) (:id . 76))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 174) (:start . 173)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "elav-gal4/+") (:form . "elav-Gal4/+") (:end . 186)\n  (:start . 175) (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 187) (:start . 186)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "uas-httexon1-q93/+") (:form . "UAS-Httexon1-Q93/+")\n  (:end . 206) (:start . 188) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 207) (:start . 206)\n  (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 209) (:start . 208)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Steffan") (:form . "Steffan") (:end . 216)\n  (:start . 209) (:id . 83))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 219) (:start . 217)\n  (:id . 84))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 223) (:start . 220)\n  (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 224) (:start . 223)\n  (:id . 86))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 229) (:start . 225)\n  (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 230) (:start . 229)\n  (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s8.289) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502541@unknown@formal@none@1@S@The HD-Q93 flies develop age-dependent neurodegenerative phenotypes in adults, which manifest as initial hyperactivity followed by a gradual loss of coordination and a decline in locomotor ability, with eventual death at around 20 days of age (Fig. 8F–H).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "develop") (:form . "develop") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "age-dependent") (:form . "age-dependent")\n  (:end . 38) (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "neurodegenerative") (:form . "neurodegenerative")\n  (:end . 56) (:start . 39) (:id . 47))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 67)\n  (:start . 57) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 77)\n  (:start . 71) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 84) (:start . 79)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "manifest") (:form . "manifest") (:end . 93)\n  (:start . 85) (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 96) (:start . 94)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 104)\n  (:start . 97) (:id . 55))\n ((:tag . "NN") (:stem . "hyperactivity") (:form . "hyperactivity")\n  (:end . 118) (:start . 105) (:id . 56))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 127)\n  (:start . 119) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 130) (:start . 128)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 132) (:start . 131)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "gradual") (:form . "gradual") (:end . 140)\n  (:start . 133) (:id . 60))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 145) (:start . 141)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n  (:id . 62))\n ((:tag . "NN") (:stem . "coordination") (:form . "coordination") (:end . 161)\n  (:start . 149) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 167) (:start . 166)\n  (:id . 65))\n ((:tag . "NN") (:stem . "decline") (:form . "decline") (:end . 175)\n  (:start . 168) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 178) (:start . 176)\n  (:id . 67))\n ((:tag . "NN") (:stem . "locomotor") (:form . "locomotor") (:end . 188)\n  (:start . 179) (:id . 68))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 196)\n  (:start . 189) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 202) (:start . 198)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "eventual") (:form . "eventual") (:end . 211)\n  (:start . 203) (:id . 72))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 217)\n  (:start . 212) (:id . 73))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 220) (:start . 218)\n  (:id . 74))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 227)\n  (:start . 221) (:id . 75))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 230) (:start . 228)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 235) (:start . 231)\n  (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 238) (:start . 236)\n  (:id . 78))\n ((:tag . "NN") (:stem . "age") (:form . "age") (:end . 242) (:start . 239)\n  (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 244) (:start . 243)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 248) (:start . 244)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "8F–H") (:form . "8F–H") (:end . 253) (:start . 249)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 254) (:start . 253)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 255) (:start . 254)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s8.290) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502542@unknown@formal@none@1@S@The HD-Q93 flies also develop a progressive degeneration of both the brain and other neuronal tissues, most prominently in the photoreceptor cells in the eye (Steffan et al., 2001).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "develop") (:form . "develop") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "progressive") (:form . "progressive") (:end . 43)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "degeneration") (:form . "degeneration") (:end . 56)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 74) (:start . 69)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 84) (:start . 79)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 93)\n  (:start . 85) (:id . 56))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 101)\n  (:start . 94) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 107) (:start . 103)\n  (:id . 59))\n ((:tag . "RB") (:stem . "prominently") (:form . "prominently") (:end . 119)\n  (:start . 108) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 62))\n ((:tag . "NN") (:stem . "photoreceptor") (:form . "photoreceptor")\n  (:end . 140) (:start . 127) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 146)\n  (:start . 141) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 66))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 157) (:start . 154)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Steffan") (:form . "Steffan") (:end . 166)\n  (:start . 159) (:id . 69))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 169) (:start . 167)\n  (:id . 70))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 173) (:start . 170)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 72))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 179) (:start . 175)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s8.291) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502543@unknown@formal@none@1@S@Loss of endogenous dhtt enhances the mobility and viability phenotypes of HD flies.@(((:tag . "NN") (:stem . "loss") (:form . "Loss") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "enhance") (:form . "enhances") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 59)\n  (:start . 50) (:id . 50))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 70)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 82) (:start . 77)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s8.292) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502544@unknown@formal@none@1@S@(A–D) Retinal organization, as revealed by pseudopupil imaging of 7-day-old adult eyes.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–D") (:form . "A–D") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "retinal") (:form . "Retinal") (:end . 13)\n  (:start . 6) (:id . 45))\n ((:tag . "NN") (:stem . "organization") (:form . "organization") (:end . 26)\n  (:start . 14) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "reveal") (:form . "revealed") (:end . 39)\n  (:start . 31) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "pseudopupil") (:form . "pseudopupil") (:end . 54)\n  (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "imaging") (:form . "imaging") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "7-day-old") (:form . "7-day-old") (:end . 75)\n  (:start . 66) (:id . 54))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 81) (:start . 76)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "eye") (:form . "eyes") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.293) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502545@unknown@formal@none@1@S@Both wild-type (A) and dhtt-ko flies (B) had well-patterned ommatidium with seven rhabdomeres in each.@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 30)\n  (:start . 23) (:id . 48))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 36) (:start . 31)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 39) (:start . 38)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 40) (:start . 39)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 44) (:start . 41)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "well-patterned") (:form . "well-patterned")\n  (:end . 59) (:start . 45) (:id . 54))\n ((:tag . "NN") (:stem . "ommatidium") (:form . "ommatidium") (:end . 70)\n  (:start . 60) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . "CD") (:stem . "seven") (:form . "seven") (:end . 81) (:start . 76)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "rhabdomere") (:form . "rhabdomeres") (:end . 93)\n  (:start . 82) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 101) (:start . 97)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s8.294) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502546@unknown@formal@none@1@S@Adult eyes from HD-Q93 (C) and HD-Q93; dhtt-ko (D) flies both showed an extensive loss of photoreceptors (arrows highlight ommatidia with only three or four rhabdomeres).@(((:tag . "JJ") (:stem . "adult") (:form . "Adult") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "eye") (:form . "eyes") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 26) (:start . 25)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 37)\n  (:start . 31) (:id . 50))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 38) (:start . 37)\n  (:id . 51))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 46)\n  (:start . 39) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 49) (:start . 48)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "fly") (:form . "flies") (:end . 56) (:start . 51)\n  (:id . 56))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 61) (:start . 57)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 68) (:start . 62)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 71) (:start . 69)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 81)\n  (:start . 72) (:id . 60))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 86) (:start . 82)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "photoreceptor") (:form . "photoreceptors")\n  (:end . 104) (:start . 90) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 112)\n  (:start . 106) (:id . 65))\n ((:tag . "VBP") (:stem . "highlight") (:form . "highlight") (:end . 122)\n  (:start . 113) (:id . 66))\n ((:tag . "NN") (:stem . "ommatidia") (:form . "ommatidia") (:end . 132)\n  (:start . 123) (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 137) (:start . 133)\n  (:id . 68))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 142) (:start . 138)\n  (:id . 69))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 148)\n  (:start . 143) (:id . 70))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 151) (:start . 149)\n  (:id . 71))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 156) (:start . 152)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "rhabdomere") (:form . "rhabdomeres") (:end . 168)\n  (:start . 157) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s8.295) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502547@unknown@formal@none@1@S@(E) Histogram showing the number of remaining photoreceptors per ommatidium in 11-day-old adults.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Histogram") (:form . "Histogram") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 21)\n  (:start . 14) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 32)\n  (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 45)\n  (:start . 36) (:id . 50))\n ((:tag . "NNS") (:stem . "photoreceptor") (:form . "photoreceptors")\n  (:end . 60) (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "ommatidium") (:form . "ommatidium") (:end . 75)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "11-day-old") (:form . "11-day-old") (:end . 89)\n  (:start . 79) (:id . 55))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 96)\n  (:start . 90) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.296) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502548@unknown@formal@none@1@S@A similar profile of degeneration was observed for HD-Q93 flies (red) and HD-Q93; dhtt-ko flies (blue).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "degeneration") (:form . "degeneration") (:end . 33)\n  (:start . 21) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 57)\n  (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 68) (:start . 65)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 80)\n  (:start . 74) (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 89)\n  (:start . 82) (:id . 58))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 95) (:start . 90)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 101) (:start . 97)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s8.297) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502549@unknown@formal@none@1@S@(F–H) Quantification of climbing ability (F), spontaneous locomotion (G) and age-dependent survival rate (H).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "F–H") (:form . "F–H") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Quantification") (:form . "Quantification")\n  (:end . 20) (:start . 6) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "climb") (:form . "climbing") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "spontaneous") (:form . "spontaneous") (:end . 57)\n  (:start . 46) (:id . 53))\n ((:tag . "NN") (:stem . "locomotion") (:form . "locomotion") (:end . 68)\n  (:start . 58) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "age-dependent") (:form . "age-dependent")\n  (:end . 90) (:start . 77) (:id . 59))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 99)\n  (:start . 91) (:id . 60))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 104) (:start . 100)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 107) (:start . 106)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s8.298) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502550@unknown@formal@none@1@S@The genotypes for each of the fly lines tested are provided within each chart.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "fly") (:form . "fly") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 39) (:start . 34)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 46) (:start . 40)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 59)\n  (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "chart") (:form . "chart") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.299) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502551@unknown@formal@none@1@S@HD flies with a background dhtt-ko mutation show an accelerated loss of mobility (F,G) and earlier lethality (H).@(((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "fly") (:form . "flies") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 26)\n  (:start . 16) (:id . 46))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "accelerate") (:form . "accelerated") (:end . 63)\n  (:start . 52) (:id . 51))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 80)\n  (:start . 72) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "F,G") (:form . "F,G") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "JJR") (:stem . "early") (:form . "earlier") (:end . 98)\n  (:start . 91) (:id . 59))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 108)\n  (:start . 99) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 111) (:start . 110)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.300) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502552@unknown@formal@none@1@S@The data in (E–H) are presented as the means±s.e.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "E–H") (:form . "E–H") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 31)\n  (:start . 22) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 34) (:start . 32)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 51))\n ((:tag . "NN") (:stem . "means±s.e") (:form . "means±s.e") (:end . 48)\n  (:start . 39) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s8.301) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502553@unknown@formal@none@1@S@After introducing HD-Q93 into the dhtt mutant background (‘HD-Q93; dhtt-ko’ flies; genotype: elav-Gal4/+; UAS-Httexon1-Q93/+; dhtt-ko/dhtt-ko), we examined the eye degeneration phenotype by quantifying the number of rhabdomeres in each ommatidia as the animals age.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "introduce") (:form . "introducing") (:end . 17)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 24)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 59) (:start . 58)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 65)\n  (:start . 59) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 74)\n  (:start . 67) (:id . 54))\n ((:tag . "POS") (:stem . "’") (:form . "’") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 91)\n  (:start . 83) (:id . 58))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "elav-gal4/+") (:form . "elav-Gal4/+") (:end . 104)\n  (:start . 93) (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 105) (:start . 104)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "uas-httexon1-q93/+") (:form . "UAS-Httexon1-Q93/+")\n  (:end . 124) (:start . 106) (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 125) (:start . 124)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dhtt-ko/dhtt-ko") (:form . "dhtt-ko/dhtt-ko")\n  (:end . 141) (:start . 126) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 66))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 146) (:start . 144)\n  (:id . 67))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 155)\n  (:start . 147) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 69))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 163) (:start . 160)\n  (:id . 70))\n ((:tag . "NN") (:stem . "degeneration") (:form . "degeneration") (:end . 176)\n  (:start . 164) (:id . 71))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 186)\n  (:start . 177) (:id . 72))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 189) (:start . 187)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "quantify") (:form . "quantifying") (:end . 201)\n  (:start . 190) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 205) (:start . 202)\n  (:id . 75))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 212)\n  (:start . 206) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 215) (:start . 213)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "rhabdomere") (:form . "rhabdomeres") (:end . 227)\n  (:start . 216) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 230) (:start . 228)\n  (:id . 79))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 235) (:start . 231)\n  (:id . 80))\n ((:tag . "NN") (:stem . "ommatidia") (:form . "ommatidia") (:end . 245)\n  (:start . 236) (:id . 81))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 248) (:start . 246)\n  (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 252) (:start . 249)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 260)\n  (:start . 253) (:id . 84))\n ((:tag . "NN") (:stem . "age") (:form . "age") (:end . 264) (:start . 261)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s8.302) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502554@unknown@formal@none@1@S@The loss of photoreceptor cells in HD-Q93 flies was not significantly enhanced in the absence of endogenous dhtt (Fig. 8A–E).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "photoreceptor") (:form . "photoreceptor")\n  (:end . 25) (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 69) (:start . 56) (:id . 52))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 78)\n  (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 93)\n  (:start . 86) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 107)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 112) (:start . 108)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 118) (:start . 114)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "8A–E") (:form . "8A–E") (:end . 123) (:start . 119)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.303) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502555@unknown@formal@none@1@S@For example, at 11 days of age, approximately 40% of ommatidia lost three photoreceptors in both HD-Q93 and HD-Q93; dhtt-ko flies (Fig. 8E) (number of ommatidia with four photoreceptors: HD-Q93=42.6±2.9%, n=562, eight adult eyes analyzed; HD-Q93; dhtt-ko=37.6±4.1%, n=266, seven adult eyes analyzed; the difference was statistically insignificant, P>0.5).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 23) (:start . 19)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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5502557@unknown@formal@none@1@S@Interestingly, although these HD-Q93; dhtt-ko flies showed normal mobility at the beginning of their adult life, they displayed a declining mobility that could be detected as early as 5 days of age and that rapidly deteriorated over the next few days (supplementary material Movies 4–8).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 29) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 36)\n  (:start . 30) (:id . 46))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . 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5502558@unknown@formal@none@1@S@During this time, the flies become progressively uncoordinated, showing an increasing frequency of both faltering while walking and falling during climbing (Fig. 8G; supplementary material Movies 4–8).@(((:tag . "IN") (:stem . "during") (:form . "During") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "become") (:form . "become") (:end . 34)\n  (:start . 28) (:id . 48))\n ((:tag . "RB") (:stem . "progressively") (:form . "progressively")\n  (:end . 48) (:start . 35) (:id . 49))\n ((:tag . "JJ") (:stem . "uncoordinated") (:form . "uncoordinated")\n  (:end . 62) (:start . 49) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 85)\n  (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 95)\n  (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 56))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 103) (:start . 99)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "falter") (:form . "faltering") (:end . 113)\n  (:start . 104) (:id . 58))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 119)\n  (:start . 114) (:id . 59))\n ((:tag . "VBG") (:stem . "walk") (:form . "walking") (:end . 127)\n  (:start . 120) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "fall") (:form . "falling") (:end . 139)\n  (:start . 132) (:id . 62))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 146)\n  (:start . 140) (:id . 63))\n ((:tag . "VBG") (:stem . "climb") (:form . "climbing") (:end . 155)\n  (:start . 147) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 161) (:start . 157)\n  (:id . 66))\n ((:tag . "NN") (:stem . "8g") (:form . "8G") (:end . 164) (:start . 162)\n  (:id . 67))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 165) (:start . 164)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 179) (:start . 166) (:id . 69))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 188)\n  (:start . 180) (:id . 70))\n ((:tag . "NNP") (:stem . "Movie") (:form . "Movies") (:end . 195)\n  (:start . 189) (:id . 71))\n ((:tag . "CD") (:stem . "4–8") (:form . "4–8") (:end . 199) (:start . 196)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 200) (:start . 199)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.307) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502559@unknown@formal@none@1@S@In a standard climbing assay, almost all 3-day-old HD-Q93; dhtt-ko flies could successfully climb to the top of a vial, which is similar to that observed for wild-type controls.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 13)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "climbing") (:form . "climbing") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "3-day-old") (:form . "3-day-old") (:end . 50)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 57)\n  (:start . 51) (:id . 51))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 78) (:start . 73)\n  (:id . 55))\n ((:tag . "RB") (:stem . "successfully") (:form . "successfully") (:end . 91)\n  (:start . 79) (:id . 56))\n ((:tag . "VB") (:stem . "climb") (:form . "climb") (:end . 97) (:start . 92)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "top") (:form . "top") (:end . 108) (:start . 105)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . "NN") (:stem . "vial") (:form . "vial") (:end . 118) (:start . 114)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 125)\n  (:start . 120) (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 128) (:start . 126)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 136)\n  (:start . 129) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n  (:id . 68))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 144) (:start . 140)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 153)\n  (:start . 145) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 157) (:start . 154)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 167)\n  (:start . 158) (:id . 72))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 176)\n  (:start . 168) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.308) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502560@unknown@formal@none@1@S@However, by day 11, only around 10% of viable HD-Q93; dhtt-ko flies could make it to the top, whereas the success rate was 61% for HD-Q93 flies, and more than 94% for wild-type and dhtt-ko flies (Fig. 8F) [based on an average of at least five independent assays of 20 flies for each genotype at the given age; compared with wild-type controls on day 11, the results from dhtt-ko flies were not significant (P=0.30), whereas the results from HD-Q93 and HD-Q93; dhtt-ko flies were significant (P<0.0001)].@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . 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5502561@unknown@formal@none@1@S@Similarly, when spontaneous locomotion was tested, the HD-Q93; dhtt-ko flies showed a more rapid decline in motility over time, and by day 9, these flies were less than half as active as those in the other groups (Fig. 8G) (activity was measured by the number of spontaneous turns performed every 4 minutes; on day 9, HD-Q93; dhtt-ko=26.4±5.9, n=9; HD-Q93=66.5±5.0, n=8; elav-Gal4; dhtt-ko control=60.6±4.3, n=9; UAS-Httex1Q93; dhtt-ko control=66.2±3.0, n=9; the HD-Q93; dhtt-ko results were statistically significant when compared with UAS-Httex1Q93; dhtt-ko control flies, P=0.00002).@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "spontaneous") (:form . 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5502562@unknown@formal@none@1@S@Furthermore, the life span of HD-Q93; dhtt-ko flies was shortened significantly, with half of them dying by day 8 and almost all of them by day 14.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "span") (:form . "span") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 45)\n  (:start . 38) (:id . 50))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "shorten") (:form . "shortened") (:end . 65)\n  (:start . 56) (:id . 53))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 79) (:start . 66) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "NN") (:stem . "half") (:form . "half") (:end . 90) (:start . 86)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "die") (:form . "dying") (:end . 104) (:start . 99)\n  (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 107) (:start . 105)\n  (:id . 61))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 111) (:start . 108)\n  (:id . 62))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 64))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 124)\n  (:start . 118) (:id . 65))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 128) (:start . 125)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n  (:id . 67))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 136) (:start . 132)\n  (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 139) (:start . 137)\n  (:id . 69))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 143) (:start . 140)\n  (:id . 70))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 146) (:start . 144)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s8.311) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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"(") (:end . 209) (:start . 208)\n  (:id . 91))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 213) (:start . 209)\n  (:id . 92))\n ((:tag . "CD") (:stem . "eight") (:form . "eight") (:end . 219)\n  (:start . 214) (:id . 93))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 229)\n  (:start . 220) (:id . 94))\n ((:tag . "NNS") (:stem . "crosse") (:form . "crosses") (:end . 237)\n  (:start . 230) (:id . 95))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 238) (:start . 237)\n  (:id . 96))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 239) (:start . 238)\n  (:id . 97))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 243) (:start . 240)\n  (:id . 98))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 254)\n  (:start . 244) (:id . 99))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 262)\n  (:start . 255) (:id . 100))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 269)\n  (:start . 263) (:id . 101))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 273) (:start . 270)\n  (:id . 102))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 280)\n  (:start . 274) (:id . 103))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 281) (:start . 280)\n  (:id . 104))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 289)\n  (:start . 282) (:id . 105))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 295) (:start . 290)\n  (:id . 106))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 299) (:start . 296)\n  (:id . 107))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n  (:end . 313) (:start . 300) (:id . 108))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 325)\n  (:start . 314) (:id . 109))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 326) (:start . 325)\n  (:id . 110))\n ((:tag . "NN") (:stem . "p=0.0003") (:form . "P=0.0003") (:end . 335)\n  (:start . 327) (:id . 111))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 336) (:start . 335)\n  (:id . 112))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 337) (:start . 336)\n  (:id . 113)))@@@1@72@((:identifiers (:sid . :s8.312) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502564@unknown@formal@none@1@S@Notably, at day 15, dhtt-ko mutants were healthy and displayed similar mobility to wild-type controls (Fig. 5A,B).@(((:tag . "RB") (:stem . "notably") (:form . "Notably") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 27)\n  (:start . 20) (:id . 48))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 35)\n  (:start . 28) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 40) (:start . 36)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "healthy") (:form . "healthy") (:end . 48)\n  (:start . 41) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 62)\n  (:start . 53) (:id . 53))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 70)\n  (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 79)\n  (:start . 71) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 92)\n  (:start . 83) (:id . 57))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 101)\n  (:start . 93) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 107) (:start . 103)\n  (:id . 60))\n ((:tag . "CD") (:stem . "5A,B") (:form . "5A,B") (:end . 112) (:start . 108)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s8.313) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502565@unknown@formal@none@1@S@To understand the underlying pathology of these phenotypes, we further examined the brain structure of these flies.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "understand") (:form . "understand") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "underlying") (:form . "underlying") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "pathology") (:form . "pathology") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 47) (:start . 42)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 58)\n  (:start . 48) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 70)\n  (:start . 63) (:id . 52))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 89) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 99)\n  (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 57))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 108)\n  (:start . 103) (:id . 58))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 114) (:start . 109)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s8.314) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502566@unknown@formal@none@1@S@Compared with HD-Q93 flies of the same age, the brains of HD-Q93; dhtt-ko flies had already developed a more severe pathology at 5 days.@(((:tag . "VBN") (:stem . "compare") (:form . "Compared") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "age") (:form . "age") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 64)\n  (:start . 58) (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 73)\n  (:start . 66) (:id . 56))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 79) (:start . 74)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 83) (:start . 80)\n  (:id . 58))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 91)\n  (:start . 84) (:id . 59))\n ((:tag . "VBN") (:stem . "develop") (:form . "developed") (:end . 101)\n  (:start . 92) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 115)\n  (:start . 109) (:id . 63))\n ((:tag . "NN") (:stem . "pathology") (:form . "pathology") (:end . 125)\n  (:start . 116) (:id . 64))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 128) (:start . 126)\n  (:id . 65))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 130) (:start . 129)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 135) (:start . 131)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.315) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502567@unknown@formal@none@1@S@Notably, the MBs appeared less organized – the characteristic bulged tip of the vertical α-axonal lobes, which were prominent in HD-Q93 flies (Fig. 9C, white arrows) (n=14) and other controls, was largely unrecognizable in 95% of HD-Q93; dhtt-ko flies (n=17/18) (Fig. 9H, white arrows) (supplementary material Figs S7 and S8).@(((:tag . "RB") (:stem . "notably") (:form . "Notably") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "mb") (:form . "MBs") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "organized") (:form . "organized") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "–") (:form . "–") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 61) (:start . 47) (:id . 51))\n ((:tag . "VBN") (:stem . "bulge") (:form . "bulged") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "tip") (:form . "tip") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "vertical") (:form . "vertical") (:end . 88)\n  (:start . 80) (:id . 56))\n ((:tag . "JJ") (:stem . "α-axonal") (:form . "α-axonal") (:end . 97)\n  (:start . 89) (:id . 57))\n ((:tag . "NNS") (:stem . "lobe") (:form . "lobes") (:end . 103) (:start . 98)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 110)\n  (:start . 105) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 115) (:start . 111)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "prominent") (:form . "prominent") (:end . 125)\n  (:start . 116) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 63))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 135)\n  (:start . 129) (:id . 64))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 141) (:start . 136)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 147) (:start . 143)\n  (:id . 67))\n ((:tag . "NN") (:stem . "9c") (:form . "9C") (:end . 150) (:start . 148)\n  (:id . 68))\n ((:tag . 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",") (:end . 192) (:start . 191)\n  (:id . 79))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 196) (:start . 193)\n  (:id . 80))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 204)\n  (:start . 197) (:id . 81))\n ((:tag . "JJ") (:stem . "unrecognizable") (:form . "unrecognizable")\n  (:end . 219) (:start . 205) (:id . 82))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 222) (:start . 220)\n  (:id . 83))\n ((:tag . "CD") (:stem . "95") (:form . "95") (:end . 225) (:start . 223)\n  (:id . 84))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 226) (:start . 225)\n  (:id . 85))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 229) (:start . 227)\n  (:id . 86))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 236)\n  (:start . 230) (:id . 87))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 237) (:start . 236)\n  (:id . 88))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 245)\n  (:start . 238) (:id . 89))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 251) (:start . 246)\n  (:id . 90))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 253) (:start . 252)\n  (:id . 91))\n ((:tag . "NN") (:stem . "n=17/18") (:form . "n=17/18") (:end . 260)\n  (:start . 253) (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 261) (:start . 260)\n  (:id . 93))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 263) (:start . 262)\n  (:id . 94))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 267) (:start . 263)\n  (:id . 95))\n ((:tag . "NN") (:stem . "9h") (:form . "9H") (:end . 270) (:start . 268)\n  (:id . 96))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 271) (:start . 270)\n  (:id . 97))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 277)\n  (:start . 272) (:id . 98))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 284)\n  (:start . 278) (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 285) (:start . 284)\n  (:id . 100))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 287) (:start . 286)\n  (:id . 101))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 300) (:start . 287) (:id . 102))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 309)\n  (:start . 301) (:id . 103))\n ((:tag . "NNP") (:stem . "Fig") (:form . "Figs") (:end . 314) (:start . 310)\n  (:id . 104))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 317) (:start . 315)\n  (:id . 105))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 321) (:start . 318)\n  (:id . 106))\n ((:tag . "NN") (:stem . "s8") (:form . "S8") (:end . 324) (:start . 322)\n  (:id . 107))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 325) (:start . 324)\n  (:id . 108))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 326) (:start . 325)\n  (:id . 109)))@@@1@68@((:identifiers (:sid . :s8.316) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502568@unknown@formal@none@1@S@The clear separation, along the midline, between the pair of medially projected ß-lobes, which was obvious in HD-Q93 flies (Fig. 9C, white arrow) (supplementary material Figs S7 and S8) (n=14) and wild-type flies (Fig. 7J), also became less distinct and often appeared to be merged in HD-Q93; dhtt-ko flies (n=13/18) (Fig. 9H, white arrow) (supplementary material Figs S7 and S8).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . 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5502569@unknown@formal@none@1@S@In addition, the anti-FasII staining of the MBs was not as strong in HD-Q93; dhtt-ko flies as in HD-Q93 flies (Fig. 9C,H; supplementary material Figs S7 and S8).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "anti-fasii") (:form . "anti-FasII") (:end . 27)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "mb") (:form . "MBs") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 65)\n  (:start . 59) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 75)\n  (:start . 69) (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 76) (:start . 75)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 84)\n  (:start . 77) (:id . 58))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 90) (:start . 85)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 61))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 103)\n  (:start . 97) (:id . 62))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 109) (:start . 104)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 115) (:start . 111)\n  (:id . 65))\n ((:tag . "CD") (:stem . "9C,H") (:form . "9C,H") (:end . 120) (:start . 116)\n  (:id . 66))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 121) (:start . 120)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 135) (:start . 122) (:id . 68))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 144)\n  (:start . 136) (:id . 69))\n ((:tag . "NNP") (:stem . "Fig") (:form . "Figs") (:end . 149) (:start . 145)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 152) (:start . 150)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 72))\n ((:tag . "NN") (:stem . "s8") (:form . "S8") (:end . 159) (:start . 157)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s8.318) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5502571@unknown@formal@none@1@S@The γ-lobe signals were too weak to be reliably tracked in both HD-Q93 and HD-Q93; dhtt-ko flies, so only the α- and ß-lobes in each MB were measured (average MB size: HD-Q93=11,137±314 µm2, n=6; HD-Q93; dhtt-ko=10,412±212 µm2, n=7; P=0.04).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "γ-lobe") (:form . "γ-lobe") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "weak") (:form . "weak") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . 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5502572@unknown@formal@none@1@S@The average signal intensity of FasII signals in the MBs of dhtt-ko mutants was also decreased, by around 31% (Fig. 9L) (relative signal intensity of α- and ß-lobes in the MBs: HD-Q93=100±6.7 µm2; dhtt-ko mutant=69.3±4.0 µm2; P=0.0004).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "FasII") (:form . "FasII") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "mb") (:form . "MBs") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 67)\n  (:start . 60) (:id . 53))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 75)\n  (:start . 68) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "decrease") (:form . "decreased") (:end . 94)\n  (:start . 85) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 105)\n  (:start . 99) (:id . 60))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 108) (:start . 106)\n  (:id . 61))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 115) (:start . 111)\n  (:id . 64))\n ((:tag . "NN") (:stem . "9l") (:form . "9L") (:end . 118) (:start . 116)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 129)\n  (:start . 121) (:id . 68))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 136)\n  (:start . 130) (:id . 69))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 146)\n  (:start . 137) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "α-") (:form . "α-") (:end . 152) (:start . 150)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "ß-lobe") (:form . "ß-lobes") (:end . 164)\n  (:start . 157) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 167) (:start . 165)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 171) (:start . 168)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "mb") (:form . "MBs") (:end . 175) (:start . 172)\n  (:id . 77))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 176) (:start . 175)\n  (:id . 78))\n ((:tag . "NN") (:stem . "hd-q93=100±6.7") (:form . "HD-Q93=100±6.7")\n  (:end . 191) (:start . 177) (:id . 79))\n ((:tag . "NN") (:stem . "µm2") (:form . "µm2") (:end . 195) (:start . 192)\n  (:id . 80))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 196) (:start . 195)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 204)\n  (:start . 197) (:id . 82))\n ((:tag . "NN") (:stem . "mutant=69.3±4.0") (:form . "mutant=69.3±4.0")\n  (:end . 220) (:start . 205) (:id . 83))\n ((:tag . "NN") (:stem . "µm2") (:form . "µm2") (:end . 224) (:start . 221)\n  (:id . 84))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 225) (:start . 224)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "P=0.0004") (:form . "P=0.0004") (:end . 234)\n  (:start . 226) (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 235) (:start . 234)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 236) (:start . 235)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s8.321) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5502575@unknown@formal@none@1@S@Together, these results suggest that there is increased disorganization and an increase in neuronal loss in the brains of HD-Q93; dhtt-ko flies.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "disorganization") (:form . "disorganization")\n  (:end . 71) (:start . 56) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 99)\n  (:start . 91) (:id . 56))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 104) (:start . 100)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 118)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 128)\n  (:start . 122) (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 129) (:start . 128)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 137)\n  (:start . 130) (:id . 64))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 143) (:start . 138)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x8.324.1) (:span 24 31)))\n (:hscopes ((:id . :x8.324.1) (:span 24 143)))\n (:identifiers (:sid . :s8.324) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502576@unknown@formal@none@1@S@Thus, loss of endogenous dhtt renders animals more vulnerable to the toxicity associated with polyQ-expanded Htt.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 24)\n  (:start . 14) (:id . 46))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "render") (:form . "renders") (:end . 37)\n  (:start . 30) (:id . 48))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "vulnerable") (:form . "vulnerable") (:end . 61)\n  (:start . 51) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "toxicity") (:form . "toxicity") (:end . 77)\n  (:start . 69) (:id . 54))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 88)\n  (:start . 78) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "polyq-expanded") (:form . "polyQ-expanded")\n  (:end . 108) (:start . 94) (:id . 57))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 112) (:start . 109)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s8.325) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502577@unknown@formal@none@1@S@Loss of endogenous dhtt affects the pathogenesis of HD flies.@(((:tag . "NN") (:stem . "loss") (:form . "Loss") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "affect") (:form . "affects") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 48)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 60) (:start . 55)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s8.326) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502578@unknown@formal@none@1@S@(A–J) Loss of endogenous dhtt causes enhanced brain pathology in HD flies.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–J") (:form . "A–J") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NN") (:stem . "loss") (:form . "Loss") (:end . 10) (:start . 6)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 24)\n  (:start . 14) (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 29) (:start . 25)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 36)\n  (:start . 30) (:id . 49))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 45)\n  (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "pathology") (:form . "pathology") (:end . 61)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 73) (:start . 68)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.327) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502579@unknown@formal@none@1@S@Confocal images of adult brains showing the distribution of neuronal cells (anti-Elav, green), cell nuclei (DAPI, white) and MBs (anti-FasII, red) in 5-day-old HD-Q93 (D–H) and HD-Q93; dhtt-ko (I–M) brains.@(((:tag . "JJ") (:stem . "confocal") (:form . "Confocal") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 56)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "anti-elav") (:form . "anti-Elav") (:end . 85)\n  (:start . 76) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 92) (:start . 87)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 99) (:start . 95)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 106)\n  (:start . 100) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "DAPI") (:form . "DAPI") (:end . 112) (:start . 108)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 119)\n  (:start . 114) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "MB") (:form . "MBs") (:end . 128) (:start . 125)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "anti-fasii") (:form . "anti-FasII") (:end . 140)\n  (:start . 130) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 145) (:start . 142)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "5-day-old") (:form . "5-day-old") (:end . 159)\n  (:start . 150) (:id . 74))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 166)\n  (:start . 160) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 168) (:start . 167)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "D–H") (:form . "D–H") (:end . 171) (:start . 168)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 183)\n  (:start . 177) (:id . 80))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 184) (:start . 183)\n  (:id . 81))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 192)\n  (:start . 185) (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 194) (:start . 193)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "I–M") (:form . "I–M") (:end . 197) (:start . 194)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 198) (:start . 197)\n  (:id . 85))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 205)\n  (:start . 199) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s8.328) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502580@unknown@formal@none@1@S@As cells in the fly brain are mainly localized at its surface, the anterior (A,B,F,G) and posterior (D,E,I,J) halves of the brains are projected separately for better visualization of the distribution pattern.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 25) (:start . 20)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "RB") (:stem . "mainly") (:form . "mainly") (:end . 36)\n  (:start . 30) (:id . 49))\n ((:tag . "VBN") (:stem . "localize") (:form . "localized") (:end . 46)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 61)\n  (:start . 54) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 75)\n  (:start . 67) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "A,B,F,G") (:form . "A,B,F,G") (:end . 84)\n  (:start . 77) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 99)\n  (:start . 90) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "D,E,I,J") (:form . "D,E,I,J") (:end . 108)\n  (:start . 101) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 109) (:start . 108)\n  (:id . 64))\n ((:tag . "VBZ") (:stem . "halve") (:form . "halves") (:end . 116)\n  (:start . 110) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 130)\n  (:start . 124) (:id . 68))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 134) (:start . 131)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "project") (:form . "projected") (:end . 144)\n  (:start . 135) (:id . 70))\n ((:tag . "RB") (:stem . "separately") (:form . "separately") (:end . 155)\n  (:start . 145) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 159) (:start . 156)\n  (:id . 72))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 166)\n  (:start . 160) (:id . 73))\n ((:tag . "NN") (:stem . "visualization") (:form . "visualization")\n  (:end . 180) (:start . 167) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 183) (:start . 181)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 187) (:start . 184)\n  (:id . 76))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 200)\n  (:start . 188) (:id . 77))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 208)\n  (:start . 201) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s8.329) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502581@unknown@formal@none@1@S@Note the enlarged regions devoid of neuronal cells in the HD-Q93; dhtt-ko brain (F) (the areas within the white lines) compared with the corresponding regions in the HD-Q93 brain (A).@(((:tag . "VB") (:stem . "note") (:form . "Note") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "enlarged") (:form . "enlarged") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "devoid") (:form . "devoid") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 64)\n  (:start . 58) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 73)\n  (:start . 66) (:id . 54))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 79) (:start . 74)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 94) (:start . 89)\n  (:id . 61))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 101)\n  (:start . 95) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 111)\n  (:start . 106) (:id . 64))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 117)\n  (:start . 112) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 127)\n  (:start . 119) (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 132) (:start . 128)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 150)\n  (:start . 137) (:id . 70))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 158)\n  (:start . 151) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 161) (:start . 159)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 73))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 172)\n  (:start . 166) (:id . 74))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 178)\n  (:start . 173) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 180) (:start . 179)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 181) (:start . 180)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 182) (:start . 181)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s8.330) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502582@unknown@formal@none@1@S@The arrows in (I) indicate the areas lacking neuronal cells at the posterior of the brain.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "i") (:form . "I") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 26)\n  (:start . 18) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 36) (:start . 31)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "lack") (:form . "lacking") (:end . 44)\n  (:start . 37) (:id . 51))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 53)\n  (:start . 45) (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 59) (:start . 54)\n  (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "posterior") (:form . "posterior") (:end . 76)\n  (:start . 67) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 58))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 89) (:start . 84)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s8.331) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502583@unknown@formal@none@1@S@(C,H) The MB in the HD-Q93; dhtt-ko brain (H) is also less well organized and shows weaker signal intensity than in the HD-Q93 brain (C).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C,H") (:form . "C,H") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 9) (:start . 6)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mb") (:form . "MB") (:end . 12) (:start . 10)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 48))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 26)\n  (:start . 20) (:id . 49))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 27) (:start . 26)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 35)\n  (:start . 28) (:id . 51))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 41) (:start . 36)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 44) (:start . 43)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 48) (:start . 46)\n  (:id . 56))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 53) (:start . 49)\n  (:id . 57))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 58) (:start . 54)\n  (:id . 58))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 63) (:start . 59)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "organize") (:form . "organized") (:end . 73)\n  (:start . 64) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 83) (:start . 78)\n  (:id . 62))\n ((:tag . "JJR") (:stem . "weak") (:form . "weaker") (:end . 90) (:start . 84)\n  (:id . 63))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 97)\n  (:start . 91) (:id . 64))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 107)\n  (:start . 98) (:id . 65))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 112) (:start . 108)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 68))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 126)\n  (:start . 120) (:id . 69))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 132)\n  (:start . 127) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 135) (:start . 134)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.332) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502584@unknown@formal@none@1@S@The white arrowheads highlight the clear separation, along the midline, between the two medial ß-lobes in the HD-Q93; dhtt-ko brain (C), this is less distinct and appears merged in the HD-Q93 brain (H).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "arrowhead") (:form . "arrowheads") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "highlight") (:form . "highlight") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 40) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "separation") (:form . "separation") (:end . 51)\n  (:start . 41) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 58) (:start . 53)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 70)\n  (:start . 63) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 94)\n  (:start . 88) (:id . 57))\n ((:tag . "NNS") (:stem . "ß-lobe") (:form . "ß-lobes") (:end . 102)\n  (:start . 95) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 116)\n  (:start . 110) (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 117) (:start . 116)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 125)\n  (:start . 118) (:id . 63))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 131)\n  (:start . 126) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 134) (:start . 133)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 135) (:start . 134)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 68))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 141) (:start . 137)\n  (:id . 69))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 144) (:start . 142)\n  (:id . 70))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 149) (:start . 145)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 158)\n  (:start . 150) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 73))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 170)\n  (:start . 163) (:id . 74))\n ((:tag . "VBN") (:stem . "merge") (:form . "merged") (:end . 177)\n  (:start . 171) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 180) (:start . 178)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 184) (:start . 181)\n  (:id . 77))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 191)\n  (:start . 185) (:id . 78))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 197)\n  (:start . 192) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 199) (:start . 198)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 200) (:start . 199)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 201) (:start . 200)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x8.333.1) (:span 163 170)))\n (:hscopes ((:id . :x8.333.1) (:span 163 197)))\n (:identifiers (:sid . :s8.333) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502585@unknown@formal@none@1@S@White arrows indicate the bulged tip of the vertical α-lobes, which become less distinct in HD-Q93; dhtt-ko brains (H).@(((:tag . "JJ") (:stem . "white") (:form . "White") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "bulge") (:form . "bulged") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "tip") (:form . "tip") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "vertical") (:form . "vertical") (:end . 52)\n  (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "α-lobe") (:form . "α-lobes") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "become") (:form . "become") (:end . 74)\n  (:start . 68) (:id . 54))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 88)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 98)\n  (:start . 92) (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 107)\n  (:start . 100) (:id . 60))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 114)\n  (:start . 108) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s8.334) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502586@unknown@formal@none@1@S@WT=w1118 wild-type control.@(((:tag . "CD") (:stem . "wt=w1118") (:form . "WT=w1118") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 26)\n  (:start . 19) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 27) (:start . 26)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s8.335) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502587@unknown@formal@none@1@S@Bars, 50 µm (all panels).@(((:tag . "NNS") (:stem . "bar") (:form . "Bars") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 11) (:start . 9)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 16) (:start . 13)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "panel") (:form . "panels") (:end . 23)\n  (:start . 17) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 24) (:start . 23)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 25) (:start . 24)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s8.336) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502588@unknown@formal@none@1@S@(K,L) Quantification of the average MB size (K) and relative signal intensity (L) of MBs in HD-Q93 (blue) and HD-Q93; dhtt-ko mutants (red), as revealed by anti-FasII staining.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "K,L") (:form . "K,L") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Quantification") (:form . "Quantification")\n  (:end . 20) (:start . 6) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 43) (:start . 39)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "K") (:form . "K") (:end . 46) (:start . 45)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 60)\n  (:start . 52) (:id . 55))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 67)\n  (:start . 61) (:id . 56))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 77)\n  (:start . 68) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "L") (:form . "L") (:end . 80) (:start . 79)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "mb") (:form . "MBs") (:end . 88) (:start . 85)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 98)\n  (:start . 92) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 104) (:start . 100)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 116)\n  (:start . 110) (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 117) (:start . 116)\n  (:id . 70))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 125)\n  (:start . 118) (:id . 71))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 133)\n  (:start . 126) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 138) (:start . 135)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 76))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 143) (:start . 141)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "reveal") (:form . "revealed") (:end . 152)\n  (:start . 144) (:id . 78))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 155) (:start . 153)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "anti-fasii") (:form . "anti-FasII") (:end . 166)\n  (:start . 156) (:id . 80))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 175)\n  (:start . 167) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s8.337) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502589@unknown@formal@none@1@S@In both HD-Q93 and HD-Q93; dhtt-ko flies, the FasII signals for the γ-lobe in MBs were too weak to be tracked reliably (see supplementary material Figs S7 and S8); therefore, only the α- and ß-lobes in each MB were measured.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 14)\n  (:start . 8) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 34)\n  (:start . 27) (:id . 48))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "FasII") (:form . "FasII") (:end . 51) (:start . 46)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 59)\n  (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "γ-lobe") (:form . "γ-lobe") (:end . 74)\n  (:start . 68) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "MB") (:form . "MBs") (:end . 81) (:start . 78)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 86) (:start . 82)\n  (:id . 59))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 90) (:start . 87)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "weak") (:form . "weak") (:end . 95) (:start . 91)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n  (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 101) (:start . 99)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "track") (:form . "tracked") (:end . 109)\n  (:start . 102) (:id . 64))\n ((:tag . "RB") (:stem . "reliably") (:form . "reliably") (:end . 118)\n  (:start . 110) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 120) (:start . 119)\n  (:id . 66))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 123) (:start . 120)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 137) (:start . 124) (:id . 68))\n ((:tag . "NN") (:stem . "material") (:form . "material") (:end . 146)\n  (:start . 138) (:id . 69))\n ((:tag . "NNP") (:stem . "Fig") (:form . "Figs") (:end . 151) (:start . 147)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 154) (:start . 152)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 158) (:start . 155)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "S8") (:form . "S8") (:end . 161) (:start . 159)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 74))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 163) (:start . 162)\n  (:id . 75))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 173)\n  (:start . 164) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 77))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 179) (:start . 175)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n  (:id . 79))\n ((:tag . "NNPS") (:stem . "α-") (:form . "α-") (:end . 186) (:start . 184)\n  (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 190) (:start . 187)\n  (:id . 81))\n ((:tag . "NNPS") (:stem . "ß-lobe") (:form . "ß-lobes") (:end . 198)\n  (:start . 191) (:id . 82))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 201) (:start . 199)\n  (:id . 83))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 206) (:start . 202)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 209) (:start . 207)\n  (:id . 85))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 214) (:start . 210)\n  (:id . 86))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 223)\n  (:start . 215) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s8.338) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502590@unknown@formal@none@1@S@(M,N) Quantification of the average brain size (M) and the total size of the regions devoid of neuronal cells in the anterior brain (N), as revealed by using neuronal-specific staining with an antibody against Elav.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "M,N") (:form . "M,N") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Quantification") (:form . "Quantification")\n  (:end . 20) (:start . 6) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 64) (:start . 59)\n  (:id . 56))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 69) (:start . 65)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 84)\n  (:start . 77) (:id . 60))\n ((:tag . "JJ") (:stem . "devoid") (:form . "devoid") (:end . 91)\n  (:start . 85) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 103)\n  (:start . 95) (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 109)\n  (:start . 104) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 125)\n  (:start . 117) (:id . 67))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 131)\n  (:start . 126) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 134) (:start . 133)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 135) (:start . 134)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 72))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 139) (:start . 137)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "reveal") (:form . "revealed") (:end . 148)\n  (:start . 140) (:id . 74))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 151) (:start . 149)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 157) (:start . 152)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "neuronal-specific") (:form . "neuronal-specific")\n  (:end . 175) (:start . 158) (:id . 77))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 184)\n  (:start . 176) (:id . 78))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 189) (:start . 185)\n  (:id . 79))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 192) (:start . 190)\n  (:id . 80))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 201)\n  (:start . 193) (:id . 81))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 209)\n  (:start . 202) (:id . 82))\n ((:tag . "NNP") (:stem . "Elav") (:form . "Elav") (:end . 214) (:start . 210)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s8.339) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502591@unknown@formal@none@1@S@The data in (K–N) are presented as the means±s.e.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "K–N") (:form . "K–N") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 31)\n  (:start . 22) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 34) (:start . 32)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 51))\n ((:tag . "NN") (:stem . "means±s.e") (:form . "means±s.e") (:end . 48)\n  (:start . 39) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s8.340) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502592@unknown@formal@none@1@S@DISCUSSION@(((:tag . "NN") (:stem . "discussion") (:form . "DISCUSSION") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s8.341) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5502593@unknown@formal@none@1@S@Htt has been characterized extensively in mammalian cell culture and in mouse systems (Cattaneo et al., 2001; Harjes and Wanker, 2003).@(((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n  (:end . 26) (:start . 13) (:id . 45))\n ((:tag . "RB") (:stem . "extensively") (:form . "extensively") (:end . 38)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 51)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 56) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 64)\n  (:start . 57) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 77) (:start . 72)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 85)\n  (:start . 78) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Cattaneo") (:form . "Cattaneo") (:end . 95)\n  (:start . 87) (:id . 56))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 98) (:start . 96)\n  (:id . 57))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 108) (:start . 104)\n  (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Harjes") (:form . "Harjes") (:end . 116)\n  (:start . 110) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Wanker") (:form . "Wanker") (:end . 127)\n  (:start . 121) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 65))\n ((:tag . "CD") (:stem . "2003") (:form . "2003") (:end . 133) (:start . 129)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.342) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502594@unknown@formal@none@1@S@However, only a few functional studies have been performed on its homologs in other model organisms.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 30)\n  (:start . 20) (:id . 47))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 74)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 83) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 89) (:start . 84)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 99)\n  (:start . 90) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s8.343) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502595@unknown@formal@none@1@S@By deleting the dhtt gene, we demonstrate that Htt is not required for normal development of Drosophila, but instead has an essential role for the long-term mobility and survival of adult animals.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "delete") (:form . "deleting") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 41)\n  (:start . 30) (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 66)\n  (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 77)\n  (:start . 71) (:id . 56))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 89)\n  (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 103)\n  (:start . 93) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "RB") (:stem . "instead") (:form . "instead") (:end . 116)\n  (:start . 109) (:id . 62))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 120) (:start . 117)\n  (:id . 63))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 133)\n  (:start . 124) (:id . 65))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 138) (:start . 134)\n  (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 142) (:start . 139)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "long-term") (:form . "long-term") (:end . 156)\n  (:start . 147) (:id . 69))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 165)\n  (:start . 157) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 169) (:start . 166)\n  (:id . 71))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 178)\n  (:start . 170) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 181) (:start . 179)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 187)\n  (:start . 182) (:id . 74))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 195)\n  (:start . 188) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.344) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502596@unknown@formal@none@1@S@Subsequent analyses revealed that loss of dhtt mildly affects the integrity of adult brains.@(((:tag . "JJ") (:stem . "subsequent") (:form . "Subsequent") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 28)\n  (:start . 20) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 45))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "RB") (:stem . "mildly") (:form . "mildly") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "VBZ") (:stem . "affect") (:form . "affects") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "integrity") (:form . "integrity") (:end . 75)\n  (:start . 66) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 84) (:start . 79)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 91)\n  (:start . 85) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.345) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502597@unknown@formal@none@1@S@Further, in the absence of endogenous dhtt, the neurodegenerative phenotypes associated with a Drosophila model of polyQ toxicity were enhanced significantly.@(((:tag . "RB") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 37)\n  (:start . 27) (:id . 48))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "neurodegenerative") (:form . "neurodegenerative")\n  (:end . 65) (:start . 48) (:id . 52))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 76)\n  (:start . 66) (:id . 53))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 87)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 92) (:start . 88)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 56))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 105)\n  (:start . 95) (:id . 57))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 111)\n  (:start . 106) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 59))\n ((:tag . "NN") (:stem . "polyq") (:form . "polyQ") (:end . 120)\n  (:start . 115) (:id . 60))\n ((:tag . "NN") (:stem . "toxicity") (:form . "toxicity") (:end . 129)\n  (:start . 121) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 134) (:start . 130)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 143)\n  (:start . 135) (:id . 63))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 157) (:start . 144) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s8.346) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502598@unknown@formal@none@1@S@The role of Htt homologs in animal development@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "animal") (:form . "animal") (:end . 34)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 46)\n  (:start . 35) (:id . 49)))@@@1@8@((:identifiers (:sid . :s8.347) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502599@unknown@formal@none@1@S@Earlier studies showed that mice lacking Htt die during early embryogenesis (Duyao et al., 1995; Nasir et al., 1995; Zeitlin et al., 1995).@(((:tag . "JJR") (:stem . "early") (:form . "Earlier") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 22) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "lack") (:form . "lacking") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "die") (:form . "die") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 75) (:start . 62) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Duyao") (:form . "Duyao") (:end . 82) (:start . 77)\n  (:id . 54))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Nasir") (:form . "Nasir") (:end . 102)\n  (:start . 97) (:id . 60))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 63))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 115) (:start . 111)\n  (:id . 64))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Zeitlin") (:form . "Zeitlin") (:end . 124)\n  (:start . 117) (:id . 66))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 127) (:start . 125)\n  (:id . 67))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 131) (:start . 128)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 69))\n ((:tag . "CD") (:stem . "1995") (:form . "1995") (:end . 137) (:start . 133)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s8.348) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502600@unknown@formal@none@1@S@It is surprising to find that dhtt is dispensable during Drosophila development.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "surprising") (:form . "surprising") (:end . 16)\n  (:start . 6) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "VB") (:stem . "find") (:form . "find") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dispensable") (:form . "dispensable") (:end . 49)\n  (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 56)\n  (:start . 50) (:id . 51))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 79)\n  (:start . 68) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s8.349) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502601@unknown@formal@none@1@S@As no other Htt homolog exists in the fly genome (Li et al., 1999), such a mild phenotype is unlikely to be caused by a functional redundancy resulting from another Htt-like gene in Drosophila.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "VBZ") (:stem . "exist") (:form . "exists") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 48)\n  (:start . 42) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Li") (:form . "Li") (:end . 52) (:start . 50)\n  (:id . 53))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 55) (:start . 53)\n  (:id . 54))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 59) (:start . 56)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 65) (:start . 61)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 59))\n ((:tag . "PDT") (:stem . "such") (:form . "such") (:end . 72) (:start . 68)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 74) (:start . 73)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "mild") (:form . "mild") (:end . 79) (:start . 75)\n  (:id . 62))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 89)\n  (:start . 80) (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 92) (:start . 90)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 101)\n  (:start . 93) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n  (:id . 66))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 107) (:start . 105)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 114)\n  (:start . 108) (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 117) (:start . 115)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 119) (:start . 118)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 130)\n  (:start . 120) (:id . 71))\n ((:tag . "NN") (:stem . "redundancy") (:form . "redundancy") (:end . 141)\n  (:start . 131) (:id . 72))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 151)\n  (:start . 142) (:id . 73))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 156) (:start . 152)\n  (:id . 74))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 164)\n  (:start . 157) (:id . 75))\n ((:tag . "JJ") (:stem . "htt-like") (:form . "Htt-like") (:end . 173)\n  (:start . 165) (:id . 76))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 178) (:start . 174)\n  (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 181) (:start . 179)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 192)\n  (:start . 182) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x8.350.1) (:span 93 101)))\n (:hscopes ((:id . :x8.350.1) (:span 68 192)))\n (:identifiers (:sid . :s8.350) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502602@unknown@formal@none@1@S@Considering the evolutionary distance between Drosophila and mammals, such an observation might indicate that the Drosophila and mammalian Htt proteins, with their relatively restricted sequence homology, are not functionally conserved.@(((:tag . "VBG") (:stem . "consider") (:form . "Considering") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 28)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 37)\n  (:start . 29) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 45)\n  (:start . 38) (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 56)\n  (:start . 46) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mammal") (:form . "mammals") (:end . 68)\n  (:start . 61) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 50))\n ((:tag . "PDT") (:stem . "such") (:form . "such") (:end . 74) (:start . 70)\n  (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 77) (:start . 75)\n  (:id . 52))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 89)\n  (:start . 78) (:id . 53))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 95) (:start . 90)\n  (:id . 54))\n ((:tag . "VB") (:stem . "indicate") (:form . "indicate") (:end . 104)\n  (:start . 96) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 109) (:start . 105)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 124)\n  (:start . 114) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 138)\n  (:start . 129) (:id . 60))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 142) (:start . 139)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 151)\n  (:start . 143) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 157) (:start . 153)\n  (:id . 64))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 163)\n  (:start . 158) (:id . 65))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 174)\n  (:start . 164) (:id . 66))\n ((:tag . "JJ") (:stem . "restricted") (:form . "restricted") (:end . 185)\n  (:start . 175) (:id . 67))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 194)\n  (:start . 186) (:id . 68))\n ((:tag . "NN") (:stem . "homology") (:form . "homology") (:end . 203)\n  (:start . 195) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 204) (:start . 203)\n  (:id . 70))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 208) (:start . 205)\n  (:id . 71))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 212) (:start . 209)\n  (:id . 72))\n ((:tag . "RB") (:stem . "functionally") (:form . "functionally") (:end . 225)\n  (:start . 213) (:id . 73))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 235)\n  (:start . 226) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 236) (:start . 235)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x8.351.1) (:span 96 109)) ((:id . :x8.351.2) (:span 90 95)))\n (:hscopes ((:id . :x8.351.1) (:span 96 235))\n  ((:id . :x8.351.2) (:span 90 235)))\n (:identifiers (:sid . :s8.351) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502603@unknown@formal@none@1@S@However, this phenotypic discrepancy might also reflect intrinsic differences during mouse and fly embryogenesis.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "phenotypic") (:form . "phenotypic") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "discrepancy") (:form . "discrepancy") (:end . 36)\n  (:start . 25) (:id . 46))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 42) (:start . 37)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "VB") (:stem . "reflect") (:form . "reflect") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "JJ") (:stem . "intrinsic") (:form . "intrinsic") (:end . 65)\n  (:start . 56) (:id . 50))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 77)\n  (:start . 66) (:id . 51))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 84)\n  (:start . 78) (:id . 52))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 90) (:start . 85)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 54))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 98) (:start . 95)\n  (:id . 55))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 112) (:start . 99) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x8.352.1) (:span 37 42)))\n (:hscopes ((:id . :x8.352.1) (:span 37 112)))\n (:identifiers (:sid . :s8.352) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502604@unknown@formal@none@1@S@In a chimeric analysis of Htt mutant mice, Dragatsis et al. showed that the early embryonic lethality of Htt-null mice was primarily the result of a crucial role of Hdh in extraembryonic membranes (Dragatsis et al., 1998).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "chimeric") (:form . "chimeric") (:end . 13)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Dragatsis") (:form . "Dragatsis") (:end . 52)\n  (:start . 43) (:id . 51))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 66) (:start . 60)\n  (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 71) (:start . 67)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 81) (:start . 76)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 91)\n  (:start . 82) (:id . 58))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 101)\n  (:start . 92) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "htt-null") (:form . "Htt-null") (:end . 113)\n  (:start . 105) (:id . 61))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 118)\n  (:start . 114) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 122) (:start . 119)\n  (:id . 63))\n ((:tag . "RB") (:stem . "primarily") (:form . "primarily") (:end . 132)\n  (:start . 123) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 65))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 143)\n  (:start . 137) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 146) (:start . 144)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 148) (:start . 147)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "crucial") (:form . "crucial") (:end . 156)\n  (:start . 149) (:id . 69))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 161) (:start . 157)\n  (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 164) (:start . 162)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Hdh") (:form . "Hdh") (:end . 168) (:start . 165)\n  (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 171) (:start . 169)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "extraembryonic") (:form . "extraembryonic")\n  (:end . 186) (:start . 172) (:id . 74))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 196)\n  (:start . 187) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 198) (:start . 197)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Dragatsis") (:form . "Dragatsis") (:end . 207)\n  (:start . 198) (:id . 77))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 210) (:start . 208)\n  (:id . 78))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 214) (:start . 211)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 215) (:start . 214)\n  (:id . 80))\n ((:tag . "CD") (:stem . "1998") (:form . "1998") (:end . 220) (:start . 216)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.353) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502605@unknown@formal@none@1@S@It is probable that Drosophila does not require equivalent tissues, such as extraembryonic membranes, to support its early development and that its embryogenesis can proceed normally in the absence of dhtt.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "probable") (:form . "probable") (:end . 14)\n  (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 30)\n  (:start . 20) (:id . 46))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "VB") (:stem . "require") (:form . "require") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "JJ") (:stem . "equivalent") (:form . "equivalent") (:end . 58)\n  (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "extraembryonic") (:form . "extraembryonic")\n  (:end . 90) (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 100)\n  (:start . 91) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "VB") (:stem . "support") (:form . "support") (:end . 112)\n  (:start . 105) (:id . 59))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 122)\n  (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 134)\n  (:start . 123) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n  (:id . 63))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 143) (:start . 139)\n  (:id . 64))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 147) (:start . 144)\n  (:id . 65))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 161) (:start . 148) (:id . 66))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 165) (:start . 162)\n  (:id . 67))\n ((:tag . "VB") (:stem . "proceed") (:form . "proceed") (:end . 173)\n  (:start . 166) (:id . 68))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 182)\n  (:start . 174) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 185) (:start . 183)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 189) (:start . 186)\n  (:id . 71))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 197)\n  (:start . 190) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 200) (:start . 198)\n  (:id . 73))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 205) (:start . 201)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x8.354.1) (:span 6 14)))\n (:hscopes ((:id . :x8.354.1) (:span 6 205)))\n (:identifiers (:sid . :s8.354) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502606@unknown@formal@none@1@S@Although an Htt homolog is found in Drosophila and vertebrates, no Htt homolog has been found in yeast or C. elegans(Li et al., 1999).@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 46)\n  (:start . 36) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 62)\n  (:start . 51) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 78)\n  (:start . 71) (:id . 55))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 87) (:start . 83)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 93) (:start . 88)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 102) (:start . 97)\n  (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 108) (:start . 106)\n  (:id . 62))\n ((:tag . "FW") (:stem . "elegans(Li") (:form . "elegans(Li") (:end . 119)\n  (:start . 109) (:id . 63))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 122) (:start . 120)\n  (:id . 64))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 126) (:start . 123)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 66))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 132) (:start . 128)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s8.355) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502607@unknown@formal@none@1@S@The absence of an Htt homolog in C. elegans suggests that Htt does not have a function that is essential for the development of invertebrates in general, which is in agreement with our observation that dhtt is dispensable for normal development of Drosophila.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "homolog") (:form . "homolog") (:end . 29)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 43)\n  (:start . 36) (:id . 50))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 52)\n  (:start . 44) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n  (:id . 57))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 86)\n  (:start . 78) (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 91) (:start . 87)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 94) (:start . 92)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 104)\n  (:start . 95) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 108) (:start . 105)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 63))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 124)\n  (:start . 113) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "invertebrate") (:form . "invertebrates")\n  (:end . 141) (:start . 128) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 152)\n  (:start . 145) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 69))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 159)\n  (:start . 154) (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 162) (:start . 160)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 165) (:start . 163)\n  (:id . 72))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 175)\n  (:start . 166) (:id . 73))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 180) (:start . 176)\n  (:id . 74))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 184) (:start . 181)\n  (:id . 75))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 196)\n  (:start . 185) (:id . 76))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 201) (:start . 197)\n  (:id . 77))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 206) (:start . 202)\n  (:id . 78))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 209) (:start . 207)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "dispensable") (:form . "dispensable") (:end . 221)\n  (:start . 210) (:id . 80))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 225) (:start . 222)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 232)\n  (:start . 226) (:id . 82))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 244)\n  (:start . 233) (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 247) (:start . 245)\n  (:id . 84))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 258)\n  (:start . 248) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 259) (:start . 258)\n  (:id . 86)))@@@1@45@((:hcues ((:id . :x8.356.1) (:span 44 52)))\n (:hscopes ((:id . :x8.356.1) (:span 44 258)))\n (:identifiers (:sid . :s8.356) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502608@unknown@formal@none@1@S@Interestingly, a phylogenetic comparison of Htt proteins from different species postulates that Htt in the protostome (which includes Drosophilids) might be dispensable because, when compared with the deuterostome branch, evolution of the Htt genes along the protostome branch is more heterogeneous (Tartari et al., 2008).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 29)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Htt") (:form . 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"(") (:end . 300) (:start . 299)\n  (:id . 88))\n ((:tag . "NNP") (:stem . "Tartari") (:form . "Tartari") (:end . 307)\n  (:start . 300) (:id . 89))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 310) (:start . 308)\n  (:id . 90))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 314) (:start . 311)\n  (:id . 91))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 315) (:start . 314)\n  (:id . 92))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 320) (:start . 316)\n  (:id . 93))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 321) (:start . 320)\n  (:id . 94))\n ((:tag . ".") (:stem . ".") (:form . ".") 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5502609@unknown@formal@none@1@S@Further studies will be required to determine whether the mammalian Htt gene can rescue Drosophila dhtt-null phenotypes.@(((:tag . "JJR") (:stem . "far") (:form . "Further") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 45)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "mammalian") (:form . "mammalian") (:end . 67)\n  (:start . 58) (:id . 51))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "VB") (:stem . "rescue") (:form . "rescue") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 98)\n  (:start . 88) (:id . 56))\n ((:tag . "JJ") (:stem . "dhtt-null") (:form . "dhtt-null") (:end . 108)\n  (:start . 99) (:id . 57))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 119)\n  (:start . 109) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x8.358.1) (:span 77 80)) ((:id . :x8.358.2) (:span 46 53)))\n (:hscopes ((:id . :x8.358.1) (:span 77 119))\n  ((:id . :x8.358.2) (:span 46 119)))\n (:identifiers (:sid . :s8.358) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502610@unknown@formal@none@1@S@Analyses of dhtt-ko mutants suggest that loss of dhtt does not affect synapse formation, neurotransmission or axonal transport (Figs 3–6), which is in agreement with the absence of an Htt homolog in the worm, in which the essential components of these cellular processes are conserved.@(((:tag . "NNS") (:stem . "analysis") (:form . "Analyses") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . 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5502611@unknown@formal@none@1@S@It is possible that Htt still regulates these cellular processes, but with a minor role.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 14)\n  (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "regulate") (:form . "regulates") (:end . 39)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "minor") (:form . "minor") (:end . 82) (:start . 77)\n  (:id . 56))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 87) (:start . 83)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x8.360.1) (:span 6 14)))\n (:hscopes ((:id . :x8.360.1) (:span 6 87)))\n (:identifiers (:sid . :s8.360) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502612@unknown@formal@none@1@S@Extrapolating, there is a possibility that the function of Htt is associated with a novel cellular process and/or animal function that has been acquired during evolution.@(((:tag . "VBG") (:stem . "extrapolate") (:form . "Extrapolating") (:end . 13)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 76)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 89) (:start . 84)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 98)\n  (:start . 90) (:id . 58))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 106)\n  (:start . 99) (:id . 59))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 113)\n  (:start . 107) (:id . 60))\n ((:tag . "NN") (:stem . "animal") (:form . "animal") (:end . 120)\n  (:start . 114) (:id . 61))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 129)\n  (:start . 121) (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 134) (:start . 130)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 138) (:start . 135)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 143) (:start . 139)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "acquire") (:form . "acquired") (:end . 152)\n  (:start . 144) (:id . 66))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 159)\n  (:start . 153) (:id . 67))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 169)\n  (:start . 160) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x8.361.1) (:span 26 37)))\n (:hscopes ((:id . :x8.361.1) (:span 26 169)))\n (:identifiers (:sid . :s8.361) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502613@unknown@formal@none@1@S@For example, although dhtt is dispensable for Drosophila development, it is important for maintaining the long-term mobility and viability of adult animals (Figs 5 and 6).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dispensable") (:form . "dispensable") (:end . 41)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 68)\n  (:start . 57) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 85)\n  (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "maintain") (:form . "maintaining") (:end . 101)\n  (:start . 90) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "long-term") (:form . "long-term") (:end . 115)\n  (:start . 106) (:id . 59))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 124)\n  (:start . 116) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 61))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 138)\n  (:start . 129) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 141) (:start . 139)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 147)\n  (:start . 142) (:id . 64))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 155)\n  (:start . 148) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Fig") (:form . "Figs") (:end . 161) (:start . 157)\n  (:id . 67))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 163) (:start . 162)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 69))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 169) (:start . 168)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s8.362) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502614@unknown@formal@none@1@S@Compared to the worm, Drosophila has a relatively long life span, a more complex nervous system and a more active life cycle, raising an intriguing possibility that the function of Htt might be directly related to these higher functions in adult animals.@(((:tag . "VBN") (:stem . "compare") (:form . "Compared") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "worm") (:form . "worm") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 32)\n  (:start . 22) (:id . 47))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 49)\n  (:start . 39) (:id . 50))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "span") (:form . "span") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 72) (:start . 68)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 80)\n  (:start . 73) (:id . 57))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 88)\n  (:start . 81) (:id . 58))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 95)\n  (:start . 89) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 101) (:start . 100)\n  (:id . 61))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 106) (:start . 102)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 113)\n  (:start . 107) (:id . 63))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 118) (:start . 114)\n  (:id . 64))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 124)\n  (:start . 119) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "raise") (:form . "raising") (:end . 133)\n  (:start . 126) (:id . 67))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 136) (:start . 134)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "intriguing") (:form . "intriguing") (:end . 147)\n  (:start . 137) (:id . 69))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 159)\n  (:start . 148) (:id . 70))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 164) (:start . 160)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 72))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 177)\n  (:start . 169) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 180) (:start . 178)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 184) (:start . 181)\n  (:id . 75))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 190)\n  (:start . 185) (:id . 76))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 193) (:start . 191)\n  (:id . 77))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 202)\n  (:start . 194) (:id . 78))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 210)\n  (:start . 203) (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 213) (:start . 211)\n  (:id . 80))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 219)\n  (:start . 214) (:id . 81))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 226)\n  (:start . 220) (:id . 82))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 236)\n  (:start . 227) (:id . 83))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 239) (:start . 237)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 245)\n  (:start . 240) (:id . 85))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 253)\n  (:start . 246) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 254) (:start . 253)\n  (:id . 87)))@@@1@46@((:hcues ((:id . :x8.363.1) (:span 185 190))\n  ((:id . :x8.363.2) (:span 126 159)))\n (:hscopes ((:id . :x8.363.1) (:span 165 253))\n  ((:id . :x8.363.2) (:span 126 253)))\n (:identifiers (:sid . :s8.363) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502615@unknown@formal@none@1@S@The role of Htt in adult brain@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 24) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 30) (:start . 25)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s8.364) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502616@unknown@formal@none@1@S@Although dhtt is dispensable for normal Drosophila development, dhtt mutants show significantly reduced mobility and viability as they age, indicating an important role of dhtt in maintaining the long-term functioning and survival of adult animals (Fig. 5).@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "dispensable") (:form . "dispensable") (:end . 28)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 50)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 62)\n  (:start . 51) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 76)\n  (:start . 69) (:id . 52))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 81) (:start . 77)\n  (:id . 53))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 95) (:start . 82) (:id . 54))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 103)\n  (:start . 96) (:id . 55))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 112)\n  (:start . 104) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 57))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 126)\n  (:start . 117) (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 129) (:start . 127)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 134) (:start . 130)\n  (:id . 60))\n ((:tag . "NN") (:stem . "age") (:form . "age") (:end . 138) (:start . 135)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 150)\n  (:start . 140) (:id . 63))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 153) (:start . 151)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 163)\n  (:start . 154) (:id . 65))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 168) (:start . 164)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 67))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 176) (:start . 172)\n  (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 179) (:start . 177)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "maintain") (:form . "maintaining") (:end . 191)\n  (:start . 180) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 195) (:start . 192)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "long-term") (:form . "long-term") (:end . 205)\n  (:start . 196) (:id . 72))\n ((:tag . "NN") (:stem . "functioning") (:form . "functioning") (:end . 217)\n  (:start . 206) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 221) (:start . 218)\n  (:id . 74))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 230)\n  (:start . 222) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 233) (:start . 231)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 239)\n  (:start . 234) (:id . 77))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 247)\n  (:start . 240) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 249) (:start . 248)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 253) (:start . 249)\n  (:id . 80))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 255) (:start . 254)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 256) (:start . 255)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x8.365.1) (:span 140 150)))\n (:hscopes ((:id . :x8.365.1) (:span 140 247)))\n (:identifiers (:sid . :s8.365) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502617@unknown@formal@none@1@S@Analysis of dhtt mutants revealed a mild abnormality in MB structure and a reduction in the complexity of axonal termini in the brain (Fig. 7).@(((:tag . "NNP") (:stem . "Analysis") (:form . "Analysis") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "mild") (:form . "mild") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "abnormality") (:form . "abnormality") (:end . 52)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 84)\n  (:start . 75) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 102)\n  (:start . 92) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 112)\n  (:start . 106) (:id . 60))\n ((:tag . "NNS") (:stem . "terminus") (:form . "termini") (:end . 120)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 133)\n  (:start . 128) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 139) (:start . 135)\n  (:id . 66))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 141) (:start . 140)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s8.366) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502618@unknown@formal@none@1@S@Similarly, Htt mutant mice with a reduced level of Htt expression display severe brain abnormalities, even though non-neuronal tissue forms normally (White et al., 1997).@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "mouse") (:form . "mice") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 65)\n  (:start . 55) (:id . 53))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 73)\n  (:start . 66) (:id . 54))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 80)\n  (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 86) (:start . 81)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "abnormality") (:form . "abnormalities")\n  (:end . 100) (:start . 87) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 113)\n  (:start . 107) (:id . 60))\n ((:tag . "JJ") (:stem . "non-neuronal") (:form . "non-neuronal") (:end . 126)\n  (:start . 114) (:id . 61))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 133)\n  (:start . 127) (:id . 62))\n ((:tag . "NNS") (:stem . "form") (:form . "forms") (:end . 139)\n  (:start . 134) (:id . 63))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 148)\n  (:start . 140) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "White") (:form . "White") (:end . 155)\n  (:start . 150) (:id . 66))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 158) (:start . 156)\n  (:id . 67))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 162) (:start . 159)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 69))\n ((:tag . "CD") (:stem . "1997") (:form . "1997") (:end . 168) (:start . 164)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s8.367) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502619@unknown@formal@none@1@S@Targeted inactivation of Hdh in the mouse forebrain also causes a progressive neurodegeneration phenotype, suggesting that Hdh is required in the development and survival of neuronal cells (Dragatsis et al., 2000).@(((:tag . "VBN") (:stem . "target") (:form . "Targeted") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "inactivation") (:form . "inactivation") (:end . 21)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Hdh") (:form . "Hdh") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "forebrain") (:form . "forebrain") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 63)\n  (:start . 57) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "progressive") (:form . "progressive") (:end . 77)\n  (:start . 66) (:id . 53))\n ((:tag . "NN") (:stem . "neurodegeneration") (:form . "neurodegeneration")\n  (:end . 95) (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 105)\n  (:start . 96) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 117)\n  (:start . 107) (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 122) (:start . 118)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Hdh") (:form . "Hdh") (:end . 126) (:start . 123)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 129) (:start . 127)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 138)\n  (:start . 130) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 63))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 157)\n  (:start . 146) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 65))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 170)\n  (:start . 162) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 182)\n  (:start . 174) (:id . 68))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 188)\n  (:start . 183) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 190) (:start . 189)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Dragatsis") (:form . "Dragatsis") (:end . 199)\n  (:start . 190) (:id . 71))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 202) (:start . 200)\n  (:id . 72))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 206) (:start . 203)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 207) (:start . 206)\n  (:id . 74))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 212) (:start . 208)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x8.368.1) (:span 107 117)))\n (:hscopes ((:id . :x8.368.1) (:span 107 188)))\n (:identifiers (:sid . :s8.368) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502620@unknown@formal@none@1@S@It remains to be determined whether common underlying molecular mechanisms are responsible for the observed brain phenotypes in the fly and mouse.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 27)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 53)\n  (:start . 43) (:id . 49))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 63)\n  (:start . 54) (:id . 50))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 74)\n  (:start . 64) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 78) (:start . 75)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "responsible") (:form . "responsible") (:end . 90)\n  (:start . 79) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 94) (:start . 91)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 107)\n  (:start . 99) (:id . 56))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 113)\n  (:start . 108) (:id . 57))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 124)\n  (:start . 114) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 127) (:start . 125)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 60))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 135) (:start . 132)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 145)\n  (:start . 140) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x8.369.1) (:span 28 35)))\n (:hscopes ((:id . :x8.369.1) (:span 28 145)))\n (:identifiers (:sid . :s8.369) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5502624@unknown@formal@none@1@S@Synapse complexity can be modulated by many factors, including neuronal activity and membrane and cytoskeleton dynamics.@(((:tag . "NNP") (:stem . "Synapse") (:form . "Synapse") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "modulate") (:form . "modulated") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 62)\n  (:start . 53) (:id . 51))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 71)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 80)\n  (:start . 72) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 54))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 93)\n  (:start . 85) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cytoskeleton") (:form . "cytoskeleton") (:end . 110)\n  (:start . 98) (:id . 57))\n ((:tag . "NNS") (:stem . "dynamic") (:form . "dynamics") (:end . 119)\n  (:start . 111) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x8.373.1) (:span 19 22)))\n (:hscopes ((:id . :x8.373.1) (:span 0 119)))\n (:identifiers (:sid . :s8.373) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502625@unknown@formal@none@1@S@In the future, many questions remain to be answered, such as the significance of this axonal terminal phenotype, the exact function of Htt in axonal termini complexity and the possibility of a causal link between this brain defect and the observed adult mobility and viability phenotypes.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "future") (:form . "future") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "question") (:form . "questions") (:end . 29)\n  (:start . 20) (:id . 47))\n ((:tag . "VBP") (:stem . "remain") (:form . "remain") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "TO") (:stem . 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5502626@unknown@formal@none@1@S@The role of endogenous dhtt in HD pathogenesis@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 22)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 46)\n  (:start . 34) (:id . 49)))@@@1@8@((:identifiers (:sid . :s8.375) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502627@unknown@formal@none@1@S@Extensive studies on HD and other polyQ diseases have demonstrated that an expanded polyQ tract can itself be neurotoxic (Zoghbi and Orr, 2000).@(((:tag . "JJ") (:stem . "extensive") (:form . "Extensive") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 17)\n  (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "polyq") (:form . "polyQ") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "disease") (:form . "diseases") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "demonstrate") (:form . "demonstrated") (:end . 66)\n  (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "expand") (:form . "expanded") (:end . 83)\n  (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "polyq") (:form . "polyQ") (:end . 89) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "tract") (:form . "tract") (:end . 95) (:start . 90)\n  (:id . 56))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 99) (:start . 96)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 106)\n  (:start . 100) (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 109) (:start . 107)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "neurotoxic") (:form . "neurotoxic") (:end . 120)\n  (:start . 110) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Zoghbi") (:form . "Zoghbi") (:end . 128)\n  (:start . 122) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Orr") (:form . "Orr") (:end . 136) (:start . 133)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 65))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 142) (:start . 138)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.376) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502628@unknown@formal@none@1@S@Given that the distinctive neuronal loss observed in each polyQ disease is caused by otherwise unrelated disease genes that are widely expressed, it has been hypothesized that other cellular factors affect disease pathogenesis (Cattaneo et al., 2001; Zoghbi and Orr, 2000).@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "distinctive") (:form . "distinctive") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 49)\n  (:start . 41) (:id . 48))\n ((:tag . 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5502629@unknown@formal@none@1@S@In HD, accumulating evidence from cell culture and mutant mouse studies suggest that wild-type Htt has a neuroprotective function (Cattaneo et al., 2001).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 44))\n ((:tag . "VBG") (:stem . "accumulate") (:form . "accumulating") (:end . 19)\n  (:start . 7) (:id . 45))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 57)\n  (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 71)\n  (:start . 64) (:id . 53))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "neuroprotective") (:form . "neuroprotective")\n  (:end . 120) (:start . 105) (:id . 60))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 129)\n  (:start . 121) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Cattaneo") (:form . "Cattaneo") (:end . 139)\n  (:start . 131) (:id . 63))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 146) (:start . 143)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 66))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 152) (:start . 148)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x8.378.1) (:span 72 79)))\n (:hscopes ((:id . :x8.378.1) (:span 72 129)))\n (:identifiers (:sid . :s8.378) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502630@unknown@formal@none@1@S@When endogenous wild-type Hdh is replaced by yeast artificial chromosomes (YACs) containing full-length human Htt with an expanded polyQ tract (YAC46, YAC72 and YAC128) (Leavitt et al., 2001; Van Raamsdonk et al., 2005), the mice develop massive cell death in the testes that can be suppressed by the wild-type Hdh gene, suggesting that the normal function of Htt might mitigate the cellular toxicity associated with the polyQ-expanded mutant Htt protein (Leavitt et al., 2001; Van Raamsdonk et al., 2005).@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "NNP") (:stem . "Hdh") (:form . "Hdh") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . 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5502631@unknown@formal@none@1@S@In addition, a genome-wide study of HD animal models and postmortem tissues has shown that neuronal genes regulated by the transcriptional repressor REST/NRSF, including the gene encoding BDNF, could be similarly repressed by either the presence of the polyQ-expanded Htt protein or by depleting endogenous wild-type Htt (Zuccato et al., 2007).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "genome-wide") (:form . "genome-wide") (:end . 26)\n  (:start . 15) (:id . 46))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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5502632@unknown@formal@none@1@S@Together, these and other studies support the hypothesis that loss of normal Htt function affects HD pathogenesis.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 76)\n  (:start . 70) (:id . 54))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . "VBZ") (:stem . "affect") (:form . "affects") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 113)\n  (:start . 101) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x8.381.1) (:span 46 56)))\n (:hscopes ((:id . :x8.381.1) (:span 46 113)))\n (:identifiers (:sid . :s8.381) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502633@unknown@formal@none@1@S@We were able to examine the effect of removing endogenous dhtt on the pathogenesis of an established Drosophila HD model for polyQ toxicity (HD-Q93).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 34)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "remove") (:form . "removing") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 57)\n  (:start . 47) (:id . 51))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 82)\n  (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "establish") (:form . "established") (:end . 100)\n  (:start . 89) (:id . 58))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 111)\n  (:start . 101) (:id . 59))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 120)\n  (:start . 115) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 124) (:start . 121)\n  (:id . 62))\n ((:tag . "NN") (:stem . "polyq") (:form . "polyQ") (:end . 130)\n  (:start . 125) (:id . 63))\n ((:tag . "NN") (:stem . "toxicity") (:form . "toxicity") (:end . 139)\n  (:start . 131) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 147)\n  (:start . 141) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.382) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502634@unknown@formal@none@1@S@Our results show that the phenotypes of HD-Q93 flies, including mobility, viability and brain pathology, are significantly exacerbated in the absence of endogenous dhtt, providing in vivo evidence that loss of normal Htt function can accelerate HD pathogenesis.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 36)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "hd-q93") (:form . "HD-Q93") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 83)\n  (:start . 74) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "pathology") (:form . "pathology") (:end . 103)\n  (:start . 94) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 108) (:start . 105)\n  (:id . 60))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 122) (:start . 109) (:id . 61))\n ((:tag . "VBN") (:stem . "exacerbate") (:form . "exacerbated") (:end . 134)\n  (:start . 123) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 137) (:start . 135)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 64))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 149)\n  (:start . 142) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 163)\n  (:start . 153) (:id . 67))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 168) (:start . 164)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "provide") (:form . "providing") (:end . 179)\n  (:start . 170) (:id . 70))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 182) (:start . 180)\n  (:id . 71))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 187) (:start . 183)\n  (:id . 72))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 196)\n  (:start . 188) (:id . 73))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 201) (:start . 197)\n  (:id . 74))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 206) (:start . 202)\n  (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 209) (:start . 207)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 216)\n  (:start . 210) (:id . 77))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 220) (:start . 217)\n  (:id . 78))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 229)\n  (:start . 221) (:id . 79))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 233) (:start . 230)\n  (:id . 80))\n ((:tag . "VB") (:stem . "accelerate") (:form . "accelerate") (:end . 244)\n  (:start . 234) (:id . 81))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 247) (:start . 245)\n  (:id . 82))\n ((:tag . "NN") (:stem . "pathogenesis") (:form . "pathogenesis") (:end . 260)\n  (:start . 248) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 261) (:start . 260)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s8.383) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502635@unknown@formal@none@1@S@It should be noted that our results do not directly demonstrate that loss of the endogenous Htt protein specifically affects HD pathogenesis, because the enhanced pathology might be the result of an additive effect of two detrimental factors in the animals, namely the presence of a toxic polyQ tract and the disturbance of the normal function of Htt.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "result") (:form . 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5502636@unknown@formal@none@1@S@Although dhtt-ko mutants exhibit only a mild age-dependent adult phenotype, it is possible that, in the absence of endogenous dhtt, some undetected cellular defects might develop that render the animals more susceptible to other cellular attacks.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "exhibit") (:form . "exhibit") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 39) (:start . 38)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "mild") (:form . "mild") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "age-dependent") (:form . "age-dependent")\n  (:end . 58) (:start . 45) (:id . 49))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 64) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 74)\n  (:start . 65) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 90)\n  (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 95) (:start . 91)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 59))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 111)\n  (:start . 104) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 125)\n  (:start . 115) (:id . 62))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 130) (:start . 126)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 64))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 136) (:start . 132)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "undetected") (:form . "undetected") (:end . 147)\n  (:start . 137) (:id . 66))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 156)\n  (:start . 148) (:id . 67))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 164)\n  (:start . 157) (:id . 68))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 170)\n  (:start . 165) (:id . 69))\n ((:tag . "VB") (:stem . "develop") (:form . "develop") (:end . 178)\n  (:start . 171) (:id . 70))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 183) (:start . 179)\n  (:id . 71))\n ((:tag . "VBP") (:stem . "render") (:form . "render") (:end . 190)\n  (:start . 184) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 194) (:start . 191)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 202)\n  (:start . 195) (:id . 74))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 207) (:start . 203)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "susceptible") (:form . "susceptible") (:end . 219)\n  (:start . 208) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 222) (:start . 220)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 228)\n  (:start . 223) (:id . 78))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 237)\n  (:start . 229) (:id . 79))\n ((:tag . "NNS") (:stem . "attack") (:form . "attacks") (:end . 245)\n  (:start . 238) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x8.385.1) (:span 165 170)) ((:id . :x8.385.2) (:span 82 90)))\n (:hscopes ((:id . :x8.385.1) (:span 165 245))\n  ((:id . :x8.385.2) (:span 82 245)))\n (:identifiers (:sid . :s8.385) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502637@unknown@formal@none@1@S@In the presence of a toxic polyQ tract, this vulnerability might be exposed further, leading to additive phenotypes.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 15)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "toxic") (:form . "toxic") (:end . 26) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "polyq") (:form . "polyQ") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "tract") (:form . "tract") (:end . 38) (:start . 33)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 44) (:start . 40)\n  (:id . 51))\n ((:tag . "NN") (:stem . "vulnerability") (:form . "vulnerability")\n  (:end . 58) (:start . 45) (:id . 52))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 64) (:start . 59)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 75)\n  (:start . 68) (:id . 55))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 83)\n  (:start . 76) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 92)\n  (:start . 85) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "additive") (:form . "additive") (:end . 104)\n  (:start . 96) (:id . 60))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 115)\n  (:start . 105) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x8.386.1) (:span 59 64)))\n (:hscopes ((:id . :x8.386.1) (:span 40 115)))\n (:identifiers (:sid . :s8.386) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502638@unknown@formal@none@1@S@Our result is in agreement with the early hypothesis that HD might be caused by the combination of an acquired toxicity, conferred by the expanded polyQ tract in the mutated Htt, and an incurred neuronal vulnerability, arising from the loss of endogenous Htt function (Cattaneo et al., 2001).@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 66) (:start . 61)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 76)\n  (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 95)\n  (:start . 84) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . 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"(") (:end . 269) (:start . 268)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "Cattaneo") (:form . "Cattaneo") (:end . 277)\n  (:start . 269) (:id . 90))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 280) (:start . 278)\n  (:id . 91))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 284) (:start . 281)\n  (:id . 92))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 285) (:start . 284)\n  (:id . 93))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 290) (:start . 286)\n  (:id . 94))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 291) (:start . 290)\n  (:id . 95))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 292) (:start . 291)\n  (:id . 96)))@@@1@55@((:hcues ((:id . :x8.387.1) (:span 61 66)) ((:id . :x8.387.2) (:span 42 52)))\n (:hscopes ((:id . :x8.387.1) (:span 58 267))\n  ((:id . :x8.387.2) (:span 42 267)))\n (:identifiers (:sid . :s8.387) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502639@unknown@formal@none@1@S@It is important to note that previous studies have demonstrated that expansion of polyQ tracts within the Htt protein does not abolish its endogenous function, as full-length Htt with an expanded polyQ tract can fully support the development of Htt-null mice (Leavitt et al., 2001; Van Raamsdonk et al., 2005; White et al., 1997).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 15)\n  (:start . 6) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "VB") (:stem . "note") (:form . "note") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "previous") (:form . 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5502640@unknown@formal@none@1@S@Recently, RNAi-mediated depletion of the polyQ-expanded Htt protein has been proposed as a therapeutic approach against HD (Farah, 2007).@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "rnai-mediated") (:form . "RNAi-mediated")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "depletion") (:form . "depletion") (:end . 33)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "polyq-expanded") (:form . "polyQ-expanded")\n  (:end . 55) (:start . 41) (:id . 48))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 59) (:start . 56)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 67)\n  (:start . 60) (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 71) (:start . 68)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 76) (:start . 72)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 85)\n  (:start . 77) (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "therapeutic") (:form . "therapeutic") (:end . 102)\n  (:start . 91) (:id . 56))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 111)\n  (:start . 103) (:id . 57))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 119)\n  (:start . 112) (:id . 58))\n ((:tag . "NNP") (:stem . "HD") (:form . "HD") (:end . 122) (:start . 120)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Farah") (:form . "Farah") (:end . 129)\n  (:start . 124) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "CD") (:stem . "2007") (:form . "2007") (:end . 135) (:start . 131)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s8.389) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502641@unknown@formal@none@1@S@Our data, together with previous mammalian studies, suggest that the normal function of Htt has a conserved neuroprotective role in the brain and that its depletion could render neuronal cells more vulnerable to the toxicity associated with the polyQ tract (Auerbach et al., 2001; Cattaneo et al., 2001; Dragatsis et al., 2000; Leavitt et al., 2001).@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 18)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "JJ") (:stem . "mammalian") (:form . 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(:end . 350) (:start . 349)\n  (:id . 109)))@@@1@68@((:hcues ((:id . :x8.390.1) (:span 165 170)) ((:id . :x8.390.2) (:span 52 59)))\n (:hscopes ((:id . :x8.390.1) (:span 165 256))\n  ((:id . :x8.390.2) (:span 52 256)))\n (:identifiers (:sid . :s8.390) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502642@unknown@formal@none@1@S@Application of such an RNAi-based strategy requires a consideration that the normal Htt function be preserved.@(((:tag . "NN") (:stem . "application") (:form . "Application") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "rnai-based") (:form . "RNAi-based") (:end . 33)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "consideration") (:form . "consideration")\n  (:end . 67) (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 72) (:start . 68)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 83)\n  (:start . 77) (:id . 53))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 87) (:start . 84)\n  (:id . 54))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 96)\n  (:start . 88) (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 99) (:start . 97)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "preserve") (:form . "preserved") (:end . 109)\n  (:start . 100) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s8.391) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502643@unknown@formal@none@1@S@Given the devastating consequence of fully progressed HD, together with the observations that Htt-null neurons can develop and survive in the adult mouse brain and that dhtt-ko animals are largely normal with only mild adult brain defects, our data indicate that the benefit gained from balanced administration of RNAi knockdown therapy in the adult brain might justify the relatively mild loss caused by depletion of the Htt-associated neuroprotective function.@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "devastate") (:form . "devastating") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "consequence") (:form . "consequence") (:end . 33)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "RB") (:stem . 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"depletion") (:end . 414)\n  (:start . 405) (:id . 107))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 417) (:start . 415)\n  (:id . 108))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 421) (:start . 418)\n  (:id . 109))\n ((:tag . "JJ") (:stem . "htt-associated") (:form . "Htt-associated")\n  (:end . 436) (:start . 422) (:id . 110))\n ((:tag . "JJ") (:stem . "neuroprotective") (:form . "neuroprotective")\n  (:end . 452) (:start . 437) (:id . 111))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 461)\n  (:start . 453) (:id . 112))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 462) (:start . 461)\n  (:id . 113)))@@@1@72@((:hcues ((:id . :x8.392.1) (:span 356 361))\n  ((:id . :x8.392.2) (:span 249 262)) ((:id . :x8.392.3) (:span 111 114)))\n (:hscopes ((:id . :x8.392.1) (:span 356 461))\n  ((:id . :x8.392.2) (:span 249 461)) ((:id . :x8.392.3) (:span 111 159)))\n (:identifiers (:sid . :s8.392) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502644@unknown@formal@none@1@S@METHODS@(((:tag . "NNS") (:stem . "methods") (:form . "METHODS") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s8.393) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5502645@unknown@formal@none@1@S@Drosophila stocks and genetics@(((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "stock") (:form . "stocks") (:end . 17)\n  (:start . 11) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "genetic") (:form . "genetics") (:end . 30)\n  (:start . 22) (:id . 45)))@@@1@4@((:identifiers (:sid . :s8.394) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502646@unknown@formal@none@1@S@Flies were maintained at 25°C and raised on standard Drosophila medium unless specified otherwise.@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "maintain") (:form . "maintained") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "25°c") (:form . "25°C") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "raise") (:form . "raised") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 52)\n  (:start . 44) (:id . 50))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 63)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 70)\n  (:start . 64) (:id . 52))\n ((:tag . "IN") (:stem . "unless") (:form . "unless") (:end . 77)\n  (:start . 71) (:id . 53))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 87)\n  (:start . 78) (:id . 54))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 97)\n  (:start . 88) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.395) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502647@unknown@formal@none@1@S@To establish transgenic animals, DNA constructs were injected into w1118 embryos together with the pπ25.7wc helper plasmid to generate germ line transformation; transformants were then selected in the next generation, according to standard procedures.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "establish") (:form . "establish") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 31)\n  (:start . 24) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "construct") (:form . "constructs") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "CD") (:stem . "w1118") (:form . "w1118") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 80)\n  (:start . 73) (:id . 53))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 56))\n ((:tag . "NN") (:stem . "pπ25.7wc") (:form . "pπ25.7wc") (:end . 107)\n  (:start . 99) (:id . 57))\n ((:tag . "NN") (:stem . "helper") (:form . "helper") (:end . 114)\n  (:start . 108) (:id . 58))\n ((:tag . "NN") (:stem . "plasmid") (:form . "plasmid") (:end . 122)\n  (:start . 115) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 125) (:start . 123)\n  (:id . 60))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 134)\n  (:start . 126) (:id . 61))\n ((:tag . "NN") (:stem . "germ") (:form . "germ") (:end . 139) (:start . 135)\n  (:id . 62))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 144) (:start . 140)\n  (:id . 63))\n ((:tag . "NN") (:stem . "transformation") (:form . "transformation")\n  (:end . 159) (:start . 145) (:id . 64))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 160) (:start . 159)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "transformant") (:form . "transformants")\n  (:end . 174) (:start . 161) (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 179) (:start . 175)\n  (:id . 67))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 184) (:start . 180)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 193)\n  (:start . 185) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 196) (:start . 194)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 200) (:start . 197)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 205) (:start . 201)\n  (:id . 72))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 216)\n  (:start . 206) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 217) (:start . 216)\n  (:id . 74))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 227)\n  (:start . 218) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 230) (:start . 228)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 239)\n  (:start . 231) (:id . 77))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 250)\n  (:start . 240) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 251) (:start . 250)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s8.396) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502648@unknown@formal@none@1@S@Unless specified otherwise, flies of the genotype w1118/w1118 were used as controls in all assays because the dhtt-ko mutant allele was generated from this w1118 genetic background during the genetic crosses.@(((:tag . "IN") (:stem . "unless") (:form . "Unless") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 16)\n  (:start . 7) (:id . 43))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 26)\n  (:start . 17) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "w1118/w1118") (:form . "w1118/w1118") (:end . 61)\n  (:start . 50) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 83)\n  (:start . 75) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 97)\n  (:start . 91) (:id . 57))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 105)\n  (:start . 98) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 117)\n  (:start . 110) (:id . 60))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 124)\n  (:start . 118) (:id . 61))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 131)\n  (:start . 125) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 135) (:start . 132)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 145)\n  (:start . 136) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 150) (:start . 146)\n  (:id . 65))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 155) (:start . 151)\n  (:id . 66))\n ((:tag . "NN") (:stem . "w1118") (:form . "w1118") (:end . 161)\n  (:start . 156) (:id . 67))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 169)\n  (:start . 162) (:id . 68))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 180)\n  (:start . 170) (:id . 69))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 187)\n  (:start . 181) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 199)\n  (:start . 192) (:id . 72))\n ((:tag . "NNS") (:stem . "crosse") (:form . "crosses") (:end . 207)\n  (:start . 200) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.397) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502649@unknown@formal@none@1@S@The p-element line d08071, piggyBac insertional line f05417 and the FLP recombinase transgene line [genotype: y, w, pCaspeR-(hs-flipase)] were from Exelixis (Parks et al., 2004).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "p-element") (:form . "p-element") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "d08071") (:form . "d08071") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "piggybac") (:form . "piggyBac") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "JJ") (:stem . "insertional") (:form . "insertional") (:end . 47)\n  (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "f05417") (:form . "f05417") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "FLP") (:form . "FLP") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "recombinase") (:form . "recombinase") (:end . 83)\n  (:start . 72) (:id . 54))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 93)\n  (:start . 84) (:id . 55))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 98) (:start . 94)\n  (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 108)\n  (:start . 100) (:id . 58))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "NN") (:stem . "y") (:form . "y") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "NN") (:stem . "w") (:form . "w") (:end . 114) (:start . 113)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "pCaspeR-(hs-flipase)")\n  (:form . "pCaspeR-(hs-flipase)") (:end . 136) (:start . 116) (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 137) (:start . 136)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 142) (:start . 138)\n  (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 147) (:start . 143)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Exelixis") (:form . "Exelixis") (:end . 156)\n  (:start . 148) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 158) (:start . 157)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Park") (:form . "Parks") (:end . 163)\n  (:start . 158) (:id . 70))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 166) (:start . 164)\n  (:id . 71))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 170) (:start . 167)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 73))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 176) (:start . 172)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 177) (:start . 176)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.398) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502650@unknown@formal@none@1@S@To analyze the A307-Gal4 labeled neurons in adult brains, flies with genotypes of A307-Gal4/+; dhtt-ko/TM6C, Tb and UAS-mCD8-eGFP/+; dhtt-ko/TM6C, Tb were generated and crossed together; their adult progenies carrying A307-Gal4/UAS-mCD8-eGFP; dhtt-ko/dhtt-ko were selected and analyzed.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "analyze") (:form . "analyze") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "a307-gal4") (:form . "A307-Gal4") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "fly") (:form . "flies") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 78)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "a307-gal4/+") (:form . "A307-Gal4/+") (:end . 93)\n  (:start . 82) (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dhtt-ko/tm6c") (:form . "dhtt-ko/TM6C") (:end . 107)\n  (:start . 95) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Tb") (:form . "Tb") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "uas-mcd8-egfp/+") (:form . "UAS-mCD8-eGFP/+")\n  (:end . 131) (:start . 116) (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 132) (:start . 131)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dhtt-ko/tm6c") (:form . "dhtt-ko/TM6C") (:end . 145)\n  (:start . 133) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Tb") (:form . "Tb") (:end . 149) (:start . 147)\n  (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 154) (:start . 150)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 164)\n  (:start . 155) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "cross") (:form . "crossed") (:end . 176)\n  (:start . 169) (:id . 70))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 185)\n  (:start . 177) (:id . 71))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 186) (:start . 185)\n  (:id . 72))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 192)\n  (:start . 187) (:id . 73))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 198)\n  (:start . 193) (:id . 74))\n ((:tag . "NNS") (:stem . "progeny") (:form . "progenies") (:end . 208)\n  (:start . 199) (:id . 75))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 217)\n  (:start . 209) (:id . 76))\n ((:tag . "NNP") (:stem . "A307-Gal4/UAS-mCD8-eGFP")\n  (:form . "A307-Gal4/UAS-mCD8-eGFP") (:end . 241) (:start . 218) (:id . 77))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 242) (:start . 241)\n  (:id . 78))\n ((:tag . "NN") (:stem . "dhtt-ko/dhtt-ko") (:form . "dhtt-ko/dhtt-ko")\n  (:end . 258) (:start . 243) (:id . 79))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 263) (:start . 259)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 272)\n  (:start . 264) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 276) (:start . 273)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 285)\n  (:start . 277) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 286) (:start . 285)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s8.399) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502651@unknown@formal@none@1@S@The controls were the progenies from crossing the A307-Gal4 line with the UAS-mCD8-eGFP line.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "progeny") (:form . "progenies") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "cross") (:form . "crossing") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "a307-gal4") (:form . "A307-Gal4") (:end . 59)\n  (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 69) (:start . 65)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "UAS-mCD8-eGFP") (:form . "UAS-mCD8-eGFP")\n  (:end . 87) (:start . 74) (:id . 54))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 92) (:start . 88)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.400) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502652@unknown@formal@none@1@S@HD-Q93 flies were obtained by crossing the pan-neuronal line elav-Gal4 (C155) with the UAS-Httexon1-Q93 line (P468) provided generously by L. Thompson and J. L. Marsh, respectively (Steffan et al., 2001).@(((:tag . "NNP") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "cross") (:form . "crossing") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "pan-neuronal") (:form . "pan-neuronal") (:end . 55)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "elav-gal4") (:form . "elav-Gal4") (:end . 70)\n  (:start . 61) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "NN") (:stem . "c155") (:form . "C155") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "uas-httexon1-q93") (:form . "UAS-Httexon1-Q93")\n  (:end . 103) (:start . 87) (:id . 57))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 108) (:start . 104)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 59))\n ((:tag . "NN") (:stem . "p468") (:form . "P468") (:end . 114) (:start . 110)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "provide") (:form . "provided") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . "RB") (:stem . "generously") (:form . "generously") (:end . 135)\n  (:start . 125) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 138) (:start . 136)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "L.") (:form . "L.") (:end . 141) (:start . 139)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Thompson") (:form . "Thompson") (:end . 150)\n  (:start . 142) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "J.") (:form . "J.") (:end . 157) (:start . 155)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "L.") (:form . "L.") (:end . 160) (:start . 158)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Marsh") (:form . "Marsh") (:end . 166)\n  (:start . 161) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 180)\n  (:start . 168) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 182) (:start . 181)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Steffan") (:form . "Steffan") (:end . 189)\n  (:start . 182) (:id . 74))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 192) (:start . 190)\n  (:id . 75))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 196) (:start . 193)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 77))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 202) (:start . 198)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 203) (:start . 202)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s8.401) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502653@unknown@formal@none@1@S@To generate ‘HD-Q93; dhtt-ko’ flies, flies with genotypes of elav-Gal4(c155)/+; dhtt-ko/TM6C, Tb and UAS-Httexon1-Q93/Cyo; dhtt-ko/TM6C, Tb were established and then crossed together; adult progenies with the genotype of elav-Gal4/+; UAS-Httexon1-Q93/+; dhtt-ko/dhtt-ko were then selected and analyzed.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "HD-Q93") (:form . "HD-Q93") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 28)\n  (:start . 21) (:id . 47))\n ((:tag . "POS") (:stem . "’") (:form . "’") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 35) (:start . 30)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "fly") (:form . "flies") (:end . 42) (:start . 37)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 57)\n  (:start . 48) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 54))\n ((:tag . "CD") (:stem . "elav-Gal4(c155)/+") (:form . "elav-Gal4(c155)/+")\n  (:end . 78) (:start . 61) (:id . 55))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dhtt-ko/tm6c") (:form . "dhtt-ko/TM6C") (:end . 92)\n  (:start . 80) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Tb") (:form . "Tb") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "UAS-Httexon1-Q93/Cyo")\n  (:form . "UAS-Httexon1-Q93/Cyo") (:end . 121) (:start . 101) (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . "NN") (:stem . "dhtt-ko/tm6c") (:form . "dhtt-ko/TM6C") (:end . 135)\n  (:start . 123) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Tb") (:form . "Tb") (:end . 139) (:start . 137)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 144) (:start . 140)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "establish") (:form . "established") (:end . 156)\n  (:start . 145) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 68))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 165) (:start . 161)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "cross") (:form . "crossed") (:end . 173)\n  (:start . 166) (:id . 70))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 182)\n  (:start . 174) (:id . 71))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 183) (:start . 182)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 189)\n  (:start . 184) (:id . 73))\n ((:tag . "NNS") (:stem . "progeny") (:form . "progenies") (:end . 199)\n  (:start . 190) (:id . 74))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 204) (:start . 200)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 208) (:start . 205)\n  (:id . 76))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 217)\n  (:start . 209) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 220) (:start . 218)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "elav-gal4/+") (:form . "elav-Gal4/+") (:end . 232)\n  (:start . 221) (:id . 79))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 233) (:start . 232)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "uas-httexon1-q93/+") (:form . "UAS-Httexon1-Q93/+")\n  (:end . 252) (:start . 234) (:id . 81))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 253) (:start . 252)\n  (:id . 82))\n ((:tag . "NN") (:stem . "dhtt-ko/dhtt-ko") (:form . "dhtt-ko/dhtt-ko")\n  (:end . 269) (:start . 254) (:id . 83))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 274) (:start . 270)\n  (:id . 84))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 279) (:start . 275)\n  (:id . 85))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 288)\n  (:start . 280) (:id . 86))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 292) (:start . 289)\n  (:id . 87))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 301)\n  (:start . 293) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 302) (:start . 301)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s8.402) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502654@unknown@formal@none@1@S@Controls flies had the following genotypes: elav-Gal4 (C155)/+; UAS-Httexon1-Q93/+; elav-Gal4 (C155)/+; dhtt-ko/dhtt-ko; and UAS-Httexon1-Q93/+; dhtt-ko/dhtt-ko.@(((:tag . "NNP") (:stem . "Control") (:form . "Controls") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "following") (:form . "following") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "elav-gal4") (:form . "elav-Gal4") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "C155)/+") (:form . "C155)/+") (:end . 62)\n  (:start . 55) (:id . 51))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "uas-httexon1-q93/+") (:form . "UAS-Httexon1-Q93/+")\n  (:end . 82) (:start . 64) (:id . 53))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "NN") (:stem . "elav-gal4") (:form . "elav-Gal4") (:end . 93)\n  (:start . 84) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "VB") (:stem . "C155)/+") (:form . "C155)/+") (:end . 102)\n  (:start . 95) (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "NN") (:stem . "dhtt-ko/dhtt-ko") (:form . "dhtt-ko/dhtt-ko")\n  (:end . 119) (:start . 104) (:id . 59))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 120) (:start . 119)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "uas-httexon1-q93/+") (:form . "UAS-Httexon1-Q93/+")\n  (:end . 143) (:start . 125) (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 144) (:start . 143)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dhtt-ko/dhtt-ko") (:form . "dhtt-ko/dhtt-ko")\n  (:end . 160) (:start . 145) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s8.403) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502655@unknown@formal@none@1@S@Genetics and molecular clonings to generate the dhtt-ko mutant allele@(((:tag . "NNP") (:stem . "Genetic") (:form . "Genetics") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "cloning") (:form . "clonings") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 62)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 69)\n  (:start . 63) (:id . 51)))@@@1@10@((:identifiers (:sid . :s8.404) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502656@unknown@formal@none@1@S@The Df(98E2) deficiency, in which both CG9990 and dhtt are deleted, was generated by following the Flp-FRT-based procedure, as described previously (Parks et al., 2004).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "deficiency") (:form . "deficiency") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "delete") (:form . "deleted") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 81)\n  (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 84) (:start . 82)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 94)\n  (:start . 85) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "flp-frt-based") (:form . "Flp-FRT-based")\n  (:end . 112) (:start . 99) (:id . 60))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 122)\n  (:start . 113) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 126) (:start . 124)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 136)\n  (:start . 127) (:id . 64))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 147)\n  (:start . 137) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 149) (:start . 148)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Park") (:form . "Parks") (:end . 154)\n  (:start . 149) (:id . 67))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 157) (:start . 155)\n  (:id . 68))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 161) (:start . 158)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 70))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 167) (:start . 163)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 168) (:start . 167)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s8.405) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502657@unknown@formal@none@1@S@Briefly, the p-element line d08071 (inserted at the 5' end of the neighboring CG9990 gene) was crossed to virgin flies carrying an FLP recombinase transgene [genotype: y, w, pCaspeR-(hs-flipase)].@(((:tag . "NNP") (:stem . "Briefly") (:form . "Briefly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "p-element") (:form . "p-element") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "d08071") (:form . "d08071") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 54) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 58) (:start . 55)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "neighbor") (:form . "neighboring") (:end . 77)\n  (:start . 66) (:id . 57))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 84)\n  (:start . 78) (:id . 58))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 89) (:start . 85)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 94) (:start . 91)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "cross") (:form . "crossed") (:end . 102)\n  (:start . 95) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n  (:id . 63))\n ((:tag . "NN") (:stem . "virgin") (:form . "virgin") (:end . 112)\n  (:start . 106) (:id . 64))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 118) (:start . 113)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 127)\n  (:start . 119) (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 130) (:start . 128)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "FLP") (:form . "FLP") (:end . 134) (:start . 131)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "recombinase") (:form . "recombinase") (:end . 146)\n  (:start . 135) (:id . 69))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 156)\n  (:start . 147) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 158) (:start . 157)\n  (:id . 71))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 166)\n  (:start . 158) (:id . 72))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 167) (:start . 166)\n  (:id . 73))\n ((:tag . "NN") (:stem . "y") (:form . "y") (:end . 169) (:start . 168)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 170) (:start . 169)\n  (:id . 75))\n ((:tag . "NN") (:stem . "w") (:form . "w") (:end . 172) (:start . 171)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "pCaspeR-(hs-flipase)")\n  (:form . "pCaspeR-(hs-flipase)") (:end . 194) (:start . 174) (:id . 78))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 195) (:start . 194)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s8.406) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502658@unknown@formal@none@1@S@For the next generation (F1), the male progenies carrying both the d08071 and the hs-flipase lines were selected and mated with virgins carrying the f05417 line, inserted near the 3' end of the dhtt gene.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "F1") (:form . "F1") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "male") (:form . "male") (:end . 38) (:start . 34)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "progeny") (:form . "progenies") (:end . 48)\n  (:start . 39) (:id . 52))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 57)\n  (:start . 49) (:id . 53))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 62) (:start . 58)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "d08071") (:form . "d08071") (:end . 73)\n  (:start . 67) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 58))\n ((:tag . "NN") (:stem . "hs-flipase") (:form . "hs-flipase") (:end . 92)\n  (:start . 82) (:id . 59))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 98) (:start . 93)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 103) (:start . 99)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 112)\n  (:start . 104) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "mat") (:form . "mated") (:end . 122) (:start . 117)\n  (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 127) (:start . 123)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "virgin") (:form . "virgins") (:end . 135)\n  (:start . 128) (:id . 66))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 144)\n  (:start . 136) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 68))\n ((:tag . "NN") (:stem . "f05417") (:form . "f05417") (:end . 155)\n  (:start . 149) (:id . 69))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 160) (:start . 156)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "insert") (:form . "inserted") (:end . 170)\n  (:start . 162) (:id . 72))\n ((:tag . "IN") (:stem . "near") (:form . "near") (:end . 175) (:start . 171)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 74))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 181) (:start . 180)\n  (:id . 75))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 182) (:start . 181)\n  (:id . 76))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 186) (:start . 183)\n  (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 189) (:start . 187)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 193) (:start . 190)\n  (:id . 79))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 198) (:start . 194)\n  (:id . 80))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 203) (:start . 199)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s8.407) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502659@unknown@formal@none@1@S@The progenies (i.e. the F1 flies) from the above crosses were heat-shocked at 37°C for 1 hour, 48 hours after egg-laying, and were then heat-shocked for a further 1 hour during each of the following 4 days.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "progeny") (:form . "progenies") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "f1") (:form . "F1") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 33) (:start . 32)\n  (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 38) (:start . 34)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 48) (:start . 43)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "crosse") (:form . "crosses") (:end . 56)\n  (:start . 49) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "heat-shocke") (:form . "heat-shocked") (:end . 74)\n  (:start . 62) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 82) (:start . 78)\n  (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 88) (:start . 87)\n  (:id . 59))\n ((:tag . "NN") (:stem . "hour") (:form . "hour") (:end . 93) (:start . 89)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 61))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 97) (:start . 95)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 103) (:start . 98)\n  (:id . 63))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 109)\n  (:start . 104) (:id . 64))\n ((:tag . "JJ") (:stem . "egg-laying") (:form . "egg-laying") (:end . 120)\n  (:start . 110) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 67))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 130) (:start . 126)\n  (:id . 68))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 135) (:start . 131)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "heat-shocked") (:form . "heat-shocked") (:end . 148)\n  (:start . 136) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 152) (:start . 149)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 154) (:start . 153)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 162)\n  (:start . 155) (:id . 73))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 164) (:start . 163)\n  (:id . 74))\n ((:tag . "NN") (:stem . "hour") (:form . "hour") (:end . 169) (:start . 165)\n  (:id . 75))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 176)\n  (:start . 170) (:id . 76))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 181) (:start . 177)\n  (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n  (:id . 79))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 198)\n  (:start . 189) (:id . 80))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 200) (:start . 199)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 205) (:start . 201)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.408) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502660@unknown@formal@none@1@S@In the third generation (F2), the virgin females were collected and crossed to males carrying balancer chromosomes (w; TM3, Sb/TM6B, Tb, Hu).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "F2") (:form . "F2") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 50))\n ((:tag . "NN") (:stem . "virgin") (:form . "virgin") (:end . 40)\n  (:start . 34) (:id . 51))\n ((:tag . "NNS") (:stem . "female") (:form . "females") (:end . 48)\n  (:start . 41) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 53) (:start . 49)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 63)\n  (:start . 54) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "cross") (:form . "crossed") (:end . 75)\n  (:start . 68) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "male") (:form . "males") (:end . 84) (:start . 79)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 93)\n  (:start . 85) (:id . 59))\n ((:tag . "NN") (:stem . "balancer") (:form . "balancer") (:end . 102)\n  (:start . 94) (:id . 60))\n ((:tag . "NNS") (:stem . "chromosome") (:form . "chromosomes") (:end . 114)\n  (:start . 103) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 62))\n ((:tag . "NN") (:stem . "w") (:form . "w") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 118) (:start . 117)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "TM3") (:form . "TM3") (:end . 122) (:start . 119)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Sb/TM6B") (:form . "Sb/TM6B") (:end . 131)\n  (:start . 124) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Tb") (:form . "Tb") (:end . 135) (:start . 133)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Hu") (:form . "Hu") (:end . 139) (:start . 137)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s8.409) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502661@unknown@formal@none@1@S@In the fourth generation (F3), progeny flies carrying the Df(98E2) deletion from the above crosses (between F2 flies) were selected based on their darker eye color, and crossed with flies carrying balancer chromosomes to establish individual fly lines.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "fourth") (:form . "fourth") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "F3") (:form . "F3") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 49))\n ((:tag . "NN") (:stem . "progeny") (:form . "progeny") (:end . 38)\n  (:start . 31) (:id . 50))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 44) (:start . 39)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 53)\n  (:start . 45) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 66)\n  (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 75)\n  (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 90) (:start . 85)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "crosse") (:form . "crosses") (:end . 98)\n  (:start . 91) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 107)\n  (:start . 100) (:id . 61))\n ((:tag . "NN") (:stem . "f2") (:form . "F2") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 116) (:start . 111)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 117) (:start . 116)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 122) (:start . 118)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 131)\n  (:start . 123) (:id . 66))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 137)\n  (:start . 132) (:id . 67))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 140) (:start . 138)\n  (:id . 68))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 146)\n  (:start . 141) (:id . 69))\n ((:tag . "NN") (:stem . "darker") (:form . "darker") (:end . 153)\n  (:start . 147) (:id . 70))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 157) (:start . 154)\n  (:id . 71))\n ((:tag . "NN") (:stem . "color") (:form . "color") (:end . 163)\n  (:start . 158) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "cross") (:form . "crossed") (:end . 176)\n  (:start . 169) (:id . 75))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 181) (:start . 177)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 187) (:start . 182)\n  (:id . 77))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 196)\n  (:start . 188) (:id . 78))\n ((:tag . "NN") (:stem . "balancer") (:form . "balancer") (:end . 205)\n  (:start . 197) (:id . 79))\n ((:tag . "NNS") (:stem . "chromosome") (:form . "chromosomes") (:end . 217)\n  (:start . 206) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 220) (:start . 218)\n  (:id . 81))\n ((:tag . "VB") (:stem . "establish") (:form . "establish") (:end . 230)\n  (:start . 221) (:id . 82))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 241)\n  (:start . 231) (:id . 83))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 245) (:start . 242)\n  (:id . 84))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 251)\n  (:start . 246) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s8.410) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502662@unknown@formal@none@1@S@The presence of the deletion in these lines was confirmed by PCR analysis of extracted genomic DNA and by DNA sequencing.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 57)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 73)\n  (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 86)\n  (:start . 77) (:id . 56))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 94)\n  (:start . 87) (:id . 57))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 98) (:start . 95)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 105) (:start . 103)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 109) (:start . 106)\n  (:id . 61))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 120)\n  (:start . 110) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s8.411) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502663@unknown@formal@none@1@S@To generate the genomic rescue construct for the CG9990 gene, a 24.7 kb genomic DNA fragment, covering the CG9990 genomic region, was isolated from the bacterial artificial chromosome (BAC) clone BACR10P23 (CHORI) following double digestion with the restriction enzymes XbaI and XmaI.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 40)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "CD") (:stem . "24.7") (:form . "24.7") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 79)\n  (:start . 72) (:id . 56))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 92)\n  (:start . 84) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "cover") (:form . "covering") (:end . 102)\n  (:start . 94) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 113)\n  (:start . 107) (:id . 62))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 121)\n  (:start . 114) (:id . 63))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 128)\n  (:start . 122) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 142)\n  (:start . 134) (:id . 67))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 147) (:start . 143)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "bacterial") (:form . "bacterial") (:end . 161)\n  (:start . 152) (:id . 70))\n ((:tag . "JJ") (:stem . "artificial") (:form . "artificial") (:end . 172)\n  (:start . 162) (:id . 71))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 183)\n  (:start . 173) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "BAC") (:form . "BAC") (:end . 188) (:start . 185)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 75))\n ((:tag . "NN") (:stem . "clone") (:form . "clone") (:end . 195)\n  (:start . 190) (:id . 76))\n ((:tag . "NNP") (:stem . "BACR10P23") (:form . "BACR10P23") (:end . 205)\n  (:start . 196) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 207) (:start . 206)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "CHORI") (:form . "CHORI") (:end . 212)\n  (:start . 207) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n  (:id . 80))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 223)\n  (:start . 214) (:id . 81))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 230)\n  (:start . 224) (:id . 82))\n ((:tag . "NN") (:stem . "digestion") (:form . "digestion") (:end . 240)\n  (:start . 231) (:id . 83))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 245) (:start . 241)\n  (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 249) (:start . 246)\n  (:id . 85))\n ((:tag . "NN") (:stem . "restriction") (:form . "restriction") (:end . 261)\n  (:start . 250) (:id . 86))\n ((:tag . "NNS") (:stem . "enzyme") (:form . "enzymes") (:end . 269)\n  (:start . 262) (:id . 87))\n ((:tag . "NNP") (:stem . "XbaI") (:form . "XbaI") (:end . 274) (:start . 270)\n  (:id . 88))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 278) (:start . 275)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "XmaI") (:form . "XmaI") (:end . 283) (:start . 279)\n  (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 284) (:start . 283)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s8.412) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502664@unknown@formal@none@1@S@This 24.7 kb genomic DNA fragment starts at an XbaI site near the end of the neighboring CG9989 gene, 2.66 kb from the inserted site of the p-element line d08071, and ends at the XmaI site within the second exon of the dhtt gene, thus covering the whole genomic region of the CG9990 gene (Fig. 1B).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "24.7") (:form . "24.7") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "VBZ") (:stem . "start") (:form . "starts") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "XbaI") (:form . "XbaI") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "IN") (:stem . "near") (:form . "near") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "neighbor") (:form . "neighboring") (:end . 88)\n  (:start . 77) (:id . 58))\n ((:tag . "NN") (:stem . "cg9989") (:form . 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"NN") (:stem . "p-element") (:form . "p-element") (:end . 149)\n  (:start . 140) (:id . 70))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 154) (:start . 150)\n  (:id . 71))\n ((:tag . "NN") (:stem . "d08071") (:form . "d08071") (:end . 161)\n  (:start . 155) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n  (:id . 74))\n ((:tag . "VBZ") (:stem . "end") (:form . "ends") (:end . 171) (:start . 167)\n  (:id . 75))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 174) (:start . 172)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "XmaI") (:form . "XmaI") (:end . 183) (:start . 179)\n  (:id . 78))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 188) (:start . 184)\n  (:id . 79))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 195)\n  (:start . 189) (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 199) (:start . 196)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 206)\n  (:start . 200) (:id . 82))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 211) (:start . 207)\n  (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 214) (:start . 212)\n  (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 218) (:start . 215)\n  (:id . 85))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 223) (:start . 219)\n  (:id . 86))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 228) (:start . 224)\n  (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 229) (:start . 228)\n  (:id . 88))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 234) (:start . 230)\n  (:id . 89))\n ((:tag . "VBG") (:stem . "cover") (:form . "covering") (:end . 243)\n  (:start . 235) (:id . 90))\n ((:tag . 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"1B") (:end . 296) (:start . 294)\n  (:id . 101))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 297) (:start . 296)\n  (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 298) (:start . 297)\n  (:id . 103)))@@@1@62@((:identifiers (:sid . :s8.413) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502665@unknown@formal@none@1@S@To generate the CG9990 rescue transgene, this 24.7 kb genomic DNA fragment was cloned into the NotI and SmaI sites in the pCaspeR-4 transgenic vector.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "CD") (:stem . "24.7") (:form . "24.7") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 74)\n  (:start . 66) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "clone") (:form . "cloned") (:end . 85)\n  (:start . 79) (:id . 56))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 90) (:start . 86)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "NotI") (:form . "NotI") (:end . 99) (:start . 95)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "SmaI") (:form . "SmaI") (:end . 108) (:start . 104)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 114)\n  (:start . 109) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 64))\n ((:tag . "NN") (:stem . "pcasper-4") (:form . "pCaspeR-4") (:end . 131)\n  (:start . 122) (:id . 65))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 142)\n  (:start . 132) (:id . 66))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 149)\n  (:start . 143) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.414) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502666@unknown@formal@none@1@S@The DNA for the pCaspeR-4–CG9990 genomic rescue construct was injected into w1118 embryos and transformants were then selected following standard procedures.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "pcasper-4–cg9990") (:form . "pCaspeR-4–CG9990")\n  (:end . 32) (:start . 16) (:id . 46))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 47)\n  (:start . 41) (:id . 48))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "inject") (:form . "injected") (:end . 70)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 75) (:start . 71)\n  (:id . 52))\n ((:tag . "NN") (:stem . "w1118") (:form . "w1118") (:end . 81) (:start . 76)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 89)\n  (:start . 82) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "transformant") (:form . "transformants")\n  (:end . 107) (:start . 94) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 112) (:start . 108)\n  (:id . 57))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 117) (:start . 113)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 126)\n  (:start . 118) (:id . 59))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 136)\n  (:start . 127) (:id . 60))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 145)\n  (:start . 137) (:id . 61))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 156)\n  (:start . 146) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s8.415) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502667@unknown@formal@none@1@S@Three independent CG9990 transgenic lines were established and then tested by crossing them into the Df(98E2) deletion.@(((:tag . "CD") (:stem . "three") (:form . "Three") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 17)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 24)\n  (:start . 18) (:id . 44))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 35)\n  (:start . 25) (:id . 45))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 41) (:start . 36)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 46) (:start . 42)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "establish") (:form . "established") (:end . 58)\n  (:start . 47) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 49))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 67) (:start . 63)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 74) (:start . 68)\n  (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 77) (:start . 75)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "cross") (:form . "crossing") (:end . 86)\n  (:start . 78) (:id . 53))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 91) (:start . 87)\n  (:id . 54))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 96) (:start . 92)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 109)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 118)\n  (:start . 110) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s8.416) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502668@unknown@formal@none@1@S@Flies with the Df(98E2) deletion, which removes both CG9990 and dhtt, are homozygous lethal at the embryonic stage.@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "remove") (:form . "removes") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 59)\n  (:start . 53) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 84)\n  (:start . 74) (:id . 56))\n ((:tag . "NN") (:stem . "lethal") (:form . "lethal") (:end . 91)\n  (:start . 85) (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 108)\n  (:start . 99) (:id . 60))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 114)\n  (:start . 109) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.417) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502669@unknown@formal@none@1@S@Through genetic crossings, we reintroduced the CG9990 genomic rescue transgene back into the Df(98E2) deletion background, generating fly lines that are defective at the molecular level for only the dhtt gene (referred to as dhtt-ko flies).@(((:tag . "IN") (:stem . "through") (:form . "Through") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "crossing") (:form . "crossings") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "reintroduce") (:form . "reintroduced") (:end . 42)\n  (:start . 30) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 68)\n  (:start . 62) (:id . 51))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 78)\n  (:start . 69) (:id . 52))\n ((:tag . "RB") (:stem . "back") (:form . "back") (:end . 83) (:start . 79)\n  (:id . 53))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 88) (:start . 84)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 101)\n  (:start . 93) (:id . 56))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 110)\n  (:start . 102) (:id . 57))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 121)\n  (:start . 111) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "generate") (:form . "generating") (:end . 133)\n  (:start . 123) (:id . 60))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 137) (:start . 134)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 143)\n  (:start . 138) (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 148) (:start . 144)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 152) (:start . 149)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "defective") (:form . "defective") (:end . 162)\n  (:start . 153) (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 165) (:start . 163)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 179)\n  (:start . 170) (:id . 68))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 185)\n  (:start . 180) (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 189) (:start . 186)\n  (:id . 70))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 194) (:start . 190)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 198) (:start . 195)\n  (:id . 72))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 203) (:start . 199)\n  (:id . 73))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 208) (:start . 204)\n  (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 210) (:start . 209)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 218)\n  (:start . 210) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 221) (:start . 219)\n  (:id . 77))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 224) (:start . 222)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 232)\n  (:start . 225) (:id . 79))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 238) (:start . 233)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 239) (:start . 238)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 240) (:start . 239)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s8.418) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502670@unknown@formal@none@1@S@Three independent genomic CG9990 transgenic lines were tested by crossing them into the Df(98E2) deletion; all of them rescued the embryonic lethality of the Df(98E2) deletion, producing viable adults.@(((:tag . "CD") (:stem . "three") (:form . "Three") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 17)\n  (:start . 6) (:id . 43))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 25)\n  (:start . 18) (:id . 44))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 32)\n  (:start . 26) (:id . 45))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 43)\n  (:start . 33) (:id . 46))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 49) (:start . 44)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 54) (:start . 50)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 61) (:start . 55)\n  (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "cross") (:form . "crossing") (:end . 73)\n  (:start . 65) (:id . 51))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 78) (:start . 74)\n  (:id . 52))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 83) (:start . 79)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 96)\n  (:start . 88) (:id . 55))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 105)\n  (:start . 97) (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 106) (:start . 105)\n  (:id . 57))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 110) (:start . 107)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 118) (:start . 114)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "rescue") (:form . "rescued") (:end . 126)\n  (:start . 119) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 140)\n  (:start . 131) (:id . 63))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 150)\n  (:start . 141) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 153) (:start . 151)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 166)\n  (:start . 158) (:id . 67))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 175)\n  (:start . 167) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 176) (:start . 175)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 186)\n  (:start . 177) (:id . 70))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 193)\n  (:start . 187) (:id . 71))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 200)\n  (:start . 194) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s8.419) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502671@unknown@formal@none@1@S@Thus, dhtt-ko flies, which carry both the Df(98E2) and the CG9990 transgene, are homozygous viable and can fully develop into adulthood, demonstrating that the lethality observed with the Df(98E2) deletion is caused by the loss of CG9990.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 13)\n  (:start . 6) (:id . 44))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 26) (:start . 21)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "carry") (:form . "carry") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 65)\n  (:start . 59) (:id . 54))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 75)\n  (:start . 66) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 91)\n  (:start . 81) (:id . 58))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 98)\n  (:start . 92) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "RB") (:stem . "fully") (:form . "fully") (:end . 112)\n  (:start . 107) (:id . 62))\n ((:tag . "VB") (:stem . "develop") (:form . "develop") (:end . 120)\n  (:start . 113) (:id . 63))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 125) (:start . 121)\n  (:id . 64))\n ((:tag . "NN") (:stem . "adulthood") (:form . "adulthood") (:end . 135)\n  (:start . 126) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating")\n  (:end . 150) (:start . 137) (:id . 67))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 155) (:start . 151)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 69))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 169)\n  (:start . 160) (:id . 70))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 178)\n  (:start . 170) (:id . 71))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 183) (:start . 179)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 187) (:start . 184)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "Df(98E2)") (:form . "Df(98E2)") (:end . 196)\n  (:start . 188) (:id . 74))\n ((:tag . "NN") (:stem . "deletion") (:form . "deletion") (:end . 205)\n  (:start . 197) (:id . 75))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 208) (:start . 206)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 215)\n  (:start . 209) (:id . 77))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 218) (:start . 216)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 222) (:start . 219)\n  (:id . 79))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 227) (:start . 223)\n  (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 230) (:start . 228)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "CG9990") (:form . "CG9990") (:end . 237)\n  (:start . 231) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s8.420) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502672@unknown@formal@none@1@S@To verify further that the dhtt gene is indeed deleted, as expected, in this dhtt-ko allele, we extracted genomic DNA from the homozygous dhtt-ko and wild-type control adults and performed Southern blots.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "verify") (:form . "verify") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "RB") (:stem . "indeed") (:form . "indeed") (:end . 46)\n  (:start . 40) (:id . 50))\n ((:tag . "VBN") (:stem . "delete") (:form . "deleted") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 67)\n  (:start . 59) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n  (:id . 56))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 76) (:start . 72)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 84)\n  (:start . 77) (:id . 58))\n ((:tag . "NN") (:stem . "allele") (:form . "allele") (:end . 91)\n  (:start . 85) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 95) (:start . 93)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "extract") (:form . "extracted") (:end . 105)\n  (:start . 96) (:id . 62))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 113)\n  (:start . 106) (:id . 63))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 117) (:start . 114)\n  (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 122) (:start . 118)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 137)\n  (:start . 127) (:id . 67))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 145)\n  (:start . 138) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 149) (:start . 146)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 159)\n  (:start . 150) (:id . 70))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 167)\n  (:start . 160) (:id . 71))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 174)\n  (:start . 168) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 178) (:start . 175)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 188)\n  (:start . 179) (:id . 74))\n ((:tag . "JJ") (:stem . "southern") (:form . "Southern") (:end . 197)\n  (:start . 189) (:id . 75))\n ((:tag . "NNS") (:stem . "blot") (:form . "blots") (:end . 203)\n  (:start . 198) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s8.421) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502673@unknown@formal@none@1@S@Genomic DNA was extracted from the dhtt-ko adults or from control w1118 adults and digested with the restriction enzyme BamHI.@(((:tag . "JJ") (:stem . "genomic") (:form . "Genomic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "CD") (:stem . "w1118") (:form . "w1118") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 78)\n  (:start . 72) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "digest") (:form . "digested") (:end . 91)\n  (:start . 83) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "restriction") (:form . "restriction") (:end . 112)\n  (:start . 101) (:id . 59))\n ((:tag . "NN") (:stem . "enzyme") (:form . "enzyme") (:end . 119)\n  (:start . 113) (:id . 60))\n ((:tag . "NNP") (:stem . "BamHI") (:form . "BamHI") (:end . 125)\n  (:start . 120) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.422) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502674@unknown@formal@none@1@S@DNA fragments were separated on a 1% agarose gel and transferred onto a nitrocellular membrane, according to the standard protocol for Southern blotting.@(((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 35) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "NN") (:stem . "agarose") (:form . "agarose") (:end . 44)\n  (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "transfer") (:form . "transferred") (:end . 64)\n  (:start . 53) (:id . 53))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 69) (:start . 65)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "nitrocellular") (:form . "nitrocellular")\n  (:end . 85) (:start . 72) (:id . 56))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 94)\n  (:start . 86) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 105)\n  (:start . 96) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 121)\n  (:start . 113) (:id . 62))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 130)\n  (:start . 122) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 134) (:start . 131)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "southern") (:form . "Southern") (:end . 143)\n  (:start . 135) (:id . 65))\n ((:tag . "NN") (:stem . "blotting") (:form . "blotting") (:end . 152)\n  (:start . 144) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s8.423) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502675@unknown@formal@none@1@S@DNA fragments specifically targeting all exons of the dhtt gene were labeled with 32P-dCTP using the Klenow polymerase and random-hexamer primer method (Amersham) and used as probe.@(((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 26)\n  (:start . 14) (:id . 44))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 36)\n  (:start . 27) (:id . 45))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 40) (:start . 37)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 46) (:start . 41)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 63) (:start . 59)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "label") (:form . "labeled") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 81) (:start . 77)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "32P-dCTP") (:form . "32P-dCTP") (:end . 90)\n  (:start . 82) (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Klenow") (:form . "Klenow") (:end . 107)\n  (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 118)\n  (:start . 108) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "random-hexamer") (:form . "random-hexamer")\n  (:end . 137) (:start . 123) (:id . 61))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 144)\n  (:start . 138) (:id . 62))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 151)\n  (:start . 145) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Amersham") (:form . "Amersham") (:end . 161)\n  (:start . 153) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 171) (:start . 167)\n  (:id . 68))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 174) (:start . 172)\n  (:id . 69))\n ((:tag . "NN") (:stem . "probe") (:form . "probe") (:end . 180)\n  (:start . 175) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s8.424) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502676@unknown@formal@none@1@S@Hybridization was performed overnight at 65°C and the fragments were subsequently washed with SDS/SSC buffers, following standard procedures for Southern blotting.@(((:tag . "NNP") (:stem . "Hybridization") (:form . "Hybridization")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 17) (:start . 14)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 27)\n  (:start . 18) (:id . 44))\n ((:tag . "RB") (:stem . "overnight") (:form . "overnight") (:end . 37)\n  (:start . 28) (:id . 45))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 40) (:start . 38)\n  (:id . 46))\n ((:tag . "NN") (:stem . "65°c") (:form . "65°C") (:end . 45) (:start . 41)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 63)\n  (:start . 54) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 81)\n  (:start . 69) (:id . 52))\n ((:tag . "VBN") (:stem . "wash") (:form . "washed") (:end . 88) (:start . 82)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 93) (:start . 89)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "SDS/SSC") (:form . "SDS/SSC") (:end . 101)\n  (:start . 94) (:id . 55))\n ((:tag . "NNS") (:stem . "buffer") (:form . "buffers") (:end . 109)\n  (:start . 102) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 120)\n  (:start . 111) (:id . 58))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 129)\n  (:start . 121) (:id . 59))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 140)\n  (:start . 130) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 144) (:start . 141)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "southern") (:form . "Southern") (:end . 153)\n  (:start . 145) (:id . 62))\n ((:tag . "NN") (:stem . "blotting") (:form . "blotting") (:end . 162)\n  (:start . 154) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.425) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502677@unknown@formal@none@1@S@The size of the genomic region covering dhtt is about 43 kb (Li et al., 1999), which is too large to be cloned into a transgenic vector by conventional approaches.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "VBG") (:stem . "cover") (:form . "covering") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "RB") (:stem . "about") (:form . "about") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Li") (:form . "Li") (:end . 63) (:start . 61)\n  (:id . 55))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 66) (:start . 64)\n  (:id . 56))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 70) (:start . 67)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 76) (:start . 72)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 84) (:start . 79)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 87) (:start . 85)\n  (:id . 63))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 91) (:start . 88)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 97) (:start . 92)\n  (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 66))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 103) (:start . 101)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "clone") (:form . "cloned") (:end . 110)\n  (:start . 104) (:id . 68))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 115) (:start . 111)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 117) (:start . 116)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 128)\n  (:start . 118) (:id . 71))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 135)\n  (:start . 129) (:id . 72))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 138) (:start . 136)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "conventional") (:form . "conventional") (:end . 151)\n  (:start . 139) (:id . 74))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 162)\n  (:start . 152) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.426) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502678@unknown@formal@none@1@S@Therefore, we engineered a dhtt minigene rescue construct that expresses full-length dhtt under the control of its own endogenous regulatory region.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "engineer") (:form . "engineered") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "minigene") (:form . "minigene") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "express") (:form . "expresses") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 84)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 89) (:start . 85)\n  (:id . 54))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 95) (:start . 90)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 56))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 107)\n  (:start . 100) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 58))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 114) (:start . 111)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 118) (:start . 115)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 129)\n  (:start . 119) (:id . 61))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 140)\n  (:start . 130) (:id . 62))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 147)\n  (:start . 141) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.427) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502679@unknown@formal@none@1@S@In Drosophila, the regulatory elements controlling the endogenous expression pattern of a gene are normally located at the 5' region of the gene, within the upstream 5' untranscribed region and in the first few introns.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "VBG") (:stem . "control") (:form . "controlling") (:end . 50)\n  (:start . 39) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 65)\n  (:start . 55) (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 76)\n  (:start . 66) (:id . 51))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 84)\n  (:start . 77) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 89) (:start . 88)\n  (:id . 54))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 98) (:start . 95)\n  (:id . 56))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 107)\n  (:start . 99) (:id . 57))\n ((:tag . "VBN") (:stem . "locate") (:form . "located") (:end . 115)\n  (:start . 108) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 118) (:start . 116)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 60))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 124) (:start . 123)\n  (:id . 61))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 125) (:start . 124)\n  (:id . 62))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 132)\n  (:start . 126) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 65))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 144) (:start . 140)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 67))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 152)\n  (:start . 146) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "upstream") (:form . "upstream") (:end . 165)\n  (:start . 157) (:id . 70))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 168) (:start . 167)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "untranscribed") (:form . "untranscribed")\n  (:end . 182) (:start . 169) (:id . 73))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 189)\n  (:start . 183) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 193) (:start . 190)\n  (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 196) (:start . 194)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 200) (:start . 197)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 206)\n  (:start . 201) (:id . 78))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 210) (:start . 207)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "intron") (:form . "introns") (:end . 218)\n  (:start . 211) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s8.428) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502680@unknown@formal@none@1@S@In addition, the expression level of a gene is also affected by its 3' untranslated region.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 27)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 43) (:start . 39)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 46) (:start . 44)\n  (:id . 51))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 51) (:start . 47)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "affect") (:form . "affected") (:end . 60)\n  (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 69) (:start . 68)\n  (:id . 56))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 70) (:start . 69)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "untranslated") (:form . "untranslated") (:end . 83)\n  (:start . 71) (:id . 58))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 90)\n  (:start . 84) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s8.429) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502681@unknown@formal@none@1@S@As a result, we isolated a 14.9 kb genomic DNA fragment from the BAC clone BACR10P23 (CHORI) following double digestion with the restriction enzymes XbaI and AscI.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "isolate") (:form . "isolated") (:end . 24)\n  (:start . 16) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 48))\n ((:tag . "CD") (:stem . "14.9") (:form . "14.9") (:end . 31) (:start . 27)\n  (:id . 49))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 34) (:start . 32)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 42)\n  (:start . 35) (:id . 51))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 46) (:start . 43)\n  (:id . 52))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 55)\n  (:start . 47) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 60) (:start . 56)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "BAC") (:form . "BAC") (:end . 68) (:start . 65)\n  (:id . 56))\n ((:tag . "NN") (:stem . "clone") (:form . "clone") (:end . 74) (:start . 69)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "BACR10P23") (:form . "BACR10P23") (:end . 84)\n  (:start . 75) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "CHORI") (:form . "CHORI") (:end . 91) (:start . 86)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 102)\n  (:start . 93) (:id . 62))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 109)\n  (:start . 103) (:id . 63))\n ((:tag . "NN") (:stem . "digestion") (:form . "digestion") (:end . 119)\n  (:start . 110) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 124) (:start . 120)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n  (:id . 66))\n ((:tag . "NN") (:stem . "restriction") (:form . "restriction") (:end . 140)\n  (:start . 129) (:id . 67))\n ((:tag . "NNS") (:stem . "enzyme") (:form . "enzymes") (:end . 148)\n  (:start . 141) (:id . 68))\n ((:tag . "NNP") (:stem . "XbaI") (:form . "XbaI") (:end . 153) (:start . 149)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "AscI") (:form . "AscI") (:end . 162) (:start . 158)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s8.430) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502682@unknown@formal@none@1@S@The XbaI site was located at the end of the CG9990 gene and the AscI site was within the tenth exon of the dhtt-coding region, thus the DNA fragment covered all of the 5' untranscribed region of the dhtt gene together with the first ten introns and exons of the gene.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "XbaI") (:form . "XbaI") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "locate") (:form . "located") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cg9990") (:form . "CG9990") (:end . 50)\n  (:start . 44) (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AscI") (:form . "AscI") (:end . 68) (:start . 64)\n  (:id . 56))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 73) (:start . 69)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 77) (:start . 74)\n  (:id . 58))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 84)\n  (:start . 78) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 60))\n ((:tag . "NN") (:stem . "tenth") (:form . "tenth") (:end . 94) (:start . 89)\n  (:id . 61))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 99) (:start . 95)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "dhtt-coding") (:form . "dhtt-coding") (:end . 118)\n  (:start . 107) (:id . 65))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 125)\n  (:start . 119) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 67))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 131) (:start . 127)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 135) (:start . 132)\n  (:id . 69))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 139) (:start . 136)\n  (:id . 70))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 148)\n  (:start . 140) (:id . 71))\n ((:tag . "VBD") (:stem . "cover") (:form . "covered") (:end . 156)\n  (:start . 149) (:id . 72))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 160) (:start . 157)\n  (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 75))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 169) (:start . 168)\n  (:id . 76))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 170) (:start . 169)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "untranscribed") (:form . "untranscribed")\n  (:end . 184) (:start . 171) (:id . 78))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 191)\n  (:start . 185) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 194) (:start . 192)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 198) (:start . 195)\n  (:id . 81))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 203) (:start . 199)\n  (:id . 82))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 208) (:start . 204)\n  (:id . 83))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 217)\n  (:start . 209) (:id . 84))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 222) (:start . 218)\n  (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 226) (:start . 223)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 232)\n  (:start . 227) (:id . 87))\n ((:tag . "CD") (:stem . "ten") (:form . "ten") (:end . 236) (:start . 233)\n  (:id . 88))\n ((:tag . "NNS") (:stem . "intron") (:form . "introns") (:end . 244)\n  (:start . 237) (:id . 89))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 248) (:start . 245)\n  (:id . 90))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 254)\n  (:start . 249) (:id . 91))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 257) (:start . 255)\n  (:id . 92))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 261) (:start . 258)\n  (:id . 93))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 266) (:start . 262)\n  (:id . 94))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 267) (:start . 266)\n  (:id . 95)))@@@1@54@((:identifiers (:sid . :s8.431) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502683@unknown@formal@none@1@S@We also isolated a 1.2 kb genomic DNA fragment, by double digestion with StuI-EcoRI, that covers the 3' end of the dhtt gene, including the last exon of dhtt and the remaining polyA sites and untranscribed region at the 3' end of the gene.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "isolate") (:form . "isolated") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "CD") (:stem . "1.2") (:form . "1.2") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 57)\n  (:start . 51) (:id . 53))\n ((:tag . "NN") (:stem . "digestion") (:form . "digestion") (:end . 67)\n  (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "StuI-EcoRI") (:form . "StuI-EcoRI") (:end . 83)\n  (:start . 73) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 89) (:start . 85)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "cover") (:form . "covers") (:end . 96)\n  (:start . 90) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 103) (:start . 102)\n  (:id . 62))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 107) (:start . 104)\n  (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 65))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 119) (:start . 115)\n  (:id . 66))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 124) (:start . 120)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 135)\n  (:start . 126) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 144) (:start . 140)\n  (:id . 71))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 149) (:start . 145)\n  (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n  (:id . 73))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 157) (:start . 153)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 76))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 175)\n  (:start . 166) (:id . 77))\n ((:tag . "NN") (:stem . "polya") (:form . "polyA") (:end . 181)\n  (:start . 176) (:id . 78))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 187)\n  (:start . 182) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 191) (:start . 188)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "untranscribed") (:form . "untranscribed")\n  (:end . 205) (:start . 192) (:id . 81))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 212)\n  (:start . 206) (:id . 82))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 215) (:start . 213)\n  (:id . 83))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 219) (:start . 216)\n  (:id . 84))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 221) (:start . 220)\n  (:id . 85))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 222) (:start . 221)\n  (:id . 86))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 226) (:start . 223)\n  (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 229) (:start . 227)\n  (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 233) (:start . 230)\n  (:id . 89))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 238) (:start . 234)\n  (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s8.432) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502684@unknown@formal@none@1@S@Next, we assembled and isolated a 6.6 kb dhtt cDNA fragment, by digestion with AscI and StuI, that covered most of the 3' cDNA region of dhtt, from the single AscI site within the tenth exon to the StuI site within the last exon.@(((:tag . "RB") (:stem . "next") (:form . "Next") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "assemble") (:form . "assembled") (:end . 18)\n  (:start . 9) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "isolate") (:form . "isolated") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "CD") (:stem . "6.6") (:form . "6.6") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . 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(:end . 229) (:start . 228)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s8.433) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502685@unknown@formal@none@1@S@The dhtt minigene rescue construct was generated by ligating and fusing, in frame, the three fragments that cover all of the dhtt regulatory and coding regions: (1) the 5' 14.9 kb genomic DNA fragment that covered all of the 5' untranscribed region of the dhtt gene, as well as the first ten introns and exons of dhtt; (2) the middle 6.6 kb of the dhtt cDNA fragment that covered from exon 10 to exon 29; and (3) the 3' 1.2 kb genomic DNA fragment that covered exon 29 and the polyA sites at the 3' end of the gene, as well as the remaining 3' untranscribed region.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "minigene") (:form . "minigene") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . 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"the") (:end . 495) (:start . 492)\n  (:id . 150))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 497) (:start . 496)\n  (:id . 151))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 498) (:start . 497)\n  (:id . 152))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 502) (:start . 499)\n  (:id . 153))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 505) (:start . 503)\n  (:id . 154))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 509) (:start . 506)\n  (:id . 155))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 514) (:start . 510)\n  (:id . 156))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 515) (:start . 514)\n  (:id . 157))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 518) (:start . 516)\n  (:id . 158))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 523) (:start . 519)\n  (:id . 159))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 526) (:start . 524)\n  (:id . 160))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 530) (:start . 527)\n  (:id . 161))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 540)\n  (:start . 531) (:id . 162))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 542) (:start . 541)\n  (:id . 163))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 543) (:start . 542)\n  (:id . 164))\n ((:tag . "JJ") (:stem . "untranscribed") (:form . "untranscribed")\n  (:end . 557) (:start . 544) (:id . 165))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 564)\n  (:start . 558) (:id . 166))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 565) (:start . 564)\n  (:id . 167)))@@@1@126@((:identifiers (:sid . :s8.434) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502686@unknown@formal@none@1@S@The 22.7 kb dhtt minigene was cloned into the NotI and XbaI sites in the pCaspeR-4 transgenic vector.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "22.7") (:form . "22.7") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "minigene") (:form . "minigene") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "clone") (:form . "cloned") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "NotI") (:form . "NotI") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "XbaI") (:form . "XbaI") (:end . 59) (:start . 55)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "NN") (:stem . "pcasper-4") (:form . "pCaspeR-4") (:end . 82)\n  (:start . 73) (:id . 57))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 93)\n  (:start . 83) (:id . 58))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 100)\n  (:start . 94) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s8.435) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502687@unknown@formal@none@1@S@After generating transgenic flies with this dhtt minigene rescue construct, we crossed these animals into the dhtt-ko mutant background to test whether the mobility and viability phenotypes of dhtt-ko mutants could be rescued.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "generate") (:form . "generating") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 27)\n  (:start . 17) (:id . 44))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 33) (:start . 28)\n  (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "NN") (:stem . "minigene") (:form . "minigene") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 64)\n  (:start . 58) (:id . 50))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 74)\n  (:start . 65) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "cross") (:form . "crossed") (:end . 86)\n  (:start . 79) (:id . 54))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 92) (:start . 87)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 100)\n  (:start . 93) (:id . 56))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 105) (:start . 101)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 117)\n  (:start . 110) (:id . 59))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 124)\n  (:start . 118) (:id . 60))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 135)\n  (:start . 125) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 138) (:start . 136)\n  (:id . 62))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 143) (:start . 139)\n  (:id . 63))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 151)\n  (:start . 144) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 65))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 164)\n  (:start . 156) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 67))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 178)\n  (:start . 169) (:id . 68))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 189)\n  (:start . 179) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 192) (:start . 190)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 200)\n  (:start . 193) (:id . 71))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 208)\n  (:start . 201) (:id . 72))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 214)\n  (:start . 209) (:id . 73))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 217) (:start . 215)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 225)\n  (:start . 218) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x8.436.1) (:span 209 214))\n  ((:id . :x8.436.2) (:span 144 151)))\n (:hscopes ((:id . :x8.436.1) (:span 152 225))\n  ((:id . :x8.436.2) (:span 144 225)))\n (:identifiers (:sid . :s8.436) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502688@unknown@formal@none@1@S@Based on the published dhtt cDNA sequence (Li et al., 1999), we isolated overlapping fragments covering the full-length of the dhtt cDNA by PCR amplification using Pfu polymerase.@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "publish") (:form . "published") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "cdna") (:form . "cDNA") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Li") (:form . "Li") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 58) (:start . 54)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 59) (:start . 58)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 63) (:start . 61)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "isolate") (:form . "isolated") (:end . 72)\n  (:start . 64) (:id . 58))\n ((:tag . "VBG") (:stem . "overlap") (:form . "overlapping") (:end . 84)\n  (:start . 73) (:id . 59))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 94)\n  (:start . 85) (:id . 60))\n ((:tag . "VBG") (:stem . "cover") (:form . "covering") (:end . 103)\n  (:start . 95) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 62))\n ((:tag . "NN") (:stem . "full-length") (:form . "full-length") (:end . 119)\n  (:start . 108) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 65))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 131) (:start . 127)\n  (:id . 66))\n ((:tag . "NN") (:stem . "cdna") (:form . "cDNA") (:end . 136) (:start . 132)\n  (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 139) (:start . 137)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 143) (:start . 140)\n  (:id . 69))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 157) (:start . 144) (:id . 70))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 163) (:start . 158)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Pfu") (:form . "Pfu") (:end . 167) (:start . 164)\n  (:id . 72))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 178)\n  (:start . 168) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.437) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502689@unknown@formal@none@1@S@We then assembled a full-length dhtt cDNA construct using these sequencing-verified dhtt fragments, cloned it into a pUASP vector, and generated transgenic fly lines by following standard protocols.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "assemble") (:form . "assembled") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cdna") (:form . "cDNA") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "sequencing-verified")\n  (:form . "sequencing-verified") (:end . 83) (:start . 64) (:id . 52))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 88) (:start . 84)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "fragment") (:form . "fragments") (:end . 98)\n  (:start . 89) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "clone") (:form . "cloned") (:end . 106)\n  (:start . 100) (:id . 56))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 109) (:start . 107)\n  (:id . 57))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 114) (:start . 110)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 116) (:start . 115)\n  (:id . 59))\n ((:tag . "NN") (:stem . "puasp") (:form . "pUASP") (:end . 122)\n  (:start . 117) (:id . 60))\n ((:tag . "NN") (:stem . "vector") (:form . "vector") (:end . 129)\n  (:start . 123) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 144)\n  (:start . 135) (:id . 64))\n ((:tag . "JJ") (:stem . "transgenic") (:form . "transgenic") (:end . 155)\n  (:start . 145) (:id . 65))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 159) (:start . 156)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 165)\n  (:start . 160) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 168) (:start . 166)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 178)\n  (:start . 169) (:id . 69))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 187)\n  (:start . 179) (:id . 70))\n ((:tag . "NNS") (:stem . "protocol") (:form . "protocols") (:end . 197)\n  (:start . 188) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s8.438) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502690@unknown@formal@none@1@S@Total RNA samples were isolated, using Trizol reagent (Invitrogen), from adult animals of the following genotypes: w1118 wild-type control, homozygous dhtt-ko mutants and dhtt-ko Rescue.@(((:tag . "JJ") (:stem . "total") (:form . "Total") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Trizol") (:form . "Trizol") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "reagent") (:form . "reagent") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 65)\n  (:start . 55) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 78) (:start . 73)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 86)\n  (:start . 79) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 103)\n  (:start . 94) (:id . 60))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 113)\n  (:start . 104) (:id . 61))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 114) (:start . 113)\n  (:id . 62))\n ((:tag . "CD") (:stem . "w1118") (:form . "w1118") (:end . 120)\n  (:start . 115) (:id . 63))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 130)\n  (:start . 121) (:id . 64))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 138)\n  (:start . 131) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "homozygous") (:form . "homozygous") (:end . 150)\n  (:start . 140) (:id . 67))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 158)\n  (:start . 151) (:id . 68))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 166)\n  (:start . 159) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 170) (:start . 167)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 178)\n  (:start . 171) (:id . 71))\n ((:tag . "NN") (:stem . "rescue") (:form . "Rescue") (:end . 185)\n  (:start . 179) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s8.439) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502691@unknown@formal@none@1@S@RT-PCR reactions were performed using Superscript one-step RT-PCR with Platinum Taq (Invitrogen) following the manufacturer’s instructions.@(((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "reaction") (:form . "reactions") (:end . 16)\n  (:start . 7) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 37) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "superscript") (:form . "Superscript") (:end . 49)\n  (:start . 38) (:id . 47))\n ((:tag . "JJ") (:stem . "one-step") (:form . "one-step") (:end . 58)\n  (:start . 50) (:id . 48))\n ((:tag . "NN") (:stem . "rt-pcr") (:form . "RT-PCR") (:end . 65)\n  (:start . 59) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 70) (:start . 66)\n  (:id . 50))\n ((:tag . "NN") (:stem . "platinum") (:form . "Platinum") (:end . 79)\n  (:start . 71) (:id . 51))\n ((:tag . "NNP") (:stem . "Taq") (:form . "Taq") (:end . 83) (:start . 80)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 95)\n  (:start . 85) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 106)\n  (:start . 97) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 57))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 123)\n  (:start . 111) (:id . 58))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 125) (:start . 124)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 138)\n  (:start . 126) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s8.440) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502692@unknown@formal@none@1@S@PCR primers were designed as follows: rp49 control: forward (in exon 1 of rp49) 5'-ACCATCCGCCCAGCATACAGG-3', reverse (in exon 2 of rp49) 5' -TTGGCGCGCTCGACAATCTCC-3'; dhtt-N: forward (in exon 5 of dhtt) 5' -GCCAATGTAGCCAGAGTCTG-3', reverse (in exon 6 of dhtt) 5' -CGCATTCGCTGATGCTGCGTG-3'; dhtt-M: forward (in exon 13 of dhtt) 5'-AAGCTATTCGAGCCGATGGTC-3', reverse (in exon 15 of dhtt) 5'-GCACCAGGAATCTCAGCATGG-3' ; dhtt-C: forward (in exon 23 of dhtt) 5'-TCGGGAATTGACTTTCGCAGC-3', reverse (in exon 24 of dhtt) 5'-TGCAGTTTGAGGCAGCGTTCC-3'.@(((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "rp49") (:form . "rp49") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 50)\n  (:start . 43) (:id . 50))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "RB") (:stem . "forward") (:form . "forward") (:end . 59)\n  (:start . 52) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . 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":") (:end . 174) (:start . 173)\n  (:id . 77))\n ((:tag . "RB") (:stem . "forward") (:form . "forward") (:end . 182)\n  (:start . 175) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 184) (:start . 183)\n  (:id . 79))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 186) (:start . 184)\n  (:id . 80))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 191) (:start . 187)\n  (:id . 81))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 193) (:start . 192)\n  (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 196) (:start . 194)\n  (:id . 83))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 201) (:start . 197)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 202) (:start . 201)\n  (:id . 85))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 204) (:start . 203)\n  (:id . 86))\n ((:tag . "SYM") (:stem . "'") (:form . "’") (:end . 205) (:start . 204)\n  (:id . 87))\n ((:tag . "NNP") (:stem . 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"dhtt-C") (:end . 421)\n  (:start . 415) (:id . 128))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 422) (:start . 421)\n  (:id . 129))\n ((:tag . "RB") (:stem . "forward") (:form . "forward") (:end . 430)\n  (:start . 423) (:id . 130))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 432) (:start . 431)\n  (:id . 131))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 434) (:start . 432)\n  (:id . 132))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 439) (:start . 435)\n  (:id . 133))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 442) (:start . 440)\n  (:id . 134))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 445) (:start . 443)\n  (:id . 135))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 450) (:start . 446)\n  (:id . 136))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 451) (:start . 450)\n  (:id . 137))\n ((:tag . "NN") (:stem . "5'-tcgggaattgactttcgcagc-3")\n  (:form . "5’-TCGGGAATTGACTTTCGCAGC-3") (:end . 478) (:start . 452)\n  (:id . 138))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 479) (:start . 478)\n  (:id . 139))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 480) (:start . 479)\n  (:id . 140))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 488)\n  (:start . 481) (:id . 141))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 490) (:start . 489)\n  (:id . 142))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 492) (:start . 490)\n  (:id . 143))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 497) (:start . 493)\n  (:id . 144))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 500) (:start . 498)\n  (:id . 145))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 503) (:start . 501)\n  (:id . 146))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 508) (:start . 504)\n  (:id . 147))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 509) (:start . 508)\n  (:id . 148))\n ((:tag . "NN") (:stem . "5'-tgcagtttgaggcagcgttcc-3")\n  (:form . "5’-TGCAGTTTGAGGCAGCGTTCC-3") (:end . 536) (:start . 510)\n  (:id . 149))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 537) (:start . 536)\n  (:id . 150))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 538) (:start . 537)\n  (:id . 151)))@@@1@110@((:identifiers (:sid . :s8.441) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502693@unknown@formal@none@1@S@Using the motif-predicting program developed by M.A. Andrade at the EMBL (http://www.embl-heidelberg.de/~andrade/papers/rep/search.html), both dHtt and human Htt were analyzed for the presence of HEAT repeats.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "motif-predicting") (:form . "motif-predicting")\n  (:end . 26) (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 34)\n  (:start . 27) (:id . 45))\n ((:tag . "VBN") (:stem . "develop") (:form . "developed") (:end . 44)\n  (:start . 35) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 47) (:start . 45)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "M.A.") (:form . "M.A.") (:end . 52) (:start . 48)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Andrade") (:form . "Andrade") (:end . 60)\n  (:start . 53) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "EMBL") (:form . "EMBL") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n  (:id . 53))\n ((:tag . "JJ")\n  (:stem . "http://www.embl-heidelberg.de/~andrade/papers/rep/search.html")\n  (:form . "http://www.embl-heidelberg.de/~andrade/papers/rep/search.html")\n  (:end . 135) (:start . 74) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 56))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 142) (:start . 138)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 147) (:start . 143)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 151) (:start . 148)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 157)\n  (:start . 152) (:id . 60))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 161) (:start . 158)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 166) (:start . 162)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 175)\n  (:start . 167) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 179) (:start . 176)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n  (:id . 65))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 192)\n  (:start . 184) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 195) (:start . 193)\n  (:id . 67))\n ((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 200) (:start . 196)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 208)\n  (:start . 201) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.442) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502694@unknown@formal@none@1@S@Using the default parameters at the site and including the AAA, ADB and IMB groups of HEAT repeats (Andrade et al., 2001), a total of 40 and 38 HEAT repeats were identified for Htt and dHtt, respectively.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 54)\n  (:start . 45) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AAA") (:form . "AAA") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "ADB") (:form . "ADB") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "IMB") (:form . "IMB") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 82)\n  (:start . 76) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 58))\n ((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 90) (:start . 86)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 98)\n  (:start . 91) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Andrade") (:form . "Andrade") (:end . 107)\n  (:start . 100) (:id . 62))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 110) (:start . 108)\n  (:id . 63))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 114) (:start . 111)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 65))\n ((:tag . "CD") (:stem . "2001") (:form . "2001") (:end . 120) (:start . 116)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 121) (:start . 120)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 124) (:start . 123)\n  (:id . 69))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 130)\n  (:start . 125) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 71))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 136) (:start . 134)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 73))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 143) (:start . 141)\n  (:id . 74))\n ((:tag . "NN") (:stem . "heat") (:form . "HEAT") (:end . 148) (:start . 144)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "repeat") (:form . "repeats") (:end . 156)\n  (:start . 149) (:id . 76))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 161) (:start . 157)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 172)\n  (:start . 162) (:id . 78))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 176) (:start . 173)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Htt") (:form . "Htt") (:end . 180) (:start . 177)\n  (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 184) (:start . 181)\n  (:id . 81))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 189) (:start . 185)\n  (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n  (:id . 83))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 203)\n  (:start . 191) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s8.443) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502695@unknown@formal@none@1@S@Sample preparation and staining for embryos, larval tissues and adult fly eyes have been described previously (Sullivan et al., 2000).@(((:tag . "NN") (:stem . "sample") (:form . "Sample") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "preparation") (:form . "preparation") (:end . 18)\n  (:start . 7) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "eye") (:form . "eyes") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 98)\n  (:start . 89) (:id . 57))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 109)\n  (:start . 99) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Sullivan") (:form . "Sullivan") (:end . 119)\n  (:start . 111) (:id . 60))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 126) (:start . 123)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 63))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 132) (:start . 128)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s8.444) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502696@unknown@formal@none@1@S@To analyze NMJs, wandering third instar larvae were dissected in Ca2+-free saline (128 mM NaCl, 2 mM KCl, 0.1 mM CaCl2, 4 mM MgCl2, 35.5 mM sucrose, 5 mM Hepes at pH 7.2, 1 mM EGTA) and stained, as described (Sullivan et al., 2000).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "analyze") (:form . "analyze") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "nmj") (:form . "NMJs") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "wander") (:form . "wandering") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "dissect") (:form . "dissected") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "ca2+-free") (:form . "Ca2+-free") (:end . 74)\n  (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "saline") (:form . "saline") (:end . 81)\n  (:start . 75) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "CD") (:stem . "128") (:form . "128") (:end . 86) (:start . 83)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "NaCl") (:form . "NaCl") (:end . 94) (:start . 90)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "CD") (:stem . 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",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 71))\n ((:tag . "CD") (:stem . "35.5") (:form . "35.5") (:end . 136) (:start . 132)\n  (:id . 72))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 139) (:start . 137)\n  (:id . 73))\n ((:tag . "NN") (:stem . "sucrose") (:form . "sucrose") (:end . 147)\n  (:start . 140) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 75))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 150) (:start . 149)\n  (:id . 76))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 153) (:start . 151)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "hepe") (:form . "Hepes") (:end . 159)\n  (:start . 154) (:id . 78))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 162) (:start . 160)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "pH") (:form . "pH") (:end . 165) (:start . 163)\n  (:id . 80))\n ((:tag . "CD") (:stem . "7.2") (:form . "7.2") (:end . 169) (:start . 166)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 170) (:start . 169)\n  (:id . 82))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 172) (:start . 171)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 175) (:start . 173)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "EGTA") (:form . "EGTA") (:end . 180) (:start . 176)\n  (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 181) (:start . 180)\n  (:id . 86))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n  (:id . 87))\n ((:tag . "VBD") (:stem . "stain") (:form . "stained") (:end . 193)\n  (:start . 186) (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 194) (:start . 193)\n  (:id . 89))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 197) (:start . 195)\n  (:id . 90))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 207)\n  (:start . 198) (:id . 91))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 209) (:start . 208)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "Sullivan") (:form . "Sullivan") (:end . 217)\n  (:start . 209) (:id . 93))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 220) (:start . 218)\n  (:id . 94))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 224) (:start . 221)\n  (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 225) (:start . 224)\n  (:id . 96))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 230) (:start . 226)\n  (:id . 97))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 231) (:start . 230)\n  (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 99)))@@@1@58@((:identifiers (:sid . :s8.445) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502697@unknown@formal@none@1@S@1–2 µM thin sections of embedded adult eyes were cut using a microtome and imaged directly without further dye staining.@(((:tag . "CD") (:stem . "1–2") (:form . "1–2") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "µM") (:form . "µM") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "thin") (:form . "thin") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "embed") (:form . "embedded") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "eye") (:form . "eyes") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "cut") (:form . "cut") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "microtome") (:form . "microtome") (:end . 70)\n  (:start . 61) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "image") (:form . "imaged") (:end . 81)\n  (:start . 75) (:id . 56))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 90)\n  (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 98)\n  (:start . 91) (:id . 58))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 106)\n  (:start . 99) (:id . 59))\n ((:tag . "NN") (:stem . "dye") (:form . "dye") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 119)\n  (:start . 111) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.446) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502698@unknown@formal@none@1@S@To stain and image the adult brains, flies were dissected in 1× PBS or in Drosophila M3 medium, to remove cuticles and external eye tissues, then fixed in 4% formaldehyde in 1× PBS for 1 hour at room temperature (RT), washed six times with 1× PBT for 1 hour, and stained with primary and secondary antibodies.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "stain") (:form . "stain") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "image") (:form . "image") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 35)\n  (:start . 29) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 42) (:start . 37)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "dissect") (:form . "dissected") (:end . 57)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "NN") (:stem . "1×") (:form . "1×") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "PBS") (:form . "PBS") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 70) (:start . 68)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 57))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 84)\n  (:start . 74) (:id . 58))\n ((:tag . "NNP") (:stem . "M3") (:form . "M3") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 94)\n  (:start . 88) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n  (:id . 62))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 105)\n  (:start . 99) (:id . 63))\n ((:tag . "NNS") (:stem . "cuticle") (:form . "cuticles") (:end . 114)\n  (:start . 106) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "external") (:form . "external") (:end . 127)\n  (:start . 119) (:id . 66))\n ((:tag . "NN") (:stem . "eye") (:form . "eye") (:end . 131) (:start . 128)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "tissue") (:form . "tissues") (:end . 139)\n  (:start . 132) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 69))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 145) (:start . 141)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 151) (:start . 146)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n  (:id . 72))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 156) (:start . 155)\n  (:id . 73))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 157) (:start . 156)\n  (:id . 74))\n ((:tag . "NN") (:stem . "formaldehyde") (:form . "formaldehyde") (:end . 170)\n  (:start . 158) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 173) (:start . 171)\n  (:id . 76))\n ((:tag . "CD") (:stem . "1×") (:form . "1×") (:end . 176) (:start . 174)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "PBS") (:form . "PBS") (:end . 180) (:start . 177)\n  (:id . 78))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 184) (:start . 181)\n  (:id . 79))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 186) (:start . 185)\n  (:id . 80))\n ((:tag . "NN") (:stem . "hour") (:form . "hour") (:end . 191) (:start . 187)\n  (:id . 81))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 194) (:start . 192)\n  (:id . 82))\n ((:tag . "NN") (:stem . "room") (:form . "room") (:end . 199) (:start . 195)\n  (:id . 83))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 211)\n  (:start . 200) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 213) (:start . 212)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "RT") (:form . "RT") (:end . 215) (:start . 213)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 216) (:start . 215)\n  (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 217) (:start . 216)\n  (:id . 88))\n ((:tag . "VBD") (:stem . "wash") (:form . "washed") (:end . 224)\n  (:start . 218) (:id . 89))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 228) (:start . 225)\n  (:id . 90))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 234)\n  (:start . 229) (:id . 91))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 239) (:start . 235)\n  (:id . 92))\n ((:tag . "NN") (:stem . "1×") (:form . "1×") (:end . 242) (:start . 240)\n  (:id . 93))\n ((:tag . "NN") (:stem . "pbt") (:form . "PBT") (:end . 246) (:start . 243)\n  (:id . 94))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 250) (:start . 247)\n  (:id . 95))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 252) (:start . 251)\n  (:id . 96))\n ((:tag . "NN") (:stem . "hour") (:form . "hour") (:end . 257) (:start . 253)\n  (:id . 97))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 258) (:start . 257)\n  (:id . 98))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 262) (:start . 259)\n  (:id . 99))\n ((:tag . "VBD") (:stem . "stain") (:form . "stained") (:end . 270)\n  (:start . 263) (:id . 100))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 275) (:start . 271)\n  (:id . 101))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 283)\n  (:start . 276) (:id . 102))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 287) (:start . 284)\n  (:id . 103))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 297)\n  (:start . 288) (:id . 104))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 308)\n  (:start . 298) (:id . 105))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 309) (:start . 308)\n  (:id . 106)))@@@1@65@((:identifiers (:sid . :s8.447) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502699@unknown@formal@none@1@S@Collection and fixation of Drosophila embryos, larvae tissue dissection and fixation, as well as RNA in situ hybridization were carried out according to standard procedures (Hauptmann and Gerster, 2000).@(((:tag . "NNP") (:stem . "Collection") (:form . "Collection") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "fixation") (:form . "fixation") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "larvae") (:form . "larvae") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "tissue") (:form . "tissue") (:end . 60)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "dissection") (:form . "dissection") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "NN") (:stem . "fixation") (:form . "fixation") (:end . 84)\n  (:start . 76) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 54))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "FW") (:stem . "situ") (:form . "situ") (:end . 108) (:start . 104)\n  (:id . 60))\n ((:tag . "NN") (:stem . "hybridization") (:form . "hybridization")\n  (:end . 122) (:start . 109) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 127) (:start . 123)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 135)\n  (:start . 128) (:id . 63))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 139) (:start . 136)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 149)\n  (:start . 140) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 152) (:start . 150)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 161)\n  (:start . 153) (:id . 67))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 172)\n  (:start . 162) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Hauptmann") (:form . "Hauptmann") (:end . 183)\n  (:start . 174) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 187) (:start . 184)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Gerster") (:form . "Gerster") (:end . 195)\n  (:start . 188) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n  (:id . 73))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 201) (:start . 197)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 202) (:start . 201)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.448) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502700@unknown@formal@none@1@S@The DIG-labeled RNA probes were generated according to the manufacturer’s instructions (Roche, Indianapolis, IN).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "dig-labeled") (:form . "DIG-labeled") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "probe") (:form . "probes") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 51)\n  (:start . 42) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 71)\n  (:start . 59) (:id . 51))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 73) (:start . 72)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 86)\n  (:start . 74) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Roche") (:form . "Roche") (:end . 93) (:start . 88)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Indianapolis") (:form . "Indianapolis")\n  (:end . 107) (:start . 95) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "IN") (:form . "IN") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s8.449) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502701@unknown@formal@none@1@S@The dhtt exon 8 and exon 20 sequences were used to generate dhtt-specific in situ probes, which gave similar in situ results.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "exon") (:form . "exon") (:end . 24) (:start . 20)\n  (:id . 47))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 37)\n  (:start . 28) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 59)\n  (:start . 51) (:id . 53))\n ((:tag . "JJ") (:stem . "dhtt-specific") (:form . "dhtt-specific")\n  (:end . 73) (:start . 60) (:id . 54))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "FW") (:stem . "situ") (:form . "situ") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "probe") (:form . "probes") (:end . 88)\n  (:start . 82) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 95) (:start . 90)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "give") (:form . "gave") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 108)\n  (:start . 101) (:id . 61))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 62))\n ((:tag . "FW") (:stem . "situ") (:form . "situ") (:end . 116) (:start . 112)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 124)\n  (:start . 117) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s8.450) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502702@unknown@formal@none@1@S@The samples for in situ hybridization were analyzed with a Zeiss Axiophot 2 compound microscope.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "FW") (:stem . "situ") (:form . "situ") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "hybridization") (:form . "hybridization")\n  (:end . 37) (:start . 24) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Zeiss") (:form . "Zeiss") (:end . 64) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Axiophot") (:form . "Axiophot") (:end . 73)\n  (:start . 65) (:id . 53))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "compound") (:form . "compound") (:end . 84)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "microscope") (:form . "microscope") (:end . 95)\n  (:start . 85) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.451) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502703@unknown@formal@none@1@S@To generate the antibody against dHtt, a cDNA fragment corresponding to the N-terminal 459 amino acids of dHtt was cloned into the pGEX-4T1 vector; the corresponding GST-fusion protein was purified according to manufacturer’s instructions (Promega) and used to produce polyclonal antibody in a rabbit (Convance).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dHtt") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cdna") (:form . "cDNA") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 68)\n  (:start . 55) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "n-terminal") (:form . "N-terminal") (:end . 86)\n  (:start . 76) (:id . 55))\n ((:tag . "CD") (:stem . "459") (:form . "459") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "acid") (:form . 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"the") (:end . 151) (:start . 148)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 165)\n  (:start . 152) (:id . 69))\n ((:tag . "NN") (:stem . "gst-fusion") (:form . "GST-fusion") (:end . 176)\n  (:start . 166) (:id . 70))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 184)\n  (:start . 177) (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 188) (:start . 185)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 197)\n  (:start . 189) (:id . 73))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 207)\n  (:start . 198) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 210) (:start . 208)\n  (:id . 75))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 223)\n  (:start . 211) (:id . 76))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 225) (:start . 224)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 238)\n  (:start . 226) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 240) (:start . 239)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Promega") (:form . "Promega") (:end . 247)\n  (:start . 240) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 248) (:start . 247)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 252) (:start . 249)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 257) (:start . 253)\n  (:id . 83))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 260) (:start . 258)\n  (:id . 84))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 268)\n  (:start . 261) (:id . 85))\n ((:tag . "JJ") (:stem . "polyclonal") (:form . "polyclonal") (:end . 279)\n  (:start . 269) (:id . 86))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 288)\n  (:start . 280) (:id . 87))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 291) (:start . 289)\n  (:id . 88))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 293) (:start . 292)\n  (:id . 89))\n ((:tag . "NN") (:stem . "rabbit") (:form . "rabbit") (:end . 300)\n  (:start . 294) (:id . 90))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 302) (:start . 301)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "Convance") (:form . "Convance") (:end . 310)\n  (:start . 302) (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 311) (:start . 310)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 312) (:start . 311)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s8.452) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502704@unknown@formal@none@1@S@The antiserum was affinity-purified and used at a final dilution of 1:200.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "antiserum") (:form . "antiserum") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "affinity-purifie") (:form . "affinity-purified")\n  (:end . 35) (:start . 18) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 44) (:start . 40)\n  (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dilution") (:form . "dilution") (:end . 64)\n  (:start . 56) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "CD") (:stem . "1:200") (:form . "1:200") (:end . 73) (:start . 68)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s8.453) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502705@unknown@formal@none@1@S@Primary antibodies were applied at 4°C overnight at the following dilutions: rabbit anti-GFP (1:1000, Molecular Probes); rabbit anti-fasciclin II (1:400) and anti-DIG (1:40,000), both generously provided by Mary Packard and Vivian Budnik (Budnik et al., 1996; Koh et al., 1999); rabbit anti-synaptotagmin (1:500) (Littleton et al., 1993); mouse anti-α-tubulin (1:10,000, Sigma); monoclonal mouse anti-fasciclin II (1D4, 1:20), anti-DIG (1:20), anti-CSP (1:20), anti-synapsin (1:50), anti-α-spectrin (1:20), anti-Armadillo (1:100), nc-82 (1:50) and anti-Futsch (22C10, 1:100) (all from Developmental Studies Hybridoma Bank) (Hummel et al., 2000; Roos et al., 2000); goat anti-HRP (1:500, Jackson Labs); Alexa488-, Alexa594- and Alexa647-conjugated secondary antibodies (all used at 1:500, Molecular Probes).@(((:tag . "JJ") (:stem . "primary") (:form . "Primary") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "antibody") (:form . 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"DT") (:stem . "both") (:form . "both") (:end . 183) (:start . 179)\n  (:id . 75))\n ((:tag . "RB") (:stem . "generously") (:form . "generously") (:end . 194)\n  (:start . 184) (:id . 76))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 203)\n  (:start . 195) (:id . 77))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 206) (:start . 204)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Mary") (:form . "Mary") (:end . 211) (:start . 207)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Packard") (:form . "Packard") (:end . 219)\n  (:start . 212) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 223) (:start . 220)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Vivian") (:form . "Vivian") (:end . 230)\n  (:start . 224) (:id . 82))\n ((:tag . "NNP") (:stem . "Budnik") (:form . "Budnik") (:end . 237)\n  (:start . 231) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 239) (:start . 238)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Budnik") (:form . 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(:end . 330) (:start . 327)\n  (:id . 106))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 331) (:start . 330)\n  (:id . 107))\n ((:tag . "CD") (:stem . "1993") (:form . "1993") (:end . 336) (:start . 332)\n  (:id . 108))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 337) (:start . 336)\n  (:id . 109))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 338) (:start . 337)\n  (:id . 110))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 344)\n  (:start . 339) (:id . 111))\n ((:tag . "JJ") (:stem . "anti-α-tubulin") (:form . "anti-α-tubulin")\n  (:end . 359) (:start . 345) (:id . 112))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 361) (:start . 360)\n  (:id . 113))\n ((:tag . "CD") (:stem . "1:10,000") (:form . "1:10,000") (:end . 369)\n  (:start . 361) (:id . 114))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 370) (:start . 369)\n  (:id . 115))\n ((:tag . "NNP") (:stem . "Sigma") (:form . 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5502706@unknown@formal@none@1@S@Rhodamine Red X-conjugated goat anti-HRP and CY5-conjugated secondary antibodies were used at 1:200 (both from Jackson Labs).@(((:tag . "NNP") (:stem . "Rhodamine") (:form . "Rhodamine") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Red") (:form . "Red") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "x-conjugated") (:form . "X-conjugated") (:end . 26)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "goat") (:form . "goat") (:end . 31) (:start . 27)\n  (:id . 45))\n ((:tag . "NN") (:stem . "anti-hrp") (:form . "anti-HRP") (:end . 40)\n  (:start . 32) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "cy5-conjugated") (:form . "CY5-conjugated")\n  (:end . 59) (:start . 45) (:id . 48))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 69)\n  (:start . 60) (:id . 49))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 80)\n  (:start . 70) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 85) (:start . 81)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 90) (:start . 86)\n  (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 93) (:start . 91)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1:200") (:form . "1:200") (:end . 99) (:start . 94)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 55))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 105) (:start . 101)\n  (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 110) (:start . 106)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Jackson") (:form . "Jackson") (:end . 118)\n  (:start . 111) (:id . 58))\n ((:tag . "NNPS") (:stem . "Labs") (:form . "Labs") (:end . 123)\n  (:start . 119) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s8.455) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502707@unknown@formal@none@1@S@DAPI (0.2 µg/ml, Molecular Probes) and TRITC-conjugated phalloidin (10 ng/ml, Sigma) were applied in PBS-Tween (PBST) for 30 minutes to label nuclei and F-actin, respectively.@(((:tag . "NNP") (:stem . "DAPI") (:form . "DAPI") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "CD") (:stem . "0.2") (:form . "0.2") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "µg/ml") (:form . "µg/ml") (:end . 15) (:start . 10)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Molecular") (:form . "Molecular") (:end . 26)\n  (:start . 17) (:id . 47))\n ((:tag . "NNP") (:stem . "Probes") (:form . "Probes") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "tritc-conjugated") (:form . "TRITC-conjugated")\n  (:end . 55) (:start . 39) (:id . 51))\n ((:tag . "NN") (:stem . "phalloidin") (:form . "phalloidin") (:end . 66)\n  (:start . 56) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "ng/ml") (:form . "ng/ml") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Sigma") (:form . "Sigma") (:end . 83) (:start . 78)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 89) (:start . 85)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 97)\n  (:start . 90) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "PBS-Tween") (:form . "PBS-Tween") (:end . 110)\n  (:start . 101) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "PBST") (:form . "PBST") (:end . 116) (:start . 112)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 117) (:start . 116)\n  (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 121) (:start . 118)\n  (:id . 66))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 124) (:start . 122)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "minute") (:form . "minutes") (:end . 132)\n  (:start . 125) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 69))\n ((:tag . "VB") (:stem . "label") (:form . "label") (:end . 141)\n  (:start . 136) (:id . 70))\n ((:tag . "NNS") (:stem . "nucleus") (:form . "nuclei") (:end . 148)\n  (:start . 142) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "F-actin") (:form . "F-actin") (:end . 160)\n  (:start . 153) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 74))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 174)\n  (:start . 162) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.456) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502708@unknown@formal@none@1@S@Image analysis@(((:tag . "NN") (:stem . "image") (:form . "Image") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 14)\n  (:start . 6) (:id . 43)))@@@1@2@((:identifiers (:sid . :s8.457) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502709@unknown@formal@none@1@S@To quantify MBs, adult brains were prepared for imaging as described above.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "quantify") (:form . "quantify") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "MB") (:form . "MBs") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 29)\n  (:start . 23) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 43)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "imaging") (:form . "imaging") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 68)\n  (:start . 59) (:id . 53))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s8.458) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502710@unknown@formal@none@1@S@Dissected adult brains from both wild-type controls and dhtt-ko mutants were stained side by side in a 12-well plate with mouse anti-Fas II antibody (1D4, 1:20) overnight at 4°C.@(((:tag . "VBN") (:stem . "dissect") (:form . "Dissected") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 22)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 63)\n  (:start . 56) (:id . 50))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 71)\n  (:start . 64) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 76) (:start . 72)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 84)\n  (:start . 77) (:id . 53))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 89) (:start . 85)\n  (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 92) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "12-well") (:form . "12-well") (:end . 110)\n  (:start . 103) (:id . 59))\n ((:tag . "NN") (:stem . "plate") (:form . "plate") (:end . 116)\n  (:start . 111) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 121) (:start . 117)\n  (:id . 61))\n ((:tag . "NN") (:stem . "mouse") (:form . "mouse") (:end . 127)\n  (:start . 122) (:id . 62))\n ((:tag . "NN") (:stem . "anti-fas") (:form . "anti-Fas") (:end . 136)\n  (:start . 128) (:id . 63))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 139) (:start . 137)\n  (:id . 64))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 148)\n  (:start . 140) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "NN") (:stem . "1d4") (:form . "1D4") (:end . 153) (:start . 150)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 68))\n ((:tag . "CD") (:stem . "1:20") (:form . "1:20") (:end . 159) (:start . 155)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 70))\n ((:tag . "RB") (:stem . "overnight") (:form . "overnight") (:end . 170)\n  (:start . 161) (:id . 71))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 173) (:start . 171)\n  (:id . 72))\n ((:tag . "NN") (:stem . "4°c") (:form . "4°C") (:end . 177) (:start . 174)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.459) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502711@unknown@formal@none@1@S@After washing six times with 1× PBT for 2 hours, samples were stained with Alexa-594-conjugated secondary antibodies (1:500) at RT for 2 hours, followed by extensive washing with 1× PBST for 2 hours at RT.@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "wash") (:form . "washing") (:end . 13) (:start . 6)\n  (:id . 43))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "1×") (:form . "1×") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "pbt") (:form . "PBT") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 47) (:start . 42)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 56)\n  (:start . 49) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 69)\n  (:start . 62) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 74) (:start . 70)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "alexa-594-conjugated")\n  (:form . "Alexa-594-conjugated") (:end . 95) (:start . 75) (:id . 57))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 105)\n  (:start . 96) (:id . 58))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 116)\n  (:start . 106) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1:500") (:form . "1:500") (:end . 123)\n  (:start . 118) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "RT") (:form . "RT") (:end . 130) (:start . 128)\n  (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 134) (:start . 131)\n  (:id . 65))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 136) (:start . 135)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 142)\n  (:start . 137) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 152)\n  (:start . 144) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 155) (:start . 153)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "extensive") (:form . "extensive") (:end . 165)\n  (:start . 156) (:id . 71))\n ((:tag . "NN") (:stem . "washing") (:form . "washing") (:end . 173)\n  (:start . 166) (:id . 72))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 178) (:start . 174)\n  (:id . 73))\n ((:tag . "NN") (:stem . "1×") (:form . "1×") (:end . 181) (:start . 179)\n  (:id . 74))\n ((:tag . "NN") (:stem . "pbst") (:form . "PBST") (:end . 186) (:start . 182)\n  (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 190) (:start . 187)\n  (:id . 76))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 192) (:start . 191)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 198)\n  (:start . 193) (:id . 78))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 201) (:start . 199)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "RT") (:form . "RT") (:end . 204) (:start . 202)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s8.460) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502712@unknown@formal@none@1@S@To ensure that the stained samples had a similar background signal during imaging analysis, brains from both wild-type controls and dhtt-ko mutants were mounted onto opposite ends of the same slide.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 59)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 66)\n  (:start . 60) (:id . 52))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "imaging") (:form . "imaging") (:end . 81)\n  (:start . 74) (:id . 54))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 90)\n  (:start . 82) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 98)\n  (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 103) (:start . 99)\n  (:id . 58))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 118)\n  (:start . 109) (:id . 60))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 127)\n  (:start . 119) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 139)\n  (:start . 132) (:id . 63))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 147)\n  (:start . 140) (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 152) (:start . 148)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "mount") (:form . "mounted") (:end . 160)\n  (:start . 153) (:id . 66))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 165) (:start . 161)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "opposite") (:form . "opposite") (:end . 174)\n  (:start . 166) (:id . 68))\n ((:tag . "NNS") (:stem . "end") (:form . "ends") (:end . 179) (:start . 175)\n  (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 182) (:start . 180)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 186) (:start . 183)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 191) (:start . 187)\n  (:id . 72))\n ((:tag . "NN") (:stem . "slide") (:form . "slide") (:end . 197)\n  (:start . 192) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.461) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502713@unknown@formal@none@1@S@The samples were photographed at 20× magnification, under the same optical parameters, using a Zeiss fluorescent microscope (Axioskop 2 Mot Plus).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "photograph") (:form . "photographed") (:end . 29)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "CD") (:stem . "20×") (:form . "20×") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "magnification") (:form . "magnification")\n  (:end . 50) (:start . 37) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 74)\n  (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 85)\n  (:start . 75) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 92) (:start . 87)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Zeiss") (:form . "Zeiss") (:end . 100)\n  (:start . 95) (:id . 58))\n ((:tag . "JJ") (:stem . "fluorescent") (:form . "fluorescent") (:end . 112)\n  (:start . 101) (:id . 59))\n ((:tag . "NN") (:stem . "microscope") (:form . "microscope") (:end . 123)\n  (:start . 113) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Axioskop") (:form . "Axioskop") (:end . 133)\n  (:start . 125) (:id . 62))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 135) (:start . 134)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Mot") (:form . "Mot") (:end . 139) (:start . 136)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Plus") (:form . "Plus") (:end . 144) (:start . 140)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s8.462) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502714@unknown@formal@none@1@S@The boundaries of MBs were traced manually using AxioVision Rel 4.5 software (Zeiss), and both the overall size of each MB and the total intensity of FasII staining signals within the MB boundary were computed using the same software.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "MB") (:form . "MBs") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "trace") (:form . "traced") (:end . 33)\n  (:start . 27) (:id . 47))\n ((:tag . "RB") (:stem . "manually") (:form . "manually") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 48) (:start . 43)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "AxioVision") (:form . "AxioVision") (:end . 59)\n  (:start . 49) (:id . 50))\n ((:tag . "NNP") (:stem . "Rel") (:form . "Rel") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "CD") (:stem . "4.5") (:form . "4.5") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 76)\n  (:start . 68) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Zeiss") (:form . "Zeiss") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 94) (:start . 90)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 106)\n  (:start . 99) (:id . 61))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 111) (:start . 107)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 63))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 119) (:start . 115)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 122) (:start . 120)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 136)\n  (:start . 131) (:id . 68))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 146)\n  (:start . 137) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "FasII") (:form . "FasII") (:end . 155)\n  (:start . 150) (:id . 71))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 164)\n  (:start . 156) (:id . 72))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 172)\n  (:start . 165) (:id . 73))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 179)\n  (:start . 173) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 186) (:start . 184)\n  (:id . 76))\n ((:tag . "NN") (:stem . "boundary") (:form . "boundary") (:end . 195)\n  (:start . 187) (:id . 77))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 200) (:start . 196)\n  (:id . 78))\n ((:tag . "VBN") (:stem . "compute") (:form . "computed") (:end . 209)\n  (:start . 201) (:id . 79))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 215) (:start . 210)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 219) (:start . 216)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 224) (:start . 220)\n  (:id . 82))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 233)\n  (:start . 225) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s8.463) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502715@unknown@formal@none@1@S@FasII staining signals from outside the MB boundary were also measured and used as a reference to subtract out the background signals.@(((:tag . "NNP") (:stem . "FasII") (:form . "FasII") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "IN") (:stem . "outside") (:form . "outside") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "boundary") (:form . "boundary") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 94)\n  (:start . 85) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "VB") (:stem . "subtract") (:form . "subtract") (:end . 106)\n  (:start . 98) (:id . 59))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 61))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 125)\n  (:start . 115) (:id . 62))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 133)\n  (:start . 126) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.464) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502716@unknown@formal@none@1@S@Since we could not confidently measure the thickness of the MBs in these samples, only the overall area covered by each MB was measured.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "RB") (:stem . "confidently") (:form . "confidently") (:end . 30)\n  (:start . 19) (:id . 46))\n ((:tag . "VB") (:stem . "measure") (:form . "measure") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "thickness") (:form . "thickness") (:end . 52)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "mb") (:form . "MBs") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 80)\n  (:start . 73) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 98)\n  (:start . 91) (:id . 59))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 103) (:start . 99)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 111)\n  (:start . 104) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 119) (:start . 115)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 122) (:start . 120)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 126) (:start . 123)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 135)\n  (:start . 127) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s8.465) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502717@unknown@formal@none@1@S@The average FasII signal intensity in each MB was calculated by dividing the ‘total intensity of FasII staining signals within the MB boundary’ by ‘the overall size of the MB’.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "FasII") (:form . "FasII") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 60)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "divide") (:form . "dividing") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 83) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 93)\n  (:start . 84) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "FasII") (:form . "FasII") (:end . 102)\n  (:start . 97) (:id . 59))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 111)\n  (:start . 103) (:id . 60))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 119)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 126)\n  (:start . 120) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 133) (:start . 131)\n  (:id . 64))\n ((:tag . "NN") (:stem . "boundary") (:form . "boundary") (:end . 142)\n  (:start . 134) (:id . 65))\n ((:tag . "POS") (:stem . "’") (:form . "’") (:end . 143) (:start . 142)\n  (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 146) (:start . 144)\n  (:id . 67))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 148) (:start . 147)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 159)\n  (:start . 152) (:id . 70))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 164) (:start . 160)\n  (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 167) (:start . 165)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 171) (:start . 168)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 174) (:start . 172)\n  (:id . 74))\n ((:tag . "POS") (:stem . "’") (:form . "’") (:end . 175) (:start . 174)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s8.466) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502718@unknown@formal@none@1@S@To calculate the relative signal intensity, the average signal intensity of FasII signals from all wild-type brains was calculated and its mean was set as a reference point of 100.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "calculate") (:form . "calculate") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "FasII") (:form . "FasII") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 89)\n  (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 108)\n  (:start . 99) (:id . 58))\n ((:tag . "NNS") (:stem . "brain") (:form . "brains") (:end . 115)\n  (:start . 109) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 130)\n  (:start . 120) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 138) (:start . 135)\n  (:id . 63))\n ((:tag . "NN") (:stem . "mean") (:form . "mean") (:end . 143) (:start . 139)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 147) (:start . 144)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 151) (:start . 148)\n  (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 156) (:start . 155)\n  (:id . 68))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 166)\n  (:start . 157) (:id . 69))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 172)\n  (:start . 167) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 179) (:start . 176)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s8.467) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502719@unknown@formal@none@1@S@To measure the overall brain size and the regions that were devoid of neurons in the brain, adult flies were dissected and stained with rat anti-Elav antibody (1:40), which labels all neuronal cells.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "measure") (:form . "measure") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 49)\n  (:start . 42) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "devoid") (:form . "devoid") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 77)\n  (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 90) (:start . 85)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 97) (:start . 92)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 103) (:start . 98)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "dissect") (:form . "dissected") (:end . 118)\n  (:start . 109) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 130)\n  (:start . 123) (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 135) (:start . 131)\n  (:id . 66))\n ((:tag . "NN") (:stem . "rat") (:form . "rat") (:end . 139) (:start . 136)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "anti-elav") (:form . "anti-Elav") (:end . 149)\n  (:start . 140) (:id . 68))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 158)\n  (:start . 150) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n  (:id . 70))\n ((:tag . "CD") (:stem . "1:40") (:form . "1:40") (:end . 164) (:start . 160)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 73))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 172)\n  (:start . 167) (:id . 74))\n ((:tag . "VBZ") (:stem . "label") (:form . "labels") (:end . 179)\n  (:start . 173) (:id . 75))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 183) (:start . 180)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 192)\n  (:start . 184) (:id . 77))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 198)\n  (:start . 193) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s8.468) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502720@unknown@formal@none@1@S@The boundary of the whole protocerebrum in the brain and the regions devoid of neurons were tracked manually and quantified with AxioVision Rel 4.5 software, as described above.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "boundary") (:form . "boundary") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protocerebrum") (:form . "protocerebrum")\n  (:end . 39) (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . "JJ") (:stem . "devoid") (:form . "devoid") (:end . 75)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 86)\n  (:start . 79) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 91) (:start . 87)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "track") (:form . "tracked") (:end . 99)\n  (:start . 92) (:id . 58))\n ((:tag . "RB") (:stem . "manually") (:form . "manually") (:end . 108)\n  (:start . 100) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "quantify") (:form . "quantified") (:end . 123)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 128) (:start . 124)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "AxioVision") (:form . "AxioVision") (:end . 139)\n  (:start . 129) (:id . 63))\n ((:tag . "NNP") (:stem . "Rel") (:form . "Rel") (:end . 143) (:start . 140)\n  (:id . 64))\n ((:tag . "CD") (:stem . "4.5") (:form . "4.5") (:end . 147) (:start . 144)\n  (:id . 65))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 156)\n  (:start . 148) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 160) (:start . 158)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 170)\n  (:start . 161) (:id . 69))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 176)\n  (:start . 171) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s8.469) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502721@unknown@formal@none@1@S@To quantify the size of the A307-positive axonal terminals, adult brains from both wild-type controls and dhtt-ko mutants were dissected, fixed and stained side by side with an anti-GFP antibody, as described above, then mounted on the two sides of the same slide to ensure that they had a similar background for imaging analysis.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "quantify") (:form . "quantify") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "a307-positive") (:form . 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"by") (:end . 163) (:start . 161)\n  (:id . 68))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 168) (:start . 164)\n  (:id . 69))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 173) (:start . 169)\n  (:id . 70))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 176) (:start . 174)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "anti-gfp") (:form . "anti-GFP") (:end . 185)\n  (:start . 177) (:id . 72))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 194)\n  (:start . 186) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n  (:id . 74))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 198) (:start . 196)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 208)\n  (:start . 199) (:id . 76))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 214)\n  (:start . 209) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 215) (:start . 214)\n  (:id . 78))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 220) (:start . 216)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "mount") (:form . "mounted") (:end . 228)\n  (:start . 221) (:id . 80))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 231) (:start . 229)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 235) (:start . 232)\n  (:id . 82))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 239) (:start . 236)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "side") (:form . "sides") (:end . 245)\n  (:start . 240) (:id . 84))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 248) (:start . 246)\n  (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 252) (:start . 249)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 257) (:start . 253)\n  (:id . 87))\n ((:tag . "NN") (:stem . "slide") (:form . "slide") (:end . 263)\n  (:start . 258) (:id . 88))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 266) (:start . 264)\n  (:id . 89))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 273)\n  (:start . 267) (:id . 90))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 278) (:start . 274)\n  (:id . 91))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 283) (:start . 279)\n  (:id . 92))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 287) (:start . 284)\n  (:id . 93))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 289) (:start . 288)\n  (:id . 94))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 297)\n  (:start . 290) (:id . 95))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 308)\n  (:start . 298) (:id . 96))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 312) (:start . 309)\n  (:id . 97))\n ((:tag . "VBG") (:stem . "image") (:form . "imaging") (:end . 320)\n  (:start . 313) (:id . 98))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 329)\n  (:start . 321) (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 330) (:start . 329)\n  (:id . 100)))@@@1@59@((:identifiers (:sid . :s8.470) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502722@unknown@formal@none@1@S@Both the wild-type control and dhtt-ko mutant samples were imaged by confocal microscopy at 40× magnification under the same optical parameters.@(((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "image") (:form . "imaged") (:end . 65)\n  (:start . 59) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "microscopy") (:form . "microscopy") (:end . 88)\n  (:start . 78) (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "CD") (:stem . "40×") (:form . "40×") (:end . 95) (:start . 92)\n  (:id . 56))\n ((:tag . "NN") (:stem . "magnification") (:form . "magnification")\n  (:end . 109) (:start . 96) (:id . 57))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 115)\n  (:start . 110) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 124) (:start . 120)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "optical") (:form . "optical") (:end . 132)\n  (:start . 125) (:id . 61))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 143)\n  (:start . 133) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s8.471) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502723@unknown@formal@none@1@S@A Z-serial section of confocal images covering the entire depth of each axonal terminus was collected using a Leica TCS confocal microscope and then projected into one merged image (using the Leica software) to generate the whole picture of each axonal terminus.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "z-serial") (:form . "Z-serial") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "VBG") (:stem . "cover") (:form . "covering") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 57)\n  (:start . 51) (:id . 50))\n ((:tag . "NN") (:stem . "depth") (:form . "depth") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 78)\n  (:start . 72) (:id . 54))\n ((:tag . "NN") (:stem . "terminus") (:form . "terminus") (:end . 87)\n  (:start . 79) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 101)\n  (:start . 92) (:id . 57))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 107) (:start . 102)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Leica") (:form . "Leica") (:end . 115)\n  (:start . 110) (:id . 60))\n ((:tag . "NNP") (:stem . "TCS") (:form . "TCS") (:end . 119) (:start . 116)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 128)\n  (:start . 120) (:id . 62))\n ((:tag . "NN") (:stem . "microscope") (:form . "microscope") (:end . 139)\n  (:start . 129) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 64))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 148) (:start . 144)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "project") (:form . "projected") (:end . 158)\n  (:start . 149) (:id . 66))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 163) (:start . 159)\n  (:id . 67))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 167) (:start . 164)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "merge") (:form . "merged") (:end . 174)\n  (:start . 168) (:id . 69))\n ((:tag . "NN") (:stem . "image") (:form . "image") (:end . 180)\n  (:start . 175) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 182) (:start . 181)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 187) (:start . 182)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Leica") (:form . "Leica") (:end . 197)\n  (:start . 192) (:id . 74))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 206)\n  (:start . 198) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 207) (:start . 206)\n  (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 210) (:start . 208)\n  (:id . 77))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 219)\n  (:start . 211) (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 223) (:start . 220)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 229)\n  (:start . 224) (:id . 80))\n ((:tag . "NN") (:stem . "picture") (:form . "picture") (:end . 237)\n  (:start . 230) (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 240) (:start . 238)\n  (:id . 82))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 245) (:start . 241)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 252)\n  (:start . 246) (:id . 84))\n ((:tag . "NN") (:stem . "terminus") (:form . "terminus") (:end . 261)\n  (:start . 253) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 262) (:start . 261)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s8.472) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502724@unknown@formal@none@1@S@Since the branches and boutons in the brain were too small to distinguish clearly, only the overall area covered by each axonal terminus was measured.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "branch") (:form . "branches") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "bouton") (:form . "boutons") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "VB") (:stem . "distinguish") (:form . "distinguish") (:end . 73)\n  (:start . 62) (:id . 54))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 81)\n  (:start . 74) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 87) (:start . 83)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 99)\n  (:start . 92) (:id . 59))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 104) (:start . 100)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 112)\n  (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 120) (:start . 116)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 127)\n  (:start . 121) (:id . 64))\n ((:tag . "NN") (:stem . "terminus") (:form . "terminus") (:end . 136)\n  (:start . 128) (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 140) (:start . 137)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 149)\n  (:start . 141) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.473) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502725@unknown@formal@none@1@S@Fluorescent images were analyzed and captured by fluorescent microscopy (Axioskop 2 Mot Plus, Zeiss) or by confocal microscopy (Leica TCS SP2 AOBS system).@(((:tag . "JJ") (:stem . "fluorescent") (:form . "Fluorescent") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 18)\n  (:start . 12) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "capture") (:form . "captured") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "fluorescent") (:form . "fluorescent") (:end . 60)\n  (:start . 49) (:id . 49))\n ((:tag . "NN") (:stem . "microscopy") (:form . "microscopy") (:end . 71)\n  (:start . 61) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Axioskop") (:form . "Axioskop") (:end . 81)\n  (:start . 73) (:id . 52))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 83) (:start . 82)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Mot") (:form . "Mot") (:end . 87) (:start . 84)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Plus") (:form . "Plus") (:end . 92) (:start . 88)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Zeiss") (:form . "Zeiss") (:end . 99) (:start . 94)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 106) (:start . 104)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 115)\n  (:start . 107) (:id . 61))\n ((:tag . "NN") (:stem . "microscopy") (:form . "microscopy") (:end . 126)\n  (:start . 116) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Leica") (:form . "Leica") (:end . 133)\n  (:start . 128) (:id . 64))\n ((:tag . "NNP") (:stem . "TCS") (:form . "TCS") (:end . 137) (:start . 134)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "SP2") (:form . "SP2") (:end . 141) (:start . 138)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "AOBS") (:form . "AOBS") (:end . 146) (:start . 142)\n  (:id . 67))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 153)\n  (:start . 147) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s8.474) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502726@unknown@formal@none@1@S@Confocal images were analyzed and projected using Leica confocal software (LCS).@(((:tag . "JJ") (:stem . "confocal") (:form . "Confocal") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "project") (:form . "projected") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 49) (:start . 44)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Leica") (:form . "Leica") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 73)\n  (:start . 65) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "LCS") (:form . "LCS") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s8.475) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502727@unknown@formal@none@1@S@Viability assay@(((:tag . "NN") (:stem . "viability") (:form . "Viability") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 15) (:start . 10)\n  (:id . 43)))@@@1@2@((:identifiers (:sid . :s8.476) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502728@unknown@formal@none@1@S@Drosophila viability was measured by placing 30 newly hatched female flies of each genotype into individual vials, containing fly food, at 25°C.@(((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 20)\n  (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "place") (:form . "placing") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "RB") (:stem . "newly") (:form . "newly") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "hatch") (:form . "hatched") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "JJ") (:stem . "female") (:form . "female") (:end . 68)\n  (:start . 62) (:id . 51))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 82) (:start . 78)\n  (:id . 54))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 91)\n  (:start . 83) (:id . 55))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 96) (:start . 92)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 107)\n  (:start . 97) (:id . 57))\n ((:tag . "NNS") (:stem . "vial") (:form . "vials") (:end . 113)\n  (:start . 108) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 125)\n  (:start . 115) (:id . 60))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 129) (:start . 126)\n  (:id . 61))\n ((:tag . "NN") (:stem . "food") (:form . "food") (:end . 134) (:start . 130)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 138) (:start . 136)\n  (:id . 64))\n ((:tag . "NN") (:stem . "25°c") (:form . "25°C") (:end . 143) (:start . 139)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s8.477) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502729@unknown@formal@none@1@S@The number of dead flies was recorded daily.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "dead") (:form . "dead") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "record") (:form . "recorded") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "RB") (:stem . "daily") (:form . "daily") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 44) (:start . 43)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s8.478) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502730@unknown@formal@none@1@S@Flies were transferred into a new food vial every 3–4 days to prevent them from sticking to old food.@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "transfer") (:form . "transferred") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "food") (:form . "food") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "vial") (:form . "vial") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "CD") (:stem . "3–4") (:form . "3–4") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 69)\n  (:start . 62) (:id . 54))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 74) (:start . 70)\n  (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 79) (:start . 75)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "stick") (:form . "sticking") (:end . 88)\n  (:start . 80) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "old") (:form . "old") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . "NN") (:stem . "food") (:form . "food") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s8.479) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502731@unknown@formal@none@1@S@For each genotype, at least two independent cohorts of flies, raised at different times from independent crosses, were tested and the results were averaged.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 43)\n  (:start . 32) (:id . 49))\n ((:tag . "NNS") (:stem . "cohort") (:form . "cohorts") (:end . 51)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "raise") (:form . "raised") (:end . 68)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 81)\n  (:start . 72) (:id . 56))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 87) (:start . 82)\n  (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 104)\n  (:start . 93) (:id . 59))\n ((:tag . "NNS") (:stem . "crosse") (:form . "crosses") (:end . 112)\n  (:start . 105) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 118) (:start . 114)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 125)\n  (:start . 119) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 141)\n  (:start . 134) (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 146) (:start . 142)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "averaged") (:form . "averaged") (:end . 155)\n  (:start . 147) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s8.480) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502732@unknown@formal@none@1@S@Mobility tests of adult flies and videos@(((:tag . "NN") (:stem . "mobility") (:form . "Mobility") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "video") (:form . "videos") (:end . 40)\n  (:start . 34) (:id . 48)))@@@1@7@((:identifiers (:sid . :s8.481) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502733@unknown@formal@none@1@S@Female flies were chosen in all the mobility tests.@(((:tag . "JJ") (:stem . "female") (:form . "Female") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "mobility") (:form . "mobility") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 51) (:start . 50)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s8.482) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502734@unknown@formal@none@1@S@Fly videos were captured using a Sony digital camcorder (DCR-TRV140) and edited in Apple’s iMovie program.@(((:tag . "RB") (:stem . "fly") (:form . "Fly") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "video") (:form . "videos") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "capture") (:form . "captured") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sony") (:form . "Sony") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "digital") (:form . "digital") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "camcorder") (:form . "camcorder") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "DCR-TRV140") (:form . "DCR-TRV140") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "edit") (:form . "edited") (:end . 79) (:start . 73)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Apple") (:form . "Apple") (:end . 88) (:start . 83)\n  (:id . 57))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "imovie") (:form . "iMovie") (:end . 97)\n  (:start . 91) (:id . 59))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 105)\n  (:start . 98) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s8.483) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502735@unknown@formal@none@1@S@Climbing assays were performed as described previously (Ganetzky and Flanagan, 1978; Le Bourg and Lints, 1992).@(((:tag . "VBG") (:stem . "climb") (:form . "Climbing") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 54)\n  (:start . 44) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Ganetzky") (:form . "Ganetzky") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Flanagan") (:form . "Flanagan") (:end . 77)\n  (:start . 69) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1978") (:form . "1978") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Le") (:form . "Le") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Bourg") (:form . "Bourg") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Lints") (:form . "Lints") (:end . 103)\n  (:start . 98) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1992") (:form . "1992") (:end . 109) (:start . 105)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s8.484) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502736@unknown@formal@none@1@S@Briefly, 20 flies of a specified age were knocked to the bottom of a plastic vial.@(((:tag . "RB") (:stem . "briefly") (:form . "Briefly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 32)\n  (:start . 23) (:id . 48))\n ((:tag . "NN") (:stem . "age") (:form . "age") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "knock") (:form . "knocked") (:end . 49)\n  (:start . 42) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "bottom") (:form . "bottom") (:end . 63)\n  (:start . 57) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n  (:id . 56))\n ((:tag . "NN") (:stem . "plastic") (:form . "plastic") (:end . 76)\n  (:start . 69) (:id . 57))\n ((:tag . "JJ") (:stem . "vial") (:form . "vial") (:end . 81) (:start . 77)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s8.485) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502737@unknown@formal@none@1@S@The number of flies that could climb to the top of the vial after 18 seconds was counted.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "VB") (:stem . "climb") (:form . "climb") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "top") (:form . "top") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 53))\n ((:tag . "NN") (:stem . "vial") (:form . "vial") (:end . 59) (:start . 55)\n  (:id . 54))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 65) (:start . 60)\n  (:id . 55))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 68) (:start . 66)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "second") (:form . "seconds") (:end . 76)\n  (:start . 69) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 80) (:start . 77)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "count") (:form . "counted") (:end . 88)\n  (:start . 81) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s8.486) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502738@unknown@formal@none@1@S@The test was repeated 6–7 times for each genotype at the specified age.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "repeat") (:form . "repeated") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "CD") (:stem . "6–7") (:form . "6–7") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "age") (:form . "age") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s8.487) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502739@unknown@formal@none@1@S@The assay was performed as described previously (Feany and Bender, 2000; Joiner and Griffith, 1999; Wang et al., 2004).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Feany") (:form . "Feany") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Bender") (:form . "Bender") (:end . 65)\n  (:start . 59) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "CD") (:stem . "2000") (:form . "2000") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Joiner") (:form . "Joiner") (:end . 79)\n  (:start . 73) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Griffith") (:form . "Griffith") (:end . 92)\n  (:start . 84) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1999") (:form . "1999") (:end . 98) (:start . 94)\n  (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 99) (:start . 98)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Wang") (:form . "Wang") (:end . 104) (:start . 100)\n  (:id . 62))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 107) (:start . 105)\n  (:id . 63))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 111) (:start . 108)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 65))\n ((:tag . "CD") (:stem . "2004") (:form . "2004") (:end . 117) (:start . 113)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.488) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502740@unknown@formal@none@1@S@For each genotype, 6–14 flies of a specific age were tested.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "CD") (:stem . "6–14") (:form . "6–14") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 43)\n  (:start . 35) (:id . 50))\n ((:tag . "NN") (:stem . "age") (:form . "age") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 52) (:start . 48)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 59) (:start . 53)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s8.489) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502741@unknown@formal@none@1@S@Flies were fed 30 mM of methyl viologen (Sigma) in instant Drosophila medium (Carolina), providing a dosage of paraquat that kills about 50% of wild-type flies after 48 hours of exposure.@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "feed") (:form . "fed") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "methyl") (:form . "methyl") (:end . 30)\n  (:start . 24) (:id . 48))\n ((:tag . "NN") (:stem . "viologen") (:form . "viologen") (:end . 39)\n  (:start . 31) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sigma") (:form . "Sigma") (:end . 46) (:start . 41)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "instant") (:form . "instant") (:end . 58)\n  (:start . 51) (:id . 54))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 69)\n  (:start . 59) (:id . 55))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 76)\n  (:start . 70) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Carolina") (:form . "Carolina") (:end . 86)\n  (:start . 78) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "provide") (:form . "providing") (:end . 98)\n  (:start . 89) (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n  (:id . 62))\n ((:tag . "NN") (:stem . "dosage") (:form . "dosage") (:end . 107)\n  (:start . 101) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 64))\n ((:tag . "NN") (:stem . "paraquat") (:form . "paraquat") (:end . 119)\n  (:start . 111) (:id . 65))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 124) (:start . 120)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "kill") (:form . "kills") (:end . 130)\n  (:start . 125) (:id . 67))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 136)\n  (:start . 131) (:id . 68))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 139) (:start . 137)\n  (:id . 69))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 140) (:start . 139)\n  (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 153)\n  (:start . 144) (:id . 72))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 159) (:start . 154)\n  (:id . 73))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 165)\n  (:start . 160) (:id . 74))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 168) (:start . 166)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 174)\n  (:start . 169) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n  (:id . 77))\n ((:tag . "NN") (:stem . "exposure") (:form . "exposure") (:end . 186)\n  (:start . 178) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s8.490) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502742@unknown@formal@none@1@S@Control flies were fed instant medium only.@(((:tag . "NNP") (:stem . "Control") (:form . "Control") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "feed") (:form . "fed") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "instant") (:form . "instant") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s8.491) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502743@unknown@formal@none@1@S@Adult flies that had eclosed within the last 24 hours were kept in 30 mM paraquat or in drug-free medium for 48 hours after eclosion.@(((:tag . "JJ") (:stem . "adult") (:form . "Adult") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "eclose") (:form . "eclosed") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "keep") (:form . "kept") (:end . 63) (:start . 59)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 69) (:start . 67)\n  (:id . 55))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 72) (:start . 70)\n  (:id . 56))\n ((:tag . "NN") (:stem . "paraquat") (:form . "paraquat") (:end . 81)\n  (:start . 73) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "drug-free") (:form . "drug-free") (:end . 97)\n  (:start . 88) (:id . 60))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 104)\n  (:start . 98) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 108) (:start . 105)\n  (:id . 62))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 111) (:start . 109)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 117)\n  (:start . 112) (:id . 64))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 123)\n  (:start . 118) (:id . 65))\n ((:tag . "NN") (:stem . "eclosion") (:form . "eclosion") (:end . 132)\n  (:start . 124) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s8.492) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502744@unknown@formal@none@1@S@The number of survivors was counted at 48 hours after the start of paraquat treatment.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "survivor") (:form . "survivors") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "count") (:form . "counted") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "start") (:form . "start") (:end . 63) (:start . 58)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "NN") (:stem . "paraquat") (:form . "paraquat") (:end . 75)\n  (:start . 67) (:id . 55))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 85)\n  (:start . 76) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.493) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502745@unknown@formal@none@1@S@An electrophysiological analysis of wandering-stage third instar larvae was performed in Drosophila HL3.1 saline (NaCl, 70 mM; KCl, 5 mM; MgCl2, 4 mM; CaCl2, 0.2 mM; NaHCO3, 10 mM; trehalose, 5 mM; sucrose, 115 mM; HEPES-NaOH, 5 mM; pH 7.2) using an Axoclamp 2B amplifer (Axon Instrument) at 22°C.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "electrophysiological")\n  (:form . "electrophysiological") (:end . 23) (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 32)\n  (:start . 24) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 45))\n ((:tag . "NN") (:stem . "wandering-stage") (:form . "wandering-stage")\n  (:end . 51) (:start . 36) (:id . 46))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 57) (:start . 52)\n  (:id . 47))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 64)\n  (:start . 58) (:id . 48))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 71)\n  (:start . 65) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 75) (:start . 72)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 85)\n  (:start . 76) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 52))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 99)\n  (:start . 89) (:id . 53))\n ((:tag . "NNP") (:stem . "HL3.1") (:form . "HL3.1") (:end . 105)\n  (:start . 100) (:id . 54))\n ((:tag . "NN") (:stem . "saline") (:form . "saline") (:end . 112)\n  (:start . 106) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "NaCl") (:form . "NaCl") (:end . 118) (:start . 114)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . 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"mM") (:end . 179) (:start . 177)\n  (:id . 80))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 180) (:start . 179)\n  (:id . 81))\n ((:tag . "NN") (:stem . "trehalose") (:form . "trehalose") (:end . 190)\n  (:start . 181) (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n  (:id . 83))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 193) (:start . 192)\n  (:id . 84))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 196) (:start . 194)\n  (:id . 85))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 197) (:start . 196)\n  (:id . 86))\n ((:tag . "NN") (:stem . "sucrose") (:form . "sucrose") (:end . 205)\n  (:start . 198) (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 206) (:start . 205)\n  (:id . 88))\n ((:tag . "CD") (:stem . "115") (:form . "115") (:end . 210) (:start . 207)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 213) (:start . 211)\n  (:id . 90))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 214) (:start . 213)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "HEPES-NaOH") (:form . "HEPES-NaOH") (:end . 225)\n  (:start . 215) (:id . 92))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 226) (:start . 225)\n  (:id . 93))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 228) (:start . 227)\n  (:id . 94))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 231) (:start . 229)\n  (:id . 95))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 232) (:start . 231)\n  (:id . 96))\n ((:tag . "NN") (:stem . "ph") (:form . "pH") (:end . 235) (:start . 233)\n  (:id . 97))\n ((:tag . "CD") (:stem . "7.2") (:form . "7.2") (:end . 239) (:start . 236)\n  (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 240) (:start . 239)\n  (:id . 99))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 246) (:start . 241)\n  (:id . 100))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 249) (:start . 247)\n  (:id . 101))\n ((:tag . "NNP") (:stem . "Axoclamp") (:form . "Axoclamp") (:end . 258)\n  (:start . 250) (:id . 102))\n ((:tag . "NN") (:stem . "2b") (:form . "2B") (:end . 261) (:start . 259)\n  (:id . 103))\n ((:tag . "NN") (:stem . "amplifer") (:form . "amplifer") (:end . 270)\n  (:start . 262) (:id . 104))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 272) (:start . 271)\n  (:id . 105))\n ((:tag . "NNP") (:stem . "Axon") (:form . "Axon") (:end . 276) (:start . 272)\n  (:id . 106))\n ((:tag . "NNP") (:stem . "Instrument") (:form . "Instrument") (:end . 287)\n  (:start . 277) (:id . 107))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 288) (:start . 287)\n  (:id . 108))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 291) (:start . 289)\n  (:id . 109))\n ((:tag . "NN") (:stem . "22°c") (:form . "22°C") (:end . 296) (:start . 292)\n  (:id . 110))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 297) (:start . 296)\n  (:id . 111)))@@@1@70@((:identifiers (:sid . :s8.494) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502746@unknown@formal@none@1@S@Recordings were performed at muscle fiber 6/7 of segments A3 to A5 under current clamp.@(((:tag . "NNS") (:stem . "recording") (:form . "Recordings") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "muscle") (:form . "muscle") (:end . 35)\n  (:start . 29) (:id . 46))\n ((:tag . "NN") (:stem . "fiber") (:form . "fiber") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . "CD") (:stem . "6/7") (:form . "6/7") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 57)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "a3") (:form . "A3") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "a5") (:form . "A5") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 80)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "clamp") (:form . "clamp") (:end . 86) (:start . 81)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.495) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502747@unknown@formal@none@1@S@PPF was measured by determining the peak amplitude responses (P2/P1) of two stimuli separated by the indicated latency.@(((:tag . "NNP") (:stem . "PPF") (:form . "PPF") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "determine") (:form . "determining") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "peak") (:form . "peak") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "amplitude") (:form . "amplitude") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "P2/P1") (:form . "P2/P1") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "stimulus") (:form . "stimuli") (:end . 83)\n  (:start . 76) (:id . 56))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 93)\n  (:start . 84) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 110)\n  (:start . 101) (:id . 60))\n ((:tag . "NN") (:stem . "latency") (:form . "latency") (:end . 118)\n  (:start . 111) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.496) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502748@unknown@formal@none@1@S@All error bars are s.e.m.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "bar") (:form . "bars") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "s.e.m") (:form . "s.e.m") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 25) (:start . 24)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s8.497) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502749@unknown@formal@none@1@S@In adults, extracellular field potentials were recorded by placing a sharp glass electrode near the longitudinal flight muscles after piercing the cuticle, with a reference electrode placed in the fly head.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "adult") (:form . "adults") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 24) (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "potential") (:form . "potentials") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "record") (:form . "recorded") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "place") (:form . "placing") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "sharp") (:form . "sharp") (:end . 74) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "glass") (:form . "glass") (:end . 80) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "electrode") (:form . "electrode") (:end . 90)\n  (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "near") (:form . "near") (:end . 95) (:start . 91)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "longitudinal") (:form . "longitudinal") (:end . 112)\n  (:start . 100) (:id . 58))\n ((:tag . "NN") (:stem . "flight") (:form . "flight") (:end . 119)\n  (:start . 113) (:id . 59))\n ((:tag . "NNS") (:stem . "muscle") (:form . "muscles") (:end . 127)\n  (:start . 120) (:id . 60))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 133)\n  (:start . 128) (:id . 61))\n ((:tag . "VBG") (:stem . "pierce") (:form . "piercing") (:end . 142)\n  (:start . 134) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 63))\n ((:tag . "NN") (:stem . "cuticle") (:form . "cuticle") (:end . 154)\n  (:start . 147) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n  (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 160) (:start . 156)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 162) (:start . 161)\n  (:id . 67))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 172)\n  (:start . 163) (:id . 68))\n ((:tag . "NN") (:stem . "electrode") (:form . "electrode") (:end . 182)\n  (:start . 173) (:id . 69))\n ((:tag . "VBN") (:stem . "place") (:form . "placed") (:end . 189)\n  (:start . 183) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 192) (:start . 190)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "fly") (:form . "fly") (:end . 200) (:start . 197)\n  (:id . 73))\n ((:tag . "NN") (:stem . "head") (:form . "head") (:end . 205) (:start . 201)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s8.498) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502750@unknown@formal@none@1@S@ERGs were performed as described previously (Rieckhof et al., 2003).@(((:tag . "NNP") (:stem . "ERG") (:form . "ERGs") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Rieckhof") (:form . "Rieckhof") (:end . 53)\n  (:start . 45) (:id . 49))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "CD") (:stem . "2003") (:form . "2003") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s8.499) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502751@unknown@formal@none@1@S@Temperature shifts were performed by heating mounting clay, which encompassed the fly, to the desired temperature with a peltier heating device.@(((:tag . "NN") (:stem . "temperature") (:form . "Temperature") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "shift") (:form . "shifts") (:end . 18)\n  (:start . 12) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 33)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "heat") (:form . "heating") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "VBG") (:stem . "mount") (:form . "mounting") (:end . 53)\n  (:start . 45) (:id . 48))\n ((:tag . "NN") (:stem . "clay") (:form . "clay") (:end . 58) (:start . 54)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "encompass") (:form . "encompassed") (:end . 77)\n  (:start . 66) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 53))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "desire") (:form . "desired") (:end . 101)\n  (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 113)\n  (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 118) (:start . 114)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . "NN") (:stem . "peltier") (:form . "peltier") (:end . 128)\n  (:start . 121) (:id . 62))\n ((:tag . "NN") (:stem . "heating") (:form . "heating") (:end . 136)\n  (:start . 129) (:id . 63))\n ((:tag . "NN") (:stem . "device") (:form . "device") (:end . 143)\n  (:start . 137) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s8.500) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502752@unknown@formal@none@1@S@For measurements of evoked EJP amplitude (Fig. 6A,B), the number of NMJs examined were: control, n=8; dhtt-ko, n=23.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "measurement") (:form . "measurements") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "evoke") (:form . "evoked") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "NNP") (:stem . "EJP") (:form . "EJP") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "amplitude") (:form . "amplitude") (:end . 40)\n  (:start . 31) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "CD") (:stem . "6A,B") (:form . "6A,B") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 64)\n  (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "NMJ") (:form . "NMJs") (:end . 72) (:start . 68)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 81)\n  (:start . 73) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 86) (:start . 82)\n  (:id . 58))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 87) (:start . 86)\n  (:id . 59))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 95)\n  (:start . 88) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 61))\n ((:tag . "NN") (:stem . "n=8") (:form . "n=8") (:end . 100) (:start . 97)\n  (:id . 62))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 101) (:start . 100)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 109)\n  (:start . 102) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 65))\n ((:tag . "NN") (:stem . "n=23") (:form . "n=23") (:end . 115) (:start . 111)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s8.501) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502753@unknown@formal@none@1@S@Voltage traces of evoked EJPs were recorded from muscle fiber 6 in third instar larvae in 0.2 mM extracellular calcium.@(((:tag . "NNP") (:stem . "Voltage") (:form . "Voltage") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "trace") (:form . "traces") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "evoked") (:form . "evoked") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "ejp") (:form . "EJPs") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "record") (:form . "recorded") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "muscle") (:form . "muscle") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "fiber") (:form . "fiber") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 79)\n  (:start . 73) (:id . 55))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 86)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "CD") (:stem . "0.2") (:form . "0.2") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 110) (:start . 97) (:id . 60))\n ((:tag . "NN") (:stem . "calcium") (:form . "calcium") (:end . 118)\n  (:start . 111) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.502) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502754@unknown@formal@none@1@S@Average resting potential: 60.2±1.2 mV in control animals and 62.4±0.8 mV in dhtt mutants.@(((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBG") (:stem . "rest") (:form . "resting") (:end . 15) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "potential") (:form . "potential") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "CD") (:stem . "60.2±1.2") (:form . "60.2±1.2") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "mv") (:form . "mV") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "CD") (:stem . "62.4±0.8") (:form . "62.4±0.8") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "mv") (:form . "mV") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.503) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502755@unknown@formal@none@1@S@Average EJP amplitude: 19.5±1.2 mV in control animals and 17.8±1.0 mV in dhtt mutants.@(((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "EJP") (:form . "EJP") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "amplitude") (:form . "amplitude") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "CD") (:stem . "19.5±1.2") (:form . "19.5±1.2") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "mv") (:form . "mV") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "CD") (:stem . "17.8±1.0") (:form . "17.8±1.0") (:end . 66)\n  (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "mv") (:form . "mV") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 85)\n  (:start . 78) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s8.504) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502756@unknown@formal@none@1@S@Measurements of voltage traces of PPF (Fig. 6C) were performed at 25 millisecond intervals in control (rescued) and dhtt mutant third instar larvae in 0.2 mM extracellular calcium.@(((:tag . "NNS") (:stem . "measurement") (:form . "Measurements") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "voltage") (:form . "voltage") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "trace") (:form . "traces") (:end . 30)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "PPF") (:form . "PPF") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "6c") (:form . "6C") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 52) (:start . 48)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 62)\n  (:start . 53) (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 68) (:start . 66)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "millisecond") (:form . "millisecond") (:end . 80)\n  (:start . 69) (:id . 56))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 90)\n  (:start . 81) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 101)\n  (:start . 94) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 110)\n  (:start . 103) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 120) (:start . 116)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 127)\n  (:start . 121) (:id . 65))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 133)\n  (:start . 128) (:id . 66))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 140)\n  (:start . 134) (:id . 67))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 147)\n  (:start . 141) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n  (:id . 69))\n ((:tag . "CD") (:stem . "0.2") (:form . "0.2") (:end . 154) (:start . 151)\n  (:id . 70))\n ((:tag . "NN") (:stem . "mm") (:form . "mM") (:end . 157) (:start . 155)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 171) (:start . 158) (:id . 72))\n ((:tag . "NN") (:stem . "calcium") (:form . "calcium") (:end . 179)\n  (:start . 172) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s8.505) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502757@unknown@formal@none@1@S@Quantification of PPF (the amplitude of EJP 2 divided by the amplitude of EJP 1) was performed in control and dhtt mutants for 25-, 50- and 75-millisecond intervals (Fig. 6D).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "PPF") (:form . "PPF") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "amplitude") (:form . "amplitude") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "EJP") (:form . "EJP") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "divide") (:form . "divided") (:end . 53)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "amplitude") (:form . "amplitude") (:end . 70)\n  (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "EJP") (:form . "EJP") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 79) (:start . 78)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 84) (:start . 81)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 94)\n  (:start . 85) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 97) (:start . 95)\n  (:id . 61))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 105)\n  (:start . 98) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dhtt") (:form . "dhtt") (:end . 114) (:start . 110)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 122)\n  (:start . 115) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 126) (:start . 123)\n  (:id . 66))\n ((:tag . "CD") (:stem . "25-") (:form . "25-") (:end . 130) (:start . 127)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 68))\n ((:tag . "CD") (:stem . "50-") (:form . "50-") (:end . 135) (:start . 132)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "75-millisecond") (:form . "75-millisecond")\n  (:end . 154) (:start . 140) (:id . 71))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 164)\n  (:start . 155) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 166) (:start . 165)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 170) (:start . 166)\n  (:id . 74))\n ((:tag . "NN") (:stem . "6d") (:form . "6D") (:end . 173) (:start . 171)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 174) (:start . 173)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s8.506) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502758@unknown@formal@none@1@S@The number of preparations analyzed were: control, n=9; dhtt-ko, n=8.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "preparation") (:form . "preparations") (:end . 26)\n  (:start . 14) (:id . 45))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "n=9") (:form . "n=9") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 63)\n  (:start . 56) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . "NN") (:stem . "n=8") (:form . "n=8") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s8.507) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502759@unknown@formal@none@1@S@The GF flight circuit can be activated by stimulation of the brain, and extracellular recordings can be made from the DLMs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "GF") (:form . "GF") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "flight") (:form . "flight") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "circuit") (:form . "circuit") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 38)\n  (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "stimulation") (:form . "stimulation") (:end . 53)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 66) (:start . 61)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 85) (:start . 72) (:id . 56))\n ((:tag . "NNS") (:stem . "recording") (:form . "recordings") (:end . 96)\n  (:start . 86) (:id . 57))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 108) (:start . 104)\n  (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "dlm") (:form . "DLMs") (:end . 122) (:start . 118)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s8.508) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502760@unknown@formal@none@1@S@Neither the control nor the dhtt-ko mutants displayed abnormal activity in the DLM flight muscles (data not shown).@(((:tag . "CC") (:stem . "neither") (:form . "Neither") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "CC") (:stem . "nor") (:form . "nor") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 71)\n  (:start . 63) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "DLM") (:form . "DLM") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "flight") (:form . "flight") (:end . 89)\n  (:start . 83) (:id . 55))\n ((:tag . "NNS") (:stem . "muscle") (:form . "muscles") (:end . 97)\n  (:start . 90) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 103) (:start . 99)\n  (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 113)\n  (:start . 108) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s8.509) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502761@unknown@formal@none@1@S@To measure ERGs at the elevated temperature (37°C), flies were rapidly heated from 20°C to 37°C, with test light pulses (black bar below trace in Fig. 6E) given at regular intervals.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "measure") (:form . "measure") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "erg") (:form . "ERGs") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "elevated") (:form . "elevated") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 43)\n  (:start . 32) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 57) (:start . 52)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n  (:id . 54))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 70)\n  (:start . 63) (:id . 55))\n ((:tag . "VBN") (:stem . "heat") (:form . "heated") (:end . 77) (:start . 71)\n  (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 82) (:start . 78)\n  (:id . 57))\n ((:tag . "NN") (:stem . "20°c") (:form . "20°C") (:end . 87) (:start . 83)\n  (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 95) (:start . 91)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 101) (:start . 97)\n  (:id . 62))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 106) (:start . 102)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "light") (:form . "light") (:end . 112)\n  (:start . 107) (:id . 64))\n ((:tag . "NNS") (:stem . "pulse") (:form . "pulses") (:end . 119)\n  (:start . 113) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 126)\n  (:start . 121) (:id . 67))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 130) (:start . 127)\n  (:id . 68))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 136)\n  (:start . 131) (:id . 69))\n ((:tag . "NN") (:stem . "trace") (:form . "trace") (:end . 142)\n  (:start . 137) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 145) (:start . 143)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 150) (:start . 146)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "6E") (:form . "6E") (:end . 153) (:start . 151)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 160)\n  (:start . 155) (:id . 75))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 163) (:start . 161)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 171)\n  (:start . 164) (:id . 77))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 181)\n  (:start . 172) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s8.510) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502762@unknown@formal@none@1@S@A total of ten dhtt-ko mutants, aged 1–3 days, were tested and all showed normal ERGs at 20°C and 37°C (Fig. 6E).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "CD") (:stem . "ten") (:form . "ten") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 22)\n  (:start . 15) (:id . 46))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 30)\n  (:start . 23) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "age") (:form . "aged") (:end . 36) (:start . 32)\n  (:id . 49))\n ((:tag . "CD") (:stem . "1–3") (:form . "1–3") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 45) (:start . 41)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 51) (:start . 47)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 58) (:start . 52)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 66) (:start . 63)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 73) (:start . 67)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 80)\n  (:start . 74) (:id . 58))\n ((:tag . "NNS") (:stem . "erg") (:form . "ERGs") (:end . 85) (:start . 81)\n  (:id . 59))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 88) (:start . 86)\n  (:id . 60))\n ((:tag . "NN") (:stem . "20°c") (:form . "20°C") (:end . 93) (:start . 89)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 62))\n ((:tag . "NN") (:stem . "37°c") (:form . "37°C") (:end . 102) (:start . 98)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Fig.") (:form . "Fig.") (:end . 108) (:start . 104)\n  (:id . 65))\n ((:tag . "NN") (:stem . "6e") (:form . "6E") (:end . 111) (:start . 109)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s8.511) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502763@unknown@formal@none@1@S@The number of preparations for the 40–45-day-old animals analyzed was: control, n=10; dhtt-ko, n=16.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "preparation") (:form . "preparations") (:end . 26)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "40–45-day-old") (:form . "40–45-day-old")\n  (:end . 48) (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 56)\n  (:start . 49) (:id . 49))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 65)\n  (:start . 57) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 70) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 78)\n  (:start . 71) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "NN") (:stem . "n=10") (:form . "n=10") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dhtt-ko") (:form . "dhtt-ko") (:end . 93)\n  (:start . 86) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "n=16") (:form . "n=16") (:end . 99) (:start . 95)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s8.512) (:did . :pmc2675792) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502764@unknown@formal@none@1@S@Evidence of a tick RNAi pathway by comparative genomics and reverse genetics screen of targets with known loss-of-function phenotypes in Drosophila@(((:tag . "NN") (:stem . "evidence") (:form . "Evidence") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "comparative") (:form . "comparative") (:end . 46)\n  (:start . 35) (:id . 49))\n ((:tag . "NNS") (:stem . "genomic") (:form . "genomics") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 67)\n  (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "genetic") (:form . "genetics") (:end . 76)\n  (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "screen") (:form . "screen") (:end . 83)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 94)\n  (:start . 87) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 99) (:start . 95)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 105)\n  (:start . 100) (:id . 58))\n ((:tag . "JJ") (:stem . "loss-of-function") (:form . "loss-of-function")\n  (:end . 122) (:start . 106) (:id . 59))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 133)\n  (:start . 123) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 147)\n  (:start . 137) (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.1) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5502765@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s9.2) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5502766@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s9.3) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502767@unknown@formal@none@1@S@The Arthropods are a diverse group of organisms including Chelicerata (ticks, mites, spiders), Crustacea (crabs, shrimps), and Insecta (flies, mosquitoes, beetles, silkworm).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "arthropod") (:form . "Arthropods") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "NNP") (:stem . "Chelicerata") (:form . "Chelicerata") (:end . 69)\n  (:start . 58) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 76) (:start . 71)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "mite") (:form . "mites") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "spider") (:form . "spiders") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "NN") (:stem . "crustacea") (:form . "Crustacea") (:end . 104)\n  (:start . 95) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "crab") (:form . "crabs") (:end . 111)\n  (:start . 106) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "shrimp") (:form . "shrimps") (:end . 120)\n  (:start . 113) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 121) (:start . 120)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Insecta") (:form . "Insecta") (:end . 134)\n  (:start . 127) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 136) (:start . 135)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 141) (:start . 136)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "mosquito") (:form . "mosquitoes") (:end . 153)\n  (:start . 143) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "beetle") (:form . "beetles") (:end . 162)\n  (:start . 155) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 75))\n ((:tag . "NN") (:stem . "silkworm") (:form . "silkworm") (:end . 172)\n  (:start . 164) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 173) (:start . 172)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s9.4) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502768@unknown@formal@none@1@S@The cattle tick, Rhipicephalus (Boophilus) microplus, is an economically significant ectoparasite of cattle affecting cattle industries world wide.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cattle") (:form . "cattle") (:end . 10)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Rhipicephalus") (:form . "Rhipicephalus")\n  (:end . 30) (:start . 17) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Boophilus") (:form . "Boophilus") (:end . 41)\n  (:start . 32) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "RB") (:stem . "economically") (:form . "economically") (:end . 72)\n  (:start . 60) (:id . 54))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 84)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "ectoparasite") (:form . "ectoparasite") (:end . 97)\n  (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "cattle") (:form . "cattle") (:end . 107)\n  (:start . 101) (:id . 58))\n ((:tag . "VBG") (:stem . "affect") (:form . "affecting") (:end . 117)\n  (:start . 108) (:id . 59))\n ((:tag . "NNS") (:stem . "cattle") (:form . "cattle") (:end . 124)\n  (:start . 118) (:id . 60))\n ((:tag . "NNS") (:stem . "industry") (:form . "industries") (:end . 135)\n  (:start . 125) (:id . 61))\n ((:tag . "NN") (:stem . "world") (:form . "world") (:end . 141)\n  (:start . 136) (:id . 62))\n ((:tag . "RB") (:stem . "wide") (:form . "wide") (:end . 146) (:start . 142)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.5) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502769@unknown@formal@none@1@S@With the availability of sequence reads from the first Chelicerate genome project (the Ixodes scapularis tick) and extensive R. microplus ESTs, we investigated evidence for putative RNAi proteins and studied RNA interference in tick cell cultures and adult female ticks targeting Drosophila homologues with known cell viability phenotype.@(((:tag . "IN") (:stem . "with") (:form . "With") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "availability") (:form . "availability") (:end . 21)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "VBZ") (:stem . "read") (:form . "reads") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . 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"with") (:end . 306) (:start . 302)\n  (:id . 88))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 312)\n  (:start . 307) (:id . 89))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 317) (:start . 313)\n  (:id . 90))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 327)\n  (:start . 318) (:id . 91))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 337)\n  (:start . 328) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 338) (:start . 337)\n  (:id . 93)))@@@1@52@((:identifiers (:sid . :s9.6) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502770@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s9.7) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502771@unknown@formal@none@1@S@We screened 13,643 R. microplus ESTs and I. scapularis genome reads to identify RNAi related proteins in ticks.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "screen") (:form . "screened") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "13,643") (:form . "13,643") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "CC") (:stem . "microplus") (:form . "microplus") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "NNP") (:stem . "ESTs") (:form . "ESTs") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 61)\n  (:start . 55) (:id . 51))\n ((:tag . "VBZ") (:stem . "read") (:form . "reads") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 79)\n  (:start . 71) (:id . 54))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "related") (:form . "related") (:end . 92)\n  (:start . 85) (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 101)\n  (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 110)\n  (:start . 105) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s9.8) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502772@unknown@formal@none@1@S@Our analysis identified 31 RNAi proteins including a putative tick Dicer, RISC associated (Ago-2 and FMRp), RNA dependent RNA polymerase (EGO-1) and 23 homologues implicated in dsRNA uptake and processing.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 50)\n  (:start . 41) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 89)\n  (:start . 79) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Ago-2") (:form . "Ago-2") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "FMRp") (:form . "FMRp") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 111) (:start . 108)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "dependent") (:form . "dependent") (:end . 121)\n  (:start . 112) (:id . 63))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 125) (:start . 122)\n  (:id . 64))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 136)\n  (:start . 126) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 66))\n ((:tag . "NN") (:stem . "ego-1") (:form . "EGO-1") (:end . 143)\n  (:start . 138) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n  (:id . 69))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 151) (:start . 149)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 162)\n  (:start . 152) (:id . 71))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 173)\n  (:start . 163) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 176) (:start . 174)\n  (:id . 73))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 182)\n  (:start . 177) (:id . 74))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 189)\n  (:start . 183) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 193) (:start . 190)\n  (:id . 76))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 204)\n  (:start . 194) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s9.9) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502773@unknown@formal@none@1@S@We selected 10 R. microplus ESTs with >80% similarity to D. melanogaster proteins associated with cell viability for RNAi functional screens in both BME26 R. microplus embryonic cells and female ticks in vivo.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "NNS") (:stem . "est") (:form . "ESTs") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "CD") (:stem . ">80") (:form . ">80") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 53)\n  (:start . 43) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 72)\n  (:start . 60) (:id . 54))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 92)\n  (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 97) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 102) (:start . 98)\n  (:id . 58))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 112)\n  (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 121) (:start . 117)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 132)\n  (:start . 122) (:id . 62))\n ((:tag . "NNS") (:stem . "screen") (:form . "screens") (:end . 140)\n  (:start . 133) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 143) (:start . 141)\n  (:id . 64))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 148) (:start . 144)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "BME26") (:form . "BME26") (:end . 154)\n  (:start . 149) (:id . 66))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 157) (:start . 155)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "microplu") (:form . "microplus") (:end . 167)\n  (:start . 158) (:id . 68))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 177)\n  (:start . 168) (:id . 69))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 183)\n  (:start . 178) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 187) (:start . 184)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "female") (:form . "female") (:end . 194)\n  (:start . 188) (:id . 72))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 200)\n  (:start . 195) (:id . 73))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 203) (:start . 201)\n  (:id . 74))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 208) (:start . 204)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s9.10) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502774@unknown@formal@none@1@S@Only genes associated with proteasomes had an effect on cell viability in vitro.@(((:tag . "RB") (:stem . "only") (:form . "Only") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "proteasome") (:form . "proteasomes") (:end . 38)\n  (:start . 27) (:id . 46))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 52)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 70)\n  (:start . 61) (:id . 52))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s9.11) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502775@unknown@formal@none@1@S@In vivo RNAi showed that 9 genes had significant effects either causing lethality or impairing egg laying.@(((:tag . "FW") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 19) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 48)\n  (:start . 37) (:id . 50))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "VBG") (:stem . "cause") (:form . "causing") (:end . 71)\n  (:start . 64) (:id . 53))\n ((:tag . "NN") (:stem . "lethality") (:form . "lethality") (:end . 81)\n  (:start . 72) (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "impair") (:form . "impairing") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "laying") (:form . "laying") (:end . 105)\n  (:start . 99) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s9.12) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502776@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s9.13) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502777@unknown@formal@none@1@S@We have identified key RNAi-related proteins in ticks and along with our loss-of-function studies support a functional RNAi pathway in R. microplus.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "rnai-related") (:form . "RNAi-related") (:end . 35)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 53) (:start . 48)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "loss-of-function") (:form . "loss-of-function")\n  (:end . 89) (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 97)\n  (:start . 90) (:id . 55))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 105)\n  (:start . 98) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 107) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 118)\n  (:start . 108) (:id . 58))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 123) (:start . 119)\n  (:id . 59))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 131)\n  (:start . 124) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 137) (:start . 135)\n  (:id . 62))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 147)\n  (:start . 138) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.14) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502778@unknown@formal@none@1@S@Our preliminary studies indicate that tick RNAi pathways may differ from that of other Arthropods such as insects.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "preliminary") (:form . "preliminary") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 56)\n  (:start . 48) (:id . 49))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "VB") (:stem . "differ") (:form . "differ") (:end . 67)\n  (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 86) (:start . 81)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "arthropod") (:form . "Arthropods") (:end . 97)\n  (:start . 87) (:id . 56))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 102) (:start . 98)\n  (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "insect") (:form . "insects") (:end . 113)\n  (:start . 106) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x9.15.1) (:span 57 60)) ((:id . :x9.15.2) (:span 24 37)))\n (:hscopes ((:id . :x9.15.1) (:span 57 113)) ((:id . :x9.15.2) (:span 24 113)))\n (:identifiers (:sid . :s9.15) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502779@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s9.16) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5502780@unknown@formal@none@1@S@The understanding of gene function in a poorly studied Arthropod such as the cattle tick Rhipicephalus (Boophilus) microplus (subphylum Chelicerata: order Acari: suborder Ixodida) can benefit from the knowledge generated by genome-wide resources of the model insect Drosophila melanogaster (subphylum Mandibulata: order Hexapoda: suborder Insecta).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "understanding") (:form . "understanding")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . 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5502781@unknown@formal@none@1@S@The genome of the fruit fly D. melanogaster was among the first eukaryotic genomes to be sequenced and assembled [1].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 43)\n  (:start . 31) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 63) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "eukaryotic") (:form . "eukaryotic") (:end . 74)\n  (:start . 64) (:id . 54))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 82)\n  (:start . 75) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "sequence") (:form . "sequenced") (:end . 98)\n  (:start . 89) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "assemble") (:form . "assembled") (:end . 112)\n  (:start . 103) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 116) (:start . 115)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.18) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502782@unknown@formal@none@1@S@D. melanogaster and R. microplus evolved from a common ancestor ca. 500 million years ago [2].@(((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "VBD") (:stem . "evolve") (:form . "evolved") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 54)\n  (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "ancestor") (:form . "ancestor") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "RB") (:stem . "ca.") (:form . "ca.") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "CD") (:stem . "500") (:form . "500") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "CD") (:stem . "million") (:form . "million") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 85) (:start . 80)\n  (:id . 55))\n ((:tag . "RB") (:stem . "ago") (:form . "ago") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 93) (:start . 92)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s9.19) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502783@unknown@formal@none@1@S@In comparison to the existing comprehensive genome resources for the fruit fly D. melanogaster, the cattle tick genome resources are limited to approximately 45,000 EST sequences [3].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "JJ") (:stem . "comprehensive") (:form . "comprehensive")\n  (:end . 43) (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 50)\n  (:start . 44) (:id . 48))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 64) (:start . 61)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 51))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 94)\n  (:start . 82) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "cattle") (:form . "cattle") (:end . 106)\n  (:start . 100) (:id . 58))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 111) (:start . 107)\n  (:id . 59))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 118)\n  (:start . 112) (:id . 60))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 128)\n  (:start . 119) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 132) (:start . 129)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 140)\n  (:start . 133) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n  (:id . 64))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 157) (:start . 144) (:id . 65))\n ((:tag . "CD") (:stem . "45,000") (:form . "45,000") (:end . 164)\n  (:start . 158) (:id . 66))\n ((:tag . "NNP") (:stem . "EST") (:form . "EST") (:end . 168) (:start . 165)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 178)\n  (:start . 169) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 180) (:start . 179)\n  (:id . 69))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 181) (:start . 180)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 182) (:start . 181)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.20) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502784@unknown@formal@none@1@S@In addition, the tick genome size of 7.1 Gbp [2] compared to the D. melanogaster of 139 Mbp [4] will likely delay the generation of a complete R. microplus genome sequence [5].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 28)\n  (:start . 22) (:id . 47))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "CD") (:stem . "7.1") (:form . "7.1") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Gbp") (:form . "Gbp") (:end . 44) (:start . 41)\n  (:id . 51))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 46) (:start . 45)\n  (:id . 52))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 47) (:start . 46)\n  (:id . 53))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 48) (:start . 47)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 57)\n  (:start . 49) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 67) (:start . 65)\n  (:id . 58))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 80)\n  (:start . 68) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 60))\n ((:tag . "CD") (:stem . "139") (:form . "139") (:end . 87) (:start . 84)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Mbp") (:form . "Mbp") (:end . 91) (:start . 88)\n  (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 93) (:start . 92)\n  (:id . 63))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 94) (:start . 93)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 95) (:start . 94)\n  (:id . 65))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 100) (:start . 96)\n  (:id . 66))\n ((:tag . "RB") (:stem . "likely") (:form . "likely") (:end . 107)\n  (:start . 101) (:id . 67))\n ((:tag . "VB") (:stem . "delay") (:form . "delay") (:end . 113)\n  (:start . 108) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 69))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 128)\n  (:start . 118) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 133) (:start . 132)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 142)\n  (:start . 134) (:id . 73))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 145) (:start . 143)\n  (:id . 74))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 155)\n  (:start . 146) (:id . 75))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 162)\n  (:start . 156) (:id . 76))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 171)\n  (:start . 163) (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 173) (:start . 172)\n  (:id . 78))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 174) (:start . 173)\n  (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 175) (:start . 174)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x9.21.1) (:span 101 107)))\n (:hscopes ((:id . :x9.21.1) (:span 101 171)))\n (:identifiers (:sid . :s9.21) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502785@unknown@formal@none@1@S@A genome project for the related tick species, Ixodes scapularis, with an estimated genome size of 2.1 Gbp, is currently underway [6].@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "project") (:form . "project") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Ixodes") (:form . "Ixodes") (:end . 53)\n  (:start . 47) (:id . 51))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 64)\n  (:start . 54) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "estimate") (:form . "estimated") (:end . 83)\n  (:start . 74) (:id . 56))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 90)\n  (:start . 84) (:id . 57))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "CD") (:stem . "2.1") (:form . "2.1") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . "NN") (:stem . "gbp") (:form . "Gbp") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 110) (:start . 108)\n  (:id . 63))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 120)\n  (:start . 111) (:id . 64))\n ((:tag . "RB") (:stem . "underway") (:form . "underway") (:end . 129)\n  (:start . 121) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 131) (:start . 130)\n  (:id . 66))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 132) (:start . 131)\n  (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 133) (:start . 132)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s9.22) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502786@unknown@formal@none@1@S@Although there are many invertebrate genomes completed including worms, nematodes, beetle, wasp, honey bee, flies, and mosquitoes http://www.genome.gov/, I. scapularis will be the first Chelicerate:Arachnida genome sequence available representing mites, ticks, scorpions and spiders.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "invertebrate") (:form . "invertebrate") (:end . 36)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "VBN") (:stem . "complete") (:form . "completed") (:end . 54)\n  (:start . 45) (:id . 48))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 64)\n  (:start . 55) (:id . 49))\n ((:tag . "NNS") (:stem . "worm") (:form . "worms") (:end . 70) (:start . 65)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "nematode") (:form . "nematodes") (:end . 81)\n  (:start . 72) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 53))\n ((:tag . "NN") (:stem . "beetle") (:form . "beetle") (:end . 89)\n  (:start . 83) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "wasp") (:form . "wasp") (:end . 95) (:start . 91)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "honey") (:form . "honey") (:end . 102) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "bee") (:form . "bee") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 113) (:start . 108)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "mosquitoe") (:form . "mosquitoes") (:end . 129)\n  (:start . 119) (:id . 64))\n ((:tag . "NNP") (:stem . "http://www.genome.gov/")\n  (:form . "http://www.genome.gov/") (:end . 152) (:start . 130) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 156) (:start . 154)\n  (:id . 67))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 167)\n  (:start . 157) (:id . 68))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 172) (:start . 168)\n  (:id . 69))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 175) (:start . 173)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 185)\n  (:start . 180) (:id . 72))\n ((:tag . "NNP") (:stem . "Chelicerate:Arachnida")\n  (:form . "Chelicerate:Arachnida") (:end . 207) (:start . 186) (:id . 73))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 214)\n  (:start . 208) (:id . 74))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 223)\n  (:start . 215) (:id . 75))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 233)\n  (:start . 224) (:id . 76))\n ((:tag . "VBG") (:stem . "represent") (:form . "representing") (:end . 246)\n  (:start . 234) (:id . 77))\n ((:tag . "NNS") (:stem . "mite") (:form . "mites") (:end . 252)\n  (:start . 247) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 253) (:start . 252)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 259)\n  (:start . 254) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 260) (:start . 259)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "scorpion") (:form . "scorpions") (:end . 270)\n  (:start . 261) (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 274) (:start . 271)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "spider") (:form . "spiders") (:end . 282)\n  (:start . 275) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 283) (:start . 282)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s9.23) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502787@unknown@formal@none@1@S@Among the many methods available for reverse genetic studies, RNA interference (RNAi) has gained popularity because of its demonstrated efficient post transcriptional gene-silencing effects in plants, fungi, nematodes, flies and cultured mammalians cells (reviewed by [7-11]).@(((:tag . "IN") (:stem . "among") (:form . "Among") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "interference") (:form . "interference") (:end . 78)\n  (:start . 66) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "gain") (:form . "gained") (:end . 96) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "popularity") (:form . "popularity") (:end . 107)\n  (:start . 97) (:id . 59))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 115)\n  (:start . 108) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n  (:id . 61))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 122) (:start . 119)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "demonstrate") (:form . "demonstrated") (:end . 135)\n  (:start . 123) (:id . 63))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 145)\n  (:start . 136) (:id . 64))\n ((:tag . "NN") (:stem . "post") (:form . "post") (:end . 150) (:start . 146)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 166) (:start . 151) (:id . 66))\n ((:tag . "JJ") (:stem . "gene-silencing") (:form . "gene-silencing")\n  (:end . 181) (:start . 167) (:id . 67))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 189)\n  (:start . 182) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 192) (:start . 190)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "plant") (:form . "plants") (:end . 199)\n  (:start . 193) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "fungus") (:form . "fungi") (:end . 206)\n  (:start . 201) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 207) (:start . 206)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "nematode") (:form . "nematodes") (:end . 217)\n  (:start . 208) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 218) (:start . 217)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 224) (:start . 219)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 228) (:start . 225)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 237)\n  (:start . 229) (:id . 78))\n ((:tag . "NNS") (:stem . "mammalian") (:form . "mammalians") (:end . 248)\n  (:start . 238) (:id . 79))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 254)\n  (:start . 249) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 256) (:start . 255)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "review") (:form . "reviewed") (:end . 264)\n  (:start . 256) (:id . 82))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 267) (:start . 265)\n  (:id . 83))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 269) (:start . 268)\n  (:id . 84))\n ((:tag . "NN") (:stem . "7-11") (:form . "7-11") (:end . 273) (:start . 269)\n  (:id . 85))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 274) (:start . 273)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 275) (:start . 274)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 276) (:start . 275)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s9.24) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502788@unknown@formal@none@1@S@RNA mediated gene silencing is a widely conserved mechanism in eukaryotes and can be categorized into two partially overlapping pathways, the RNAi pathway and the microRNA (miRNA) pathway.@(((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "mediate") (:form . "mediated") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "RB") (:stem . "widely") (:form . "widely") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 59)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "eukaryote") (:form . "eukaryotes") (:end . 73)\n  (:start . 63) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "categorize") (:form . "categorized") (:end . 96)\n  (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 101) (:start . 97)\n  (:id . 57))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 105) (:start . 102)\n  (:id . 58))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 115)\n  (:start . 106) (:id . 59))\n ((:tag . "VBG") (:stem . "overlap") (:form . "overlapping") (:end . 127)\n  (:start . 116) (:id . 60))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 136)\n  (:start . 128) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 146) (:start . 142)\n  (:id . 64))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 154)\n  (:start . 147) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 158) (:start . 155)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "microRNA") (:form . "microRNA") (:end . 171)\n  (:start . 163) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 173) (:start . 172)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "miRNA") (:form . "miRNA") (:end . 178)\n  (:start . 173) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 71))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 187)\n  (:start . 180) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s9.25) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502789@unknown@formal@none@1@S@The RNAi pathway is triggered by exogenous or endogenous dsRNAs that are recognized by Dicer RNase III proteins which 'dice' these molecules into double-stranded small interfering RNAs (siRNAs) of 21–23 nt in length [12].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "trigger") (:form . "triggered") (:end . 29)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "exogenous") (:form . "exogenous") (:end . 42)\n  (:start . 33) (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "dsrna") (:form . "dsRNAs") (:end . 63)\n  (:start . 57) (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "recognize") (:form . "recognized") (:end . 83)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 92) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "RNase") (:form . "RNase") (:end . 98) (:start . 93)\n  (:id . 57))\n ((:tag . "CD") (:stem . "iii") (:form . "III") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 111)\n  (:start . 103) (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 117)\n  (:start . 112) (:id . 60))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 119) (:start . 118)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "dice") (:form . "dice") (:end . 123) (:start . 119)\n  (:id . 62))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 130)\n  (:start . 125) (:id . 64))\n ((:tag . "NNS") (:stem . "molecule") (:form . "molecules") (:end . 140)\n  (:start . 131) (:id . 65))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 145) (:start . 141)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "double-stranded") (:form . "double-stranded")\n  (:end . 161) (:start . 146) (:id . 67))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 167)\n  (:start . 162) (:id . 68))\n ((:tag . "VBG") (:stem . "interfere") (:form . "interfering") (:end . 179)\n  (:start . 168) (:id . 69))\n ((:tag . "NNS") (:stem . "rna") (:form . "RNAs") (:end . 184) (:start . 180)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 186) (:start . 185)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 192)\n  (:start . 186) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 193) (:start . 192)\n  (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 196) (:start . 194)\n  (:id . 74))\n ((:tag . "CD") (:stem . "21–23") (:form . "21–23") (:end . 202)\n  (:start . 197) (:id . 75))\n ((:tag . "NN") (:stem . "nt") (:form . "nt") (:end . 205) (:start . 203)\n  (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 208) (:start . 206)\n  (:id . 77))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 215)\n  (:start . 209) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 217) (:start . 216)\n  (:id . 79))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 219) (:start . 217)\n  (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 220) (:start . 219)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 221) (:start . 220)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s9.26) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502790@unknown@formal@none@1@S@A typical eukaryotic Dicer consists of 2 helicase domains, a PAZ domain, 2 RNAse domains and a dsRNA-binding domain (dsRBD) [12,13], however some variations in this domain structure have been noted for insect Dicers [14].@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "typical") (:form . "typical") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "JJ") (:stem . "eukaryotic") (:form . "eukaryotic") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "helicase") (:form . "helicase") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 60) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "PAZ") (:form . "PAZ") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 71)\n  (:start . 65) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "RNAse") (:form . "RNAse") (:end . 80) (:start . 75)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 88)\n  (:start . 81) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "dsrna-binding") (:form . "dsRNA-binding")\n  (:end . 108) (:start . 95) (:id . 61))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 115)\n  (:start . 109) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dsrbd") (:form . "dsRBD") (:end . 122)\n  (:start . 117) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n  (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 125) (:start . 124)\n  (:id . 66))\n ((:tag . "CD") (:stem . "12,13") (:form . "12,13") (:end . 130)\n  (:start . 125) (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 131) (:start . 130)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 69))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 140)\n  (:start . 133) (:id . 70))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 145) (:start . 141)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "variation") (:form . "variations") (:end . 156)\n  (:start . 146) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 159) (:start . 157)\n  (:id . 73))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 164) (:start . 160)\n  (:id . 74))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 171)\n  (:start . 165) (:id . 75))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 181)\n  (:start . 172) (:id . 76))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 186) (:start . 182)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 191) (:start . 187)\n  (:id . 78))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 197)\n  (:start . 192) (:id . 79))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 201) (:start . 198)\n  (:id . 80))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 208)\n  (:start . 202) (:id . 81))\n ((:tag . "NNS") (:stem . "dicer") (:form . "Dicers") (:end . 215)\n  (:start . 209) (:id . 82))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 217) (:start . 216)\n  (:id . 83))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 219) (:start . 217)\n  (:id . 84))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 220) (:start . 219)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 221) (:start . 220)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s9.27) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502791@unknown@formal@none@1@S@D. melanogaster has 2 Dicer enzymes, Dcr-1 and Dcr-2 which are responsible for miRNA and siRNA production respectively [15].@(((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "enzyme") (:form . "enzymes") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "dcr-1") (:form . "Dcr-1") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dcr-2") (:form . "Dcr-2") (:end . 52) (:start . 47)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "responsible") (:form . "responsible") (:end . 74)\n  (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "mirna") (:form . "miRNA") (:end . 84) (:start . 79)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 94) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 105)\n  (:start . 95) (:id . 59))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 118)\n  (:start . 106) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 123) (:start . 122)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.28) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502792@unknown@formal@none@1@S@By contrast most other animals contain a single Dicer that generates both siRNAs and miRNAs.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "generate") (:form . "generates") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 80)\n  (:start . 74) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "mirna") (:form . "miRNAs") (:end . 91)\n  (:start . 85) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s9.29) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502793@unknown@formal@none@1@S@The next phase in the RNAi pathway involves the loading of siRNAs into RNA-induced silencing complexes (RISCs).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "phase") (:form . "phase") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 34)\n  (:start . 27) (:id . 48))\n ((:tag . "VBZ") (:stem . "involve") (:form . "involves") (:end . 43)\n  (:start . 35) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "loading") (:form . "loading") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 65)\n  (:start . 59) (:id . 53))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "rna-induced") (:form . "RNA-induced") (:end . 82)\n  (:start . 71) (:id . 55))\n ((:tag . "JJ") (:stem . "silencing") (:form . "silencing") (:end . 92)\n  (:start . 83) (:id . 56))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 102)\n  (:start . 93) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISCs") (:end . 109)\n  (:start . 104) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s9.30) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502794@unknown@formal@none@1@S@dsRNA binding motif proteins (dsRBM), such as D. melanogaster R2D2 and Caenorhabditiselegans Rde-4 help siRNAs to be loaded properly into silencing complexes [16,17].@(((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "dsRBM") (:form . "dsRBM") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 45) (:start . 43)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 48) (:start . 46)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 61)\n  (:start . 49) (:id . 53))\n ((:tag . "NN") (:stem . "r2d2") (:form . "R2D2") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "NNPS") (:stem . "Caenorhabditiselegans")\n  (:form . "Caenorhabditiselegans") (:end . 92) (:start . 71) (:id . 56))\n ((:tag . "NN") (:stem . "rde-4") (:form . "Rde-4") (:end . 98) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "help") (:form . "help") (:end . 103) (:start . 99)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 110)\n  (:start . 104) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 116) (:start . 114)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "load") (:form . "loaded") (:end . 123)\n  (:start . 117) (:id . 62))\n ((:tag . "RB") (:stem . "properly") (:form . "properly") (:end . 132)\n  (:start . 124) (:id . 63))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 137) (:start . 133)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "silencing") (:form . "silencing") (:end . 147)\n  (:start . 138) (:id . 65))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 157)\n  (:start . 148) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 159) (:start . 158)\n  (:id . 67))\n ((:tag . "CD") (:stem . "16,17") (:form . "16,17") (:end . 164)\n  (:start . 159) (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 165) (:start . 164)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s9.31) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502795@unknown@formal@none@1@S@Using the siRNAs as a guide, RISCs find target mRNAs and cleave them.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "guide") (:form . "guide") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "risc") (:form . "RISCs") (:end . 34) (:start . 29)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 39) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 46)\n  (:start . 40) (:id . 51))\n ((:tag . "NNS") (:stem . "mrna") (:form . "mRNAs") (:end . 52) (:start . 47)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . "VB") (:stem . "cleave") (:form . "cleave") (:end . 63)\n  (:start . 57) (:id . 54))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s9.32) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502796@unknown@formal@none@1@S@Argonaute (Ago) family proteins are the main components of silencing complexes, mediating target recognition and silencing [18-20].@(((:tag . "NNP") (:stem . "Argonaute") (:form . "Argonaute") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Ago") (:form . "Ago") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 22)\n  (:start . 16) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "main") (:form . "main") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 55)\n  (:start . 45) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "silencing") (:form . "silencing") (:end . 68)\n  (:start . 59) (:id . 53))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 78)\n  (:start . 69) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "mediate") (:form . "mediating") (:end . 89)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 96)\n  (:start . 90) (:id . 57))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 108)\n  (:start . 97) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 122)\n  (:start . 113) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 124) (:start . 123)\n  (:id . 61))\n ((:tag . "CD") (:stem . "18-20") (:form . "18-20") (:end . 129)\n  (:start . 124) (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.33) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502797@unknown@formal@none@1@S@Most organisms have multiple members of the Ago proteins, for example both insect species D. melanogaster and Tribolium castaneum (beetle) have 5, whereas C. elegans (nematode) has 27 [14,21-25].@(((:tag . "JJS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Ago") (:form . "Ago") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 69)\n  (:start . 62) (:id . 53))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 81)\n  (:start . 75) (:id . 55))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 105)\n  (:start . 93) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "NN") (:stem . "tribolium") (:form . "Tribolium") (:end . 119)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "castaneum") (:form . "castaneum") (:end . 129)\n  (:start . 120) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 62))\n ((:tag . "NN") (:stem . "beetle") (:form . "beetle") (:end . 137)\n  (:start . 131) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 143) (:start . 139)\n  (:id . 65))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 67))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 154)\n  (:start . 147) (:id . 68))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 157) (:start . 155)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 165)\n  (:start . 158) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . "NN") (:stem . "nematode") (:form . "nematode") (:end . 175)\n  (:start . 167) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 73))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 180) (:start . 177)\n  (:id . 74))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 183) (:start . 181)\n  (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 185) (:start . 184)\n  (:id . 76))\n ((:tag . "CD") (:stem . "14,21-25") (:form . "14,21-25") (:end . 193)\n  (:start . 185) (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 194) (:start . 193)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s9.34) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502798@unknown@formal@none@1@S@In Drosophila Ago-1 and Ago-2 are known to be associated with RISC [21].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "Ago-1") (:form . "Ago-1") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Ago-2") (:form . "Ago-2") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 56)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s9.35) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502799@unknown@formal@none@1@S@In C. elegans, the primary siRNAs processed by Dicer can also trigger the amplification of siRNAs through a RNA-dependent RNA polymerase (RdRP) to produce secondary dsRNAs in a two-step mechanism involving secondary Argonaute proteins [26-28].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 13)\n  (:start . 6) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 26)\n  (:start . 19) (:id . 47))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . "VBN") (:stem . "process") (:form . "processed") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 52) (:start . 47)\n  (:id . 51))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "VB") (:stem . "trigger") (:form . "trigger") (:end . 69)\n  (:start . 62) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 87) (:start . 74) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 97)\n  (:start . 91) (:id . 58))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 105)\n  (:start . 98) (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "rna-dependent") (:form . "RNA-dependent")\n  (:end . 121) (:start . 108) (:id . 61))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 125) (:start . 122)\n  (:id . 62))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 136)\n  (:start . 126) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 142) (:start . 138)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 146) (:start . 144)\n  (:id . 67))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 154)\n  (:start . 147) (:id . 68))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 164)\n  (:start . 155) (:id . 69))\n ((:tag . "NNS") (:stem . "dsrna") (:form . "dsRNAs") (:end . 171)\n  (:start . 165) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 174) (:start . 172)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 176) (:start . 175)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "two-step") (:form . "two-step") (:end . 185)\n  (:start . 177) (:id . 73))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 195)\n  (:start . 186) (:id . 74))\n ((:tag . "VBG") (:stem . "involve") (:form . "involving") (:end . 205)\n  (:start . 196) (:id . 75))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 215)\n  (:start . 206) (:id . 76))\n ((:tag . "NNP") (:stem . "Argonaute") (:form . "Argonaute") (:end . 225)\n  (:start . 216) (:id . 77))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 234)\n  (:start . 226) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 236) (:start . 235)\n  (:id . 79))\n ((:tag . "CD") (:stem . "26-28") (:form . "26-28") (:end . 241)\n  (:start . 236) (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 242) (:start . 241)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s9.36) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502800@unknown@formal@none@1@S@This mechanism has not been demonstrated in other animals to date and is commonly found in plants rather than animals.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "demonstrate") (:form . "demonstrated") (:end . 40)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 87) (:start . 82)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "plant") (:form . "plants") (:end . 97)\n  (:start . 91) (:id . 58))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 104)\n  (:start . 98) (:id . 59))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 117)\n  (:start . 110) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.37) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502801@unknown@formal@none@1@S@An additional phenomenon identified in plants and C. elegans is the systemic spread of RNAi from cell to cell throughout the organism and its potential systemic transfer to subsequent generations through the germ-line [29-31].@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "phenomenon") (:form . "phenomenon") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 35)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "plant") (:form . "plants") (:end . 45)\n  (:start . 39) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 76)\n  (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "spread") (:form . "spread") (:end . 83)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 120)\n  (:start . 110) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n  (:id . 62))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 133)\n  (:start . 125) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 64))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 141) (:start . 138)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 151)\n  (:start . 142) (:id . 66))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 160)\n  (:start . 152) (:id . 67))\n ((:tag . "NN") (:stem . "transfer") (:form . "transfer") (:end . 169)\n  (:start . 161) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 172) (:start . 170)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 183)\n  (:start . 173) (:id . 70))\n ((:tag . "NNS") (:stem . "generation") (:form . "generations") (:end . 195)\n  (:start . 184) (:id . 71))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 203)\n  (:start . 196) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 207) (:start . 204)\n  (:id . 73))\n ((:tag . "NN") (:stem . "germ-line") (:form . "germ-line") (:end . 217)\n  (:start . 208) (:id . 74))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 219) (:start . 218)\n  (:id . 75))\n ((:tag . "CD") (:stem . "29-31") (:form . "29-31") (:end . 224)\n  (:start . 219) (:id . 76))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 225) (:start . 224)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x9.38.1) (:span 142 151)))\n (:hscopes ((:id . :x9.38.1) (:span 142 217)))\n (:identifiers (:sid . :s9.38) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502802@unknown@formal@none@1@S@Proteins related to this phenomenon in C. elegans include Sid-1, which encodes a multi-transmembrane domain protein thought to act as a channel for dsRNA uptake, and RNAi spreading defective proteins (Rsd-2, Rsd-3 and Rsd-6) shown to be required for the systemic RNAi response [32,33].@(((:tag . "NNPS") (:stem . "Protein") (:form . "Proteins") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "phenomenon") (:form . "phenomenon") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "sid-1") (:form . "Sid-1") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 78)\n  (:start . 71) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "multi-transmembrane")\n  (:form . "multi-transmembrane") (:end . 100) (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 107)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 115)\n  (:start . 108) (:id . 58))\n ((:tag . "VBN") (:stem . 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5502803@unknown@formal@none@1@S@Originally, systemic RNAi was thought to be unique to C. elegans in animals, however preliminary evidence suggests that silkworm, honeybee, wasp and beetle utilize a Sid-1-like (sil) protein not found in mosquitoes or flies (reviewed by Tomoyasu et al [14]).@(((:tag . "RB") (:stem . "originally") (:form . "Originally") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . 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5502804@unknown@formal@none@1@S@Furthermore, over 20 genes identified as necessary for dsRNA uptake in Drosophila cultured cells have also been identified in other insect species [14,34-36].@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 60) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 67)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 81)\n  (:start . 71) (:id . 54))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 90)\n  (:start . 82) (:id . 55))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 101) (:start . 97)\n  (:id . 57))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 106) (:start . 102)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 111) (:start . 107)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 122)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 125) (:start . 123)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 131)\n  (:start . 126) (:id . 62))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 138)\n  (:start . 132) (:id . 63))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 146)\n  (:start . 139) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 148) (:start . 147)\n  (:id . 65))\n ((:tag . "CD") (:stem . "14,34-36") (:form . "14,34-36") (:end . 156)\n  (:start . 148) (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s9.41) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502805@unknown@formal@none@1@S@The specific mechanisms associated with dsRNA uptake and systemic RNAi in Arthropods including some insect species are thus currently undefined.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 34)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 45) (:start . 40)\n  (:id . 47))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 52)\n  (:start . 46) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 65)\n  (:start . 57) (:id . 50))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 70) (:start . 66)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Arthropod") (:form . "Arthropods") (:end . 84)\n  (:start . 74) (:id . 53))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 94)\n  (:start . 85) (:id . 54))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 99) (:start . 95)\n  (:id . 55))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 106)\n  (:start . 100) (:id . 56))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 114)\n  (:start . 107) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 123) (:start . 119)\n  (:id . 59))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 133)\n  (:start . 124) (:id . 60))\n ((:tag . "JJ") (:stem . "undefined") (:form . "undefined") (:end . 143)\n  (:start . 134) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.42) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502806@unknown@formal@none@1@S@Of the above described proteins associated with RNAi pathways, only one RNAi tick protein has been identified to date, a putative R. microplus Ago-2 [37].@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 42)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 109)\n  (:start . 99) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 117) (:start . 113)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 129)\n  (:start . 121) (:id . 64))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 142)\n  (:start . 133) (:id . 66))\n ((:tag . "NN") (:stem . "ago-2") (:form . "Ago-2") (:end . 148)\n  (:start . 143) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 150) (:start . 149)\n  (:id . 68))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 152) (:start . 150)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 153) (:start . 152)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s9.43) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502807@unknown@formal@none@1@S@RNAi pathways in Arthropods other than fruit flies and mosquitoes are beginning to demonstrate that there are evolutionary variations in these pathways with a higher level of divergence within the Arthropoda than previously thought [14,38-41].@(((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "arthropod") (:form . "Arthropods") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "mosquito") (:form . "mosquitoes") (:end . 65)\n  (:start . 55) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "begin") (:form . "beginning") (:end . 79)\n  (:start . 70) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "VB") (:stem . "demonstrate") (:form . "demonstrate") (:end . 94)\n  (:start . 83) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 105)\n  (:start . 100) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 109) (:start . 106)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 122)\n  (:start . 110) (:id . 59))\n ((:tag . "NNS") (:stem . "variation") (:form . "variations") (:end . 133)\n  (:start . 123) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 61))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 142)\n  (:start . 137) (:id . 62))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 151)\n  (:start . 143) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 156) (:start . 152)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 158) (:start . 157)\n  (:id . 65))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 165)\n  (:start . 159) (:id . 66))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 171)\n  (:start . 166) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 174) (:start . 172)\n  (:id . 68))\n ((:tag . "NN") (:stem . "divergence") (:form . "divergence") (:end . 185)\n  (:start . 175) (:id . 69))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 192)\n  (:start . 186) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Arthropoda") (:form . "Arthropoda") (:end . 207)\n  (:start . 197) (:id . 72))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 212) (:start . 208)\n  (:id . 73))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 223)\n  (:start . 213) (:id . 74))\n ((:tag . "VBN") (:stem . "think") (:form . "thought") (:end . 231)\n  (:start . 224) (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 233) (:start . 232)\n  (:id . 76))\n ((:tag . "CD") (:stem . "14,38-41") (:form . "14,38-41") (:end . 241)\n  (:start . 233) (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 242) (:start . 241)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x9.44.1) (:span 83 94)))\n (:hscopes ((:id . :x9.44.1) (:span 83 231)))\n (:identifiers (:sid . :s9.44) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502808@unknown@formal@none@1@S@Similarly, long dsRNAs have been successfully applied in R. microplus [42] and other tick species (e.g. Amblyomma, Ixodes, Haemaphysalis, and Dermacentor spp.) for targeted gene knockdown to demonstrate the function of tick-specific genes in various tick life stages, with some studies producing evidence of systemic RNAi spread into subsequent stages (reviewed by de la Fuente et al [37]).@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "dsrna") (:form . "dsRNAs") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . 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5502809@unknown@formal@none@1@S@With the advent of increasing Arthropod genome resources, it may be feasible to identify more putative tick homologues of essential RNAi pathway-associated proteins to better elucidate the tick RNAi mechanism.@(((:tag . "IN") (:stem . "with") (:form . "With") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "advent") (:form . "advent") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "arthropod") (:form . "Arthropod") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 46)\n  (:start . 40) (:id . 48))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 56)\n  (:start . 47) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "feasible") (:form . "feasible") (:end . 76)\n  (:start . 68) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 88)\n  (:start . 80) (:id . 56))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 93) (:start . 89)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 102)\n  (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 107) (:start . 103)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 118)\n  (:start . 108) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 131)\n  (:start . 122) (:id . 62))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 136) (:start . 132)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "pathway-associated") (:form . "pathway-associated")\n  (:end . 155) (:start . 137) (:id . 64))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 164)\n  (:start . 156) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 167) (:start . 165)\n  (:id . 66))\n ((:tag . "RBR") (:stem . "well") (:form . "better") (:end . 174)\n  (:start . 168) (:id . 67))\n ((:tag . "VB") (:stem . "elucidate") (:form . "elucidate") (:end . 184)\n  (:start . 175) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n  (:id . 69))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 193) (:start . 189)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 198) (:start . 194)\n  (:id . 71))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 208)\n  (:start . 199) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x9.46.1) (:span 61 64)))\n (:hscopes ((:id . :x9.46.1) (:span 61 208)))\n (:identifiers (:sid . :s9.46) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502810@unknown@formal@none@1@S@Improving the understanding of the mechanisms used by ticks for gene knockdown will assist to develop specific tick RNA interference reagents and improved techniques for gene functional studies.@(((:tag . "VBG") (:stem . "improve") (:form . "Improving") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "understanding") (:form . "understanding")\n  (:end . 27) (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 45)\n  (:start . 35) (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 50) (:start . 46)\n  (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . "VB") (:stem . "assist") (:form . "assist") (:end . 90)\n  (:start . 84) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 56))\n ((:tag . "VB") (:stem . "develop") (:form . "develop") (:end . 101)\n  (:start . 94) (:id . 57))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 110)\n  (:start . 102) (:id . 58))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "NN") (:stem . "interference") (:form . "interference") (:end . 132)\n  (:start . 120) (:id . 61))\n ((:tag . "NNS") (:stem . "reagent") (:form . "reagents") (:end . 141)\n  (:start . 133) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "improve") (:form . "improved") (:end . 154)\n  (:start . 146) (:id . 64))\n ((:tag . "NNS") (:stem . "technique") (:form . "techniques") (:end . 165)\n  (:start . 155) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 169) (:start . 166)\n  (:id . 66))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 174) (:start . 170)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 185)\n  (:start . 175) (:id . 68))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 193)\n  (:start . 186) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s9.47) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502811@unknown@formal@none@1@S@In this study we provide evidence for the presence of RNAi pathway associated proteins in R. microplus ESTs and I. scapularis genome reads, including a tick homologue for Dicer, Argonaute proteins, RdRP and proteins associated with dsRNA uptake and processing, and thus propose a putative tick RNAi pathway.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . 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"associated") (:end . 226)\n  (:start . 216) (:id . 79))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 231) (:start . 227)\n  (:id . 80))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 237)\n  (:start . 232) (:id . 81))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 244)\n  (:start . 238) (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 248) (:start . 245)\n  (:id . 83))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 259)\n  (:start . 249) (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 260) (:start . 259)\n  (:id . 85))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 264) (:start . 261)\n  (:id . 86))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 269) (:start . 265)\n  (:id . 87))\n ((:tag . "VB") (:stem . "propose") (:form . "propose") (:end . 277)\n  (:start . 270) (:id . 88))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 279) (:start . 278)\n  (:id . 89))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 288)\n  (:start . 280) (:id . 90))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 293) (:start . 289)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 298) (:start . 294)\n  (:id . 92))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 306)\n  (:start . 299) (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 307) (:start . 306)\n  (:id . 94)))@@@1@53@((:hcues ((:id . :x9.48.1) (:span 280 288)) ((:id . :x9.48.2) (:span 270 277)))\n (:hscopes ((:id . :x9.48.1) (:span 280 306))\n  ((:id . :x9.48.2) (:span 270 306)))\n (:identifiers (:sid . :s9.48) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502812@unknown@formal@none@1@S@We then determined whether targeting genes in the cattle tick which are homologous to D. melanogaster genes with known RNAi in vitro phenotypes [43] would similarly result in abnormal phenotypes.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "determine") (:form . "determined") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 42) (:start . 37)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cattle") (:form . "cattle") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 82)\n  (:start . 72) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 101)\n  (:start . 89) (:id . 57))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 107)\n  (:start . 102) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 112) (:start . 108)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 118)\n  (:start . 113) (:id . 60))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 126) (:start . 124)\n  (:id . 62))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 132)\n  (:start . 127) (:id . 63))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 143)\n  (:start . 133) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 145) (:start . 144)\n  (:id . 65))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 147) (:start . 145)\n  (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 148) (:start . 147)\n  (:id . 67))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 154)\n  (:start . 149) (:id . 68))\n ((:tag . "RB") (:stem . "similarly") (:form . "similarly") (:end . 164)\n  (:start . 155) (:id . 69))\n ((:tag . "VB") (:stem . "result") (:form . "result") (:end . 171)\n  (:start . 165) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 174) (:start . 172)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "abnormal") (:form . "abnormal") (:end . 183)\n  (:start . 175) (:id . 72))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 194)\n  (:start . 184) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x9.49.1) (:span 149 154)) ((:id . :x9.49.2) (:span 19 26)))\n (:hscopes ((:id . :x9.49.1) (:span 149 194))\n  ((:id . :x9.49.2) (:span 19 194)))\n (:identifiers (:sid . :s9.49) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502813@unknown@formal@none@1@S@We identified 10 candidate genes and conducted in vitro and in vivo (female tick injections) RNAi loss-of-function assays.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "conduct") (:form . "conducted") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "female") (:form . "female") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "injection") (:form . "injections") (:end . 91)\n  (:start . 81) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 97) (:start . 93)\n  (:id . 59))\n ((:tag . "NN") (:stem . "loss-of-function") (:form . "loss-of-function")\n  (:end . 114) (:start . 98) (:id . 60))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 121)\n  (:start . 115) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.50) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502814@unknown@formal@none@1@S@Interestingly, only proteasomal genes impaired tick cell viability in vitro, whilst 9 candidates impaired tick egg and larval development in vivo.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "proteasomal") (:form . "proteasomal") (:end . 31)\n  (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 37) (:start . 32)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "impair") (:form . "impaired") (:end . 46)\n  (:start . 38) (:id . 47))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 56) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 66)\n  (:start . 57) (:id . 50))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 75) (:start . 70)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "IN") (:stem . "whilst") (:form . "whilst") (:end . 83)\n  (:start . 77) (:id . 54))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 85) (:start . 84)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 96)\n  (:start . 86) (:id . 56))\n ((:tag . "VBD") (:stem . "impair") (:form . "impaired") (:end . 105)\n  (:start . 97) (:id . 57))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 110) (:start . 106)\n  (:id . 58))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 114) (:start . 111)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 125)\n  (:start . 119) (:id . 61))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 137)\n  (:start . 126) (:id . 62))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n  (:id . 63))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 145) (:start . 141)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s9.51) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502815@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s9.52) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5502816@unknown@formal@none@1@S@Evidence of putative RNAi pathway in R. microplus@(((:tag . "NN") (:stem . "evidence") (:form . "Evidence") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "microplu") (:form . "microplus") (:end . 49)\n  (:start . 40) (:id . 49)))@@@1@8@((:hcues ((:id . :x9.53.1) (:span 12 20)))\n (:hscopes ((:id . :x9.53.1) (:span 12 33)))\n (:identifiers (:sid . :s9.53) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502817@unknown@formal@none@1@S@A Dicer homologue was not confirmed in R. microplus however conserved domains commonly found in Dicer proteins of higher eukaryotes were identified in the R. microplus BmiGI2 EST database ([3](summarized in Additional File 1).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 59)\n  (:start . 52) (:id . 51))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 69)\n  (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 86)\n  (:start . 78) (:id . 54))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 92) (:start . 87)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 101)\n  (:start . 96) (:id . 57))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 110)\n  (:start . 102) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 59))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 120)\n  (:start . 114) (:id . 60))\n ((:tag . "NNS") (:stem . "eukaryote") (:form . "eukaryotes") (:end . 131)\n  (:start . 121) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 136) (:start . 132)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 147)\n  (:start . 137) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 157) (:start . 155)\n  (:id . 66))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 167)\n  (:start . 158) (:id . 67))\n ((:tag . "NNP") (:stem . "BmiGI2") (:form . "BmiGI2") (:end . 174)\n  (:start . 168) (:id . 68))\n ((:tag . "NNP") (:stem . "EST") (:form . "EST") (:end . 178) (:start . 175)\n  (:id . 69))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 187)\n  (:start . 179) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n  (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 190) (:start . 189)\n  (:id . 72))\n ((:tag . "VBD") (:stem . "3](summarized") (:form . "3](summarized")\n  (:end . 203) (:start . 190) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 206) (:start . 204)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 217)\n  (:start . 207) (:id . 75))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 222) (:start . 218)\n  (:id . 76))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 224) (:start . 223)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 225) (:start . 224)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s9.54) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502818@unknown@formal@none@1@S@A single R. microplus EST sequence (TC9337) was identified as containing an ORF of 250 amino acids (aa) encoding a putative RNase III (Pfam:PF00636) domain.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "NNP") (:stem . "EST") (:form . "EST") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "tc9337") (:form . "TC9337") (:end . 42)\n  (:start . 36) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 58)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 72)\n  (:start . 62) (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "orf") (:form . "ORF") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "CD") (:stem . "250") (:form . "250") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 92) (:start . 87)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 98) (:start . 93)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 61))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 102) (:start . 100)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 103) (:start . 102)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "encode") (:form . "encoding") (:end . 112)\n  (:start . 104) (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 114) (:start . 113)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 123)\n  (:start . 115) (:id . 66))\n ((:tag . "NNP") (:stem . "RNase") (:form . "RNase") (:end . 129)\n  (:start . 124) (:id . 67))\n ((:tag . "CD") (:stem . "iii") (:form . "III") (:end . 133) (:start . 130)\n  (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Pfam:PF00636") (:form . "Pfam:PF00636")\n  (:end . 147) (:start . 135) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 71))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 155)\n  (:start . 149) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s9.55) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502819@unknown@formal@none@1@S@The pairwise alignment of the ORF with the amino acid sequence of C. elegans Dcr-1 [GenBank:NP_498761] showed 24% identity and an e-value of 8e-12 (Additional File 1).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "pairwise") (:form . "pairwise") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "orf") (:form . "ORF") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 62)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 76)\n  (:start . 69) (:id . 55))\n ((:tag . "NN") (:stem . "dcr-1") (:form . "Dcr-1") (:end . 82) (:start . 77)\n  (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "GenBank:NP_498761") (:form . "GenBank:NP_498761")\n  (:end . 101) (:start . 84) (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 109)\n  (:start . 103) (:id . 60))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 122)\n  (:start . 114) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 64))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 129) (:start . 127)\n  (:id . 65))\n ((:tag . "NN") (:stem . "e-value") (:form . "e-value") (:end . 137)\n  (:start . 130) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n  (:id . 67))\n ((:tag . "CD") (:stem . "8e-12") (:form . "8e-12") (:end . 146)\n  (:start . 141) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 158)\n  (:start . 148) (:id . 70))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 163) (:start . 159)\n  (:id . 71))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 165) (:start . 164)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s9.56) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502820@unknown@formal@none@1@S@A Dicer tick homologue with the expected domain structure for a eukaryotic Dicer was identified in I. scapularis in a recently assembled supercontig [GenBank: DS643033] from the Ixodes Genome Project (IGP) [6].@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "eukaryotic") (:form . "eukaryotic") (:end . 74)\n  (:start . 64) (:id . 53))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 80) (:start . 75)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 95)\n  (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 101) (:start . 99)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 112)\n  (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 126)\n  (:start . 118) (:id . 62))\n ((:tag . "VBN") (:stem . "assemble") (:form . "assembled") (:end . 136)\n  (:start . 127) (:id . 63))\n ((:tag . "NN") (:stem . "supercontig") (:form . "supercontig") (:end . 148)\n  (:start . 137) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 150) (:start . 149)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 157)\n  (:start . 150) (:id . 66))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 158) (:start . 157)\n  (:id . 67))\n ((:tag . "NN") (:stem . "ds643033") (:form . "DS643033") (:end . 167)\n  (:start . 159) (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 168) (:start . 167)\n  (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 173) (:start . 169)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Ixodes") (:form . "Ixodes") (:end . 184)\n  (:start . 178) (:id . 72))\n ((:tag . "NNP") (:stem . "Genome") (:form . "Genome") (:end . 191)\n  (:start . 185) (:id . 73))\n ((:tag . "NNP") (:stem . "Project") (:form . "Project") (:end . 199)\n  (:start . 192) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 201) (:start . 200)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "IGP") (:form . "IGP") (:end . 204) (:start . 201)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 205) (:start . 204)\n  (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 207) (:start . 206)\n  (:id . 78))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 208) (:start . 207)\n  (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 209) (:start . 208)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s9.57) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502821@unknown@formal@none@1@S@This supercontig represents a 350 kb region of the I. scapularis tick genome and we identified a 22.3 kb genomic region containing a single gene that has 14 exons (the annotation described here has been submitted to the IGP).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "supercontig") (:form . "supercontig") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 27)\n  (:start . 17) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 45))\n ((:tag . "CD") (:stem . "350") (:form . "350") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 64)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 76)\n  (:start . 70) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 94)\n  (:start . 84) (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . "CD") (:stem . "22.3") (:form . "22.3") (:end . 101) (:start . 97)\n  (:id . 59))\n ((:tag . "NN") (:stem . "kb") (:form . "kb") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 112)\n  (:start . 105) (:id . 61))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 119)\n  (:start . 113) (:id . 62))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 130)\n  (:start . 120) (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 132) (:start . 131)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 139)\n  (:start . 133) (:id . 65))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 144) (:start . 140)\n  (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 149) (:start . 145)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 153) (:start . 150)\n  (:id . 68))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 156) (:start . 154)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 162)\n  (:start . 157) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 72))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 178)\n  (:start . 168) (:id . 73))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 188)\n  (:start . 179) (:id . 74))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 193) (:start . 189)\n  (:id . 75))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 197) (:start . 194)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 202) (:start . 198)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "submit") (:form . "submitted") (:end . 212)\n  (:start . 203) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 215) (:start . 213)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 219) (:start . 216)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "IGP") (:form . "IGP") (:end . 223) (:start . 220)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 224) (:start . 223)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s9.58) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502822@unknown@formal@none@1@S@The predicted I. scapularis Dicer protein is 1799aa long and has 31% similarity to the predicted Dicer-1 isoform 4 from the dog Canis lupus familiaris [GenBank:XP_868526].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "1799aa") (:form . "1799aa") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "RB") (:stem . "long") (:form . "long") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 79)\n  (:start . 69) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 96)\n  (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "dicer-1") (:form . "Dicer-1") (:end . 104)\n  (:start . 97) (:id . 59))\n ((:tag . "NN") (:stem . "isoform") (:form . "isoform") (:end . 112)\n  (:start . 105) (:id . 60))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 119) (:start . 115)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dog") (:form . "dog") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Canis") (:form . "Canis") (:end . 133)\n  (:start . 128) (:id . 65))\n ((:tag . "NN") (:stem . "lupus") (:form . "lupus") (:end . 139)\n  (:start . 134) (:id . 66))\n ((:tag . "NN") (:stem . "familiaris") (:form . "familiaris") (:end . 150)\n  (:start . 140) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 152) (:start . 151)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "GenBank:XP_868526") (:form . "GenBank:XP_868526")\n  (:end . 169) (:start . 152) (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 170) (:start . 169)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s9.59) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502823@unknown@formal@none@1@S@Furthermore, Figure 1a shows that the predicted I. scapularis Dcr-1 homologue has the same domain composition as its counterparts in D. melanogaster and C. elegans.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "i.") (:form . "I.") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 61)\n  (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "dcr-1") (:form . "Dcr-1") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 77)\n  (:start . 68) (:id . 53))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 90) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 97)\n  (:start . 91) (:id . 57))\n ((:tag . "NN") (:stem . "composition") (:form . "composition") (:end . 109)\n  (:start . 98) (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 112) (:start . 110)\n  (:id . 59))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "counterpart") (:form . "counterparts") (:end . 129)\n  (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 135) (:start . 133)\n  (:id . 63))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 148)\n  (:start . 136) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 155) (:start . 153)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 163)\n  (:start . 156) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s9.60) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502824@unknown@formal@none@1@S@The identified I. scapularis Dicer homologue clusters with the Dicer protein from the bovine Bos taurus (Figure 1b).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 44)\n  (:start . 35) (:id . 47))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 53)\n  (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 58) (:start . 54)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 68) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 76)\n  (:start . 69) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 81) (:start . 77)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "bovine") (:form . "bovine") (:end . 92)\n  (:start . 86) (:id . 55))\n ((:tag . "NNP") (:stem . "Bos") (:form . "Bos") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "taurus") (:form . "taurus") (:end . 103)\n  (:start . 97) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 111)\n  (:start . 105) (:id . 59))\n ((:tag . "NN") (:stem . "1b") (:form . "1b") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.61) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502825@unknown@formal@none@1@S@The schematic domain structure of Dicer proteins.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "schematic") (:form . "schematic") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s9.62) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502826@unknown@formal@none@1@S@(a) Comparison of the conserved domain structures of D. melanogaster Dicer-1 and Dicer-2, C. elegans DCR-1 and our predicted I. scapularis Dicer-1 protein.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Comparison") (:form . "Comparison") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 31)\n  (:start . 22) (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 38)\n  (:start . 32) (:id . 49))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 49)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 68)\n  (:start . 56) (:id . 53))\n ((:tag . "NN") (:stem . "dicer-1") (:form . "Dicer-1") (:end . 76)\n  (:start . 69) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "dicer-2") (:form . "Dicer-2") (:end . 88)\n  (:start . 81) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 100)\n  (:start . 93) (:id . 59))\n ((:tag . "NN") (:stem . "dcr-1") (:form . "DCR-1") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 114) (:start . 111)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 124)\n  (:start . 115) (:id . 63))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 127) (:start . 125)\n  (:id . 64))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 138)\n  (:start . 128) (:id . 65))\n ((:tag . "NN") (:stem . "dicer-1") (:form . "Dicer-1") (:end . 146)\n  (:start . 139) (:id . 66))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 154)\n  (:start . 147) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s9.63) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502827@unknown@formal@none@1@S@Names and IDs of the conserved domains are given as stored in the Pfam database. * =@(((:tag . "NNPS") (:stem . "Name") (:form . "Names") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNPS") (:stem . "ID") (:form . "IDs") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 30)\n  (:start . 21) (:id . 47))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "store") (:form . "stored") (:end . 58)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 70) (:start . 66)\n  (:id . 55))\n ((:tag . "NN") (:stem . "database.") (:form . "database.") (:end . 80)\n  (:start . 71) (:id . 56))\n ((:tag . "NN") (:stem . "*") (:form . "*") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 84) (:start . 83)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s9.64) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502828@unknown@formal@none@1@S@The Pfam search did not detect a signal for this domain in the sequence of the Dicer-1 protein of D. melanogaster.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 39)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 48) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 55)\n  (:start . 49) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 71)\n  (:start . 63) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dicer-1") (:form . "Dicer-1") (:end . 86)\n  (:start . 79) (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 94)\n  (:start . 87) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 100) (:start . 98)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 113) (:start . 101) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s9.65) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502829@unknown@formal@none@1@S@(b) Phylogenetic analysis of full-length Dicer proteins (Bos = B. taurus, Cele = C. elegans, Dmel = D. melanogaster, Iscap = I. scapularis, Tcas = T. castaneum).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "Phylogenetic") (:end . 16)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 40)\n  (:start . 29) (:id . 48))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Bos") (:form . "Bos") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "FW") (:stem . "b.") (:form . "B.") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "FW") (:stem . "taurus") (:form . "taurus") (:end . 72)\n  (:start . 66) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Cele") (:form . "Cele") (:end . 78) (:start . 74)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "=") (:form . "=") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 83) (:start . 81)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 91)\n  (:start . 84) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Dmel") (:form . "Dmel") (:end . 97) (:start . 93)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "=") (:form . "=") (:end . 99) (:start . 98)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 102) (:start . 100)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 115) (:start . 103) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Iscap") (:form . "Iscap") (:end . 122)\n  (:start . 117) (:id . 67))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 124) (:start . 123)\n  (:id . 68))\n ((:tag . "FW") (:stem . "i.") (:form . "I.") (:end . 127) (:start . 125)\n  (:id . 69))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 138)\n  (:start . 128) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Tcas") (:form . "Tcas") (:end . 144) (:start . 140)\n  (:id . 72))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 146) (:start . 145)\n  (:id . 73))\n ((:tag . "FW") (:stem . "t.") (:form . "T.") (:end . 149) (:start . 147)\n  (:id . 74))\n ((:tag . "NN") (:stem . "castaneum") (:form . "castaneum") (:end . 159)\n  (:start . 150) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s9.66) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502830@unknown@formal@none@1@S@The analysis of R. microplus ESTs and I. scapularis genome reads identified putative tick homologues of D. melanogaster Argonaute-1 and 2 proteins in both species (Table 1, Figures 2 and 3).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "CC") (:stem . "microplus") (:form . "microplus") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "NNP") (:stem . "ESTs") (:form . "ESTs") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 51)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 58)\n  (:start . 52) (:id . 51))\n ((:tag . "VBZ") (:stem . "read") (:form . "reads") (:end . 64) (:start . 59)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 75)\n  (:start . 65) (:id . 53))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 84)\n  (:start . 76) (:id . 54))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 89) (:start . 85)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 100)\n  (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 119) (:start . 107) (:id . 59))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 131)\n  (:start . 120) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 61))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 137) (:start . 136)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 146)\n  (:start . 138) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 64))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 154) (:start . 150)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 162)\n  (:start . 155) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 169)\n  (:start . 164) (:id . 68))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 171) (:start . 170)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 180)\n  (:start . 173) (:id . 71))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 182) (:start . 181)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 186) (:start . 183)\n  (:id . 73))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 188) (:start . 187)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s9.67) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502831@unknown@formal@none@1@S@Putative tick RNAi candidate homologues@(((:tag . "JJ") (:stem . "putative") (:form . "Putative") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 39)\n  (:start . 29) (:id . 46)))@@@1@5@((:identifiers (:sid . :s9.68) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5502832@unknown@formal@none@1@S@Domain structure and phylogenetic tree of tick Argonaute-1 proteins.@(((:tag . "NN") (:stem . "domain") (:form . "Domain") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 16)\n  (:start . 7) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 33)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "tree") (:form . "tree") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 58)\n  (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 67)\n  (:start . 59) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s9.69) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502833@unknown@formal@none@1@S@(a) Schematic structure of the Argonaute-1 proteins from D. melanogaster and our predictions of the structures of the I. scapularis and R. microplus Argonaute-1 homologues.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 23)\n  (:start . 14) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 42)\n  (:start . 31) (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 51)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 72)\n  (:start . 60) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 92)\n  (:start . 81) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 110)\n  (:start . 100) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 120) (:start . 118)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 131)\n  (:start . 121) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 138) (:start . 136)\n  (:id . 65))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 148)\n  (:start . 139) (:id . 66))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 160)\n  (:start . 149) (:id . 67))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 171)\n  (:start . 161) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s9.70) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502834@unknown@formal@none@1@S@(b) Phylogenetic analysis of Argonaute-1 proteins.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "Phylogenetic") (:end . 16)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 40)\n  (:start . 29) (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 50) (:start . 49)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s9.71) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502835@unknown@formal@none@1@S@(Bos = B. taurus, Cat = R. microplus, Cele = C. elegans, Dmel = D. melanogaster, Iscap = I. scapularis, Tcas = T. castaneum).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Bos") (:form . "Bos") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 6) (:start . 5)\n  (:id . 44))\n ((:tag . "FW") (:stem . "b.") (:form . "B.") (:end . 9) (:start . 7)\n  (:id . 45))\n ((:tag . "FW") (:stem . "taurus") (:form . "taurus") (:end . 16)\n  (:start . 10) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Cat") (:form . "Cat") (:end . 21) (:start . 18)\n  (:id . 48))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 23) (:start . 22)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 26) (:start . 24)\n  (:id . 50))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 36)\n  (:start . 27) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Cele") (:form . "Cele") (:end . 42) (:start . 38)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "=") (:form . "=") (:end . 44) (:start . 43)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 47) (:start . 45)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 55)\n  (:start . 48) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Dmel") (:form . "Dmel") (:end . 61) (:start . 57)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "=") (:form . "=") (:end . 63) (:start . 62)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 66) (:start . 64)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 79)\n  (:start . 67) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Iscap") (:form . "Iscap") (:end . 86) (:start . 81)\n  (:id . 63))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 88) (:start . 87)\n  (:id . 64))\n ((:tag . "FW") (:stem . "i.") (:form . "I.") (:end . 91) (:start . 89)\n  (:id . 65))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 102)\n  (:start . 92) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Tcas") (:form . "Tcas") (:end . 108) (:start . 104)\n  (:id . 68))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 110) (:start . 109)\n  (:id . 69))\n ((:tag . "FW") (:stem . "t.") (:form . "T.") (:end . 113) (:start . 111)\n  (:id . 70))\n ((:tag . "NN") (:stem . "castaneum") (:form . "castaneum") (:end . 123)\n  (:start . 114) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s9.72) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502836@unknown@formal@none@1@S@Domain structure and phylogenetic tree of tick Argonaute-2 proteins.@(((:tag . "NN") (:stem . "domain") (:form . "Domain") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 16)\n  (:start . 7) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 33)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "tree") (:form . "tree") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 58)\n  (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 67)\n  (:start . 59) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s9.73) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502837@unknown@formal@none@1@S@(a) The structure of the predicted Argonaute-2 proteins from I. scapularis and R. microplus in comparison to the structure of Argonaute-2 in D. melanogaster.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 17)\n  (:start . 8) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 34)\n  (:start . 25) (:id . 49))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 46)\n  (:start . 35) (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 74)\n  (:start . 64) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 91)\n  (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 105)\n  (:start . 95) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 61))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 122)\n  (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 63))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 137)\n  (:start . 126) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 143) (:start . 141)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 156) (:start . 144) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s9.74) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502838@unknown@formal@none@1@S@The predicted structural property of both tick Argonaute-2 candidates is similar to the structure of the fruit fly Argonaute-2 protein.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "property") (:form . "property") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 58)\n  (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 69)\n  (:start . 59) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 80)\n  (:start . 73) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 54))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 97)\n  (:start . 88) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 57))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 110)\n  (:start . 105) (:id . 58))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 114) (:start . 111)\n  (:id . 59))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 126)\n  (:start . 115) (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 134)\n  (:start . 127) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.75) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502839@unknown@formal@none@1@S@No R. microplus ORF with a Piwi domain similar to Argonaute-2 Piwi was identified.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 15)\n  (:start . 6) (:id . 44))\n ((:tag . "NN") (:stem . "orf") (:form . "ORF") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Piwi") (:form . "Piwi") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 38)\n  (:start . 32) (:id . 49))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 46)\n  (:start . 39) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 61)\n  (:start . 50) (:id . 52))\n ((:tag . "NNP") (:stem . "Piwi") (:form . "Piwi") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 81)\n  (:start . 71) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s9.76) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502840@unknown@formal@none@1@S@(b) Phylogenetic analysis of Argonaute-2 proteins (Bos = B. taurus, Cat = R. microplus, Cele = C. elegans, Dmel = D. melanogaster, Iscap = I. scapularis, Tcas = T. castaneum).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "Phylogenetic") (:end . 16)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 40)\n  (:start . 29) (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Bos") (:form . "Bos") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "FW") (:stem . "b.") (:form . "B.") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "FW") (:stem . "taurus") (:form . "taurus") (:end . 66)\n  (:start . 60) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Cat") (:form . "Cat") (:end . 71) (:start . 68)\n  (:id . 56))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 76) (:start . 74)\n  (:id . 58))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 86)\n  (:start . 77) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Cele") (:form . "Cele") (:end . 92) (:start . 88)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "=") (:form . "=") (:end . 94) (:start . 93)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 97) (:start . 95)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 105)\n  (:start . 98) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Dmel") (:form . "Dmel") (:end . 111) (:start . 107)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "=") (:form . "=") (:end . 113) (:start . 112)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 116) (:start . 114)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 129) (:start . 117) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Iscap") (:form . "Iscap") (:end . 136)\n  (:start . 131) (:id . 71))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 138) (:start . 137)\n  (:id . 72))\n ((:tag . "FW") (:stem . "i.") (:form . "I.") (:end . 141) (:start . 139)\n  (:id . 73))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 152)\n  (:start . 142) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Tcas") (:form . "Tcas") (:end . 158) (:start . 154)\n  (:id . 76))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 160) (:start . 159)\n  (:id . 77))\n ((:tag . "FW") (:stem . "t.") (:form . "T.") (:end . 163) (:start . 161)\n  (:id . 78))\n ((:tag . "NN") (:stem . "castaneum") (:form . "castaneum") (:end . 173)\n  (:start . 164) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 174) (:start . 173)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s9.77) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502841@unknown@formal@none@1@S@Figure 2a summarizes the domain structure of the identified tick Ago-1 proteins.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "summarize") (:form . "summarizes") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 59)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "ago-1") (:form . "Ago-1") (:end . 70) (:start . 65)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s9.78) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502842@unknown@formal@none@1@S@The cattle tick Argonaute-1 protein (Cat-Ago-1) is partially encoded by two ESTs (Figure 2a).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cattle") (:form . "cattle") (:end . 10)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "tick") (:form . "tick") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 27)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cat-ago-1") (:form . "Cat-Ago-1") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 60)\n  (:start . 51) (:id . 51))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "est") (:form . "ESTs") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 88)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s9.79) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502843@unknown@formal@none@1@S@TC13769 encodes an ORF of 352aa containing the DUF1785 domain located from aa 162 to 213 and a PAZ domain from aa 226 to 350.@(((:tag . "NNP") (:stem . "TC13769") (:form . "TC13769") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "orf") (:form . "ORF") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "352aa") (:form . "352aa") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "duf1785") (:form . "DUF1785") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 61)\n  (:start . 55) (:id . 51))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 69)\n  (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 74) (:start . 70)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "aa") (:form . "aa") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "CD") (:stem . "162") (:form . "162") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . "CD") (:stem . "213") (:form . "213") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "PAZ") (:form . "PAZ") (:end . 98) (:start . 95)\n  (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 105)\n  (:start . 99) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 110) (:start . 106)\n  (:id . 62))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 113) (:start . 111)\n  (:id . 63))\n ((:tag . "CD") (:stem . "226") (:form . "226") (:end . 117) (:start . 114)\n  (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 120) (:start . 118)\n  (:id . 65))\n ((:tag . "CD") (:stem . "350") (:form . "350") (:end . 124) (:start . 121)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s9.80) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502844@unknown@formal@none@1@S@A pairwise alignment using blastp showed 43% identity with the respective domains of D. melanogaster Argonaute-1 protein.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "pairwise") (:form . "pairwise") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "blastp") (:form . "blastp") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 40) (:start . 34)\n  (:id . 47))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 73)\n  (:start . 63) (:id . 53))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 81)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 100) (:start . 88) (:id . 57))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 112)\n  (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 120)\n  (:start . 113) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s9.81) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502845@unknown@formal@none@1@S@Another EST, TC6448 encodes the putative Piwi domain of the Cat-Ago-1 protein, which has 46% identity with the Piwi domain of D. melanogaster Ago-1.@(((:tag . "DT") (:stem . "another") (:form . "Another") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "EST") (:form . "EST") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "tc6448") (:form . "TC6448") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "NNP") (:stem . "Piwi") (:form . "Piwi") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cat-ago-1") (:form . "Cat-Ago-1") (:end . 69)\n  (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 77)\n  (:start . 70) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 84) (:start . 79)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 101)\n  (:start . 93) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 106) (:start . 102)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Piwi") (:form . "Piwi") (:end . 115) (:start . 111)\n  (:id . 63))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 122)\n  (:start . 116) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 128) (:start . 126)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 141) (:start . 129) (:id . 67))\n ((:tag . "NN") (:stem . "ago-1") (:form . "Ago-1") (:end . 147)\n  (:start . 142) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x9.82.1) (:span 32 40)))\n (:hscopes ((:id . :x9.82.1) (:span 32 77)))\n (:identifiers (:sid . :s9.82) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502846@unknown@formal@none@1@S@The Piwi domain encoded in TC6448 is located from aa 120 to 430.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Piwi") (:form . "Piwi") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "tc6448") (:form . "TC6448") (:end . 33)\n  (:start . 27) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "CD") (:stem . "120") (:form . "120") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "CD") (:stem . "430") (:form . "430") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s9.83) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502847@unknown@formal@none@1@S@The I. scapularis contig ABJB010128003.1 (Iscap-Ago-1) encodes an ORF of 967aa containing all three known domains of Ago-1 proteins (Figure 2a).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NNP") (:stem . "ABJB010128003.1") (:form . "ABJB010128003.1")\n  (:end . 40) (:start . 25) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 47))\n ((:tag . "NN") (:stem . "iscap-ago-1") (:form . "Iscap-Ago-1") (:end . 53)\n  (:start . 42) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 62)\n  (:start . 55) (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "orf") (:form . "ORF") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "967aa") (:form . "967aa") (:end . 78) (:start . 73)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 89)\n  (:start . 79) (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 93) (:start . 90)\n  (:id . 56))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 99) (:start . 94)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 105)\n  (:start . 100) (:id . 58))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 113)\n  (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "NN") (:stem . "ago-1") (:form . "Ago-1") (:end . 122)\n  (:start . 117) (:id . 61))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 131)\n  (:start . 123) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 139)\n  (:start . 133) (:id . 64))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 142) (:start . 140)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s9.84) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502848@unknown@formal@none@1@S@The PAZ domain of Iscap-Ago-1 has 41% and 47% similarity with the PAZ domains of Dmel-Ago-1 and Cat-Ago-1, respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "PAZ") (:form . "PAZ") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Iscap-Ago-1") (:form . "Iscap-Ago-1") (:end . 29)\n  (:start . 18) (:id . 46))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 56)\n  (:start . 46) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PAZ") (:form . "PAZ") (:end . 69) (:start . 66)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 77)\n  (:start . 70) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 58))\n ((:tag . "NN") (:stem . "dmel-ago-1") (:form . "Dmel-Ago-1") (:end . 91)\n  (:start . 81) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 60))\n ((:tag . "NN") (:stem . "cat-ago-1") (:form . "Cat-Ago-1") (:end . 105)\n  (:start . 96) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 62))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 119)\n  (:start . 107) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.85) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502849@unknown@formal@none@1@S@Interestingly, the Piwi domain of Iscap-Ago-1 shows a higher sequence similarity, being 52% and 57% identical to its counterpart in Drosophila and cattle tick.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Piwi") (:form . "Piwi") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Iscap-Ago-1") (:form . "Iscap-Ago-1") (:end . 45)\n  (:start . 34) (:id . 48))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 51) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 60) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 69)\n  (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 80)\n  (:start . 70) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 87) (:start . 82)\n  (:id . 55))\n ((:tag . "CD") (:stem . "52") (:form . "52") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "CD") (:stem . "57") (:form . "57") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 99) (:start . 98)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 109)\n  (:start . 100) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 116) (:start . 113)\n  (:id . 63))\n ((:tag . "NN") (:stem . "counterpart") (:form . "counterpart") (:end . 128)\n  (:start . 117) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 131) (:start . 129)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 142)\n  (:start . 132) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 146) (:start . 143)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "cattle") (:form . "cattle") (:end . 153)\n  (:start . 147) (:id . 68))\n ((:tag . "VBP") (:stem . "tick") (:form . "tick") (:end . 158) (:start . 154)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s9.86) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502850@unknown@formal@none@1@S@Based on the multiple sequence alignments of the DUF1785 and PAZ of the Argonaute-1 proteins a clustering of I. scapularis and R. microplus is observed (Figure 2b).@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "DUF1785") (:form . "DUF1785") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "PAZ") (:form . "PAZ") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 83)\n  (:start . 72) (:id . 55))\n ((:tag . "VBZ") (:stem . "protein") (:form . "proteins") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "clustering") (:form . "clustering") (:end . 105)\n  (:start . 95) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 122)\n  (:start . 112) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 139)\n  (:start . 130) (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 142) (:start . 140)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 151)\n  (:start . 143) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 159)\n  (:start . 153) (:id . 68))\n ((:tag . "NNP") (:stem . "2b") (:form . "2b") (:end . 162) (:start . 160)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 163) (:start . 162)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s9.87) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502851@unknown@formal@none@1@S@The second cluster consists of the sequences from the insect species T. castaneum and D. melanogaster.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "FW") (:stem . "t.") (:form . "T.") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "castaneum") (:form . "castaneum") (:end . 81)\n  (:start . 72) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 101) (:start . 89) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s9.88) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502852@unknown@formal@none@1@S@The sequences of the Argonaute-1 proteins from C. elegans and B. taurus form two separate outlying groups.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 32)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "B.") (:form . "B.") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "tauru") (:form . "taurus") (:end . 71)\n  (:start . 65) (:id . 53))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . "VBG") (:stem . "outlye") (:form . "outlying") (:end . 98)\n  (:start . 90) (:id . 57))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 105)\n  (:start . 99) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s9.89) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502853@unknown@formal@none@1@S@Figure 3a summarizes the domain structure of the identified tick Ago-2 proteins.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "3a") (:form . "3a") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "summarize") (:form . "summarizes") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 59)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "ago-2") (:form . "Ago-2") (:end . 70) (:start . 65)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s9.90) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502854@unknown@formal@none@1@S@TC8091 represents a putative cattle tick Argonaute-2 protein (Cat-Ago-2) encoding an ORF of 269aa harboring the DUF1785 and PAZ domains located from aa 81 to 134 and aa 135 to 269 (27% identity), respectively.@(((:tag . "NNP") (:stem . "TC8091") (:form . "TC8091") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 17)\n  (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "cattle") (:form . "cattle") (:end . 35)\n  (:start . 29) (:id . 46))\n ((:tag . "VBP") (:stem . "tick") (:form . "tick") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 52)\n  (:start . 41) (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 60)\n  (:start . 53) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cat-ago-2") (:form . "Cat-Ago-2") (:end . 71)\n  (:start . 62) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "encode") (:form . "encoding") (:end . 81)\n  (:start . 73) (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "NN") (:stem . "orf") (:form . "ORF") (:end . 88) (:start . 85)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "NN") (:stem . "269aa") (:form . "269aa") (:end . 97) (:start . 92)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "harbor") (:form . "harboring") (:end . 107)\n  (:start . 98) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "DUF1785") (:form . "DUF1785") (:end . 119)\n  (:start . 112) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "PAZ") (:form . "PAZ") (:end . 127) (:start . 124)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 135)\n  (:start . 128) (:id . 63))\n ((:tag . "VBN") (:stem . "locate") (:form . "located") (:end . 143)\n  (:start . 136) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 148) (:start . 144)\n  (:id . 65))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 151) (:start . 149)\n  (:id . 66))\n ((:tag . "CD") (:stem . "81") (:form . "81") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 157) (:start . 155)\n  (:id . 68))\n ((:tag . "CD") (:stem . "134") (:form . "134") (:end . 161) (:start . 158)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 70))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 168) (:start . 166)\n  (:id . 71))\n ((:tag . "CD") (:stem . "135") (:form . "135") (:end . 172) (:start . 169)\n  (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 175) (:start . 173)\n  (:id . 73))\n ((:tag . "CD") (:stem . "269") (:form . "269") (:end . 179) (:start . 176)\n  (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 181) (:start . 180)\n  (:id . 75))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 183) (:start . 181)\n  (:id . 76))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 184) (:start . 183)\n  (:id . 77))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 193)\n  (:start . 185) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n  (:id . 80))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 208)\n  (:start . 196) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s9.91) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502855@unknown@formal@none@1@S@The R. microplus Ago-2 homologue TC984 (TC9244/TC16832, BmiGI2) identified by de la Fuente et al [37] was also confirmed in our search and appears to encode a Piwi domain.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "ago-2") (:form . "Ago-2") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "tc984") (:form . "TC984") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "TC9244/TC16832") (:form . "TC9244/TC16832")\n  (:end . 54) (:start . 40) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "BmiGI2") (:form . "BmiGI2") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 74)\n  (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "FW") (:stem . "de") (:form . "de") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "FW") (:stem . "la") (:form . "la") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Fuente") (:form . "Fuente") (:end . 90)\n  (:start . 84) (:id . 57))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "FW") (:stem . "al") (:form . "al") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 98) (:start . 97)\n  (:id . 60))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 100) (:start . 98)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 101) (:start . 100)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 105) (:start . 102)\n  (:id . 63))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 110) (:start . 106)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 120)\n  (:start . 111) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n  (:id . 66))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 127) (:start . 124)\n  (:id . 67))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 134)\n  (:start . 128) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n  (:id . 69))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 146)\n  (:start . 139) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n  (:id . 71))\n ((:tag . "VB") (:stem . "encode") (:form . "encode") (:end . 156)\n  (:start . 150) (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 158) (:start . 157)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Piwi") (:form . "Piwi") (:end . 163) (:start . 159)\n  (:id . 74))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 170)\n  (:start . 164) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x9.92.1) (:span 139 146)))\n (:hscopes ((:id . :x9.92.1) (:span 139 170)))\n (:identifiers (:sid . :s9.92) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502856@unknown@formal@none@1@S@Interestingly, the pairwise alignment using blastp with both D. melanogaster Argonaute proteins showed an overall identity of 42% with Argonaute-1 and 39% with Argonaute-2.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "pairwise") (:form . "pairwise") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 43) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "blastp") (:form . "blastp") (:end . 50)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 55) (:start . 51)\n  (:id . 49))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 76)\n  (:start . 64) (:id . 52))\n ((:tag . "NNP") (:stem . "Argonaute") (:form . "Argonaute") (:end . 86)\n  (:start . 77) (:id . 53))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 95)\n  (:start . 87) (:id . 54))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 102)\n  (:start . 96) (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 105) (:start . 103)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 113)\n  (:start . 106) (:id . 57))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 122)\n  (:start . 114) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 59))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 128) (:start . 126)\n  (:id . 60))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 129) (:start . 128)\n  (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 134) (:start . 130)\n  (:id . 62))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 146)\n  (:start . 135) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 64))\n ((:tag . "CD") (:stem . "39") (:form . "39") (:end . 153) (:start . 151)\n  (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 154) (:start . 153)\n  (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 159) (:start . 155)\n  (:id . 67))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 171)\n  (:start . 160) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s9.93) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502857@unknown@formal@none@1@S@The I. scapularis contig ABJB010009424.1 (Iscap-Ago-2, Figure 3a) encodes an ORF of 896aa consisting of a DUF1785 domain from aa 304 to 357, a PAZ domain from aa 358 to 498 and a Piwi domain located in the region from aa 640 to 896.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NNP") (:stem . "ABJB010009424.1") (:form . "ABJB010009424.1")\n  (:end . 40) (:start . 25) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Iscap-Ago-2") (:form . "Iscap-Ago-2") (:end . 53)\n  (:start . 42) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 61)\n  (:start . 55) (:id . 50))\n ((:tag . "NN") (:stem . "3a") (:form . "3a") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 73)\n  (:start . 66) (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "orf") (:form . "ORF") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "NN") (:stem . "896aa") (:form . "896aa") (:end . 89) (:start . 84)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "consist") (:form . "consisting") (:end . 100)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "NN") (:stem . "duf1785") (:form . "DUF1785") (:end . 113)\n  (:start . 106) (:id . 61))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 120)\n  (:start . 114) (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 125) (:start . 121)\n  (:id . 63))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 128) (:start . 126)\n  (:id . 64))\n ((:tag . "CD") (:stem . "304") (:form . "304") (:end . 132) (:start . 129)\n  (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 66))\n ((:tag . "CD") (:stem . "357") (:form . "357") (:end . 139) (:start . 136)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 142) (:start . 141)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "PAZ") (:form . "PAZ") (:end . 146) (:start . 143)\n  (:id . 70))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 153)\n  (:start . 147) (:id . 71))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 158) (:start . 154)\n  (:id . 72))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 161) (:start . 159)\n  (:id . 73))\n ((:tag . "CD") (:stem . "358") (:form . "358") (:end . 165) (:start . 162)\n  (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 168) (:start . 166)\n  (:id . 75))\n ((:tag . "CD") (:stem . "498") (:form . "498") (:end . 172) (:start . 169)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n  (:id . 77))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 178) (:start . 177)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Piwi") (:form . "Piwi") (:end . 183) (:start . 179)\n  (:id . 79))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 190)\n  (:start . 184) (:id . 80))\n ((:tag . "VBN") (:stem . "locate") (:form . "located") (:end . 198)\n  (:start . 191) (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 201) (:start . 199)\n  (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 205) (:start . 202)\n  (:id . 83))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 212)\n  (:start . 206) (:id . 84))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 217) (:start . 213)\n  (:id . 85))\n ((:tag . "NN") (:stem . "aa") (:form . "aa") (:end . 220) (:start . 218)\n  (:id . 86))\n ((:tag . "CD") (:stem . "640") (:form . "640") (:end . 224) (:start . 221)\n  (:id . 87))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 227) (:start . 225)\n  (:id . 88))\n ((:tag . "CD") (:stem . "896") (:form . "896") (:end . 231) (:start . 228)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s9.94) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502858@unknown@formal@none@1@S@Sequence comparison of the putative Iscap-Ago-2 with the Dmel-Ago-1 ([GenBank:NP_725341.1], 27% identity) and Dmel-Ago-2 ([GenBank:NP_730054.1], 41% identity) proteins revealed a higher homology between Iscap-Ago-2 and Dmel-Ago-1, nevertheless the predicted domain structure of this putative I. scapularis Argonaute was more similar to Dmel-Ago-2 (Figure 3a).@(((:tag . "NN") (:stem . "sequence") (:form . "Sequence") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 19)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "iscap-ago-2") (:form . "Iscap-Ago-2") (:end . 47)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 52) (:start . 48)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dmel-ago-1") (:form . "Dmel-Ago-1") (:end . 67)\n  (:start . 57) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 51))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 70) (:start . 69)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "GenBank:NP_725341.1")\n  (:form . "GenBank:NP_725341.1") (:end . 89) (:start . 70) (:id . 53))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 90) (:start . 89)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 55))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 104)\n  (:start . 96) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Dmel-Ago-2") (:form . "Dmel-Ago-2") (:end . 120)\n  (:start . 110) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 123) (:start . 122)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "GenBank:NP_730054.1")\n  (:form . "GenBank:NP_730054.1") (:end . 142) (:start . 123) (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 143) (:start . 142)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 66))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 147) (:start . 145)\n  (:id . 67))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 148) (:start . 147)\n  (:id . 68))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 157)\n  (:start . 149) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 167)\n  (:start . 159) (:id . 71))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 176)\n  (:start . 168) (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 178) (:start . 177)\n  (:id . 73))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 185)\n  (:start . 179) (:id . 74))\n ((:tag . "NN") (:stem . "homology") (:form . "homology") (:end . 194)\n  (:start . 186) (:id . 75))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 202)\n  (:start . 195) (:id . 76))\n ((:tag . "NN") (:stem . "iscap-ago-2") (:form . "Iscap-Ago-2") (:end . 214)\n  (:start . 203) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 218) (:start . 215)\n  (:id . 78))\n ((:tag . "NN") (:stem . "dmel-ago-1") (:form . "Dmel-Ago-1") (:end . 229)\n  (:start . 219) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 230) (:start . 229)\n  (:id . 80))\n ((:tag . "RB") (:stem . "nevertheless") (:form . "nevertheless") (:end . 243)\n  (:start . 231) (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 247) (:start . 244)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 257)\n  (:start . 248) (:id . 83))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 264)\n  (:start . 258) (:id . 84))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 274)\n  (:start . 265) (:id . 85))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 277) (:start . 275)\n  (:id . 86))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 282) (:start . 278)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 291)\n  (:start . 283) (:id . 88))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 294) (:start . 292)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 305)\n  (:start . 295) (:id . 90))\n ((:tag . "NNP") (:stem . "Argonaute") (:form . "Argonaute") (:end . 315)\n  (:start . 306) (:id . 91))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 319) (:start . 316)\n  (:id . 92))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 324) (:start . 320)\n  (:id . 93))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 332)\n  (:start . 325) (:id . 94))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 335) (:start . 333)\n  (:id . 95))\n ((:tag . "NNP") (:stem . "Dmel-Ago-2") (:form . "Dmel-Ago-2") (:end . 346)\n  (:start . 336) (:id . 96))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 348) (:start . 347)\n  (:id . 97))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 354)\n  (:start . 348) (:id . 98))\n ((:tag . "NN") (:stem . "3a") (:form . "3a") (:end . 357) (:start . 355)\n  (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 358) (:start . 357)\n  (:id . 100))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 359) (:start . 358)\n  (:id . 101)))@@@1@60@((:identifiers (:sid . :s9.95) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502859@unknown@formal@none@1@S@The phylogenetic tree of the Argonaute-2 proteins shows three clusters (Figure 3b).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "tree") (:form . "tree") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 40)\n  (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 49)\n  (:start . 41) (:id . 48))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 61) (:start . 56)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 70)\n  (:start . 62) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 78)\n  (:start . 72) (:id . 53))\n ((:tag . "NN") (:stem . "3b") (:form . "3b") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s9.96) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502860@unknown@formal@none@1@S@The I. scapularis and R. microplus sequences group together, the second cluster consists of the Argonaute-2 proteins from D. melanogaster and T. castaneum, and in the third group the sequences from C. elegans and B. taurus are clustered.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 71)\n  (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 88)\n  (:start . 80) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 107)\n  (:start . 96) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 116)\n  (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 121) (:start . 117)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 124) (:start . 122)\n  (:id . 61))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 137)\n  (:start . 125) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "T.") (:form . "T.") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "NN") (:stem . "castaneum") (:form . "castaneum") (:end . 154)\n  (:start . 145) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 162) (:start . 160)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 172)\n  (:start . 167) (:id . 70))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 178)\n  (:start . 173) (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 182) (:start . 179)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 192)\n  (:start . 183) (:id . 73))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 197) (:start . 193)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 200) (:start . 198)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 208)\n  (:start . 201) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 212) (:start . 209)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "B.") (:form . "B.") (:end . 215) (:start . 213)\n  (:id . 78))\n ((:tag . "NN") (:stem . "taurus") (:form . "taurus") (:end . 222)\n  (:start . 216) (:id . 79))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 226) (:start . 223)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "cluster") (:form . "clustered") (:end . 236)\n  (:start . 227) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 237) (:start . 236)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s9.97) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502861@unknown@formal@none@1@S@Available R. microplus ESTs and I. scapularis genomic contigs were screened for homologous genes to C. elegans proteins involved in RNAi systemic spread (Rsd-2, Rsd-3, and Rsd-6) and dsRNA uptake (Epn-1) (Table 1).@(((:tag . "NNP") (:stem . "Available") (:form . "Available") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NNP") (:stem . "ESTs") (:form . "ESTs") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "scapulari") (:form . "scapularis") (:end . 45)\n  (:start . 35) (:id . 48))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "NNS") (:stem . "contig") (:form . "contigs") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "screen") (:form . "screened") (:end . 75)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 90)\n  (:start . 80) (:id . 54))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 96) (:start . 91)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 99) (:start . 97)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 102) (:start . 100)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 110)\n  (:start . 103) (:id . 58))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 119)\n  (:start . 111) (:id . 59))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 128)\n  (:start . 120) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 131) (:start . 129)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 136) (:start . 132)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 145)\n  (:start . 137) (:id . 63))\n ((:tag . "NN") (:stem . "spread") (:form . "spread") (:end . 152)\n  (:start . 146) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Rsd-2") (:form . "Rsd-2") (:end . 159)\n  (:start . 154) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Rsd-3") (:form . "Rsd-3") (:end . 166)\n  (:start . 161) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Rsd-6") (:form . "Rsd-6") (:end . 177)\n  (:start . 172) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 178) (:start . 177)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 182) (:start . 179)\n  (:id . 73))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 188)\n  (:start . 183) (:id . 74))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 195)\n  (:start . 189) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 197) (:start . 196)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Epn-1") (:form . "Epn-1") (:end . 202)\n  (:start . 197) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 203) (:start . 202)\n  (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 205) (:start . 204)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 210)\n  (:start . 205) (:id . 80))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 212) (:start . 211)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s9.98) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502862@unknown@formal@none@1@S@We identified putative hits to Rsd-3 and Epn-1 in both R. microplus and I. scapularis with 45% and 48% (Rsd-3) and 71% and 43% (Epn-1) identities, respectively.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Rsd-3") (:form . "Rsd-3") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "epn-1") (:form . "Epn-1") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 67)\n  (:start . 58) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 85)\n  (:start . 75) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n  (:id . 57))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 60))\n ((:tag . "CD") (:stem . "48") (:form . "48") (:end . 101) (:start . 99)\n  (:id . 61))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Rsd-3") (:form . "Rsd-3") (:end . 109)\n  (:start . 104) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 66))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 117) (:start . 115)\n  (:id . 67))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 118) (:start . 117)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 69))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 125) (:start . 123)\n  (:id . 70))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 126) (:start . 125)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 72))\n ((:tag . "NN") (:stem . "epn-1") (:form . "Epn-1") (:end . 133)\n  (:start . 128) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "identity") (:form . "identities") (:end . 145)\n  (:start . 135) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 76))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 159)\n  (:start . 147) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x9.99.1) (:span 14 22)))\n (:hscopes ((:id . :x9.99.1) (:span 14 46)))\n (:identifiers (:sid . :s9.99) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502863@unknown@formal@none@1@S@Screening for tick homologues against the 30 D. melanogaster proteins implicated in dsRNA uptake and processing [35] identified 14 and 16 homologues in R. microplus and I. scapularis, respectively, at varying levels of similarity for the 23 hits (22–91%).@(((:tag . "NN") (:stem . "screening") (:form . "Screening") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 60)\n  (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 69)\n  (:start . 61) (:id . 51))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 80)\n  (:start . 70) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 83) (:start . 81)\n  (:id . 53))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 89) (:start . 84)\n  (:id . 54))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 96)\n  (:start . 90) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 56))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 111)\n  (:start . 101) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 113) (:start . 112)\n  (:id . 58))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 115) (:start . 113)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 116) (:start . 115)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 127)\n  (:start . 117) (:id . 61))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 148)\n  (:start . 138) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 151) (:start . 149)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 164)\n  (:start . 155) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 171) (:start . 169)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 182)\n  (:start . 172) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 72))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 196)\n  (:start . 184) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 74))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 200) (:start . 198)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "vary") (:form . "varying") (:end . 208)\n  (:start . 201) (:id . 76))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 215)\n  (:start . 209) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 218) (:start . 216)\n  (:id . 78))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 229)\n  (:start . 219) (:id . 79))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 233) (:start . 230)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 237) (:start . 234)\n  (:id . 81))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 240) (:start . 238)\n  (:id . 82))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 245) (:start . 241)\n  (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 247) (:start . 246)\n  (:id . 84))\n ((:tag . "CD") (:stem . "22–91") (:form . "22–91") (:end . 252)\n  (:start . 247) (:id . 85))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 253) (:start . 252)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 254) (:start . 253)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 255) (:start . 254)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s9.100) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502864@unknown@formal@none@1@S@The highest similarity was observed with dsRNA uptake homologues associated with vesicle mediated transport, intracellular transport, oogenesis, endosome transport and ATPase for both tick species (Table 1).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 11) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 46) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 64)\n  (:start . 54) (:id . 50))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 75)\n  (:start . 65) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 80) (:start . 76)\n  (:id . 52))\n ((:tag . "NN") (:stem . "vesicle") (:form . "vesicle") (:end . 88)\n  (:start . 81) (:id . 53))\n ((:tag . "JJ") (:stem . "mediated") (:form . "mediated") (:end . 97)\n  (:start . 89) (:id . 54))\n ((:tag . "NN") (:stem . "transport") (:form . "transport") (:end . 107)\n  (:start . 98) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "intracellular") (:form . "intracellular")\n  (:end . 122) (:start . 109) (:id . 57))\n ((:tag . "NN") (:stem . "transport") (:form . "transport") (:end . 132)\n  (:start . 123) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 59))\n ((:tag . "NN") (:stem . "oogenesis") (:form . "oogenesis") (:end . 143)\n  (:start . 134) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 61))\n ((:tag . "NN") (:stem . "endosome") (:form . "endosome") (:end . 153)\n  (:start . 145) (:id . 62))\n ((:tag . "NN") (:stem . "transport") (:form . "transport") (:end . 163)\n  (:start . 154) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 64))\n ((:tag . "NN") (:stem . "atpase") (:form . "ATPase") (:end . 174)\n  (:start . 168) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 178) (:start . 175)\n  (:id . 66))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 183) (:start . 179)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "tick") (:form . "tick") (:end . 188) (:start . 184)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 196)\n  (:start . 189) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 198) (:start . 197)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 203)\n  (:start . 198) (:id . 71))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 205) (:start . 204)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s9.101) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502865@unknown@formal@none@1@S@Similarity searches with the protein sequences of the putative RNA helicases Armitage and Rm62, involved in the assembly of RISC, resulted in best hits on R. microplus sequences TC9347 and TC14966 respectively but no homologues of Spindle E were found (Table 1).@(((:tag . "NN") (:stem . "similarity") (:form . "Similarity") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 24) (:start . 20)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 46)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "helicas") (:form . "helicases") (:end . 76)\n  (:start . 67) (:id . 52))\n ((:tag . "NNP") (:stem . "Armitage") (:form . "Armitage") (:end . 85)\n  (:start . 77) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Rm62") (:form . "Rm62") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 104)\n  (:start . 96) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 120)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 128) (:start . 124)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 138)\n  (:start . 130) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n  (:id . 65))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 146) (:start . 142)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 151) (:start . 147)\n  (:id . 67))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 154) (:start . 152)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 157) (:start . 155)\n  (:id . 69))\n ((:tag . "CC") (:stem . "microplus") (:form . "microplus") (:end . 167)\n  (:start . 158) (:id . 70))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 177)\n  (:start . 168) (:id . 71))\n ((:tag . "NNP") (:stem . "TC9347") (:form . "TC9347") (:end . 184)\n  (:start . 178) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 188) (:start . 185)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "TC14966") (:form . "TC14966") (:end . 196)\n  (:start . 189) (:id . 74))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 209)\n  (:start . 197) (:id . 75))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 213) (:start . 210)\n  (:id . 76))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 216) (:start . 214)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 227)\n  (:start . 217) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 230) (:start . 228)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Spindle") (:form . "Spindle") (:end . 238)\n  (:start . 231) (:id . 80))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 240) (:start . 239)\n  (:id . 81))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 245) (:start . 241)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 251)\n  (:start . 246) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 253) (:start . 252)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 258)\n  (:start . 253) (:id . 85))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 260) (:start . 259)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 261) (:start . 260)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 262) (:start . 261)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s9.102) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502866@unknown@formal@none@1@S@Searches using D. melanogaster protein sequences for FMRp and TudorSN returned best hits on the R. microplus ESTs BEAE145TR (53% identity) and BEAFW62TR (46% identity), respectively.@(((:tag . "NNP") (:stem . "Searches") (:form . "Searches") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 30)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 48)\n  (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 52) (:start . 49)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "FMRp") (:form . "FMRp") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "TudorSN") (:form . "TudorSN") (:end . 69)\n  (:start . 62) (:id . 51))\n ((:tag . "VBD") (:stem . "return") (:form . "returned") (:end . 78)\n  (:start . 70) (:id . 52))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 83) (:start . 79)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 88) (:start . 84)\n  (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 98) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 108)\n  (:start . 99) (:id . 58))\n ((:tag . "NNP") (:stem . "EST") (:form . "ESTs") (:end . 113) (:start . 109)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "BEAE145TR") (:form . "BEAE145TR") (:end . 123)\n  (:start . 114) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "CD") (:stem . "53") (:form . "53") (:end . 127) (:start . 125)\n  (:id . 62))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 128) (:start . 127)\n  (:id . 63))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 137)\n  (:start . 129) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "BEAFW62TR") (:form . "BEAFW62TR") (:end . 152)\n  (:start . 143) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 68))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 156) (:start . 154)\n  (:id . 69))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 157) (:start . 156)\n  (:id . 70))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 166)\n  (:start . 158) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 73))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 181)\n  (:start . 169) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s9.103) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502867@unknown@formal@none@1@S@It must be noted that only one SN domain was identified in the putative homologue which either indicates that it is not a true TudorSN homologue or that the consensus sequence is currently incomplete.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "sn") (:form . "SN") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 40)\n  (:start . 34) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 44) (:start . 41)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 55)\n  (:start . 45) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 71)\n  (:start . 63) (:id . 55))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 81)\n  (:start . 72) (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 87) (:start . 82)\n  (:id . 57))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 94)\n  (:start . 88) (:id . 58))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 104)\n  (:start . 95) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 119) (:start . 116)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 126) (:start . 122)\n  (:id . 65))\n ((:tag . "NN") (:stem . "tudorsn") (:form . "TudorSN") (:end . 134)\n  (:start . 127) (:id . 66))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 144)\n  (:start . 135) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 147) (:start . 145)\n  (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 152) (:start . 148)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 70))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 166)\n  (:start . 157) (:id . 71))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 175)\n  (:start . 167) (:id . 72))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 178) (:start . 176)\n  (:id . 73))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 188)\n  (:start . 179) (:id . 74))\n ((:tag . "JJ") (:stem . "incomplete") (:form . "incomplete") (:end . 199)\n  (:start . 189) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x9.104.1) (:span 95 109))\n  ((:id . :x9.104.2) (:span 88 94 145 147)))\n (:hscopes ((:id . :x9.104.1) (:span 95 144))\n  ((:id . :x9.104.2) (:span 88 199)))\n (:identifiers (:sid . :s9.104) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502868@unknown@formal@none@1@S@However, a recent GenBank submission indicates the presence of a putative I. scapularis TudorSN identified simultaneously with this study ([GenBank:EEC18716.1] Ixodes scapularis Genome Project Consortium).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 17)\n  (:start . 11) (:id . 45))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "submission") (:form . "submission") (:end . 36)\n  (:start . 26) (:id . 47))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 73)\n  (:start . 65) (:id . 53))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 87)\n  (:start . 77) (:id . 55))\n ((:tag . "NNP") (:stem . "TudorSN") (:form . "TudorSN") (:end . 95)\n  (:start . 88) (:id . 56))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 106)\n  (:start . 96) (:id . 57))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n  (:end . 121) (:start . 107) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 126) (:start . 122)\n  (:id . 59))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 131) (:start . 127)\n  (:id . 60))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 137)\n  (:start . 132) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 140) (:start . 139)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "GenBank:EEC18716.1") (:form . "GenBank:EEC18716.1")\n  (:end . 158) (:start . 140) (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 159) (:start . 158)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Ixodes") (:form . "Ixodes") (:end . 166)\n  (:start . 160) (:id . 66))\n ((:tag . "VBZ") (:stem . "scapulari") (:form . "scapularis") (:end . 177)\n  (:start . 167) (:id . 67))\n ((:tag . "NNP") (:stem . "Genome") (:form . "Genome") (:end . 184)\n  (:start . 178) (:id . 68))\n ((:tag . "NNP") (:stem . "Project") (:form . "Project") (:end . 192)\n  (:start . 185) (:id . 69))\n ((:tag . "NNP") (:stem . "Consortium") (:form . "Consortium") (:end . 203)\n  (:start . 193) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 204) (:start . 203)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x9.105.1) (:span 37 46)))\n (:hscopes ((:id . :x9.105.1) (:span 37 204)))\n (:identifiers (:sid . :s9.105) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502869@unknown@formal@none@1@S@The EGO-1 protein from C. elegans has RNA-directed RNA polymerase (RdRP) activity and is associated with the C. elegans transitive RNAi pathway by amplifying the trigger dsRNA and/or siRNAs [28].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "ego-1") (:form . "EGO-1") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "rna-directed") (:form . "RNA-directed") (:end . 50)\n  (:start . 38) (:id . 49))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 65)\n  (:start . 55) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 99)\n  (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 104) (:start . 100)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 111) (:start . 109)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 119)\n  (:start . 112) (:id . 62))\n ((:tag . "JJ") (:stem . "transitive") (:form . "transitive") (:end . 130)\n  (:start . 120) (:id . 63))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 135) (:start . 131)\n  (:id . 64))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 143)\n  (:start . 136) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 146) (:start . 144)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "amplify") (:form . "amplifying") (:end . 157)\n  (:start . 147) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 68))\n ((:tag . "NN") (:stem . "trigger") (:form . "trigger") (:end . 169)\n  (:start . 162) (:id . 69))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 175)\n  (:start . 170) (:id . 70))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 182)\n  (:start . 176) (:id . 71))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 189)\n  (:start . 183) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 191) (:start . 190)\n  (:id . 73))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 193) (:start . 191)\n  (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 194) (:start . 193)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s9.106) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502870@unknown@formal@none@1@S@The EST BEAEL55TR exhibited a 41% identity with the C. elegans RdRP – EGO-1 (Table 1).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "EST") (:form . "EST") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "BEAEL55TR") (:form . "BEAEL55TR") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "VBD") (:stem . "exhibit") (:form . "exhibited") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 42)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 62)\n  (:start . 55) (:id . 53))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "NN") (:stem . "–") (:form . "–") (:end . 69) (:start . 68)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "EGO-1") (:form . "EGO-1") (:end . 75) (:start . 70)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 82) (:start . 77)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 84) (:start . 83)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s9.107) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502871@unknown@formal@none@1@S@Nine putative I. scapularis RdRP accessions have been deposited into GenBank by the Ixodes scapularis Genome Project Consortium simultaneously with this study.@(((:tag . "CD") (:stem . "nine") (:form . "Nine") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "accession") (:form . "accessions") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 53) (:start . 49)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "deposit") (:form . "deposited") (:end . 63)\n  (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 76)\n  (:start . 69) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Ixodes") (:form . "Ixodes") (:end . 90)\n  (:start . 84) (:id . 55))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 101)\n  (:start . 91) (:id . 56))\n ((:tag . "NNP") (:stem . "Genome") (:form . "Genome") (:end . 108)\n  (:start . 102) (:id . 57))\n ((:tag . "NNP") (:stem . "Project") (:form . "Project") (:end . 116)\n  (:start . 109) (:id . 58))\n ((:tag . "NNP") (:stem . "Consortium") (:form . "Consortium") (:end . 127)\n  (:start . 117) (:id . 59))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n  (:end . 142) (:start . 128) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 147) (:start . 143)\n  (:id . 61))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 152) (:start . 148)\n  (:id . 62))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 158)\n  (:start . 153) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.108) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502872@unknown@formal@none@1@S@A total of 4 of these I. scapularis RdRP sequences share conserved regions with the partial R. microplus RdRP and thus the new Accessions EEC04985.1, EEC05952.1, EEC12509.1 and EEC12909.1 were utilized for the I. scapularis RdRP sequences in the consensus tree presented in Figure 4.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 21) (:start . 16)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 24) (:start . 22)\n  (:id . 48))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 35)\n  (:start . 25) (:id . 49))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 40) (:start . 36)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 50)\n  (:start . 41) (:id . 51))\n ((:tag . "VBP") (:stem . "share") (:form . "share") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 74)\n  (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 91)\n  (:start . 84) (:id . 57))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 104)\n  (:start . 95) (:id . 59))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 61))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 118) (:start . 114)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 126) (:start . 123)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Accessions") (:form . "Accessions") (:end . 137)\n  (:start . 127) (:id . 65))\n ((:tag . "NNP") (:stem . "EEC04985.1") (:form . "EEC04985.1") (:end . 148)\n  (:start . 138) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "EEC05952.1") (:form . "EEC05952.1") (:end . 160)\n  (:start . 150) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "EEC12509.1") (:form . "EEC12509.1") (:end . 172)\n  (:start . 162) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "EEC12909.1") (:form . "EEC12909.1") (:end . 187)\n  (:start . 177) (:id . 72))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 192) (:start . 188)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "utilize") (:form . "utilized") (:end . 201)\n  (:start . 193) (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 205) (:start . 202)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 212) (:start . 210)\n  (:id . 77))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 223)\n  (:start . 213) (:id . 78))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 228) (:start . 224)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 238)\n  (:start . 229) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 241) (:start . 239)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 245) (:start . 242)\n  (:id . 82))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 255)\n  (:start . 246) (:id . 83))\n ((:tag . "NN") (:stem . "tree") (:form . "tree") (:end . 260) (:start . 256)\n  (:id . 84))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 270)\n  (:start . 261) (:id . 85))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 273) (:start . 271)\n  (:id . 86))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 280)\n  (:start . 274) (:id . 87))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 282) (:start . 281)\n  (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 283) (:start . 282)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s9.109) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502873@unknown@formal@none@1@S@All 5 tick RdRPs demonstrate a close phylogenetic relationship with the partial R. microplus RdRP clustering with I. scapularis EEC12909.1.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "rdrp") (:form . "RdRPs") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 28)\n  (:start . 17) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "close") (:form . "close") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 49)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 62)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 79)\n  (:start . 72) (:id . 53))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 92)\n  (:start . 83) (:id . 55))\n ((:tag . "NN") (:stem . "rdrp") (:form . "RdRP") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "cluster") (:form . "clustering") (:end . 108)\n  (:start . 98) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 113) (:start . 109)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 116) (:start . 114)\n  (:id . 59))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 127)\n  (:start . 117) (:id . 60))\n ((:tag . "NN") (:stem . "eec12909.1") (:form . "EEC12909.1") (:end . 138)\n  (:start . 128) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.110) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502874@unknown@formal@none@1@S@I. scapularis sequences EEC12509.1 and EEC04985.1, and EEC05952.1, form separate branches respectively.@(((:tag . "LS") (:stem . "i.") (:form . "I.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "eec12509.1") (:form . "EEC12509.1") (:end . 34)\n  (:start . 24) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "NN") (:stem . "eec04985.1") (:form . "EEC04985.1") (:end . 49)\n  (:start . 39) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "EEC05952.1") (:form . "EEC05952.1") (:end . 65)\n  (:start . 55) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 80)\n  (:start . 72) (:id . 53))\n ((:tag . "NNS") (:stem . "branch") (:form . "branches") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 102)\n  (:start . 90) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s9.111) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502875@unknown@formal@none@1@S@The RdRP proteins from C. elegans form another distinct cluster with the tick RdRPs branching between C. elegans and those from fungi, plants and protists (Figure 4).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 63)\n  (:start . 56) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "rdrp") (:form . "RdRPs") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "branch") (:form . "branching") (:end . 93)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 101)\n  (:start . 94) (:id . 57))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 112)\n  (:start . 105) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 122)\n  (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 127) (:start . 123)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "fungus") (:form . "fungi") (:end . 133)\n  (:start . 128) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "plant") (:form . "plants") (:end . 141)\n  (:start . 135) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "protist") (:form . "protists") (:end . 154)\n  (:start . 146) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 162)\n  (:start . 156) (:id . 69))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 164) (:start . 163)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.112) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502876@unknown@formal@none@1@S@Apart from the Armitage homologue, all R. microplus hits associated with RISC components and RdRP above were confirmed in I. scapularis genome reads in this study (Table 1).@(((:tag . "RB") (:stem . "apart") (:form . "Apart") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Armitage") (:form . "Armitage") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 88)\n  (:start . 78) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 97) (:start . 93)\n  (:id . 57))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 103) (:start . 98)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 118)\n  (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 124) (:start . 122)\n  (:id . 62))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 135)\n  (:start . 125) (:id . 63))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 142)\n  (:start . 136) (:id . 64))\n ((:tag . "VBZ") (:stem . "read") (:form . "reads") (:end . 148)\n  (:start . 143) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 151) (:start . 149)\n  (:id . 66))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 156) (:start . 152)\n  (:id . 67))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 162)\n  (:start . 157) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 169)\n  (:start . 164) (:id . 70))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 171) (:start . 170)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s9.113) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502877@unknown@formal@none@1@S@Phylogenetic tree constructed from the multiple sequence alignment of the partial R. microplus RdRP domain (Cat-RdRP) and hypothetical I. scapularis RdRP proteins (Iscap) to RdRP sequences from selected plants (Nicotiana tabacum, Hordeum vulgare, Arabidopsis thaliana, Solanum lycopersicum), fungi (Schizosaccharomyces pombe, Neurospora crassa and Aspergillus fumigatus), protists (Tetrahymena thermophila and Dictyostelium discoideum) and the metazoan C. elegans (Cele-ego-1, Cele-rrf-1/3).@(((:tag . "JJ") (:stem . "phylogenetic") (:form . "Phylogenetic") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "tree") (:form . "tree") (:end . 17) (:start . 13)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 29)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 34) (:start . 30)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 47)\n  (:start . 39) (:id . 47))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 56)\n  (:start . 48) (:id . 48))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 66)\n  (:start . 57) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 81)\n  (:start . 74) (:id . 52))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 84) (:start . 82)\n  (:id . 53))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 94)\n  (:start . 85) (:id . 54))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 99) (:start . 95)\n  (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 106)\n  (:start . 100) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Cat-RdRP") (:form . "Cat-RdRP") (:end . 116)\n  (:start . 108) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 117) (:start . 116)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "hypothetical") (:form . "hypothetical") (:end . 134)\n  (:start . 122) (:id . 61))\n ((:tag . "NN") (:stem . "i.") (:form . "I.") (:end . 137) (:start . 135)\n  (:id . 62))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 148)\n  (:start . 138) (:id . 63))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 153) (:start . 149)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 162)\n  (:start . 154) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Iscap") (:form . "Iscap") (:end . 169)\n  (:start . 164) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 173) (:start . 171)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 178) (:start . 174)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 188)\n  (:start . 179) (:id . 71))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 193) (:start . 189)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 202)\n  (:start . 194) (:id . 73))\n ((:tag . "NNS") (:stem . "plant") (:form . "plants") (:end . 209)\n  (:start . 203) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 211) (:start . 210)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Nicotiana") (:form . "Nicotiana") (:end . 220)\n  (:start . 211) (:id . 76))\n ((:tag . "NNP") (:stem . "tabacum") (:form . "tabacum") (:end . 228)\n  (:start . 221) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 229) (:start . 228)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Hordeum") (:form . "Hordeum") (:end . 237)\n  (:start . 230) (:id . 79))\n ((:tag . "NNP") (:stem . "vulgare") (:form . "vulgare") (:end . 245)\n  (:start . 238) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 246) (:start . 245)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Arabidopsis") (:form . "Arabidopsis") (:end . 258)\n  (:start . 247) (:id . 82))\n ((:tag . "NNP") (:stem . "thaliana") (:form . "thaliana") (:end . 267)\n  (:start . 259) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 268) (:start . 267)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Solanum") (:form . "Solanum") (:end . 276)\n  (:start . 269) (:id . 85))\n ((:tag . "NN") (:stem . "lycopersicum") (:form . "lycopersicum") (:end . 289)\n  (:start . 277) (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 290) (:start . 289)\n  (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 291) (:start . 290)\n  (:id . 88))\n ((:tag . "NN") (:stem . "fungi") (:form . "fungi") (:end . 297)\n  (:start . 292) (:id . 89))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 299) (:start . 298)\n  (:id . 90))\n ((:tag . "FW") (:stem . "schizosaccharomyces")\n  (:form . "Schizosaccharomyces") (:end . 318) (:start . 299) (:id . 91))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 324)\n  (:start . 319) (:id . 92))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 325) (:start . 324)\n  (:id . 93))\n ((:tag . "NNP") (:stem . "Neurospora") (:form . "Neurospora") (:end . 336)\n  (:start . 326) (:id . 94))\n ((:tag . "NN") (:stem . "crassa") (:form . "crassa") (:end . 343)\n  (:start . 337) (:id . 95))\n ((:tag . "CC") (:stem . "and") (:form . 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5502878@unknown@formal@none@1@S@The branch labels display the consensus support in %.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "branch") (:form . "branch") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "label") (:form . "labels") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 47)\n  (:start . 40) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s9.115) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502879@unknown@formal@none@1@S@Figure 5 shows a schematic diagram of a putative tick RNAi pathway.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "schematic") (:form . "schematic") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 54)))@@@1@13@((:hcues ((:id . :x9.116.1) (:span 40 48)))\n (:hscopes ((:id . :x9.116.1) (:span 40 66)))\n (:identifiers (:sid . :s9.116) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502880@unknown@formal@none@1@S@Putative proteins identified in R. microplus ESTs have been described using the 'Cat' (Cattle tick) prefix.@(((:tag . "JJ") (:stem . "putative") (:form . "Putative") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 28)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 44)\n  (:start . 35) (:id . 47))\n ((:tag . "NNS") (:stem . "est") (:form . "ESTs") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 69)\n  (:start . 60) (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 75) (:start . 70)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 53))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 81) (:start . 80)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Cat") (:form . "Cat") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Cattle") (:form . "Cattle") (:end . 93)\n  (:start . 87) (:id . 58))\n ((:tag . "NNP") (:stem . "tick") (:form . "tick") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 60))\n ((:tag . "NN") (:stem . "prefix") (:form . "prefix") (:end . 106)\n  (:start . 100) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x9.117.1) (:span 0 8)))\n (:hscopes ((:id . :x9.117.1) (:span 0 49)))\n (:identifiers (:sid . :s9.117) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502881@unknown@formal@none@1@S@dsRNA is taken up by tick cells and the RNAi effect spreads to subsequent tick stages by an unknown mechanism [42].@(((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 31) (:start . 26)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 44) (:start . 40)\n  (:id . 51))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 51)\n  (:start . 45) (:id . 52))\n ((:tag . "VBZ") (:stem . "spread") (:form . "spreads") (:end . 59)\n  (:start . 52) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 73)\n  (:start . 63) (:id . 55))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 78) (:start . 74)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 85)\n  (:start . 79) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 99)\n  (:start . 92) (:id . 60))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 109)\n  (:start . 100) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 111) (:start . 110)\n  (:id . 62))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 113) (:start . 111)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 114) (:start . 113)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s9.118) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502882@unknown@formal@none@1@S@It is yet unconfirmed whether a SID-1 or Sil-1 homologue exist in ticks, however, it is feasible that RdRP and associated proteins are involved in germ-line spread similar to the C. elegans RdRP pathway [28].@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "unconfirmed") (:form . "unconfirmed") (:end . 21)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sid-1") (:form . "SID-1") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "sil-1") (:form . "Sil-1") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 56)\n  (:start . 47) (:id . 51))\n ((:tag . "VBP") (:stem . "exist") (:form . "exist") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 80)\n  (:start . 73) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "feasible") (:form . "feasible") (:end . 96)\n  (:start . 88) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 101) (:start . 97)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 106) (:start . 102)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 121)\n  (:start . 111) (:id . 64))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 130)\n  (:start . 122) (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 134) (:start . 131)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 143)\n  (:start . 135) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n  (:id . 68))\n ((:tag . "NN") (:stem . "germ-line") (:form . "germ-line") (:end . 156)\n  (:start . 147) (:id . 69))\n ((:tag . "NN") (:stem . "spread") (:form . "spread") (:end . 163)\n  (:start . 157) (:id . 70))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 171)\n  (:start . 164) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 174) (:start . 172)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 181) (:start . 179)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 189)\n  (:start . 182) (:id . 75))\n ((:tag . "NN") (:stem . "rdrp") (:form . "RdRP") (:end . 194) (:start . 190)\n  (:id . 76))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 202)\n  (:start . 195) (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 204) (:start . 203)\n  (:id . 78))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 206) (:start . 204)\n  (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 207) (:start . 206)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x9.119.1) (:span 88 96)) ((:id . :x9.119.2) (:span 22 29))\n  ((:id . :x9.119.3) (:span 10 21)))\n (:hscopes ((:id . :x9.119.1) (:span 88 202)) ((:id . :x9.119.2) (:span 22 71))\n  ((:id . :x9.119.3) (:span 10 71)))\n (:identifiers (:sid . :s9.119) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502883@unknown@formal@none@1@S@Here we postulate the potential amplification of both trigger dsRNA and secondary siRNAs through the involvement of a Cat-RdRP.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "postulate") (:form . "postulate") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 45) (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 53) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "trigger") (:form . "trigger") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 67) (:start . 62)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 81)\n  (:start . 72) (:id . 53))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 88)\n  (:start . 82) (:id . 54))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 96)\n  (:start . 89) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 56))\n ((:tag . "NN") (:stem . "involvement") (:form . "involvement") (:end . 112)\n  (:start . 101) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 117) (:start . 116)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Cat-RdRP") (:form . "Cat-RdRP") (:end . 126)\n  (:start . 118) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x9.120.1) (:span 22 31)) ((:id . :x9.120.2) (:span 8 17)))\n (:hscopes ((:id . :x9.120.1) (:span 22 88)) ((:id . :x9.120.2) (:span 8 126)))\n (:identifiers (:sid . :s9.120) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502884@unknown@formal@none@1@S@A R. microplus Dicer was not identified, although a homologue was identified in the I. scapularis genome reads as described above.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 14)\n  (:start . 5) (:id . 44))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 39)\n  (:start . 29) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 61)\n  (:start . 52) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 76)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 97)\n  (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 104)\n  (:start . 98) (:id . 59))\n ((:tag . "VBZ") (:stem . "read") (:form . "reads") (:end . 110)\n  (:start . 105) (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 123)\n  (:start . 114) (:id . 62))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 129)\n  (:start . 124) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.121) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502885@unknown@formal@none@1@S@A definitive dsRNA binding protein (such as D. melanogaster R2D2 or C. elegans Rde-4) potentially associated with Dicer was not found using the current tick sequence resources.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "definitive") (:form . "definitive") (:end . 12)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 59)\n  (:start . 47) (:id . 51))\n ((:tag . "NN") (:stem . "r2d2") (:form . "R2D2") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 78)\n  (:start . 71) (:id . 55))\n ((:tag . "NN") (:stem . "rde-4") (:form . "Rde-4") (:end . 84) (:start . 79)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 57))\n ((:tag . "RB") (:stem . "potentially") (:form . "potentially") (:end . 97)\n  (:start . 86) (:id . 58))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 108)\n  (:start . 98) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 113) (:start . 109)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 119)\n  (:start . 114) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 123) (:start . 120)\n  (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 133)\n  (:start . 128) (:id . 64))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 139) (:start . 134)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 151)\n  (:start . 144) (:id . 67))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 156) (:start . 152)\n  (:id . 68))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 165)\n  (:start . 157) (:id . 69))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 175)\n  (:start . 166) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x9.122.1) (:span 86 97)))\n (:hscopes ((:id . :x9.122.1) (:span 0 119)))\n (:identifiers (:sid . :s9.122) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502886@unknown@formal@none@1@S@A confirmed tick Rde-1 was not identified but has been associated with the RdRP pathway if present [25].@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 11)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "rde-1") (:form . "Rde-1") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 41)\n  (:start . 31) (:id . 48))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 65)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 70) (:start . 66)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 87)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "present") (:form . "present") (:end . 98)\n  (:start . 91) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.123) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502887@unknown@formal@none@1@S@Dicer guides the siRNA to the RISC structure which has been adapted from the Sontheimer RNAi published diagram [44].@(((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "guide") (:form . "guides") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 44)\n  (:start . 35) (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "adapt") (:form . "adapted") (:end . 67)\n  (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Sontheimer") (:form . "Sontheimer") (:end . 87)\n  (:start . 77) (:id . 56))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 92) (:start . 88)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "publish") (:form . "published") (:end . 102)\n  (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 110)\n  (:start . 103) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 112) (:start . 111)\n  (:id . 60))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s9.124) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502888@unknown@formal@none@1@S@The RISC structure demonstrates homologues for a cattle tick Drosophila Fragile × protein (Cat-FMRp), tick TudorSN (Ixodes scapularis Genome Project Consortium) and the Cat-Ago-2 described above [44-46].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "VBZ") (:stem . "demonstrate") (:form . "demonstrates") (:end . 31)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 42)\n  (:start . 32) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 46) (:start . 43)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cattle") (:form . "cattle") (:end . 55)\n  (:start . 49) (:id . 49))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "NNP") (:stem . "Fragile") (:form . "Fragile") (:end . 79)\n  (:start . 72) (:id . 52))\n ((:tag . "NNP") (:stem . "×") (:form . "×") (:end . 81) (:start . 80)\n  (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 89)\n  (:start . 82) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Cat-FMRp") (:form . "Cat-FMRp") (:end . 99)\n  (:start . 91) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "TudorSN") (:form . "TudorSN") (:end . 114)\n  (:start . 107) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Ixodes") (:form . "Ixodes") (:end . 122)\n  (:start . 116) (:id . 62))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 133)\n  (:start . 123) (:id . 63))\n ((:tag . "NNP") (:stem . "Genome") (:form . "Genome") (:end . 140)\n  (:start . 134) (:id . 64))\n ((:tag . "NNP") (:stem . "Project") (:form . "Project") (:end . 148)\n  (:start . 141) (:id . 65))\n ((:tag . "NNP") (:stem . "Consortium") (:form . "Consortium") (:end . 159)\n  (:start . 149) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 69))\n ((:tag . "NN") (:stem . "cat-ago-2") (:form . "Cat-Ago-2") (:end . 178)\n  (:start . 169) (:id . 70))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 188)\n  (:start . 179) (:id . 71))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 194)\n  (:start . 189) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 196) (:start . 195)\n  (:id . 73))\n ((:tag . "CD") (:stem . "44-46") (:form . "44-46") (:end . 201)\n  (:start . 196) (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 202) (:start . 201)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s9.125) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502889@unknown@formal@none@1@S@Other proteins putatively associated with dsRNA uptake, systemic or germ-line RNAi listed in Table 1 were not included in this diagram.@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "RB") (:stem . "putatively") (:form . "putatively") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 36)\n  (:start . 26) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 41) (:start . 37)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 47) (:start . 42)\n  (:id . 47))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 54)\n  (:start . 48) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "germ-line") (:form . "germ-line") (:end . 77)\n  (:start . 68) (:id . 52))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 82) (:start . 78)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "list") (:form . "listed") (:end . 89) (:start . 83)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 105) (:start . 101)\n  (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 118)\n  (:start . 110) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 61))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 126) (:start . 122)\n  (:id . 62))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 134)\n  (:start . 127) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x9.126.1) (:span 15 25)))\n (:hscopes ((:id . :x9.126.1) (:span 0 82)))\n (:identifiers (:sid . :s9.126) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502890@unknown@formal@none@1@S@Schematic representation of a putative tick RNAi pathway.@(((:tag . "JJ") (:stem . "schematic") (:form . "Schematic") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "representation") (:form . "representation")\n  (:end . 24) (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 56)\n  (:start . 49) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n  (:id . 50)))@@@1@9@((:hcues ((:id . :x9.127.1) (:span 30 38)))\n (:hscopes ((:id . :x9.127.1) (:span 30 56)))\n (:identifiers (:sid . :s9.127) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502891@unknown@formal@none@1@S@Cattle tick homologues are indicated using a 'Cat' prefix for proteins where Rhicipephalus (Boophilus) microplus homologues are identified in this study (GenBank Accessions are listed in Additional File 6).@(((:tag . "VB") (:stem . "cattle") (:form . "Cattle") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 42) (:start . 37)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Cat") (:form . "Cat") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "prefix") (:form . "prefix") (:end . 57)\n  (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 70)\n  (:start . 62) (:id . 54))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Rhicipephalus") (:form . "Rhicipephalus")\n  (:end . 90) (:start . 77) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Boophilus") (:form . "Boophilus") (:end . 101)\n  (:start . 92) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 112)\n  (:start . 103) (:id . 60))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 123)\n  (:start . 113) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 127) (:start . 124)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 138)\n  (:start . 128) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n  (:id . 64))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 146) (:start . 142)\n  (:id . 65))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 152)\n  (:start . 147) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 161)\n  (:start . 154) (:id . 68))\n ((:tag . "NNP") (:stem . "Accession") (:form . "Accessions") (:end . 172)\n  (:start . 162) (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 176) (:start . 173)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "list") (:form . "listed") (:end . 183)\n  (:start . 177) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 186) (:start . 184)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 197)\n  (:start . 187) (:id . 73))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 202) (:start . 198)\n  (:id . 74))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 204) (:start . 203)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 205) (:start . 204)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s9.128) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502892@unknown@formal@none@1@S@The proposed activity of the Cat-RdRP (RNA dependent RNA polymerase, EGO1-like) is indicated as amplifying trigger dsRNA or cleaved siRNAs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Cat-RdRP") (:form . "Cat-RdRP") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dependent") (:form . "dependent") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "ego1-like") (:form . "EGO1-like") (:end . 78)\n  (:start . 69) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 92)\n  (:start . 83) (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "amplify") (:form . "amplifying") (:end . 106)\n  (:start . 96) (:id . 59))\n ((:tag . "NN") (:stem . "trigger") (:form . "trigger") (:end . 114)\n  (:start . 107) (:id . 60))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 120)\n  (:start . 115) (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "cleaved") (:form . "cleaved") (:end . 131)\n  (:start . 124) (:id . 63))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 138)\n  (:start . 132) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s9.129) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502893@unknown@formal@none@1@S@Long dsRNAs are recruited to Dicer (putative tick Dicer identified in I. scapularis genome reads) via a yet to be identified dsRNA Binding Protein.@(((:tag . "JJ") (:stem . "long") (:form . "Long") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "dsrna") (:form . "dsRNAs") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "recruit") (:form . "recruited") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 55) (:start . 50)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 66)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 83)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 90)\n  (:start . 84) (:id . 56))\n ((:tag . "VBZ") (:stem . "read") (:form . "reads") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 107) (:start . 104)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 113) (:start . 111)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 124)\n  (:start . 114) (:id . 64))\n ((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 130)\n  (:start . 125) (:id . 65))\n ((:tag . "NNP") (:stem . "Binding") (:form . "Binding") (:end . 138)\n  (:start . 131) (:id . 66))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 146)\n  (:start . 139) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s9.130) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502894@unknown@formal@none@1@S@The RNA-Induced-Silencing Complex (RISC) includes a Cat-Ago-2 (Argonaute-2 homologue), tick TudorSN (I. scapularis tudor-staphylococcal nuclease – GenBank EEC18716.1) and a Cat-FmRp (representing the D. melanogaster orthologue of the fragile-X mental-retardation protein essential to RISC).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "RNA-Induced-Silencing")\n  (:form . "RNA-Induced-Silencing") (:end . 25) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Complex") (:form . "Complex") (:end . 33)\n  (:start . 26) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 35) (:start . 34)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 40) (:start . 39)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 49)\n  (:start . 41) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cat-ago-2") (:form . "Cat-Ago-2") (:end . 61)\n  (:start . 52) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 74)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 84)\n  (:start . 75) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "TudorSN") (:form . "TudorSN") (:end . 99)\n  (:start . 92) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 114)\n  (:start . 104) (:id . 60))\n ((:tag . "JJ") (:stem . "tudor-staphylococcal")\n  (:form . "tudor-staphylococcal") (:end . 135) (:start . 115) (:id . 61))\n ((:tag . "NN") (:stem . "nuclease") (:form . "nuclease") (:end . 144)\n  (:start . 136) (:id . 62))\n ((:tag . "NN") (:stem . "–") (:form . "–") (:end . 146) (:start . 145)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 154)\n  (:start . 147) (:id . 64))\n ((:tag . "NNP") (:stem . "EEC18716.1") (:form . "EEC18716.1") (:end . 165)\n  (:start . 155) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 170) (:start . 167)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 172) (:start . 171)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Cat-FmRp") (:form . "Cat-FmRp") (:end . 181)\n  (:start . 173) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 183) (:start . 182)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "represent") (:form . "representing") (:end . 195)\n  (:start . 183) (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 199) (:start . 196)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 202) (:start . 200)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 215) (:start . 203) (:id . 74))\n ((:tag . "NN") (:stem . "orthologue") (:form . "orthologue") (:end . 226)\n  (:start . 216) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 229) (:start . 227)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 233) (:start . 230)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "fragile-X") (:form . "fragile-X") (:end . 243)\n  (:start . 234) (:id . 78))\n ((:tag . "NN") (:stem . "mental-retardation") (:form . "mental-retardation")\n  (:end . 262) (:start . 244) (:id . 79))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 270)\n  (:start . 263) (:id . 80))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 280)\n  (:start . 271) (:id . 81))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 283) (:start . 281)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 288) (:start . 284)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 289) (:start . 288)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 290) (:start . 289)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s9.131) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502895@unknown@formal@none@1@S@Homologues for a tick RNA unwinding protein and a vasa intronic gene (associated with RISC) were not identified.@(((:tag . "NNS") (:stem . "homologue") (:form . "Homologues") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "unwinding") (:form . "unwinding") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "vasa") (:form . "vasa") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "intronic") (:form . "intronic") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 80)\n  (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 90) (:start . 86)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 96) (:start . 92)\n  (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 111)\n  (:start . 101) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.132) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502896@unknown@formal@none@1@S@The schematic diagram was partly adapted from Sontheimer 2005 [44] and was drawn using Solid Edge Version 20 (Siemens PLM Software, TX, USA).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "schematic") (:form . "schematic") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "RB") (:stem . "partly") (:form . "partly") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "VBN") (:stem . "adapt") (:form . "adapted") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sontheimer") (:form . "Sontheimer") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "CD") (:stem . "2005") (:form . "2005") (:end . 61) (:start . 57)\n  (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "draw") (:form . "drawn") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 86) (:start . 81)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Solid") (:form . "Solid") (:end . 92) (:start . 87)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Edge") (:form . "Edge") (:end . 97) (:start . 93)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Version") (:form . "Version") (:end . 105)\n  (:start . 98) (:id . 60))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 108) (:start . 106)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Siemens") (:form . "Siemens") (:end . 117)\n  (:start . 110) (:id . 63))\n ((:tag . "NNP") (:stem . "PLM") (:form . "PLM") (:end . 121) (:start . 118)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Software") (:form . "Software") (:end . 130)\n  (:start . 122) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "TX") (:form . "TX") (:end . 134) (:start . 132)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "USA") (:form . "USA") (:end . 139) (:start . 136)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s9.133) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502897@unknown@formal@none@1@S@Selection of R. microplus conserved homologues for RNAi gene silencing@(((:tag . "NN") (:stem . "selection") (:form . "Selection") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "CC") (:stem . "microplus") (:form . "microplus") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 46)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 55) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 70)\n  (:start . 61) (:id . 51)))@@@1@10@((:identifiers (:sid . :s9.134) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502898@unknown@formal@none@1@S@To validate further a putative functional RNAi pathway in R. microplus we conducted RNAi-mediated loss-of-function assays in vitro and in vivo.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "validate") (:form . "validate") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "CC") (:stem . "microplus") (:form . "microplus") (:end . 70)\n  (:start . 61) (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "conduct") (:form . "conducted") (:end . 83)\n  (:start . 74) (:id . 54))\n ((:tag . "JJ") (:stem . "rnai-mediated") (:form . "RNAi-mediated")\n  (:end . 97) (:start . 84) (:id . 55))\n ((:tag . "JJ") (:stem . "loss-of-function") (:form . "loss-of-function")\n  (:end . 114) (:start . 98) (:id . 56))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 121)\n  (:start . 115) (:id . 57))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 124) (:start . 122)\n  (:id . 58))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 130)\n  (:start . 125) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 60))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 137) (:start . 135)\n  (:id . 61))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 142) (:start . 138)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x9.135.1) (:span 22 30)))\n (:hscopes ((:id . :x9.135.1) (:span 22 54)))\n (:identifiers (:sid . :s9.135) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502899@unknown@formal@none@1@S@We first selected tick RNAi targets based on their homology to Drosophila genes known to display an RNAi phenotype [43].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 50)\n  (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "homology") (:form . "homology") (:end . 59)\n  (:start . 51) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 73)\n  (:start . 63) (:id . 53))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 85) (:start . 80)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "VB") (:stem . "display") (:form . "display") (:end . 96)\n  (:start . 89) (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 104) (:start . 100)\n  (:id . 59))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 114)\n  (:start . 105) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 118) (:start . 116)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 119) (:start . 118)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.136) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502900@unknown@formal@none@1@S@Of the 438 Drosophila genes known to affect growth and viability, 40 were identified in the I. scapularis genome reads and 37 in the R. microplus BmiGI2 database with 31 hits common between the tick species (results not shown).@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "438") (:form . "438") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 21)\n  (:start . 11) (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 64)\n  (:start . 55) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 73) (:start . 69)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 84)\n  (:start . 74) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 94) (:start . 92)\n  (:id . 59))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 105)\n  (:start . 95) (:id . 60))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 112)\n  (:start . 106) (:id . 61))\n ((:tag . "NNS") (:stem . "read") (:form . "reads") (:end . 118)\n  (:start . 113) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 63))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 125) (:start . 123)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 135) (:start . 133)\n  (:id . 67))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 145)\n  (:start . 136) (:id . 68))\n ((:tag . "NN") (:stem . "bmigi2") (:form . "BmiGI2") (:end . 152)\n  (:start . 146) (:id . 69))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 161)\n  (:start . 153) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 166) (:start . 162)\n  (:id . 71))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 169) (:start . 167)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 174) (:start . 170)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 181)\n  (:start . 175) (:id . 74))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 189)\n  (:start . 182) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 193) (:start . 190)\n  (:id . 76))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 198) (:start . 194)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 206)\n  (:start . 199) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 208) (:start . 207)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 215)\n  (:start . 208) (:id . 80))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 219) (:start . 216)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 225)\n  (:start . 220) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 226) (:start . 225)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s9.137) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502901@unknown@formal@none@1@S@These results were based on blastn searches with an e-value cut-off of <1e-10.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "blastn") (:form . "blastn") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "e-value") (:form . "e-value") (:end . 59)\n  (:start . 52) (:id . 51))\n ((:tag . "NN") (:stem . "cut-off") (:form . "cut-off") (:end . 67)\n  (:start . 60) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "CD") (:stem . "<1e-10") (:form . "<1e-10") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s9.138) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502902@unknown@formal@none@1@S@To select the most conserved sequences for tick in vitro studies, using high stringency searches (>80% identity, e-value <1e-50), 11 R. microplus ESTs were identified in the BmiGI2 database as homologous to D. melanogaster genes with RNAi phenotypes affecting growth and viability at z scores >3 [43] (Table 2).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "select") (:form . "select") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "stringency") (:form . "stringency") (:end . 87)\n  (:start . 77) (:id . 56))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 96)\n  (:start . 88) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "CD") (:stem . ">80") (:form . ">80") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 111)\n  (:start . 103) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 62))\n ((:tag . "NN") (:stem . "e-value") (:form . "e-value") (:end . 120)\n  (:start . 113) (:id . 63))\n ((:tag . "CD") (:stem . "<1e-50") (:form . "<1e-50") (:end . 127)\n  (:start . 121) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 66))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 132) (:start . 130)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 135) (:start . 133)\n  (:id . 68))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 145)\n  (:start . 136) (:id . 69))\n ((:tag . "NNS") (:stem . "est") (:form . "ESTs") (:end . 150) (:start . 146)\n  (:id . 70))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 155) (:start . 151)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 166)\n  (:start . 156) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 169) (:start . 167)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 173) (:start . 170)\n  (:id . 74))\n ((:tag . "NN") (:stem . "bmigi2") (:form . "BmiGI2") (:end . 180)\n  (:start . 174) (:id . 75))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 189)\n  (:start . 181) (:id . 76))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 192) (:start . 190)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 203)\n  (:start . 193) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 206) (:start . 204)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 209) (:start . 207)\n  (:id . 80))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 222)\n  (:start . 210) (:id . 81))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 228)\n  (:start . 223) (:id . 82))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 233) (:start . 229)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 238) (:start . 234)\n  (:id . 84))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 249)\n  (:start . 239) (:id . 85))\n ((:tag . "VBG") (:stem . "affect") (:form . "affecting") (:end . 259)\n  (:start . 250) (:id . 86))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 266)\n  (:start . 260) (:id . 87))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 270) (:start . 267)\n  (:id . 88))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 280)\n  (:start . 271) (:id . 89))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 283) (:start . 281)\n  (:id . 90))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 285) (:start . 284)\n  (:id . 91))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 292)\n  (:start . 286) (:id . 92))\n ((:tag . "CD") (:stem . ">3") (:form . ">3") (:end . 295) (:start . 293)\n  (:id . 93))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 297) (:start . 296)\n  (:id . 94))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 299) (:start . 297)\n  (:id . 95))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 300) (:start . 299)\n  (:id . 96))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 302) (:start . 301)\n  (:id . 97))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 307)\n  (:start . 302) (:id . 98))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 309) (:start . 308)\n  (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 310) (:start . 309)\n  (:id . 100))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 311) (:start . 310)\n  (:id . 101)))@@@1@60@((:identifiers (:sid . :s9.139) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502903@unknown@formal@none@1@S@An additional 2 highly conserved homologues were selected as negative controls, one with a lower z score (Drosophila string of perls) and one with a nil z score thus with a nil effect on cell culture growth and viability (Drosophila Tat-binding protein-1), Table 2.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 69)\n  (:start . 61) (:id . 51))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 78)\n  (:start . 70) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 53))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 90) (:start . 89)\n  (:id . 56))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 104) (:start . 99)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 116)\n  (:start . 106) (:id . 61))\n ((:tag . "NN") (:stem . "string") (:form . "string") (:end . 123)\n  (:start . 117) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "perl") (:form . "perls") (:end . 132)\n  (:start . 127) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 66))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 141) (:start . 138)\n  (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 146) (:start . 142)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 148) (:start . 147)\n  (:id . 69))\n ((:tag . "NN") (:stem . "nil") (:form . "nil") (:end . 152) (:start . 149)\n  (:id . 70))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 154) (:start . 153)\n  (:id . 71))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 160)\n  (:start . 155) (:id . 72))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 165) (:start . 161)\n  (:id . 73))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 170) (:start . 166)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 172) (:start . 171)\n  (:id . 75))\n ((:tag . "NN") (:stem . "nil") (:form . "nil") (:end . 176) (:start . 173)\n  (:id . 76))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 183)\n  (:start . 177) (:id . 77))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 186) (:start . 184)\n  (:id . 78))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 191) (:start . 187)\n  (:id . 79))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 199)\n  (:start . 192) (:id . 80))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 206)\n  (:start . 200) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 210) (:start . 207)\n  (:id . 82))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 220)\n  (:start . 211) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 222) (:start . 221)\n  (:id . 84))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 232)\n  (:start . 222) (:id . 85))\n ((:tag . "JJ") (:stem . "tat-binding") (:form . "Tat-binding") (:end . 244)\n  (:start . 233) (:id . 86))\n ((:tag . "NN") (:stem . "protein-1") (:form . "protein-1") (:end . 254)\n  (:start . 245) (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 255) (:start . 254)\n  (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 256) (:start . 255)\n  (:id . 89))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 262)\n  (:start . 257) (:id . 90))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 264) (:start . 263)\n  (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 92)))@@@1@51@((:identifiers (:sid . :s9.140) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502904@unknown@formal@none@1@S@The putative function of these 13 R. microplus ESTs were then assigned by retrieving the annotated InterPro domains of their Drosophila counterparts (Table 2).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "NNS") (:stem . "est") (:form . "ESTs") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 70)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "retrieve") (:form . "retrieving") (:end . 84)\n  (:start . 74) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 98)\n  (:start . 89) (:id . 57))\n ((:tag . "NNP") (:stem . "InterPro") (:form . "InterPro") (:end . 107)\n  (:start . 99) (:id . 58))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 115)\n  (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 124)\n  (:start . 119) (:id . 61))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 135)\n  (:start . 125) (:id . 62))\n ((:tag . "NNS") (:stem . "counterpart") (:form . "counterparts") (:end . 148)\n  (:start . 136) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 155)\n  (:start . 150) (:id . 65))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 157) (:start . 156)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x9.141.1) (:span 4 12)))\n (:hscopes ((:id . :x9.141.1) (:span 4 51)))\n (:identifiers (:sid . :s9.141) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502905@unknown@formal@none@1@S@Evaluation of the assigned functional information revealed that 5 sequences putatively have a role in ribosome and protein synthesis (TC5762, TC9037, TC12306, TC12372, TC12393), 4 in proteasome and ubiquitinylation (TC6372, TC9852, TC10417, TC13930), 3 in DNA binding (TC6116, TC12182, TC9417), and one in energy and metabolism (TC5823).@(((:tag . "NN") (:stem . "evaluation") (:form . "Evaluation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 49)\n  (:start . 38) (:id . 47))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 58)\n  (:start . 50) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 63) (:start . 59)\n  (:id . 49))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 65) (:start . 64)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 75)\n  (:start . 66) (:id . 51))\n ((:tag . "RB") (:stem . "putatively") (:form . "putatively") (:end . 86)\n  (:start . 76) (:id . 52))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 91) (:start . 87)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 93) (:start . 92)\n  (:id . 54))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 98) (:start . 94)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 101) (:start . 99)\n  (:id . 56))\n ((:tag . "NN") (:stem . "ribosome") (:form . "ribosome") (:end . 110)\n  (:start . 102) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 122)\n  (:start . 115) (:id . 59))\n ((:tag . "NN") (:stem . "synthesis") (:form . "synthesis") (:end . 132)\n  (:start . 123) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "TC5762") (:form . "TC5762") (:end . 140)\n  (:start . 134) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "TC9037") (:form . "TC9037") (:end . 148)\n  (:start . 142) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "TC12306") (:form . "TC12306") (:end . 157)\n  (:start . 150) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "TC12372") (:form . 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"(") (:end . 216) (:start . 215)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "TC6372") (:form . "TC6372") (:end . 222)\n  (:start . 216) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 223) (:start . 222)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "TC9852") (:form . "TC9852") (:end . 230)\n  (:start . 224) (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 231) (:start . 230)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "TC10417") (:form . "TC10417") (:end . 239)\n  (:start . 232) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 240) (:start . 239)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "TC13930") (:form . "TC13930") (:end . 248)\n  (:start . 241) (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 249) (:start . 248)\n  (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 250) (:start . 249)\n  (:id . 87))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 252) (:start . 251)\n  (:id . 88))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 255) (:start . 253)\n  (:id . 89))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 259) (:start . 256)\n  (:id . 90))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 267)\n  (:start . 260) (:id . 91))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 269) (:start . 268)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "TC6116") (:form . "TC6116") (:end . 275)\n  (:start . 269) (:id . 93))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 276) (:start . 275)\n  (:id . 94))\n ((:tag . "NNP") (:stem . "TC12182") (:form . "TC12182") (:end . 284)\n  (:start . 277) (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 285) (:start . 284)\n  (:id . 96))\n ((:tag . "NNP") (:stem . "TC9417") (:form . "TC9417") (:end . 292)\n  (:start . 286) (:id . 97))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 293) (:start . 292)\n  (:id . 98))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 294) (:start . 293)\n  (:id . 99))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 298) (:start . 295)\n  (:id . 100))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 302) (:start . 299)\n  (:id . 101))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 305) (:start . 303)\n  (:id . 102))\n ((:tag . "NN") (:stem . "energy") (:form . "energy") (:end . 312)\n  (:start . 306) (:id . 103))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 316) (:start . 313)\n  (:id . 104))\n ((:tag . "NN") (:stem . "metabolism") (:form . "metabolism") (:end . 327)\n  (:start . 317) (:id . 105))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 329) (:start . 328)\n  (:id . 106))\n ((:tag . "NNP") (:stem . "TC5823") (:form . "TC5823") (:end . 335)\n  (:start . 329) (:id . 107))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 336) (:start . 335)\n  (:id . 108))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 337) (:start . 336)\n  (:id . 109)))@@@1@68@((:hcues ((:id . :x9.142.1) (:span 76 86)))\n (:hscopes ((:id . :x9.142.1) (:span 64 336)))\n (:identifiers (:sid . :s9.142) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502906@unknown@formal@none@1@S@The controls used were the Drosophila string of perls (TC5762) and Tat-binding protein-1 (TC13930) homologues respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "string") (:form . "string") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "perl") (:form . "perls") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tc5762") (:form . "TC5762") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "tat-binding") (:form . "Tat-binding") (:end . 78)\n  (:start . 67) (:id . 55))\n ((:tag . "NN") (:stem . "protein-1") (:form . "protein-1") (:end . 88)\n  (:start . 79) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "tc13930") (:form . "TC13930") (:end . 97)\n  (:start . 90) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 109)\n  (:start . 99) (:id . 60))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 122)\n  (:start . 110) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.143) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502907@unknown@formal@none@1@S@R. microplus homologues with high conservation (≥ 80% identity) to 13 D. melanogaster proteins following RNAi knockdown in vitro (11 associated with significant cell viability z scores at >3 and 2 controls at<3)@(((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 46)\n  (:start . 34) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "≥") (:form . "≥") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "CD") (:stem . "80") (:form . "80") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 62)\n  (:start . 54) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 69) (:start . 67)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 72) (:start . 70)\n  (:id . 56))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 85)\n  (:start . 73) (:id . 57))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 94)\n  (:start . 86) (:id . 58))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 104)\n  (:start . 95) (:id . 59))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "knockdown") (:form . "knockdown") (:end . 119)\n  (:start . 110) (:id . 61))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 128)\n  (:start . 123) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 143)\n  (:start . 133) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 148) (:start . 144)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 160)\n  (:start . 149) (:id . 68))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 165) (:start . 161)\n  (:id . 69))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 175)\n  (:start . 166) (:id . 70))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 177) (:start . 176)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 184)\n  (:start . 178) (:id . 72))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 187) (:start . 185)\n  (:id . 73))\n ((:tag . "CD") (:stem . ">3") (:form . ">3") (:end . 190) (:start . 188)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n  (:id . 75))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 196) (:start . 195)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 205)\n  (:start . 197) (:id . 77))\n ((:tag . "CD") (:stem . "at<3") (:form . "at<3") (:end . 210) (:start . 206)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 211) (:start . 210)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s9.144) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5502908@unknown@formal@none@1@S@Although all primers for target amplification prior to RNA transcription were designed by targeting conserved consensus regions as described in the methods, amplification of TC5823 (energy and metabolism/ATP biosynthesis), TC9417 (DNA binding) and TC12372 (ribosome and protein synthesis) was inconsistent with poor yields which were inadequate for RNA transcription (not shown).@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 45) (:start . 32) (:id . 47))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 51) (:start . 46)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 58) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 72) (:start . 59) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 77) (:start . 73)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 86)\n  (:start . 78) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 89) (:start . 87)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 99)\n  (:start . 90) (:id . 55))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 109)\n  (:start . 100) (:id . 56))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 119)\n  (:start . 110) (:id . 57))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 127)\n  (:start . 120) (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 130) (:start . 128)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 140)\n  (:start . 131) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 143) (:start . 141)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 155)\n  (:start . 148) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 64))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 170) (:start . 157) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "TC5823") (:form . 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"DNA") (:end . 234) (:start . 231)\n  (:id . 77))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 242)\n  (:start . 235) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 243) (:start . 242)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 247) (:start . 244)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "TC12372") (:form . "TC12372") (:end . 255)\n  (:start . 248) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 257) (:start . 256)\n  (:id . 82))\n ((:tag . "NN") (:stem . "ribosome") (:form . "ribosome") (:end . 265)\n  (:start . 257) (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 269) (:start . 266)\n  (:id . 84))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 277)\n  (:start . 270) (:id . 85))\n ((:tag . "NN") (:stem . "synthesis") (:form . "synthesis") (:end . 287)\n  (:start . 278) (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 288) (:start . 287)\n  (:id . 87))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 292) (:start . 289)\n  (:id . 88))\n ((:tag . "JJ") (:stem . "inconsistent") (:form . "inconsistent") (:end . 305)\n  (:start . 293) (:id . 89))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 310) (:start . 306)\n  (:id . 90))\n ((:tag . "JJ") (:stem . "poor") (:form . "poor") (:end . 315) (:start . 311)\n  (:id . 91))\n ((:tag . "NNS") (:stem . "yield") (:form . "yields") (:end . 322)\n  (:start . 316) (:id . 92))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 328)\n  (:start . 323) (:id . 93))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 333) (:start . 329)\n  (:id . 94))\n ((:tag . "JJ") (:stem . "inadequate") (:form . "inadequate") (:end . 344)\n  (:start . 334) (:id . 95))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 348) (:start . 345)\n  (:id . 96))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 352) (:start . 349)\n  (:id . 97))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 366) (:start . 353) (:id . 98))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 368) (:start . 367)\n  (:id . 99))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 371) (:start . 368)\n  (:id . 100))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 377)\n  (:start . 372) (:id . 101))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 378) (:start . 377)\n  (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 379) (:start . 378)\n  (:id . 103)))@@@1@62@((:identifiers (:sid . :s9.145) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502909@unknown@formal@none@1@S@dsRNAs were transcribed successfully for the remaining 10 target genes (8 high z scores, 2 controls) used for RNAi experiments in cultured R. microplus BME26 cells and adult female ticks.@(((:tag . "NNS") (:stem . "dsrna") (:form . "dsRNAs") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "transcribe") (:form . "transcribed") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "RB") (:stem . "successfully") (:form . "successfully") (:end . 36)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 40) (:start . 37)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 54)\n  (:start . 45) (:id . 48))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 64)\n  (:start . 58) (:id . 50))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 70) (:start . 65)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 87)\n  (:start . 81) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 99)\n  (:start . 91) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 105) (:start . 101)\n  (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 114) (:start . 110)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 126)\n  (:start . 115) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 138)\n  (:start . 130) (:id . 66))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 141) (:start . 139)\n  (:id . 67))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 151)\n  (:start . 142) (:id . 68))\n ((:tag . "NN") (:stem . "bme26") (:form . "BME26") (:end . 157)\n  (:start . 152) (:id . 69))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 163)\n  (:start . 158) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 173)\n  (:start . 168) (:id . 72))\n ((:tag . "JJ") (:stem . "female") (:form . "female") (:end . 180)\n  (:start . 174) (:id . 73))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 186)\n  (:start . 181) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s9.146) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502910@unknown@formal@none@1@S@Gene silencing in cultured tick cells@(((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 37) (:start . 32)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s9.147) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502911@unknown@formal@none@1@S@None of the dsRNA treatments had significant effects on tick cell viability (Figure 6a) compared to controls and compared to z scores >3 as described for the same targets in Drosophila cells (Table 2, [43]).@(((:tag . "NN") (:stem . "none") (:form . "None") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 44)\n  (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 75)\n  (:start . 66) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 83)\n  (:start . 77) (:id . 55))\n ((:tag . "NN") (:stem . "6a") (:form . "6a") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 96)\n  (:start . 88) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 99) (:start . 97)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 108)\n  (:start . 100) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 121)\n  (:start . 113) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 126) (:start . 125)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 133)\n  (:start . 127) (:id . 65))\n ((:tag . "CD") (:stem . ">3") (:form . ">3") (:end . 136) (:start . 134)\n  (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 139) (:start . 137)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 149)\n  (:start . 140) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 153) (:start . 150)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 162) (:start . 158)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 170)\n  (:start . 163) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 173) (:start . 171)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 184)\n  (:start . 174) (:id . 74))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 190)\n  (:start . 185) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 192) (:start . 191)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 197)\n  (:start . 192) (:id . 77))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 199) (:start . 198)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n  (:id . 79))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 202) (:start . 201)\n  (:id . 80))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 204) (:start . 202)\n  (:id . 81))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 205) (:start . 204)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s9.148) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
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5502913@unknown@formal@none@1@S@An additional 2 target genes (Rpt1 TC10417, and Tat-binding protein-1 TC13930) demonstrated a slight reduction on cell viability with z scores 0.8 and 1.0 respectively.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Rpt1") (:form . "Rpt1") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "TC10417") (:form . "TC10417") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "tat-binding") (:form . "Tat-binding") (:end . 59)\n  (:start . 48) (:id . 52))\n ((:tag . "NN") (:stem . "protein-1") (:form . "protein-1") (:end . 69)\n  (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "tc13930") (:form . "TC13930") (:end . 77)\n  (:start . 70) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 91)\n  (:start . 79) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "slight") (:form . "slight") (:end . 100)\n  (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 110)\n  (:start . 101) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 118) (:start . 114)\n  (:id . 61))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 128)\n  (:start . 119) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 133) (:start . 129)\n  (:id . 63))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 135) (:start . 134)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 142)\n  (:start . 136) (:id . 65))\n ((:tag . "CD") (:stem . "0.8") (:form . "0.8") (:end . 146) (:start . 143)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 67))\n ((:tag . "CD") (:stem . "1.0") (:form . "1.0") (:end . 154) (:start . 151)\n  (:id . 68))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 167)\n  (:start . 155) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s9.150) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502914@unknown@formal@none@1@S@It is feasible that the TC13930 treatment may have had a stronger viability phenotype if the knockdown had been more effective (only 31% compared to other treatments ~>79%).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "feasible") (:form . "feasible") (:end . 14)\n  (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "tc13930") (:form . "TC13930") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 41)\n  (:start . 32) (:id . 48))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "JJR") (:stem . "strong") (:form . "stronger") (:end . 65)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 75)\n  (:start . 66) (:id . 54))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 85)\n  (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 102)\n  (:start . 93) (:id . 58))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 111) (:start . 107)\n  (:id . 60))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 116) (:start . 112)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 126)\n  (:start . 117) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 63))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 132) (:start . 128)\n  (:id . 64))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 136) (:start . 135)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 145)\n  (:start . 137) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 154)\n  (:start . 149) (:id . 69))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 165)\n  (:start . 155) (:id . 70))\n ((:tag . "CD") (:stem . "~>79") (:form . "~>79") (:end . 170) (:start . 166)\n  (:id . 71))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 171) (:start . 170)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x9.151.1) (:span 42 45)) ((:id . :x9.151.2) (:span 6 14)))\n (:hscopes ((:id . :x9.151.1) (:span 42 172))\n  ((:id . :x9.151.2) (:span 6 172)))\n (:identifiers (:sid . :s9.151) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502915@unknown@formal@none@1@S@Collectively the effects are less significant in tick cells than for their Drosophila counterparts in Drosophila cells, these 3 treatments are all associated with proteins involved in proteasome and ubiquitin function.@(((:tag . "RB") (:stem . "collectively") (:form . "Collectively") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 45)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 53) (:start . 49)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 74)\n  (:start . 69) (:id . 53))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 85)\n  (:start . 75) (:id . 54))\n ((:tag . "NNS") (:stem . "counterpart") (:form . "counterparts") (:end . 98)\n  (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 101) (:start . 99)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 112)\n  (:start . 102) (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 118)\n  (:start . 113) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 59))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 125)\n  (:start . 120) (:id . 60))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 127) (:start . 126)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 138)\n  (:start . 128) (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 142) (:start . 139)\n  (:id . 63))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 146) (:start . 143)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 157)\n  (:start . 147) (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 162) (:start . 158)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 171)\n  (:start . 163) (:id . 67))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 180)\n  (:start . 172) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 183) (:start . 181)\n  (:id . 69))\n ((:tag . "NN") (:stem . "proteasome") (:form . "proteasome") (:end . 194)\n  (:start . 184) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 198) (:start . 195)\n  (:id . 71))\n ((:tag . "NN") (:stem . "ubiquitin") (:form . "ubiquitin") (:end . 208)\n  (:start . 199) (:id . 72))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 217)\n  (:start . 209) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s9.152) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502916@unknown@formal@none@1@S@Quantitative RT-PCR analysis confirmed that all RNAi targeted genes resulted in a substantial reduction of the corresponding target mRNA (79.9 – 100%) except for TC13930 at 31% (Figure 6b).@(((:tag . "JJ") (:stem . "quantitative") (:form . "Quantitative") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 19)\n  (:start . 13) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 28)\n  (:start . 20) (:id . 44))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 38)\n  (:start . 29) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 43) (:start . 39)\n  (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 47) (:start . 44)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 52) (:start . 48)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "target") (:form . "targeted") (:end . 61)\n  (:start . 53) (:id . 49))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 67) (:start . 62)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 76)\n  (:start . 68) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 81) (:start . 80)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "substantial") (:form . "substantial") (:end . 93)\n  (:start . 82) (:id . 54))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 103)\n  (:start . 94) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 124)\n  (:start . 111) (:id . 58))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 131)\n  (:start . 125) (:id . 59))\n ((:tag . "NNP") (:stem . "mRNA") (:form . "mRNA") (:end . 136) (:start . 132)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 61))\n ((:tag . "CD") (:stem . "79.9") (:form . "79.9") (:end . 142) (:start . 138)\n  (:id . 62))\n ((:tag . "SYM") (:stem . "–") (:form . "–") (:end . 144) (:start . 143)\n  (:id . 63))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 148) (:start . 145)\n  (:id . 64))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 149) (:start . 148)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "IN") (:stem . "except") (:form . "except") (:end . 157)\n  (:start . 151) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 161) (:start . 158)\n  (:id . 68))\n ((:tag . "NN") (:stem . "tc13930") (:form . "TC13930") (:end . 169)\n  (:start . 162) (:id . 69))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 172) (:start . 170)\n  (:id . 70))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 176) (:start . 175)\n  (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 178) (:start . 177)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 184)\n  (:start . 178) (:id . 74))\n ((:tag . "NN") (:stem . "6b") (:form . "6b") (:end . 187) (:start . 185)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s9.153) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502917@unknown@formal@none@1@S@Cell culture knockdown.@(((:tag . "NN") (:stem . "cell") (:form . "Cell") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 23) (:start . 22)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s9.154) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502918@unknown@formal@none@1@S@(a).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 4) (:start . 3) (:id . 45)))@@@1@4@((:identifiers (:sid . :s9.155) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502919@unknown@formal@none@1@S@Growth and viability RNAi phenotypes expressed as inverse z-scores of genes involved in ribosome and protein synthesis (TC5762, TC9037, TC12306, TC12393), encoding proteasome components and participating in ubiquitinylation (TC6372, TC9852, TC10417, TC13930), and having DNA binding functions (TC6116, TC12182).@(((:tag . "NN") (:stem . "growth") (:form . "Growth") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 36)\n  (:start . 26) (:id . 46))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 46)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . 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5502920@unknown@formal@none@1@S@A positive z-score indicates reduced cell growth and viability.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "z-score") (:form . "z-score") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 48)\n  (:start . 42) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 62)\n  (:start . 53) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s9.157) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502921@unknown@formal@none@1@S@(b).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 4) (:start . 3) (:id . 45)))@@@1@4@((:identifiers (:sid . :s9.158) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502922@unknown@formal@none@1@S@Effect of dsRNA-induced knockdown on RNAi targets measured by quantitative RT-PCR and presented as % of gene expression levels relative to the housekeeping gene.@(((:tag . "NN") (:stem . "effect") (:form . "Effect") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "dsrna-induced") (:form . "dsRNA-induced")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 33)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 58)\n  (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 74)\n  (:start . 62) (:id . 51))\n ((:tag . "NN") (:stem . "rt-pcr") (:form . "RT-PCR") (:end . 81)\n  (:start . 75) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "present") (:form . "presented") (:end . 95)\n  (:start . 86) (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 98) (:start . 96)\n  (:id . 55))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 100) (:start . 99)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 108) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 119)\n  (:start . 109) (:id . 59))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 126)\n  (:start . 120) (:id . 60))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 135)\n  (:start . 127) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 138) (:start . 136)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n  (:id . 63))\n ((:tag . "NN") (:stem . "housekeeping") (:form . "housekeeping") (:end . 155)\n  (:start . 143) (:id . 64))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 160) (:start . 156)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s9.159) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502923@unknown@formal@none@1@S@Gene silencing in adult female ticks (reproduction phenotype)@(((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "female") (:form . "female") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "reproduction") (:form . "reproduction") (:end . 50)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s9.160) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5502924@unknown@formal@none@1@S@The same treatments were tested in live adult female ticks to measure any in vivo effects of gene silencing on tick survivability, egg output and larval hatching.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 31) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "live") (:form . "live") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "female") (:form . "female") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 58) (:start . 53)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "VB") (:stem . "measure") (:form . "measure") (:end . 69)\n  (:start . 62) (:id . 53))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 89)\n  (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 97) (:start . 93)\n  (:id . 59))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 107)\n  (:start . 98) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 110) (:start . 108)\n  (:id . 61))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 115) (:start . 111)\n  (:id . 62))\n ((:tag . "NN") (:stem . "survivability") (:form . "survivability")\n  (:end . 129) (:start . 116) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 134) (:start . 131)\n  (:id . 65))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 141)\n  (:start . 135) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 152)\n  (:start . 146) (:id . 68))\n ((:tag . "NN") (:stem . "hatching") (:form . "hatching") (:end . 161)\n  (:start . 153) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s9.161) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502925@unknown@formal@none@1@S@Eggs laid by ticks from the control groups showed no obvious morphological changes (see Figure 7a for eggs from "no treatment" group).@(((:tag . "NNP") (:stem . "Egg") (:form . "Eggs") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "lay") (:form . "laid") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 42)\n  (:start . 36) (:id . 49))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 49) (:start . 43)\n  (:id . 50))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 60)\n  (:start . 53) (:id . 52))\n ((:tag . "JJ") (:stem . "morphological") (:form . "morphological")\n  (:end . 74) (:start . 61) (:id . 53))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 82)\n  (:start . 75) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 94)\n  (:start . 88) (:id . 57))\n ((:tag . "NN") (:stem . "7a") (:form . "7a") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "egg") (:form . "eggs") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 111) (:start . 107)\n  (:id . 61))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 115) (:start . 113)\n  (:id . 63))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 125)\n  (:start . 116) (:id . 64))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 126) (:start . 125)\n  (:id . 65))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 132)\n  (:start . 127) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s9.162) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502926@unknown@formal@none@1@S@The average egg mass weight was 0.118 g for the control dsRNA group, 0.134 for the tick actin dsRNA group, 0.107 g for the PBS injection control group and 0.128 g for the negative control group (nil injection).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "weight") (:form . "weight") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "CD") (:stem . "0.118") (:form . "0.118") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "g") (:form . "g") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 55)\n  (:start . 48) (:id . 52))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 61) (:start . 56)\n  (:id . 53))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "CD") (:stem . "0.134") (:form . "0.134") (:end . 74) (:start . 69)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 78) (:start . 75)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 87) (:start . 83)\n  (:id . 59))\n ((:tag . "NN") (:stem . "actin") (:form . "actin") (:end . 93) (:start . 88)\n  (:id . 60))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 99) (:start . 94)\n  (:id . 61))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 105)\n  (:start . 100) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 63))\n ((:tag . "CD") (:stem . "0.107") (:form . "0.107") (:end . 112)\n  (:start . 107) (:id . 64))\n ((:tag . "NN") (:stem . "g") (:form . "g") (:end . 114) (:start . 113)\n  (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 118) (:start . 115)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "PBS") (:form . "PBS") (:end . 126) (:start . 123)\n  (:id . 68))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 136)\n  (:start . 127) (:id . 69))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 144)\n  (:start . 137) (:id . 70))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 150)\n  (:start . 145) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 72))\n ((:tag . "CD") (:stem . "0.128") (:form . "0.128") (:end . 160)\n  (:start . 155) (:id . 73))\n ((:tag . "NN") (:stem . "g") (:form . "g") (:end . 162) (:start . 161)\n  (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 166) (:start . 163)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 179)\n  (:start . 171) (:id . 77))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 187)\n  (:start . 180) (:id . 78))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 193)\n  (:start . 188) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 195) (:start . 194)\n  (:id . 80))\n ((:tag . "NN") (:stem . "nil") (:form . "nil") (:end . 198) (:start . 195)\n  (:id . 81))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 208)\n  (:start . 199) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 209) (:start . 208)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s9.163) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502927@unknown@formal@none@1@S@Eggs from the control groups showed a normal embryonic development time to larval hatching at 27 days.@(((:tag . "NNP") (:stem . "Egg") (:form . "Eggs") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 35) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 54)\n  (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 66)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "larval") (:form . "larval") (:end . 81)\n  (:start . 75) (:id . 54))\n ((:tag . "VBG") (:stem . "hatch") (:form . "hatching") (:end . 90)\n  (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 93) (:start . 91)\n  (:id . 56))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s9.164) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502928@unknown@formal@none@1@S@The larval hatching rates for control treatments ranged between 62.0–69.8% (Table 3).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "hatching") (:form . "hatching") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 25) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 48)\n  (:start . 38) (:id . 48))\n ((:tag . "VBD") (:stem . "range") (:form . "ranged") (:end . 55)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 63)\n  (:start . 56) (:id . 50))\n ((:tag . "CD") (:stem . "62.0–69.8") (:form . "62.0–69.8") (:end . 73)\n  (:start . 64) (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 74) (:start . 73)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s9.165) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502929@unknown@formal@none@1@S@Differences in egg morphologies following treatment of R. microplus adult female ticks with dsRNA.@(((:tag . "NNS") (:stem . "difference") (:form . "Differences") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "morphology") (:form . "morphologies") (:end . 31)\n  (:start . 19) (:id . 45))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 41)\n  (:start . 32) (:id . 46))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 51)\n  (:start . 42) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "CC") (:stem . "microplus") (:form . "microplus") (:end . 67)\n  (:start . 58) (:id . 50))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 73) (:start . 68)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "female") (:form . "female") (:end . 80)\n  (:start . 74) (:id . 52))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 86) (:start . 81)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 91) (:start . 87)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 97) (:start . 92)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s9.166) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502930@unknown@formal@none@1@S@(a) Egg from untreated females approximately 15 day after laying, (b) Eggs from females treated with TC6372 (D. melanogaster Ubiquitin 63E-like transcript) dsRNA approximately 15 days after laying.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "LS") (:stem . "a") (:form . "a") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Egg") (:form . "Egg") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 12) (:start . 8)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "untreated") (:form . "untreated") (:end . 22)\n  (:start . 13) (:id . 47))\n ((:tag . "NNS") (:stem . "female") (:form . "females") (:end . 30)\n  (:start . 23) (:id . 48))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 44) (:start . 31) (:id . 49))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "day") (:form . "day") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 57) (:start . 52)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "lay") (:form . "laying") (:end . 64) (:start . 58)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 68) (:start . 67)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Egg") (:form . "Eggs") (:end . 74) (:start . 70)\n  (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 79) (:start . 75)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "female") (:form . "females") (:end . 87)\n  (:start . 80) (:id . 60))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 95)\n  (:start . 88) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 100) (:start . 96)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "TC6372") (:form . "TC6372") (:end . 107)\n  (:start . 101) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 111) (:start . 109)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 124) (:start . 112) (:id . 66))\n ((:tag . "NNP") (:stem . "Ubiquitin") (:form . "Ubiquitin") (:end . 134)\n  (:start . 125) (:id . 67))\n ((:tag . "JJ") (:stem . "63e-like") (:form . "63E-like") (:end . 143)\n  (:start . 135) (:id . 68))\n ((:tag . "NN") (:stem . "transcript") (:form . "transcript") (:end . 154)\n  (:start . 144) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 161)\n  (:start . 156) (:id . 71))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 175) (:start . 162) (:id . 72))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 178) (:start . 176)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 183) (:start . 179)\n  (:id . 74))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 189)\n  (:start . 184) (:id . 75))\n ((:tag . "VBG") (:stem . "lay") (:form . "laying") (:end . 196)\n  (:start . 190) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s9.167) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502931@unknown@formal@none@1@S@(c) Eggs from females treated with dsRNA targeting TC12306 (D. melanogaster ribosomal protein L8-like transcript) approximately 15 days after egg laying.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "c") (:form . "c") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Egg") (:form . "Eggs") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 13) (:start . 9)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "female") (:form . "females") (:end . 21)\n  (:start . 14) (:id . 47))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 29)\n  (:start . 22) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 40) (:start . 35)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 50)\n  (:start . 41) (:id . 51))\n ((:tag . "NNP") (:stem . "TC12306") (:form . "TC12306") (:end . 58)\n  (:start . 51) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 75)\n  (:start . 63) (:id . 55))\n ((:tag . "JJ") (:stem . "ribosomal") (:form . "ribosomal") (:end . 85)\n  (:start . 76) (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 93)\n  (:start . 86) (:id . 57))\n ((:tag . "JJ") (:stem . "l8-like") (:form . "L8-like") (:end . 101)\n  (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "transcript") (:form . "transcript") (:end . 112)\n  (:start . 102) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 127) (:start . 114) (:id . 61))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 135) (:start . 131)\n  (:id . 63))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 141)\n  (:start . 136) (:id . 64))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 145) (:start . 142)\n  (:id . 65))\n ((:tag . "NN") (:stem . "laying") (:form . "laying") (:end . 152)\n  (:start . 146) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s9.168) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5502932@unknown@formal@none@1@S@Effect of tick in vivo dsRNA gene knockdown treatments on female tick survival and subsequent reproduction fecundity by targeting Drosophila homologues described in Table 2@(((:tag . "NN") (:stem . "effect") (:form . "Effect") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "female") (:form . "female") (:end . 64)\n  (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 93)\n  (:start . 83) (:id . 56))\n ((:tag . "NN") (:stem . "reproduction") (:form . "reproduction") (:end . 106)\n  (:start . 94) (:id . 57))\n ((:tag . "NN") (:stem . "fecundity") (:form . "fecundity") (:end . 116)\n  (:start . 107) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 119) (:start . 117)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 129)\n  (:start . 120) (:id . 60))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 140)\n  (:start . 130) (:id . 61))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 151)\n  (:start . 141) (:id . 62))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 161)\n  (:start . 152) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 164) (:start . 162)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 170)\n  (:start . 165) (:id . 65))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 172) (:start . 171)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s9.169) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5502933@unknown@formal@none@1@S@Ubiquitin-63E dsRNA treatment had the most significant effect on adult tick survival (average 10 days, approximately 5 days less than the controls, Table 3).@(((:tag . "NNP") (:stem . "Ubiquitin-63E") (:form . "Ubiquitin-63E")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 19) (:start . 14)\n  (:id . 43))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 29)\n  (:start . 20) (:id . 44))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 33) (:start . 30)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 54)\n  (:start . 43) (:id . 48))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 61)\n  (:start . 55) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 70) (:start . 65)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 75) (:start . 71)\n  (:id . 52))\n ((:tag . "NN") (:stem . "survival") (:form . "survival") (:end . 84)\n  (:start . 76) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 54))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 101) (:start . 97)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 116) (:start . 103) (:id . 59))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 118) (:start . 117)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 128) (:start . 124)\n  (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 133) (:start . 129)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 146)\n  (:start . 138) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 153)\n  (:start . 148) (:id . 67))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 155) (:start . 154)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s9.170) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502934@unknown@formal@none@1@S@Eggs laid by R. microplus females injected with dsRNA targeting genes associated with ribosome/protein synthesis (TC5762/string of perls; TC12306/Rpl-8; TC9037/Ribosomal protein L11; TC9852/Proteasome 26S subunit; TC12393/Ribosomal protein S13) and proteasome/ubiquitin (TC6372/Ubiquitin-63E) demonstrated the most lethal effect on tick reproduction with deformed egg morphology and no larvae hatching (Table 3).@(((:tag . "NNP") (:stem . "Egg") (:form . "Eggs") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "lay") (:form . "laid") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 25)\n  (:start . 16) (:id . 46))\n ((:tag . "NNS") (:stem . "female") (:form . 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"(") (:form . "(") (:end . 403) (:start . 402)\n  (:id . 97))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 408)\n  (:start . 403) (:id . 98))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 410) (:start . 409)\n  (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 411) (:start . 410)\n  (:id . 100))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 412) (:start . 411)\n  (:id . 101)))@@@1@60@((:identifiers (:sid . :s9.171) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502935@unknown@formal@none@1@S@RNAi targeting of TC12306 (Rpl-8) and TC6372 (Ubiquitin-63E) generated the greatest reductions in average egg output, with Ubiquitin-63E (TC6372) treated ticks again being significantly affected compared with the controls (Table 3).@(((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "TC12306") (:form . "TC12306") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "rpl-8") (:form . "Rpl-8") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "TC6372") (:form . "TC6372") (:end . 44)\n  (:start . 38) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Ubiquitin-63E") (:form . "Ubiquitin-63E")\n  (:end . 59) (:start . 46) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 70)\n  (:start . 61) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "JJS") (:stem . "great") (:form . "greatest") (:end . 83)\n  (:start . 75) (:id . 56))\n ((:tag . "NNS") (:stem . "reduction") (:form . "reductions") (:end . 94)\n  (:start . 84) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 105)\n  (:start . 98) (:id . 59))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 116)\n  (:start . 110) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 122) (:start . 118)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Ubiquitin-63E") (:form . "Ubiquitin-63E")\n  (:end . 136) (:start . 123) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . "NN") (:stem . "tc6372") (:form . "TC6372") (:end . 144)\n  (:start . 138) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "treat") (:form . "treated") (:end . 153)\n  (:start . 146) (:id . 68))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 159)\n  (:start . 154) (:id . 69))\n ((:tag . "RB") (:stem . "again") (:form . "again") (:end . 165)\n  (:start . 160) (:id . 70))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 171) (:start . 166)\n  (:id . 71))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 185) (:start . 172) (:id . 72))\n ((:tag . "VBN") (:stem . "affect") (:form . "affected") (:end . 194)\n  (:start . 186) (:id . 73))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 203)\n  (:start . 195) (:id . 74))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 208) (:start . 204)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 212) (:start . 209)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 221)\n  (:start . 213) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 223) (:start . 222)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 228)\n  (:start . 223) (:id . 79))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 230) (:start . 229)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 231) (:start . 230)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s9.172) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502936@unknown@formal@none@1@S@Figures 7b and 7c show examples of phenotypic effects on embryo development due to TC6372 (dehydrated in appearance, embryo not visible) and TC12306 (embryo smaller in size) knockdown respectively.@(((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "7b") (:form . "7b") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "7c") (:form . "7c") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "phenotypic") (:form . "phenotypic") (:end . 45)\n  (:start . 35) (:id . 49))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 75)\n  (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "due") (:form . "due") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "tc6372") (:form . "TC6372") (:end . 89)\n  (:start . 83) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "dehydrate") (:form . "dehydrated") (:end . 101)\n  (:start . 91) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 59))\n ((:tag . "NN") (:stem . "appearance") (:form . "appearance") (:end . 115)\n  (:start . 105) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 123)\n  (:start . 117) (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "visible") (:form . "visible") (:end . 135)\n  (:start . 128) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "TC12306") (:form . "TC12306") (:end . 148)\n  (:start . 141) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 68))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 156)\n  (:start . 150) (:id . 69))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 164)\n  (:start . 157) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 167) (:start . 165)\n  (:id . 71))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 172) (:start . 168)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 173) (:start . 172)\n  (:id . 73))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 183)\n  (:start . 174) (:id . 74))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 196)\n  (:start . 184) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s9.173) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502937@unknown@formal@none@1@S@Down-regulation of the TC13930/Tat-binding protein-1 also associated with proteasome/ubiquitin function, impaired embryo development leading to a poor larval hatching rate (0.4%).@(((:tag . "NN") (:stem . "down-regulation") (:form . "Down-regulation")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "tc13930/tat-binding")\n  (:form . "TC13930/Tat-binding") (:end . 42) (:start . 23) (:id . 45))\n ((:tag . "NN") (:stem . "protein-1") (:form . "protein-1") (:end . 52)\n  (:start . 43) (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 57) (:start . 53)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "associate") (:form . "associated") (:end . 68)\n  (:start . 58) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 73) (:start . 69)\n  (:id . 49))\n ((:tag . "NN") (:stem . "proteasome/ubiquitin")\n  (:form . "proteasome/ubiquitin") (:end . 94) (:start . 74) (:id . 50))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 103)\n  (:start . 95) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "impaired") (:form . "impaired") (:end . 113)\n  (:start . 105) (:id . 53))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 120)\n  (:start . 114) (:id . 54))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 132)\n  (:start . 121) (:id . 55))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 140)\n  (:start . 133) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 145) (:start . 144)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "poor") (:form . "poor") (:end . 150) (:start . 146)\n  (:id . 59))\n ((:tag . "NN") (:stem . "larval") (:form . "larval") (:end . 157)\n  (:start . 151) (:id . 60))\n ((:tag . "VBG") (:stem . "hatch") (:form . "hatching") (:end . 166)\n  (:start . 158) (:id . 61))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 171) (:start . 167)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 173) (:start . 172)\n  (:id . 63))\n ((:tag . "CD") (:stem . "0.4") (:form . "0.4") (:end . 176) (:start . 173)\n  (:id . 64))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 177) (:start . 176)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 178) (:start . 177)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s9.174) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502938@unknown@formal@none@1@S@In contrast, another gene associated with proteasome/ubiquitin (TC10417/rpt 1) had no effect on egg development and hatching rates compared with controls, although this target demonstrated a decrease in cell viability in cell culture experiments above.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 36)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "proteasome/ubiquitin")\n  (:form . "proteasome/ubiquitin") (:end . 62) (:start . 42) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "TC10417/rpt") (:form . "TC10417/rpt") (:end . 75)\n  (:start . 64) (:id . 51))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 77) (:start . 76)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 92)\n  (:start . 86) (:id . 56))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 111)\n  (:start . 100) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 60))\n ((:tag . "NN") (:stem . "hatching") (:form . "hatching") (:end . 124)\n  (:start . 116) (:id . 61))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 130)\n  (:start . 125) (:id . 62))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 139)\n  (:start . 131) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 144) (:start . 140)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 153)\n  (:start . 145) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 66))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 163)\n  (:start . 155) (:id . 67))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 168) (:start . 164)\n  (:id . 68))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 175)\n  (:start . 169) (:id . 69))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 188)\n  (:start . 176) (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 190) (:start . 189)\n  (:id . 71))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 199)\n  (:start . 191) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 202) (:start . 200)\n  (:id . 73))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 207) (:start . 203)\n  (:id . 74))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 217)\n  (:start . 208) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 220) (:start . 218)\n  (:id . 76))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 225) (:start . 221)\n  (:id . 77))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 233)\n  (:start . 226) (:id . 78))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 245)\n  (:start . 234) (:id . 79))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 251)\n  (:start . 246) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s9.175) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502939@unknown@formal@none@1@S@The 2 ESTs associated with DNA binding (TC6116 and TC12182/histone H3.3A) both induced slower embryo development and reductions in egg hatching at 3.1% and 35.2% respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "est") (:form . "ESTs") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 21)\n  (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "TC6116") (:form . "TC6116") (:end . 46)\n  (:start . 40) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "TC12182/histone") (:form . "TC12182/histone")\n  (:end . 66) (:start . 51) (:id . 52))\n ((:tag . "NNP") (:stem . "H3.3A") (:form . "H3.3A") (:end . 72) (:start . 67)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n  (:id . 54))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 78) (:start . 74)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "induce") (:form . "induced") (:end . 86)\n  (:start . 79) (:id . 56))\n ((:tag . "JJR") (:stem . "slow") (:form . "slower") (:end . 93) (:start . 87)\n  (:id . 57))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 100)\n  (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 112)\n  (:start . 101) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "reduction") (:form . "reductions") (:end . 127)\n  (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "hatch") (:form . "hatching") (:end . 143)\n  (:start . 135) (:id . 64))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 146) (:start . 144)\n  (:id . 65))\n ((:tag . "CD") (:stem . "3.1") (:form . "3.1") (:end . 150) (:start . 147)\n  (:id . 66))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 151) (:start . 150)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 155) (:start . 152)\n  (:id . 68))\n ((:tag . "CD") (:stem . "35.2") (:form . "35.2") (:end . 160) (:start . 156)\n  (:id . 69))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 161) (:start . 160)\n  (:id . 70))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 174)\n  (:start . 162) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.176) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502940@unknown@formal@none@1@S@A single (sixth) tick was harvested to confirm the relative reduction of transcript levels (% knockdown determined by qRT-PCR) for both the adult ticks and eggs (where applicable) for each Drosophila homologue treatment.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "sixth") (:form . "sixth") (:end . 15) (:start . 10)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 21) (:start . 17)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "harvest") (:form . "harvested") (:end . 35)\n  (:start . 26) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . "VB") (:stem . "confirm") (:form . "confirm") (:end . 46)\n  (:start . 39) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 59)\n  (:start . 51) (:id . 53))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 69)\n  (:start . 60) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "transcript") (:form . "transcript") (:end . 83)\n  (:start . 73) (:id . 56))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 90)\n  (:start . 84) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 93) (:start . 92)\n  (:id . 59))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 103)\n  (:start . 94) (:id . 60))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 114)\n  (:start . 104) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 117) (:start . 115)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 125)\n  (:start . 118) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 130) (:start . 127)\n  (:id . 65))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 135) (:start . 131)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 145)\n  (:start . 140) (:id . 68))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 151)\n  (:start . 146) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 155) (:start . 152)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "egg") (:form . "eggs") (:end . 160) (:start . 156)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 72))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 167)\n  (:start . 162) (:id . 73))\n ((:tag . "NN") (:stem . "applicable") (:form . "applicable") (:end . 178)\n  (:start . 168) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 183) (:start . 180)\n  (:id . 76))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 188) (:start . 184)\n  (:id . 77))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 199)\n  (:start . 189) (:id . 78))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 209)\n  (:start . 200) (:id . 79))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 219)\n  (:start . 210) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s9.177) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502941@unknown@formal@none@1@S@All treatments except TC9037 demonstrated high knockdown of transcripts in adult tick viscera (≥ 94%), with knockdown also confirmed in eggs tested (≥ 76%).@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "except") (:form . "except") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "tc9037") (:form . "TC9037") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 41)\n  (:start . 29) (:id . 46))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 46) (:start . 42)\n  (:id . 47))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 56)\n  (:start . 47) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "transcript") (:form . "transcripts") (:end . 71)\n  (:start . 60) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 80) (:start . 75)\n  (:id . 52))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 85) (:start . 81)\n  (:id . 53))\n ((:tag . "NN") (:stem . "viscera") (:form . "viscera") (:end . 93)\n  (:start . 86) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 55))\n ((:tag . "NN") (:stem . "≥") (:form . "≥") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "CD") (:stem . "94") (:form . "94") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 107) (:start . 103)\n  (:id . 61))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 117)\n  (:start . 108) (:id . 62))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 122) (:start . 118)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 132)\n  (:start . 123) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "egg") (:form . "eggs") (:end . 140) (:start . 136)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 147)\n  (:start . 141) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 149) (:start . 148)\n  (:id . 68))\n ((:tag . "NN") (:stem . "≥") (:form . "≥") (:end . 150) (:start . 149)\n  (:id . 69))\n ((:tag . "CD") (:stem . "76") (:form . "76") (:end . 153) (:start . 151)\n  (:id . 70))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 154) (:start . 153)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s9.178) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502942@unknown@formal@none@1@S@As the viscera from only one tick per treatment was harvested for RT-qPCR, it is feasible that the TC9037 treatment on this single tick was not delivered successfully, however, none of the 5 ticks injected produced viable eggs indicating a knockdown phenotype for the TC9037 treatment overall.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "viscera") (:form . "viscera") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "IN") (:stem . 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5502943@unknown@formal@none@1@S@Thus 9 of the 10 Drosophila tick homologues demonstrated either a lethal effect on reproduction or a reduction in larval hatching rates when using dsRNA targeted knockdown in vivo.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 27)\n  (:start . 17) (:id . 47))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 43)\n  (:start . 33) (:id . 49))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 56)\n  (:start . 44) (:id . 50))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 63)\n  (:start . 57) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "lethal") (:form . "lethal") (:end . 72)\n  (:start . 66) (:id . 53))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 79)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "reproduction") (:form . "reproduction") (:end . 95)\n  (:start . 83) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 98) (:start . 96)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 110)\n  (:start . 101) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 120)\n  (:start . 114) (:id . 61))\n ((:tag . "NN") (:stem . "hatching") (:form . "hatching") (:end . 129)\n  (:start . 121) (:id . 62))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 135)\n  (:start . 130) (:id . 63))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 140) (:start . 136)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 146) (:start . 141)\n  (:id . 65))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 152)\n  (:start . 147) (:id . 66))\n ((:tag . "VBD") (:stem . "target") (:form . "targeted") (:end . 161)\n  (:start . 153) (:id . 67))\n ((:tag . "JJ") (:stem . "knockdown") (:form . "knockdown") (:end . 171)\n  (:start . 162) (:id . 68))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 174) (:start . 172)\n  (:id . 69))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 179) (:start . 175)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x9.180.1) (:span 57 63 96 98)))\n (:hscopes ((:id . :x9.180.1) (:span 57 135)))\n (:identifiers (:sid . :s9.180) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502944@unknown@formal@none@1@S@The significant effects associated with the Ubiquitin-63E homologue TC6372 treatments correlates with the highest z scores for the same target in Drosophila cell viability out of the sub-set of targets used here (Table 2, [43]).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 34)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Ubiquitin-63E") (:form . "Ubiquitin-63E")\n  (:end . 57) (:start . 44) (:id . 48))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 67)\n  (:start . 58) (:id . 49))\n ((:tag . "NN") (:stem . "tc6372") (:form . "TC6372") (:end . 74)\n  (:start . 68) (:id . 50))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 85)\n  (:start . 75) (:id . 51))\n ((:tag . "VBZ") (:stem . "correlate") (:form . "correlates") (:end . 96)\n  (:start . 86) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 101) (:start . 97)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 54))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 113)\n  (:start . 106) (:id . 55))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 115) (:start . 114)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 122)\n  (:start . 116) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 126) (:start . 123)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 135) (:start . 131)\n  (:id . 60))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 142)\n  (:start . 136) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 145) (:start . 143)\n  (:id . 62))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 156)\n  (:start . 146) (:id . 63))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 161) (:start . 157)\n  (:id . 64))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 171)\n  (:start . 162) (:id . 65))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 175) (:start . 172)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 178) (:start . 176)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 182) (:start . 179)\n  (:id . 68))\n ((:tag . "NN") (:stem . "sub-set") (:form . "sub-set") (:end . 190)\n  (:start . 183) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 193) (:start . 191)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 201)\n  (:start . 194) (:id . 71))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 206) (:start . 202)\n  (:id . 72))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 211) (:start . 207)\n  (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 213) (:start . 212)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 218)\n  (:start . 213) (:id . 75))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 220) (:start . 219)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 221) (:start . 220)\n  (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 223) (:start . 222)\n  (:id . 78))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 225) (:start . 223)\n  (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 226) (:start . 225)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 227) (:start . 226)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s9.181) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502945@unknown@formal@none@1@S@Data from the FlyBase website http://flybase.org/ identified that in vivo studies involving dsRNA injection into Drosophila embryos was lethal for both Rpt1 and RpS13 (correlating to TC10417 and TC12393 above).@(((:tag . "NNP") (:stem . "Datum") (:form . "Data") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "FlyBase") (:form . "FlyBase") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "website") (:form . "website") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "http://flybase.org/")\n  (:form . "http://flybase.org/") (:end . 49) (:start . 30) (:id . 47))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 60)\n  (:start . 50) (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 65) (:start . 61)\n  (:id . 49))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 50))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 73) (:start . 69)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 81)\n  (:start . 74) (:id . 52))\n ((:tag . "VBG") (:stem . "involve") (:form . "involving") (:end . 91)\n  (:start . 82) (:id . 53))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 97) (:start . 92)\n  (:id . 54))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 107)\n  (:start . 98) (:id . 55))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 112) (:start . 108)\n  (:id . 56))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 123)\n  (:start . 113) (:id . 57))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 131)\n  (:start . 124) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 135) (:start . 132)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "lethal") (:form . "lethal") (:end . 142)\n  (:start . 136) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 146) (:start . 143)\n  (:id . 61))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 151) (:start . 147)\n  (:id . 62))\n ((:tag . "NN") (:stem . "rpt1") (:form . "Rpt1") (:end . 156) (:start . 152)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 64))\n ((:tag . "NN") (:stem . "rps13") (:form . "RpS13") (:end . 166)\n  (:start . 161) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 168) (:start . 167)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "correlate") (:form . "correlating") (:end . 179)\n  (:start . 168) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 182) (:start . 180)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "TC10417") (:form . "TC10417") (:end . 190)\n  (:start . 183) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "TC12393") (:form . "TC12393") (:end . 202)\n  (:start . 195) (:id . 71))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 208)\n  (:start . 203) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 209) (:start . 208)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s9.182) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502946@unknown@formal@none@1@S@However, Rpt1 (TC10417) was the only treatment which did not have an effect in vivo for ticks.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "Rpt1") (:form . "Rpt1") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "TC10417") (:form . "TC10417") (:end . 22)\n  (:start . 15) (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 27) (:start . 24)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 36) (:start . 32)\n  (:id . 50))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 46)\n  (:start . 37) (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 52) (:start . 47)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 65) (:start . 61)\n  (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 68) (:start . 66)\n  (:id . 56))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 75)\n  (:start . 69) (:id . 57))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 58))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 83) (:start . 79)\n  (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 87) (:start . 84)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 93) (:start . 88)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.183) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502947@unknown@formal@none@1@S@Fly in vivo knockdown studies associated with the 8 of the remaining targets were not found.@(((:tag . "RB") (:stem . "fly") (:form . "Fly") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "knockdown") (:form . "knockdown") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 68)\n  (:start . 59) (:id . 53))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 76)\n  (:start . 69) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 91) (:start . 86)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s9.184) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502948@unknown@formal@none@1@S@Discussion@(((:tag . "NN") (:stem . "discussion") (:form . "Discussion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s9.185) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5502949@unknown@formal@none@1@S@The lack of tick genome sequence resources has limited the ability to mine for RNAi protein homologues however research to date has suggested that ticks utilize a dsRNA-mediated RNAi similar to that described in insects such as flies and mosquitoes [47,48].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 42)\n  (:start . 33) (:id . 48))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 66)\n  (:start . 59) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "VB") (:stem . "mine") (:form . "mine") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 91)\n  (:start . 84) (:id . 57))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 102)\n  (:start . 92) (:id . 58))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 110)\n  (:start . 103) (:id . 59))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 119)\n  (:start . 111) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 127) (:start . 123)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 131) (:start . 128)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "suggest") (:form . "suggested") (:end . 141)\n  (:start . 132) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 146) (:start . 142)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 152)\n  (:start . 147) (:id . 66))\n ((:tag . "VBP") (:stem . "utilize") (:form . "utilize") (:end . 160)\n  (:start . 153) (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 162) (:start . 161)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "dsrna-mediated") (:form . "dsRNA-mediated")\n  (:end . 177) (:start . 163) (:id . 69))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 182) (:start . 178)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 190)\n  (:start . 183) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 193) (:start . 191)\n  (:id . 72))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 198) (:start . 194)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 208)\n  (:start . 199) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 211) (:start . 209)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "insect") (:form . "insects") (:end . 219)\n  (:start . 212) (:id . 76))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 224) (:start . 220)\n  (:id . 77))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 227) (:start . 225)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 233) (:start . 228)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 237) (:start . 234)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "mosquito") (:form . "mosquitoes") (:end . 248)\n  (:start . 238) (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 250) (:start . 249)\n  (:id . 82))\n ((:tag . "CD") (:stem . "47,48") (:form . "47,48") (:end . 255)\n  (:start . 250) (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 256) (:start . 255)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x9.186.1) (:span 132 141)))\n (:hscopes ((:id . :x9.186.1) (:span 132 248)))\n (:identifiers (:sid . :s9.186) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502950@unknown@formal@none@1@S@De la Fuente and colleagues [37] postulated a model for tick dsRNA-mediated RNAi following the identification of a putative Ago-2 protein in the R. microplus EST database.@(((:tag . "NNP") (:stem . "De") (:form . "De") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "la") (:form . "la") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Fuente") (:form . "Fuente") (:end . 12)\n  (:start . 6) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "colleague") (:form . "colleagues") (:end . 27)\n  (:start . 17) (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 32) (:start . 31)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "postulate") (:form . "postulated") (:end . 43)\n  (:start . 33) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 51) (:start . 46)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 55) (:start . 52)\n  (:id . 53))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 60) (:start . 56)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "dsrna-mediated") (:form . "dsRNA-mediated")\n  (:end . 75) (:start . 61) (:id . 55))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 90)\n  (:start . 81) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 109) (:start . 95) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 123)\n  (:start . 115) (:id . 62))\n ((:tag . "NN") (:stem . "ago-2") (:form . "Ago-2") (:end . 129)\n  (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 137)\n  (:start . 130) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 147) (:start . 145)\n  (:id . 67))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 157)\n  (:start . 148) (:id . 68))\n ((:tag . "NNP") (:stem . "EST") (:form . "EST") (:end . 161) (:start . 158)\n  (:id . 69))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 170)\n  (:start . 162) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x9.187.1) (:span 33 43)))\n (:hscopes ((:id . :x9.187.1) (:span 33 170)))\n (:identifiers (:sid . :s9.187) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502951@unknown@formal@none@1@S@Our results support the diagram represented in de la Fuente et al [37] demonstrating evidence for putative tick Dicer, RISC associated proteins and dsRNA uptake homologues, however we identified a R. microplus EGO-1 homologue known to be implicated in RNA-directed RNA polymerase activity previously not identified in animals other than C. elegans.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "diagram") (:form . "diagram") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 43)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . 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"for") (:form . "for") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 106)\n  (:start . 98) (:id . 60))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 111) (:start . 107)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 117)\n  (:start . 112) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 123) (:start . 119)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 134)\n  (:start . 124) (:id . 65))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 143)\n  (:start . 135) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n  (:id . 67))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 153)\n  (:start . 148) (:id . 68))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 160)\n  (:start . 154) (:id . 69))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 171)\n  (:start . 161) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 71))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 180)\n  (:start . 173) (:id . 72))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 183) (:start . 181)\n  (:id . 73))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 194)\n  (:start . 184) (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 196) (:start . 195)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 199) (:start . 197)\n  (:id . 76))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 209)\n  (:start . 200) (:id . 77))\n ((:tag . "NN") (:stem . "ego-1") (:form . "EGO-1") (:end . 215)\n  (:start . 210) (:id . 78))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 225)\n  (:start . 216) (:id . 79))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 231)\n  (:start . 226) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 234) (:start . 232)\n  (:id . 81))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 237) (:start . 235)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 248)\n  (:start . 238) (:id . 83))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 251) (:start . 249)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "rna-directed") (:form . "RNA-directed") (:end . 264)\n  (:start . 252) (:id . 85))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 268) (:start . 265)\n  (:id . 86))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 279)\n  (:start . 269) (:id . 87))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 288)\n  (:start . 280) (:id . 88))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 299)\n  (:start . 289) (:id . 89))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 303) (:start . 300)\n  (:id . 90))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 314)\n  (:start . 304) (:id . 91))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 317) (:start . 315)\n  (:id . 92))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 325)\n  (:start . 318) (:id . 93))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 331)\n  (:start . 326) (:id . 94))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 336) (:start . 332)\n  (:id . 95))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 339) (:start . 337)\n  (:id . 96))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 347)\n  (:start . 340) (:id . 97))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 348) (:start . 347)\n  (:id . 98)))@@@1@57@((:hcues ((:id . :x9.188.1) (:span 238 248)) ((:id . :x9.188.2) (:span 12 19)))\n (:hscopes ((:id . :x9.188.1) (:span 195 347))\n  ((:id . :x9.188.2) (:span 12 171)))\n (:identifiers (:sid . :s9.188) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502952@unknown@formal@none@1@S@We also identified a Cat-Ago-2 at higher similarity than the tick homologue identified by de la Fuente et al [37] which exhibited higher similarity to the Argonaute-1 protein of D. melanogaster in this study.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cat-ago-2") (:form . "Cat-Ago-2") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 40) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 51)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 75)\n  (:start . 66) (:id . 53))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 86)\n  (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "FW") (:stem . "de") (:form . "de") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "FW") (:stem . "la") (:form . "la") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Fuente") (:form . "Fuente") (:end . 102)\n  (:start . 96) (:id . 58))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 105) (:start . 103)\n  (:id . 59))\n ((:tag . "FW") (:stem . "al") (:form . "al") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 119)\n  (:start . 114) (:id . 64))\n ((:tag . "VBD") (:stem . "exhibit") (:form . "exhibited") (:end . 129)\n  (:start . 120) (:id . 65))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 136)\n  (:start . 130) (:id . 66))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 147)\n  (:start . 137) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 150) (:start . 148)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 69))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 166)\n  (:start . 155) (:id . 70))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 174)\n  (:start . 167) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 180) (:start . 178)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 193) (:start . 181) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 196) (:start . 194)\n  (:id . 75))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 201) (:start . 197)\n  (:id . 76))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 207)\n  (:start . 202) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s9.189) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502953@unknown@formal@none@1@S@This is the first comprehensive analysis of RNAi sequence domains for a tick species and for the Chelicerate Arthropods.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "comprehensive") (:form . "comprehensive")\n  (:end . 31) (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 57)\n  (:start . 49) (:id . 50))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 65)\n  (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 92) (:start . 89)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Chelicerate") (:form . "Chelicerate") (:end . 108)\n  (:start . 97) (:id . 59))\n ((:tag . "NNPS") (:stem . "Arthropod") (:form . "Arthropods") (:end . 119)\n  (:start . 109) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s9.190) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502954@unknown@formal@none@1@S@Compared to the vast insect genome resources (flies, mosquitoes, beetle, silkworm, wasp – to name a few), there is currently only one Chelicerate genome available with the I. scapularis tick genome project nearing completion.@(((:tag . "VBN") (:stem . "compare") (:form . "Compared") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "vast") (:form . "vast") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 51) (:start . 46)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "mosquito") (:form . "mosquitoes") (:end . 63)\n  (:start . 53) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "beetle") (:form . "beetle") (:end . 71)\n  (:start . 65) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "silkworm") (:form . "silkworm") (:end . 81)\n  (:start . 73) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "wasp") (:form . "wasp") (:end . 87) (:start . 83)\n  (:id . 58))\n ((:tag . "NN") (:stem . "–") (:form . "–") (:end . 89) (:start . 88)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n  (:id . 60))\n ((:tag . "VB") (:stem . "name") (:form . "name") (:end . 97) (:start . 93)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 103) (:start . 100)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 65))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 111)\n  (:start . 106) (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 114) (:start . 112)\n  (:id . 67))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 124)\n  (:start . 115) (:id . 68))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 129) (:start . 125)\n  (:id . 69))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 133) (:start . 130)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Chelicerate") (:form . "Chelicerate") (:end . 145)\n  (:start . 134) (:id . 71))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 152)\n  (:start . 146) (:id . 72))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 162)\n  (:start . 153) (:id . 73))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 167) (:start . 163)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 171) (:start . 168)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 174) (:start . 172)\n  (:id . 76))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 185)\n  (:start . 175) (:id . 77))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 190) (:start . 186)\n  (:id . 78))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 197)\n  (:start . 191) (:id . 79))\n ((:tag . "NN") (:stem . "project") (:form . "project") (:end . 205)\n  (:start . 198) (:id . 80))\n ((:tag . "VBG") (:stem . "near") (:form . "nearing") (:end . 213)\n  (:start . 206) (:id . 81))\n ((:tag . "NN") (:stem . "completion") (:form . "completion") (:end . 224)\n  (:start . 214) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s9.191) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502955@unknown@formal@none@1@S@To provide an evolutionary perspective to demonstrate relationships within the Ecdysozoan infraphylum it is important to note that their common ancestors may have existed over 1 billion years ago [49].@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 26)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "perspective") (:form . "perspective") (:end . 38)\n  (:start . 27) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "VB") (:stem . "demonstrate") (:form . "demonstrate") (:end . 53)\n  (:start . 42) (:id . 48))\n ((:tag . "NNS") (:stem . "relationship") (:form . "relationships")\n  (:end . 67) (:start . 54) (:id . 49))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 74)\n  (:start . 68) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Ecdysozoan") (:form . "Ecdysozoan") (:end . 89)\n  (:start . 79) (:id . 52))\n ((:tag . "NN") (:stem . "infraphylum") (:form . "infraphylum") (:end . 101)\n  (:start . 90) (:id . 53))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 104) (:start . 102)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 107) (:start . 105)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 117)\n  (:start . 108) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 120) (:start . 118)\n  (:id . 57))\n ((:tag . "VB") (:stem . "note") (:form . "note") (:end . 125) (:start . 121)\n  (:id . 58))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 130) (:start . 126)\n  (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 136)\n  (:start . 131) (:id . 60))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 143)\n  (:start . 137) (:id . 61))\n ((:tag . "NNS") (:stem . "ancestor") (:form . "ancestors") (:end . 153)\n  (:start . 144) (:id . 62))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 157) (:start . 154)\n  (:id . 63))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 162) (:start . 158)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "exist") (:form . "existed") (:end . 170)\n  (:start . 163) (:id . 65))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 175) (:start . 171)\n  (:id . 66))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 177) (:start . 176)\n  (:id . 67))\n ((:tag . "CD") (:stem . "billion") (:form . "billion") (:end . 185)\n  (:start . 178) (:id . 68))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 191)\n  (:start . 186) (:id . 69))\n ((:tag . "RB") (:stem . "ago") (:form . "ago") (:end . 195) (:start . 192)\n  (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 197) (:start . 196)\n  (:id . 71))\n ((:tag . "CD") (:stem . "49") (:form . "49") (:end . 199) (:start . 197)\n  (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 200) (:start . 199)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x9.192.1) (:span 154 157)))\n (:hscopes ((:id . :x9.192.1) (:span 154 195)))\n (:identifiers (:sid . :s9.192) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502956@unknown@formal@none@1@S@Comparative genomics between these phyla is in its infancy and pathways such as RNAi interference and gene regulation to date have been based on the fruit fly D. melanogaster as the model organism.@(((:tag . "JJ") (:stem . "comparative") (:form . "Comparative") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "genomic") (:form . "genomics") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 28)\n  (:start . 21) (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 34) (:start . 29)\n  (:id . 45))\n ((:tag . "NN") (:stem . "phyla") (:form . "phyla") (:end . 40) (:start . 35)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 48))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "infancy") (:form . "infancy") (:end . 58)\n  (:start . 51) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 71)\n  (:start . 63) (:id . 52))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "interference") (:form . "interference") (:end . 97)\n  (:start . 85) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 57))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 106) (:start . 102)\n  (:id . 58))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 117)\n  (:start . 107) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 120) (:start . 118)\n  (:id . 60))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 125) (:start . 121)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 130) (:start . 126)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 135) (:start . 131)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 141)\n  (:start . 136) (:id . 64))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 66))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 154)\n  (:start . 149) (:id . 67))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 158) (:start . 155)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 161) (:start . 159)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 174) (:start . 162) (:id . 70))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 177) (:start . 175)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 181) (:start . 178)\n  (:id . 72))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 187)\n  (:start . 182) (:id . 73))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 196)\n  (:start . 188) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s9.193) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502957@unknown@formal@none@1@S@As differences between RNAi pathway mechanisms between C. elegans and D. melanogaster are evident, it is thus feasible that Chelicerates could also vary from insects albeit their evolutionary distance is less (~500 million years) [2].@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 46)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 54)\n  (:start . 47) (:id . 48))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 65)\n  (:start . 58) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 85)\n  (:start . 73) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 89) (:start . 86)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "evident") (:form . "evident") (:end . 97)\n  (:start . 90) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 101) (:start . 99)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 109) (:start . 105)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "feasible") (:form . "feasible") (:end . 118)\n  (:start . 110) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Chelicerates") (:form . "Chelicerates")\n  (:end . 136) (:start . 124) (:id . 62))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 142)\n  (:start . 137) (:id . 63))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 147) (:start . 143)\n  (:id . 64))\n ((:tag . "VB") (:stem . "vary") (:form . "vary") (:end . 152) (:start . 148)\n  (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 157) (:start . 153)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "insect") (:form . "insects") (:end . 165)\n  (:start . 158) (:id . 67))\n ((:tag . "IN") (:stem . "albeit") (:form . "albeit") (:end . 172)\n  (:start . 166) (:id . 68))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 178)\n  (:start . 173) (:id . 69))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 191)\n  (:start . 179) (:id . 70))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 200)\n  (:start . 192) (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 203) (:start . 201)\n  (:id . 72))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 208) (:start . 204)\n  (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 210) (:start . 209)\n  (:id . 74))\n ((:tag . "CD") (:stem . "~500") (:form . "~500") (:end . 214) (:start . 210)\n  (:id . 75))\n ((:tag . "CD") (:stem . "million") (:form . "million") (:end . 222)\n  (:start . 215) (:id . 76))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 228)\n  (:start . 223) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 229) (:start . 228)\n  (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 231) (:start . 230)\n  (:id . 79))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 232) (:start . 231)\n  (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 233) (:start . 232)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x9.194.1) (:span 137 142))\n  ((:id . :x9.194.2) (:span 110 118)))\n (:hscopes ((:id . :x9.194.1) (:span 137 229))\n  ((:id . :x9.194.2) (:span 110 229)))\n (:identifiers (:sid . :s9.194) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502958@unknown@formal@none@1@S@Indeed, definitive hits for the domains and proteins here were not exclusive to the Arthropoda, with the putative tick RNAi proteins matching homologues in diverse species such as insects (beetle, silkworm, wasp), nematodes, and mammals (data not shown).@(((:tag . "RB") (:stem . "indeed") (:form . "Indeed") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "JJ") (:stem . "definitive") (:form . "definitive") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . 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"NNS") (:stem . "nematode") (:form . "nematodes") (:end . 223)\n  (:start . 214) (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 224) (:start . 223)\n  (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 228) (:start . 225)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "mammal") (:form . "mammals") (:end . 236)\n  (:start . 229) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 238) (:start . 237)\n  (:id . 85))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 242)\n  (:start . 238) (:id . 86))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 246) (:start . 243)\n  (:id . 87))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 252)\n  (:start . 247) (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 253) (:start . 252)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 254) (:start . 253)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s9.195) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502959@unknown@formal@none@1@S@While only a single Dicer protein is present in mammals and in C. elegans, in D. melanogaster siRNAs and miRNAs are produced by distinct Dicer enzymes [15].@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "mammal") (:form . "mammals") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 73)\n  (:start . 66) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 80) (:start . 78)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 93)\n  (:start . 81) (:id . 59))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 100)\n  (:start . 94) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "mirna") (:form . "miRNAs") (:end . 111)\n  (:start . 105) (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 115) (:start . 112)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 124)\n  (:start . 116) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 127) (:start . 125)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 136)\n  (:start . 128) (:id . 66))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 142)\n  (:start . 137) (:id . 67))\n ((:tag . "NNS") (:stem . "enzyme") (:form . "enzymes") (:end . 150)\n  (:start . 143) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 152) (:start . 151)\n  (:id . 69))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 154) (:start . 152)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 155) (:start . 154)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.196) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502960@unknown@formal@none@1@S@In this study we identified one putative tick Dicer in the I. scapularis genome reads however evidence for more than one Dicer cannot at this stage be confirmed.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 27)\n  (:start . 17) (:id . 46))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 51) (:start . 46)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 72)\n  (:start . 62) (:id . 54))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 79)\n  (:start . 73) (:id . 55))\n ((:tag . "VBZ") (:stem . "read") (:form . "reads") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 93)\n  (:start . 86) (:id . 57))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 102)\n  (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 111) (:start . 107)\n  (:id . 60))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 116) (:start . 112)\n  (:id . 61))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 120) (:start . 117)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 126)\n  (:start . 121) (:id . 63))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 133)\n  (:start . 127) (:id . 64))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 136) (:start . 134)\n  (:id . 65))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 141) (:start . 137)\n  (:id . 66))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 147)\n  (:start . 142) (:id . 67))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 150) (:start . 148)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 160)\n  (:start . 151) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x9.197.1) (:span 127 133 148 160)))\n (:hscopes ((:id . :x9.197.1) (:span 94 160)))\n (:identifiers (:sid . :s9.197) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502961@unknown@formal@none@1@S@This I. scapularis Dicer was found to be most similar to a Dicer-1 from a mammal.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 53)\n  (:start . 46) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "dicer-1") (:form . "Dicer-1") (:end . 66)\n  (:start . 59) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 71) (:start . 67)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "mammal") (:form . "mammal") (:end . 80)\n  (:start . 74) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s9.198) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502962@unknown@formal@none@1@S@A R. microplus Dicer could not be confirmed, however an I. scapularis homologue was also not previously identified using EST data alone.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 14)\n  (:start . 5) (:id . 44))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 52)\n  (:start . 45) (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 69)\n  (:start . 59) (:id . 54))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 79)\n  (:start . 70) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 103)\n  (:start . 93) (:id . 59))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 114)\n  (:start . 104) (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 120) (:start . 115)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "EST") (:form . "EST") (:end . 124) (:start . 121)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 129)\n  (:start . 125) (:id . 63))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 135)\n  (:start . 130) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s9.199) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502963@unknown@formal@none@1@S@Our preliminary evidence points to a 'single' tick Dicer with yet un-confirmed structure, though until complete tick genome resources are available the presence of more than one Dicer cannot be entirely dismissed.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "preliminary") (:form . "preliminary") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "VBZ") (:stem . "point") (:form . "points") (:end . 31)\n  (:start . 25) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "un-confirmed") (:form . "un-confirmed") (:end . 78)\n  (:start . 66) (:id . 55))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 88)\n  (:start . 79) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 96)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 102) (:start . 97)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 111)\n  (:start . 103) (:id . 60))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 116) (:start . 112)\n  (:id . 61))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 123)\n  (:start . 117) (:id . 62))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 133)\n  (:start . 124) (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 137) (:start . 134)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 147)\n  (:start . 138) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 66))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 160)\n  (:start . 152) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 68))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 168) (:start . 164)\n  (:id . 69))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 173) (:start . 169)\n  (:id . 70))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 177) (:start . 174)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 183)\n  (:start . 178) (:id . 72))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 190)\n  (:start . 184) (:id . 73))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 193) (:start . 191)\n  (:id . 74))\n ((:tag . "RB") (:stem . "entirely") (:form . "entirely") (:end . 202)\n  (:start . 194) (:id . 75))\n ((:tag . "VBN") (:stem . "dismiss") (:form . "dismissed") (:end . 212)\n  (:start . 203) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x9.200.1) (:span 184 212)))\n (:hscopes ((:id . :x9.200.1) (:span 148 212)))\n (:identifiers (:sid . :s9.200) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502964@unknown@formal@none@1@S@The RISC structure contains the following essential proteins: D. melanogaster R2D2 or C. elegans Rde-4 [17], D. melanogaster homologue of the Fragile × mental retardation protein (FMRP) dFXR [45], Vasa Intronic gene (VIG) and a Tudor Staphylococcal nuclease [46,50].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 51)\n  (:start . 42) (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 60)\n  (:start . 52) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 61) (:start . 60)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 77)\n  (:start . 65) (:id . 52))\n ((:tag . "NN") (:stem . "r2d2") (:form . "R2D2") (:end . 82) (:start . 78)\n  (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 85) (:start . 83)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 96)\n  (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "rde-4") (:form . "Rde-4") (:end . 102) (:start . 97)\n  (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 104) (:start . 103)\n  (:id . 58))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 111) (:start . 109)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 124) (:start . 112) (:id . 63))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 134)\n  (:start . 125) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Fragile") (:form . "Fragile") (:end . 149)\n  (:start . 142) (:id . 67))\n ((:tag . "POS") (:stem . "×") (:form . "×") (:end . 151) (:start . 150)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "mental") (:form . "mental") (:end . 158)\n  (:start . 152) (:id . 69))\n ((:tag . "NN") (:stem . "retardation") (:form . "retardation") (:end . 170)\n  (:start . 159) (:id . 70))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 178)\n  (:start . 171) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 180) (:start . 179)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "FMRP") (:form . "FMRP") (:end . 184) (:start . 180)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 185) (:start . 184)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "dFXR") (:form . "dFXR") (:end . 190) (:start . 186)\n  (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 192) (:start . 191)\n  (:id . 76))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 194) (:start . 192)\n  (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 195) (:start . 194)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Vasa") (:form . "Vasa") (:end . 201) (:start . 197)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "intronic") (:form . "Intronic") (:end . 210)\n  (:start . 202) (:id . 81))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 215) (:start . 211)\n  (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 217) (:start . 216)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "VIG") (:form . "VIG") (:end . 220) (:start . 217)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n  (:id . 85))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 225) (:start . 222)\n  (:id . 86))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 227) (:start . 226)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "Tudor") (:form . "Tudor") (:end . 233)\n  (:start . 228) (:id . 88))\n ((:tag . "JJ") (:stem . "staphylococcal") (:form . "Staphylococcal")\n  (:end . 248) (:start . 234) (:id . 89))\n ((:tag . "NN") (:stem . "nuclease") (:form . "nuclease") (:end . 257)\n  (:start . 249) (:id . 90))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 259) (:start . 258)\n  (:id . 91))\n ((:tag . "CD") (:stem . "46,50") (:form . "46,50") (:end . 264)\n  (:start . 259) (:id . 92))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 265) (:start . 264)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 266) (:start . 265)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s9.201) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502965@unknown@formal@none@1@S@We were able to confirm the presence of putative tick FMRp but no significant hits for TudorSN or VIG homologues and no significant similarity to known RNA binding proteins using the current tick resources.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VB") (:stem . "confirm") (:form . "confirm") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "FMRp") (:form . "FMRp") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 77)\n  (:start . 66) (:id . 55))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 82) (:start . 78)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 86) (:start . 83)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "TudorSN") (:form . "TudorSN") (:end . 94)\n  (:start . 87) (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "VIG") (:form . "VIG") (:end . 101) (:start . 98)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 112)\n  (:start . 102) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 119) (:start . 117)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 131)\n  (:start . 120) (:id . 64))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 142)\n  (:start . 132) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 145) (:start . 143)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 151)\n  (:start . 146) (:id . 67))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 155) (:start . 152)\n  (:id . 68))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 163)\n  (:start . 156) (:id . 69))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 172)\n  (:start . 164) (:id . 70))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 178) (:start . 173)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 182) (:start . 179)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 190)\n  (:start . 183) (:id . 73))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 195) (:start . 191)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 205)\n  (:start . 196) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s9.202) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502966@unknown@formal@none@1@S@However, a concurrent study has identified a putative I. scapularis TudorSN (GenBank, Ixodes scapularis Genome Project Consortium) yet to be confirmed in R. microplus.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "concurrent") (:form . "concurrent") (:end . 21)\n  (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . "NNP") (:stem . "TudorSN") (:form . "TudorSN") (:end . 75)\n  (:start . 68) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Ixodes") (:form . "Ixodes") (:end . 92)\n  (:start . 86) (:id . 57))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 103)\n  (:start . 93) (:id . 58))\n ((:tag . "NNP") (:stem . "Genome") (:form . "Genome") (:end . 110)\n  (:start . 104) (:id . 59))\n ((:tag . "NNP") (:stem . "Project") (:form . "Project") (:end . 118)\n  (:start . 111) (:id . 60))\n ((:tag . "NNP") (:stem . "Consortium") (:form . "Consortium") (:end . 129)\n  (:start . 119) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 150)\n  (:start . 141) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 153) (:start . 151)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 156) (:start . 154)\n  (:id . 68))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 166)\n  (:start . 157) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s9.203) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502967@unknown@formal@none@1@S@The Argonaute (Ago) family of proteins contains 2 distinct RNA-binding domains PAZ and PIWI (PPD) required to bind the siRNA and to slice the cognate RNA to be degraded, respectively and thus are essential to RISC [51,52].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Argonaute") (:form . "Argonaute") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Ago") (:form . "Ago") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 26)\n  (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 38)\n  (:start . 30) (:id . 49))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 47)\n  (:start . 39) (:id . 50))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 58)\n  (:start . 50) (:id . 52))\n ((:tag . "JJ") (:stem . "rna-binding") (:form . "RNA-binding") (:end . 70)\n  (:start . 59) (:id . 53))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 78)\n  (:start . 71) (:id . 54))\n ((:tag . "NNP") (:stem . "PAZ") (:form . "PAZ") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "PIWI") (:form . "PIWI") (:end . 91) (:start . 87)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "PPD") (:form . "PPD") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 106)\n  (:start . 98) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "VB") (:stem . "bind") (:form . "bind") (:end . 114) (:start . 110)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 64))\n ((:tag . "NN") (:stem . "sirna") (:form . "siRNA") (:end . 124)\n  (:start . 119) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 131) (:start . 129)\n  (:id . 67))\n ((:tag . "VB") (:stem . "slice") (:form . "slice") (:end . 137)\n  (:start . 132) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "cognate") (:form . "cognate") (:end . 149)\n  (:start . 142) (:id . 70))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 153) (:start . 150)\n  (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 156) (:start . 154)\n  (:id . 72))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 159) (:start . 157)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "degrade") (:form . "degraded") (:end . 168)\n  (:start . 160) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 75))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 182)\n  (:start . 170) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 186) (:start . 183)\n  (:id . 77))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 191) (:start . 187)\n  (:id . 78))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 195) (:start . 192)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 205)\n  (:start . 196) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 208) (:start . 206)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 213) (:start . 209)\n  (:id . 82))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 215) (:start . 214)\n  (:id . 83))\n ((:tag . "CD") (:stem . "51,52") (:form . "51,52") (:end . 220)\n  (:start . 215) (:id . 84))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 221) (:start . 220)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s9.204) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502968@unknown@formal@none@1@S@Our study confirmed the presence of tick Ago-1 and Ago-2 in the I. scapularis genome reads and found evidence for a complete Ago-1 protein in the R. microplus EST database.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "ago-1") (:form . "Ago-1") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "ago-2") (:form . "Ago-2") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 77)\n  (:start . 67) (:id . 55))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 84)\n  (:start . 78) (:id . 56))\n ((:tag . "NNS") (:stem . "read") (:form . "reads") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 100) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 109)\n  (:start . 101) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 113) (:start . 110)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 124)\n  (:start . 116) (:id . 63))\n ((:tag . "NN") (:stem . "ago-1") (:form . "Ago-1") (:end . 130)\n  (:start . 125) (:id . 64))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 138)\n  (:start . 131) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 148) (:start . 146)\n  (:id . 68))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 158)\n  (:start . 149) (:id . 69))\n ((:tag . "NNP") (:stem . "EST") (:form . "EST") (:end . 162) (:start . 159)\n  (:id . 70))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 171)\n  (:start . 163) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.205) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502969@unknown@formal@none@1@S@A R. microplus sequence containing a partial Ago-2 protein was also identified.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 14)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "ago-2") (:form . "Ago-2") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 58)\n  (:start . 51) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 78)\n  (:start . 68) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s9.206) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502970@unknown@formal@none@1@S@The functions of these tick Argonaute proteins remains to be confirmed and further research is required to identify the full complement of tick PPD proteins.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "argonaute") (:form . "Argonaute") (:end . 37)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "VBZ") (:stem . "remain") (:form . "remains") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 70)\n  (:start . 61) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 82)\n  (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 91)\n  (:start . 83) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 103)\n  (:start . 95) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 115)\n  (:start . 107) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 124) (:start . 120)\n  (:id . 61))\n ((:tag . "NN") (:stem . "complement") (:form . "complement") (:end . 135)\n  (:start . 125) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 63))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 143) (:start . 139)\n  (:id . 64))\n ((:tag . "NN") (:stem . "ppd") (:form . "PPD") (:end . 147) (:start . 144)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 156)\n  (:start . 148) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x9.207.1) (:span 47 70)))\n (:hscopes ((:id . :x9.207.1) (:span 0 70)))\n (:identifiers (:sid . :s9.207) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502971@unknown@formal@none@1@S@Flies and mosquitoes do not possess C. elegans Sid-1 homologues known to be responsible for systemic and germ-line RNAi.@(((:tag . "NNS") (:stem . "fly") (:form . "Flies") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "mosquito") (:form . "mosquitoes") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "VB") (:stem . "possess") (:form . "possess") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "sid-1") (:form . "Sid-1") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 63)\n  (:start . 53) (:id . 51))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "responsible") (:form . "responsible") (:end . 87)\n  (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 100)\n  (:start . 92) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "germ-line") (:form . "germ-line") (:end . 114)\n  (:start . 105) (:id . 59))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 119) (:start . 115)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s9.208) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502972@unknown@formal@none@1@S@Tick RNAi observed in this study and the literature demonstrate that a systemic RNAi silencing mechanism is active in ticks [42].@(((:tag . "NNP") (:stem . "Tick") (:form . "Tick") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "literature") (:form . "literature") (:end . 51)\n  (:start . 41) (:id . 50))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 63)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 79)\n  (:start . 71) (:id . 54))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 104)\n  (:start . 95) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 114)\n  (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 123)\n  (:start . 118) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 125) (:start . 124)\n  (:id . 62))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s9.209) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502973@unknown@formal@none@1@S@Although a tick Sid-1 was not found, we did however identify a tick homologue of the C. elegans EGO-1, an RNA dependent RNA polymerase (RdRP) known to amplify trigger dsRNA (transitive RNAi) and systemic RNAi [27,53].@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sid-1") (:form . "Sid-1") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 51)\n  (:start . 44) (:id . 52))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 60)\n  (:start . 52) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 67) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 77)\n  (:start . 68) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 95)\n  (:start . 88) (:id . 60))\n ((:tag . "NN") (:stem . "ego-1") (:form . "EGO-1") (:end . 101) (:start . 96)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 105) (:start . 103)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 109) (:start . 106)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "dependent") (:form . "dependent") (:end . 119)\n  (:start . 110) (:id . 65))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 123) (:start . 120)\n  (:id . 66))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 134)\n  (:start . 124) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 136) (:start . 135)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 140) (:start . 136)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 141) (:start . 140)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 147)\n  (:start . 142) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 150) (:start . 148)\n  (:id . 72))\n ((:tag . "VB") (:stem . "amplify") (:form . "amplify") (:end . 158)\n  (:start . 151) (:id . 73))\n ((:tag . "NN") (:stem . "trigger") (:form . "trigger") (:end . 166)\n  (:start . 159) (:id . 74))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 172)\n  (:start . 167) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "transitive") (:form . "transitive") (:end . 184)\n  (:start . 174) (:id . 77))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 189) (:start . 185)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 203)\n  (:start . 195) (:id . 81))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 208) (:start . 204)\n  (:id . 82))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 210) (:start . 209)\n  (:id . 83))\n ((:tag . "CD") (:stem . "27,53") (:form . "27,53") (:end . 215)\n  (:start . 210) (:id . 84))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 216) (:start . 215)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s9.210) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502974@unknown@formal@none@1@S@RdRP is otherwise absent in flies, mosquitoes and other animals.@(((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "absent") (:form . "absent") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mosquito") (:form . "mosquitoes") (:end . 45)\n  (:start . 35) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 55) (:start . 50)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 63)\n  (:start . 56) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 64) (:start . 63)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s9.211) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502975@unknown@formal@none@1@S@Perhaps an RdRP-based RNAi amplification mechanism within the Ecdysozoans (including ticks and C. elegans) is common, but lost in insect species?@(((:tag . "RB") (:stem . "perhaps") (:form . "Perhaps") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "rdrp-based") (:form . "RdRP-based") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 40) (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 50)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 57)\n  (:start . 51) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 49))\n ((:tag . "NNPS") (:stem . "Ecdysozoan") (:form . "Ecdysozoans") (:end . 73)\n  (:start . 62) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 84)\n  (:start . 75) (:id . 52))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 90) (:start . 85)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 97) (:start . 95)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 105)\n  (:start . 98) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 109) (:start . 107)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 116)\n  (:start . 110) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 60))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 121) (:start . 118)\n  (:id . 61))\n ((:tag . "VBD") (:stem . "lose") (:form . "lost") (:end . 126) (:start . 122)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 136)\n  (:start . 130) (:id . 64))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 144)\n  (:start . 137) (:id . 65))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 145) (:start . 144)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x9.212.1) (:span 0 7)))\n (:hscopes ((:id . :x9.212.1) (:span 0 144)))\n (:identifiers (:sid . :s9.212) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502976@unknown@formal@none@1@S@Mechanisms for cell to cell dsRNA uptake within ticks requires further investigation, as well as the confirmation of the activity of the tick RdRP and Rsd-3 homologues identified here.@(((:tag . "NNPS") (:stem . "Mechanism") (:form . "Mechanisms") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 70)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "investigation") (:form . "investigation")\n  (:end . 84) (:start . 71) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 54))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "confirmation") (:form . "confirmation") (:end . 113)\n  (:start . 101) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 129)\n  (:start . 121) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 64))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 141) (:start . 137)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 146) (:start . 142)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Rsd-3") (:form . "Rsd-3") (:end . 156)\n  (:start . 151) (:id . 68))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 167)\n  (:start . 157) (:id . 69))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 178)\n  (:start . 168) (:id . 70))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 183) (:start . 179)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.213) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502977@unknown@formal@none@1@S@Further research to identify putative tick secondary Argonautes associated with the transitive RNAi pathway in C. elegans is also warranted.@(((:tag . "JJ") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 52)\n  (:start . 43) (:id . 48))\n ((:tag . "NNS") (:stem . "argonaute") (:form . "Argonautes") (:end . 63)\n  (:start . 53) (:id . 49))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 74)\n  (:start . 64) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 79) (:start . 75)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "transitive") (:form . "transitive") (:end . 94)\n  (:start . 84) (:id . 53))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 99) (:start . 95)\n  (:id . 54))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 107)\n  (:start . 100) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 113) (:start . 111)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 121)\n  (:start . 114) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 124) (:start . 122)\n  (:id . 59))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 129) (:start . 125)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "warrant") (:form . "warranted") (:end . 139)\n  (:start . 130) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.214) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502978@unknown@formal@none@1@S@These mechanisms have not been studied in spiders, mites or ticks to date, thus confirmation of RNAi mechanisms within the Cheliceromorpha will assist to confirm potentially new evolutionary mechanisms previously not defined and which cannot be based on pathways observed in insect species.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "study") (:form . "studied") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "spider") (:form . "spiders") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "mite") (:form . "mites") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 73) (:start . 69)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 79) (:start . 75)\n  (:id . 57))\n ((:tag . "NN") (:stem . "confirmation") (:form . "confirmation") (:end . 92)\n  (:start . 80) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 111)\n  (:start . 101) (:id . 61))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 118)\n  (:start . 112) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Cheliceromorpha") (:form . "Cheliceromorpha")\n  (:end . 138) (:start . 123) (:id . 64))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 143) (:start . 139)\n  (:id . 65))\n ((:tag . "VB") (:stem . "assist") (:form . "assist") (:end . 150)\n  (:start . 144) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 153) (:start . 151)\n  (:id . 67))\n ((:tag . "VB") (:stem . "confirm") (:form . "confirm") (:end . 161)\n  (:start . 154) (:id . 68))\n ((:tag . "RB") (:stem . "potentially") (:form . "potentially") (:end . 173)\n  (:start . 162) (:id . 69))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 177) (:start . 174)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 190)\n  (:start . 178) (:id . 71))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 201)\n  (:start . 191) (:id . 72))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 212)\n  (:start . 202) (:id . 73))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 216) (:start . 213)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 224)\n  (:start . 217) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 228) (:start . 225)\n  (:id . 76))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 234)\n  (:start . 229) (:id . 77))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 241)\n  (:start . 235) (:id . 78))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 244) (:start . 242)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 250)\n  (:start . 245) (:id . 80))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 253) (:start . 251)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 262)\n  (:start . 254) (:id . 82))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 271)\n  (:start . 263) (:id . 83))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 274) (:start . 272)\n  (:id . 84))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 281)\n  (:start . 275) (:id . 85))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 289)\n  (:start . 282) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 290) (:start . 289)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s9.215) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502979@unknown@formal@none@1@S@An additional aim of our study was to investigate whether fruit fly RNAi screens of conserved genes could be associated with similar tick phenotypes and tick gene function.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "aim") (:form . "aim") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 49)\n  (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 57)\n  (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "fruit") (:form . "fruit") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "fly") (:form . "fly") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "screen") (:form . "screens") (:end . 80)\n  (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 93)\n  (:start . 84) (:id . 57))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 99) (:start . 94)\n  (:id . 58))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 105)\n  (:start . 100) (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 119)\n  (:start . 109) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 124) (:start . 120)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 132)\n  (:start . 125) (:id . 63))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 137) (:start . 133)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 148)\n  (:start . 138) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 66))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 157) (:start . 153)\n  (:id . 67))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 162) (:start . 158)\n  (:id . 68))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 171)\n  (:start . 163) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x9.216.1) (:span 100 105)) ((:id . :x9.216.2) (:span 50 57)))\n (:hscopes ((:id . :x9.216.1) (:span 58 171))\n  ((:id . :x9.216.2) (:span 50 171)))\n (:identifiers (:sid . :s9.216) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502980@unknown@formal@none@1@S@We used a stringent search to enable the selection of the most similar sequences to maximize the probability of selecting a tick sequence which following dsRNA mediated knockdown could also affect growth and viability in vitro.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 9) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "stringent") (:form . "stringent") (:end . 19)\n  (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "VB") (:stem . "enable") (:form . "enable") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 50)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 70)\n  (:start . 63) (:id . 54))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 80)\n  (:start . 71) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "VB") (:stem . "maximize") (:form . "maximize") (:end . 92)\n  (:start . 84) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 108)\n  (:start . 97) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "select") (:form . "selecting") (:end . 121)\n  (:start . 112) (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 123) (:start . 122)\n  (:id . 62))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 128) (:start . 124)\n  (:id . 63))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 137)\n  (:start . 129) (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 143)\n  (:start . 138) (:id . 65))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 153)\n  (:start . 144) (:id . 66))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 159)\n  (:start . 154) (:id . 67))\n ((:tag . "JJ") (:stem . "mediated") (:form . "mediated") (:end . 168)\n  (:start . 160) (:id . 68))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 178)\n  (:start . 169) (:id . 69))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 184)\n  (:start . 179) (:id . 70))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 189) (:start . 185)\n  (:id . 71))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 196)\n  (:start . 190) (:id . 72))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 203)\n  (:start . 197) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 207) (:start . 204)\n  (:id . 74))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 217)\n  (:start . 208) (:id . 75))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 220) (:start . 218)\n  (:id . 76))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 226)\n  (:start . 221) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x9.217.1) (:span 179 184)))\n (:hscopes ((:id . :x9.217.1) (:span 179 226)))\n (:identifiers (:sid . :s9.217) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502981@unknown@formal@none@1@S@With the exception of proteasome/ubiquitin protein homologues, the RNAi experiments with cultured R. microplus BME26 cells did not replicate the effects observed by Boutros and co-workers in D. melanogaster cells [43] for all targets.@(((:tag . "IN") (:stem . "with") (:form . "With") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "exception") (:form . "exception") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "proteasome/ubiquitin")\n  (:form . "proteasome/ubiquitin") (:end . 42) (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 50)\n  (:start . 43) (:id . 47))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 61)\n  (:start . 51) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 71) (:start . 67)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 83)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 88) (:start . 84)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 97)\n  (:start . 89) (:id . 54))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 100) (:start . 98)\n  (:id . 55))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 110)\n  (:start . 101) (:id . 56))\n ((:tag . "NN") (:stem . "bme26") (:form . "BME26") (:end . 116)\n  (:start . 111) (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 122)\n  (:start . 117) (:id . 58))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 126) (:start . 123)\n  (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 130) (:start . 127)\n  (:id . 60))\n ((:tag . "VB") (:stem . "replicate") (:form . "replicate") (:end . 140)\n  (:start . 131) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 152)\n  (:start . 145) (:id . 63))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 161)\n  (:start . 153) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 164) (:start . 162)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "boutro") (:form . "Boutros") (:end . 172)\n  (:start . 165) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "co-worker") (:form . "co-workers") (:end . 187)\n  (:start . 177) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 190) (:start . 188)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 193) (:start . 191)\n  (:id . 70))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 206)\n  (:start . 194) (:id . 71))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 212)\n  (:start . 207) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 214) (:start . 213)\n  (:id . 73))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 216) (:start . 214)\n  (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 217) (:start . 216)\n  (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 221) (:start . 218)\n  (:id . 76))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 225) (:start . 222)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 233)\n  (:start . 226) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s9.218) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502982@unknown@formal@none@1@S@However, in vivo knockdown confirmed a lethal effect for 6 of the 10 targets, with only one demonstrating nil effects on tick reproduction.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "lethal") (:form . "lethal") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 68) (:start . 66)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 76)\n  (:start . 69) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 82) (:start . 78)\n  (:id . 58))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 87) (:start . 83)\n  (:id . 59))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 91) (:start . 88)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating")\n  (:end . 105) (:start . 92) (:id . 61))\n ((:tag . "NN") (:stem . "nil") (:form . "nil") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 117)\n  (:start . 110) (:id . 63))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 120) (:start . 118)\n  (:id . 64))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 125) (:start . 121)\n  (:id . 65))\n ((:tag . "NN") (:stem . "reproduction") (:form . "reproduction") (:end . 138)\n  (:start . 126) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s9.219) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502983@unknown@formal@none@1@S@The ubiquitin-63E homologue which demonstrated the highest z score and impact on Drosophila cell viability exhibited the strongest effects on viability in our tick study both in vitro and in vivo.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "ubiquitin-63e") (:form . "ubiquitin-63E")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 27)\n  (:start . 18) (:id . 44))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 33) (:start . 28)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 46)\n  (:start . 34) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 47))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 58)\n  (:start . 51) (:id . 48))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 60) (:start . 59)\n  (:id . 49))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 66) (:start . 61)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 51))\n ((:tag . "NN") (:stem . "impact") (:form . "impact") (:end . 77)\n  (:start . 71) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 80) (:start . 78)\n  (:id . 53))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 91)\n  (:start . 81) (:id . 54))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 96) (:start . 92)\n  (:id . 55))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 106)\n  (:start . 97) (:id . 56))\n ((:tag . "VBD") (:stem . "exhibit") (:form . "exhibited") (:end . 116)\n  (:start . 107) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 58))\n ((:tag . "JJS") (:stem . "strong") (:form . "strongest") (:end . 130)\n  (:start . 121) (:id . 59))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 138)\n  (:start . 131) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 141) (:start . 139)\n  (:id . 61))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 151)\n  (:start . 142) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n  (:id . 63))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 158) (:start . 155)\n  (:id . 64))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 163) (:start . 159)\n  (:id . 65))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 169)\n  (:start . 164) (:id . 66))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 174) (:start . 170)\n  (:id . 67))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 177) (:start . 175)\n  (:id . 68))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 183)\n  (:start . 178) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 187) (:start . 184)\n  (:id . 70))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 190) (:start . 188)\n  (:id . 71))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 195) (:start . 191)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s9.220) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502984@unknown@formal@none@1@S@However the effects on tick cell growth and viability from the remaining 9 (including 2 negative controls) dsRNA targets tested did not correlate well with Drosophila demonstrating poor statistical significance at least under our in vitro conditions.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "remain") (:form . "remaining") (:end . 72)\n  (:start . 63) (:id . 53))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 85)\n  (:start . 76) (:id . 56))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 96)\n  (:start . 88) (:id . 58))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 105)\n  (:start . 97) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 112)\n  (:start . 107) (:id . 61))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 120)\n  (:start . 113) (:id . 62))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 127)\n  (:start . 121) (:id . 63))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 131) (:start . 128)\n  (:id . 64))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 135) (:start . 132)\n  (:id . 65))\n ((:tag . "VB") (:stem . "correlate") (:form . "correlate") (:end . 145)\n  (:start . 136) (:id . 66))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 150) (:start . 146)\n  (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 155) (:start . 151)\n  (:id . 68))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 166)\n  (:start . 156) (:id . 69))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating")\n  (:end . 180) (:start . 167) (:id . 70))\n ((:tag . "JJ") (:stem . "poor") (:form . "poor") (:end . 185) (:start . 181)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 197)\n  (:start . 186) (:id . 72))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 210)\n  (:start . 198) (:id . 73))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 213) (:start . 211)\n  (:id . 74))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 219)\n  (:start . 214) (:id . 75))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 225)\n  (:start . 220) (:id . 76))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 229) (:start . 226)\n  (:id . 77))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 232) (:start . 230)\n  (:id . 78))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 238)\n  (:start . 233) (:id . 79))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 249)\n  (:start . 239) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 250) (:start . 249)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s9.221) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502985@unknown@formal@none@1@S@Kurtti et al [54] found that cationic lipid-based reagents greatly improved the transfection of I. scapularis cultured tick cells as well as subsequent silencing of transgenes by dsRNAi.@(((:tag . "NNP") (:stem . "Kurtti") (:form . "Kurtti") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "FW") (:stem . "al") (:form . "al") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "CD") (:stem . "54") (:form . "54") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 23) (:start . 18)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "cationic") (:form . "cationic") (:end . 37)\n  (:start . 29) (:id . 50))\n ((:tag . "JJ") (:stem . "lipid-based") (:form . "lipid-based") (:end . 49)\n  (:start . 38) (:id . 51))\n ((:tag . "NNS") (:stem . "reagent") (:form . "reagents") (:end . 58)\n  (:start . 50) (:id . 52))\n ((:tag . "RB") (:stem . "greatly") (:form . "greatly") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "VBD") (:stem . "improve") (:form . "improved") (:end . 75)\n  (:start . 67) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 92)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 98) (:start . 96)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 109)\n  (:start . 99) (:id . 59))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 118)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 129)\n  (:start . 124) (:id . 62))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 137) (:start . 133)\n  (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 151)\n  (:start . 141) (:id . 66))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 161)\n  (:start . 152) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 164) (:start . 162)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "transgene") (:form . "transgenes") (:end . 175)\n  (:start . 165) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 178) (:start . 176)\n  (:id . 70))\n ((:tag . "NN") (:stem . "dsrnai") (:form . "dsRNAi") (:end . 185)\n  (:start . 179) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.222) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502986@unknown@formal@none@1@S@Perhaps uptake of nucleic acids by cultured tick cells is less efficient than with Drosophila cells.@(((:tag . "RB") (:stem . "perhaps") (:form . "Perhaps") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "nucleic") (:form . "nucleic") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 72)\n  (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 93)\n  (:start . 83) (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 99) (:start . 94)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x9.223.1) (:span 0 7)))\n (:hscopes ((:id . :x9.223.1) (:span 0 99)))\n (:identifiers (:sid . :s9.223) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502987@unknown@formal@none@1@S@In addition, although tick genome resources are currently incomplete, we did not identify tick homologues of Scavenger receptors (Eater and SrCI) known to be required for dsRNA uptake in Drosophila cell culture [36].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 33)\n  (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "JJ") (:stem . "incomplete") (:form . "incomplete") (:end . 68)\n  (:start . 58) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 94) (:start . 90)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 105)\n  (:start . 95) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Scavenger") (:form . "Scavenger") (:end . 118)\n  (:start . 109) (:id . 60))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 128)\n  (:start . 119) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Eater") (:form . "Eater") (:end . 135)\n  (:start . 130) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "SrCI") (:form . "SrCI") (:end . 144) (:start . 140)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 151)\n  (:start . 146) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 154) (:start . 152)\n  (:id . 68))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 157) (:start . 155)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 166)\n  (:start . 158) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 170) (:start . 167)\n  (:id . 71))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 176)\n  (:start . 171) (:id . 72))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 183)\n  (:start . 177) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 186) (:start . 184)\n  (:id . 74))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 197)\n  (:start . 187) (:id . 75))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 202) (:start . 198)\n  (:id . 76))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 210)\n  (:start . 203) (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 212) (:start . 211)\n  (:id . 78))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 214) (:start . 212)\n  (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 215) (:start . 214)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s9.224) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502988@unknown@formal@none@1@S@This suggests the recruitment of different receptors for dsRNA uptake in tick cells compared to those described in Drosophila.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "recruitment") (:form . "recruitment") (:end . 29)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 52)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 62) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "uptake") (:form . "uptake") (:end . 69)\n  (:start . 63) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 83) (:start . 78)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 92)\n  (:start . 84) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 56))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 101) (:start . 96)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 111)\n  (:start . 102) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 125)\n  (:start . 115) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x9.225.1) (:span 5 13)))\n (:hscopes ((:id . :x9.225.1) (:span 5 125)))\n (:identifiers (:sid . :s9.225) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502989@unknown@formal@none@1@S@It is also possible that the cell line types utilized in D. melanogaster and R. microplus are not directly comparable and functionally different.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 19)\n  (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 44) (:start . 39)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "utilize") (:form . "utilized") (:end . 53)\n  (:start . 45) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 72)\n  (:start . 60) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "microplu") (:form . "microplus") (:end . 89)\n  (:start . 80) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 106)\n  (:start . 98) (:id . 60))\n ((:tag . "JJ") (:stem . "comparable") (:form . "comparable") (:end . 117)\n  (:start . 107) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "RB") (:stem . "functionally") (:form . "functionally") (:end . 134)\n  (:start . 122) (:id . 63))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 144)\n  (:start . 135) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x9.226.1) (:span 11 19)))\n (:hscopes ((:id . :x9.226.1) (:span 11 144)))\n (:identifiers (:sid . :s9.226) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502990@unknown@formal@none@1@S@The 438 genes targeted by Boutros and co-workers [43] compared the effects using 2 embryonic cell lines, Kc167 which is an 'early' embryonic cell line and S2R+ which is a 'late' embryonic cell line – potentially more comparable to BME26 cells which are 'late' embryonic in origin [55-57].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "438") (:form . "438") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "target") (:form . "targeted") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "boutro") (:form . "Boutros") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NNS") (:stem . 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5502991@unknown@formal@none@1@S@However, the BME26 average cell size is smaller at 15–20 µM compared to SR2+ cells at 50 µM [56,58].@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "BME26") (:form . "BME26") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "CD") (:stem . "15–20") (:form . "15–20") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "µm") (:form . "µM") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 68)\n  (:start . 60) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "sr2+") (:form . "SR2+") (:end . 76) (:start . 72)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 82) (:start . 77)\n  (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 85) (:start . 83)\n  (:id . 58))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 88) (:start . 86)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "µM") (:form . "µM") (:end . 91) (:start . 89)\n  (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 93) (:start . 92)\n  (:id . 61))\n ((:tag . "CD") (:stem . "56,58") (:form . "56,58") (:end . 98) (:start . 93)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 99) (:start . 98)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.228) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502992@unknown@formal@none@1@S@The BME26 cell line also has a doubling time of 7 days, considerably slower than the Drosophila cell lines.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "BME26") (:form . "BME26") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "doubling") (:form . "doubling") (:end . 39)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 54) (:start . 50)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 54))\n ((:tag . "RB") (:stem . "considerably") (:form . "considerably") (:end . 68)\n  (:start . 56) (:id . 55))\n ((:tag . "JJR") (:stem . "slow") (:form . "slower") (:end . 75) (:start . 69)\n  (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 80) (:start . 76)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 95)\n  (:start . 85) (:id . 59))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 106)\n  (:start . 101) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.229) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502993@unknown@formal@none@1@S@Our in vivo studies were more convincing demonstrating lethal and inhibitory effects on tick reproduction for 9 (including the 2 controls) of the 10 targets.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "convincing") (:form . "convincing") (:end . 40)\n  (:start . 30) (:id . 48))\n ((:tag . "VBG") (:stem . "demonstrate") (:form . "demonstrating") (:end . 54)\n  (:start . 41) (:id . 49))\n ((:tag . "JJ") (:stem . "lethal") (:form . "lethal") (:end . 61)\n  (:start . 55) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "inhibitory") (:form . "inhibitory") (:end . 76)\n  (:start . 66) (:id . 52))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 84)\n  (:start . 77) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 87) (:start . 85)\n  (:id . 54))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 92) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "reproduction") (:form . "reproduction") (:end . 105)\n  (:start . 93) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 109) (:start . 106)\n  (:id . 57))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 111) (:start . 110)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 122)\n  (:start . 113) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 128) (:start . 127)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 137)\n  (:start . 129) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 141) (:start . 139)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 66))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 148) (:start . 146)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 156)\n  (:start . 149) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s9.230) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502994@unknown@formal@none@1@S@In vivo studies in C. elegans showed that 47% of the C. elegans orthologues of the 438 genes associated with the Drosophila RNAi phenotypes exhibited developmental phenotypes [43,59].@(((:tag . "FW") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 29)\n  (:start . 22) (:id . 47))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 36) (:start . 30)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 55) (:start . 53)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 63)\n  (:start . 56) (:id . 55))\n ((:tag . "NNS") (:stem . "orthologue") (:form . "orthologues") (:end . 75)\n  (:start . 64) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "CD") (:stem . "438") (:form . "438") (:end . 86) (:start . 83)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 92) (:start . 87)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 103)\n  (:start . 93) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 123)\n  (:start . 113) (:id . 64))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 128) (:start . 124)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 139)\n  (:start . 129) (:id . 66))\n ((:tag . "VBD") (:stem . "exhibit") (:form . "exhibited") (:end . 149)\n  (:start . 140) (:id . 67))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 163) (:start . 150) (:id . 68))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 174)\n  (:start . 164) (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 176) (:start . 175)\n  (:id . 70))\n ((:tag . "CD") (:stem . "43,59") (:form . "43,59") (:end . 181)\n  (:start . 176) (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 182) (:start . 181)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s9.231) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502995@unknown@formal@none@1@S@Perhaps the fact that we chose highly conserved homologues increased the probability of success in our in vivo experiments compared with C. elegans.@(((:tag . "RB") (:stem . "perhaps") (:form . "Perhaps") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 30)\n  (:start . 25) (:id . 47))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 58)\n  (:start . 48) (:id . 50))\n ((:tag . "VBD") (:stem . "increase") (:form . "increased") (:end . 68)\n  (:start . 59) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 84)\n  (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 54))\n ((:tag . "NN") (:stem . "success") (:form . "success") (:end . 95)\n  (:start . 88) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 110) (:start . 106)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 122)\n  (:start . 111) (:id . 60))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 131)\n  (:start . 123) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 136) (:start . 132)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 139) (:start . 137)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 147)\n  (:start . 140) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x9.232.1) (:span 0 7)))\n (:hscopes ((:id . :x9.232.1) (:span 0 147)))\n (:identifiers (:sid . :s9.232) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502996@unknown@formal@none@1@S@However, it is clear that tick in vitro RNAi analysis using BME26 cannot be directly correlated to available Drosophila in vitro data, unless perhaps only target genes with higher z scores (as demonstrated here for ubiquitin-63E) can be studied to increase the probability of a phenotype correlation.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 20) (:start . 15)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 30) (:start . 26)\n  (:id . 48))\n ((:tag . "FW") (:stem . 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5502997@unknown@formal@none@1@S@The challenges encountered during the initial PCR amplification of tick template DNA (results not shown) prompted re-design of conserved primer sets for targets amplified and transcribed in this study.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "challenge") (:form . "challenges") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "encounter") (:form . "encountered") (:end . 26)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 33)\n  (:start . 27) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . "NN") (:stem . "pcr") (:form . "PCR") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 63) (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 50))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 71) (:start . 67)\n  (:id . 51))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 80)\n  (:start . 72) (:id . 52))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 84) (:start . 81)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 97) (:start . 94)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 103) (:start . 98)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "prompt") (:form . "prompted") (:end . 113)\n  (:start . 105) (:id . 59))\n ((:tag . "NN") (:stem . "re-design") (:form . "re-design") (:end . 123)\n  (:start . 114) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 136)\n  (:start . 127) (:id . 62))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 143)\n  (:start . 137) (:id . 63))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 148) (:start . 144)\n  (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 152) (:start . 149)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 160)\n  (:start . 153) (:id . 66))\n ((:tag . "VBN") (:stem . "amplify") (:form . "amplified") (:end . 170)\n  (:start . 161) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 174) (:start . 171)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "transcribe") (:form . "transcribed") (:end . 186)\n  (:start . 175) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 189) (:start . 187)\n  (:id . 70))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 194) (:start . 190)\n  (:id . 71))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 200)\n  (:start . 195) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s9.234) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502998@unknown@formal@none@1@S@Other tick dsRNA studies have used cDNA clones [42] as templates for amplification and subsequent transcription verifying that perhaps the tick genomic DNA templates are not amenable for high throughput gene amplification required for RNAi functional screens.@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cdna") (:form . "cDNA") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "clone") (:form . "clones") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 54) (:start . 52)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 64)\n  (:start . 55) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 82) (:start . 69) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 97)\n  (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 111) (:start . 98) (:id . 59))\n ((:tag . "VBG") (:stem . "verify") (:form . "verifying") (:end . 121)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 126) (:start . 122)\n  (:id . 61))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 134)\n  (:start . 127) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 63))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 143) (:start . 139)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 151)\n  (:start . 144) (:id . 65))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 155) (:start . 152)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 165)\n  (:start . 156) (:id . 67))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 169) (:start . 166)\n  (:id . 68))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 173) (:start . 170)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "amenable") (:form . "amenable") (:end . 182)\n  (:start . 174) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 186) (:start . 183)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 191) (:start . 187)\n  (:id . 72))\n ((:tag . "NN") (:stem . "throughput") (:form . "throughput") (:end . 202)\n  (:start . 192) (:id . 73))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 207) (:start . 203)\n  (:id . 74))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 221) (:start . 208) (:id . 75))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 230)\n  (:start . 222) (:id . 76))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 234) (:start . 231)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 239) (:start . 235)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 250)\n  (:start . 240) (:id . 79))\n ((:tag . "NNS") (:stem . "screen") (:form . "screens") (:end . 258)\n  (:start . 251) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 259) (:start . 258)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x9.235.1) (:span 127 134)))\n (:hscopes ((:id . :x9.235.1) (:span 127 258)))\n (:identifiers (:sid . :s9.235) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5502999@unknown@formal@none@1@S@The tick genome is large (7.1 Gbp) with a high ratio of repetitive and exonic sequences [2] also confirmed here with the I. scapularis putative Dicer genomic sequence structure with 14 exons.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "CD") (:stem . "7.1") (:form . "7.1") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Gbp") (:form . "Gbp") (:end . 33) (:start . 30)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 34) (:start . 33)\n  (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 39) (:start . 35)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 46) (:start . 42)\n  (:id . 53))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 52) (:start . 47)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "repetitive") (:form . "repetitive") (:end . 66)\n  (:start . 56) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "exonic") (:form . "exonic") (:end . 77)\n  (:start . 71) (:id . 58))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 87)\n  (:start . 78) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 89) (:start . 88)\n  (:id . 60))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 90) (:start . 89)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 91) (:start . 90)\n  (:id . 62))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 96) (:start . 92)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 106)\n  (:start . 97) (:id . 64))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 111) (:start . 107)\n  (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 116) (:start . 112)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 123) (:start . 121)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "scapulari") (:form . "scapularis") (:end . 134)\n  (:start . 124) (:id . 69))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 143)\n  (:start . 135) (:id . 70))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 149)\n  (:start . 144) (:id . 71))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 157)\n  (:start . 150) (:id . 72))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 166)\n  (:start . 158) (:id . 73))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 176)\n  (:start . 167) (:id . 74))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 181) (:start . 177)\n  (:id . 75))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 184) (:start . 182)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "exon") (:form . "exons") (:end . 190)\n  (:start . 185) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s9.236) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503000@unknown@formal@none@1@S@The presence of complex intronic/exonic structure can inhibit satisfactory PCR amplification of gDNA possibly due to poor primer binding.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "JJ") (:stem . "intronic/exonic") (:form . "intronic/exonic")\n  (:end . 39) (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 49)\n  (:start . 40) (:id . 47))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 53) (:start . 50)\n  (:id . 48))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 61)\n  (:start . 54) (:id . 49))\n ((:tag . "JJ") (:stem . "satisfactory") (:form . "satisfactory") (:end . 74)\n  (:start . 62) (:id . 50))\n ((:tag . "NN") (:stem . "pcr") (:form . "PCR") (:end . 78) (:start . 75)\n  (:id . 51))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 92) (:start . 79) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 53))\n ((:tag . "NN") (:stem . "gdna") (:form . "gDNA") (:end . 100) (:start . 96)\n  (:id . 54))\n ((:tag . "RB") (:stem . "possibly") (:form . "possibly") (:end . 109)\n  (:start . 101) (:id . 55))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 113) (:start . 110)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 116) (:start . 114)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "poor") (:form . "poor") (:end . 121) (:start . 117)\n  (:id . 58))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 128)\n  (:start . 122) (:id . 59))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 136)\n  (:start . 129) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x9.237.1) (:span 101 109)))\n (:hscopes ((:id . :x9.237.1) (:span 101 136)))\n (:identifiers (:sid . :s9.237) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503001@unknown@formal@none@1@S@This was mostly overcome in this study by improving primers by targeting conserved ORFs across several arthropod species, however, amplification was not always consistent (not shown).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "mostly") (:form . "mostly") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "overcome") (:form . "overcome") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "improve") (:form . "improving") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 59)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 72)\n  (:start . 63) (:id . 53))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 82)\n  (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 94)\n  (:start . 88) (:id . 56))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 102)\n  (:start . 95) (:id . 57))\n ((:tag . "NN") (:stem . "arthropod") (:form . "arthropod") (:end . 112)\n  (:start . 103) (:id . 58))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 120)\n  (:start . 113) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 60))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 129)\n  (:start . 122) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "NN") (:stem . "amplification") (:form . "amplification")\n  (:end . 144) (:start . 131) (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 148) (:start . 145)\n  (:id . 64))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 152) (:start . 149)\n  (:id . 65))\n ((:tag . "RB") (:stem . "always") (:form . "always") (:end . 159)\n  (:start . 153) (:id . 66))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 170)\n  (:start . 160) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 68))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 175) (:start . 172)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 181)\n  (:start . 176) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 182) (:start . 181)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.238) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503002@unknown@formal@none@1@S@It may be feasible to develop short interfering RNA treatments which would be simpler to prepare than long dsRNA treatments for difficult templates such as the tick, to date siRNAs have not been applied in R. microplus loss-off-function assays.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "feasible") (:form . "feasible") (:end . 18)\n  (:start . 10) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "VB") (:stem . "develop") (:form . "develop") (:end . 29)\n  (:start . 22) (:id . 47))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "interfere") (:form . "interfering") (:end . 47)\n  (:start . 36) (:id . 49))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 62)\n  (:start . 52) (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 68) (:start . 63)\n  (:id . 52))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 74) (:start . 69)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "JJR") (:stem . "simple") (:form . "simpler") (:end . 85)\n  (:start . 78) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "VB") (:stem . "prepare") (:form . "prepare") (:end . 96)\n  (:start . 89) (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 112)\n  (:start . 107) (:id . 60))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 123)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 127) (:start . 124)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 137)\n  (:start . 128) (:id . 63))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 147)\n  (:start . 138) (:id . 64))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 152) (:start . 148)\n  (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 155) (:start . 153)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 67))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 164) (:start . 160)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 168) (:start . 166)\n  (:id . 70))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 173) (:start . 169)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 180)\n  (:start . 174) (:id . 72))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 185) (:start . 181)\n  (:id . 73))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 189) (:start . 186)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 194) (:start . 190)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 202)\n  (:start . 195) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 205) (:start . 203)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 208) (:start . 206)\n  (:id . 78))\n ((:tag . "CC") (:stem . "microplus") (:form . "microplus") (:end . 218)\n  (:start . 209) (:id . 79))\n ((:tag . "JJ") (:stem . "loss-off-function") (:form . "loss-off-function")\n  (:end . 236) (:start . 219) (:id . 80))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 243)\n  (:start . 237) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x9.239.1) (:span 69 74)) ((:id . :x9.239.2) (:span 10 18))\n  ((:id . :x9.239.3) (:span 3 6)))\n (:hscopes ((:id . :x9.239.1) (:span 69 243)) ((:id . :x9.239.2) (:span 10 62))\n  ((:id . :x9.239.3) (:span 3 243)))\n (:identifiers (:sid . :s9.239) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503003@unknown@formal@none@1@S@Long dsRNA gene silencing can also lead to off target effects and false positive RNAi phenotypes [60,61].@(((:tag . "JJ") (:stem . "long") (:form . "Long") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "VB") (:stem . "lead") (:form . "lead") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "RP") (:stem . "off") (:form . "off") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 53)\n  (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 80)\n  (:start . 72) (:id . 55))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 96)\n  (:start . 86) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "CD") (:stem . "60,61") (:form . "60,61") (:end . 103) (:start . 98)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x9.240.1) (:span 26 29)))\n (:hscopes ((:id . :x9.240.1) (:span 26 96)))\n (:identifiers (:sid . :s9.240) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503004@unknown@formal@none@1@S@Until complete annotated tick genome resources are available, false positive knockdown resulting from long dsRNA treatments and the specificity of (siRNAs) tick RNAi reagents cannot be confirmed.@(((:tag . "IN") (:stem . "until") (:form . "Until") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 36)\n  (:start . 30) (:id . 46))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 46)\n  (:start . 37) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 67) (:start . 62)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 76)\n  (:start . 68) (:id . 52))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 86)\n  (:start . 77) (:id . 53))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 96)\n  (:start . 87) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 101) (:start . 97)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 106) (:start . 102)\n  (:id . 56))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 112)\n  (:start . 107) (:id . 57))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 123)\n  (:start . 113) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 60))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 143)\n  (:start . 132) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 146) (:start . 144)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "sirna") (:form . "siRNAs") (:end . 154)\n  (:start . 148) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 65))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 160) (:start . 156)\n  (:id . 66))\n ((:tag . "NN") (:stem . "rnai") (:form . "RNAi") (:end . 165) (:start . 161)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "reagent") (:form . "reagents") (:end . 174)\n  (:start . 166) (:id . 68))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 181)\n  (:start . 175) (:id . 69))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 184) (:start . 182)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 194)\n  (:start . 185) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x9.241.1) (:span 175 194)))\n (:hscopes ((:id . :x9.241.1) (:span 128 194)))\n (:identifiers (:sid . :s9.241) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503005@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s9.242) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503006@unknown@formal@none@1@S@We utilized the existing R. microplus BmiGI2 database (13,643 ESTs) and the I. scapularis genome reads to identify 31 putative tick RNAi proteins which confirmed the presence of a putative Dicer, RISC associated, dsRNA uptake and RdRP proteins in ticks and constructed a putative tick RNAi pathway.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "utilize") (:form . "utilized") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 37)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "bmigi2") (:form . 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5503007@unknown@formal@none@1@S@Apart for proteasome/ubiquitinylation homologues, it was not feasible to replicate D. melanogaster embryonic cell culture RNAi functional data in R. microplus BME26 embryonic cells.@(((:tag . "NN") (:stem . "apart") (:form . "Apart") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "proteasome/ubiquitinylation")\n  (:form . "proteasome/ubiquitinylation") (:end . 37) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 48)\n  (:start . 38) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 52) (:start . 50)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 56) (:start . 53)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 60) (:start . 57)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "feasible") (:form . "feasible") (:end . 69)\n  (:start . 61) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "VB") (:stem . "replicate") (:form . "replicate") (:end . 82)\n  (:start . 73) (:id . 52))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 85) (:start . 83)\n  (:id . 53))\n ((:tag . "VB") (:stem . "melanogaster") (:form . "melanogaster") (:end . 98)\n  (:start . 86) (:id . 54))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 108)\n  (:start . 99) (:id . 55))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 113) (:start . 109)\n  (:id . 56))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 121)\n  (:start . 114) (:id . 57))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 126) (:start . 122)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 137)\n  (:start . 127) (:id . 59))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 142)\n  (:start . 138) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 145) (:start . 143)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 148) (:start . 146)\n  (:id . 62))\n ((:tag . "CC") (:stem . "microplus") (:form . "microplus") (:end . 158)\n  (:start . 149) (:id . 63))\n ((:tag . "NN") (:stem . "bme26") (:form . "BME26") (:end . 164)\n  (:start . 159) (:id . 64))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 174)\n  (:start . 165) (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 180)\n  (:start . 175) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x9.244.1) (:span 61 69)))\n (:hscopes ((:id . :x9.244.1) (:span 61 180)))\n (:identifiers (:sid . :s9.244) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503008@unknown@formal@none@1@S@This could either be attributed to transfection/uptake issues and/or a difference in cell types in the fly and tick embryonic cell lines.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "either") (:form . "either") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "attribute") (:form . "attributed") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "VB") (:stem . "transfection/uptake")\n  (:form . "transfection/uptake") (:end . 54) (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "issue") (:form . "issues") (:end . 61)\n  (:start . 55) (:id . 49))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 68)\n  (:start . 62) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 81)\n  (:start . 71) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 89) (:start . 85)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 95) (:start . 90)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 106) (:start . 103)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 59))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 115) (:start . 111)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 125)\n  (:start . 116) (:id . 61))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 130) (:start . 126)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 136)\n  (:start . 131) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x9.245.1) (:span 11 17 62 68)))\n (:hscopes ((:id . :x9.245.1) (:span 11 136)))\n (:identifiers (:sid . :s9.245) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503009@unknown@formal@none@1@S@We did demonstrate a correlating in vivo effect on embryogenesis for 9 of the 10 D. melanogaster tick homologues.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VB") (:stem . "demonstrate") (:form . "demonstrate") (:end . 18)\n  (:start . 7) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "correlate") (:form . "correlating") (:end . 32)\n  (:start . 21) (:id . 46))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 64) (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . "MD") (:stem . "melanogaster") (:form . "melanogaster") (:end . 96)\n  (:start . 84) (:id . 58))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 101) (:start . 97)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 112)\n  (:start . 102) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s9.246) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503010@unknown@formal@none@1@S@The findings in this manuscript support the fact that perhaps the Chelicerates may not be amenable to modeling based on insect pathways (Subphylum Mandibulata) as perhaps expected for Arthropods.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "manuscript") (:form . "manuscript") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NNPS") (:stem . "Chelicerates") (:form . "Chelicerates")\n  (:end . 78) (:start . 66) (:id . 53))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "amenable") (:form . "amenable") (:end . 98)\n  (:start . 90) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 58))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 110)\n  (:start . 102) (:id . 59))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 116)\n  (:start . 111) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . "NN") (:stem . "insect") (:form . "insect") (:end . 126)\n  (:start . 120) (:id . 62))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 135)\n  (:start . 127) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Subphylum") (:form . "Subphylum") (:end . 146)\n  (:start . 137) (:id . 65))\n ((:tag . "NNP") (:stem . "Mandibulata") (:form . "Mandibulata") (:end . 158)\n  (:start . 147) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 162) (:start . 160)\n  (:id . 68))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 170)\n  (:start . 163) (:id . 69))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 179)\n  (:start . 171) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 183) (:start . 180)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Arthropod") (:form . "Arthropods") (:end . 194)\n  (:start . 184) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x9.247.1) (:span 163 170)) ((:id . :x9.247.2) (:span 79 82))\n  ((:id . :x9.247.3) (:span 54 61)))\n (:hscopes ((:id . :x9.247.1) (:span 163 194))\n  ((:id . :x9.247.2) (:span 79 194)) ((:id . :x9.247.3) (:span 54 194)))\n (:identifiers (:sid . :s9.247) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503011@unknown@formal@none@1@S@With the evidence of a tick RdRP and the propensity for systemic or germ-line RNAi, it will be better to compare gene function and RNAi pathways between members of the Arachnida and the Superphylum Nemathelminthes (C. elegans).@(((:tag . "IN") (:stem . "with") (:form . "With") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "propensity") (:form . "propensity") (:end . 51)\n  (:start . 41) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "systemic") (:form . "systemic") (:end . 64)\n  (:start . 56) (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "germ-line") (:form . "germ-line") (:end . 77)\n  (:start . 68) (:id . 55))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 82) (:start . 78)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 86) (:start . 84)\n  (:id . 58))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 91) (:start . 87)\n  (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 94) (:start . 92)\n  (:id . 60))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 101)\n  (:start . 95) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n  (:id . 62))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 112)\n  (:start . 105) (:id . 63))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 117) (:start . 113)\n  (:id . 64))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 126)\n  (:start . 118) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 135) (:start . 131)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 144)\n  (:start . 136) (:id . 68))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 152)\n  (:start . 145) (:id . 69))\n ((:tag . "NNS") (:stem . "member") (:form . "members") (:end . 160)\n  (:start . 153) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Arachnida") (:form . "Arachnida") (:end . 177)\n  (:start . 168) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 181) (:start . 178)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Superphylum") (:form . "Superphylum") (:end . 197)\n  (:start . 186) (:id . 76))\n ((:tag . "NNP") (:stem . "Nemathelminthes") (:form . "Nemathelminthes")\n  (:end . 213) (:start . 198) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 215) (:start . 214)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 217) (:start . 215)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 225)\n  (:start . 218) (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 226) (:start . 225)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s9.248) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503012@unknown@formal@none@1@S@Until more tick and related genomes (mites and spiders) are available, such comparative studies within these Subphyla are not feasible.@(((:tag . "IN") (:stem . "until") (:form . "Until") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "NNS") (:stem . "genome") (:form . "genomes") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "mite") (:form . "mites") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "spider") (:form . "spiders") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 69)\n  (:start . 60) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "comparative") (:form . "comparative") (:end . 87)\n  (:start . 76) (:id . 57))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 95)\n  (:start . 88) (:id . 58))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 102)\n  (:start . 96) (:id . 59))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 108)\n  (:start . 103) (:id . 60))\n ((:tag . "NNP") (:stem . "Subphyla") (:form . "Subphyla") (:end . 117)\n  (:start . 109) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "feasible") (:form . "feasible") (:end . 134)\n  (:start . 126) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x9.249.1) (:span 126 134)))\n (:hscopes ((:id . :x9.249.1) (:span 71 134)))\n (:identifiers (:sid . :s9.249) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503013@unknown@formal@none@1@S@Clearly the RNAi pathways warrant further elucidation, and tick specific genome and functional data will be beneficial for tick research and for the development of improved tick control measures.@(((:tag . "RB") (:stem . "clearly") (:form . "Clearly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "VBP") (:stem . "warrant") (:form . "warrant") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "NN") (:stem . "elucidation") (:form . "elucidation") (:end . 53)\n  (:start . 42) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 50))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 63) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 72)\n  (:start . 64) (:id . 52))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 79)\n  (:start . 73) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 94)\n  (:start . 84) (:id . 55))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 104) (:start . 100)\n  (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "beneficial") (:form . "beneficial") (:end . 118)\n  (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 122) (:start . 119)\n  (:id . 60))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 127) (:start . 123)\n  (:id . 61))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 136)\n  (:start . 128) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 144) (:start . 141)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 65))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 160)\n  (:start . 149) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "improve") (:form . "improved") (:end . 172)\n  (:start . 164) (:id . 68))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 177) (:start . 173)\n  (:id . 69))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 185)\n  (:start . 178) (:id . 70))\n ((:tag . "NNS") (:stem . "measure") (:form . "measures") (:end . 194)\n  (:start . 186) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.250) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503014@unknown@formal@none@1@S@Methods@(((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s9.251) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503015@unknown@formal@none@1@S@Sources of input sequence data@(((:tag . "NNS") (:stem . "source") (:form . "Sources") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 30) (:start . 26)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s9.252) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503016@unknown@formal@none@1@S@13,643 ESTs (9,403 Tentative Consensus/TC and 4,240 singleton) sequences for R. microplus were obtained from the Boophilus microplus Gene Index (BmiGI) at http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=b_microplus (last accessed: 17/6/2008)[3].@(((:tag . "CD") (:stem . "13,643") (:form . "13,643") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "est") (:form . "ESTs") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "CD") (:stem . "9,403") (:form . "9,403") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "tentative") (:form . "Tentative") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "NNP") (:stem . "Consensus/TC") (:form . "Consensus/TC") (:end . 41)\n  (:start . 29) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "CD") (:stem . "4,240") (:form . "4,240") (:end . 51) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "singleton") (:form . "singleton") (:end . 61)\n  (:start . 52) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "microplu") (:form . "microplus") (:end . 89)\n  (:start . 80) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 103)\n  (:start . 95) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 108) (:start . 104)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Boophilus") (:form . "Boophilus") (:end . 122)\n  (:start . 113) (:id . 60))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 132)\n  (:start . 123) (:id . 61))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 137) (:start . 133)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Index") (:form . "Index") (:end . 143)\n  (:start . 138) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "BmiGI") (:form . "BmiGI") (:end . 150)\n  (:start . 145) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 66))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . "JJ")\n  (:stem\n   . "http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=b_microplus")\n  (:form\n   . "http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=b_microplus")\n  (:end . 229) (:start . 155) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 231) (:start . 230)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 235) (:start . 231)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "access") (:form . "accessed") (:end . 244)\n  (:start . 236) (:id . 71))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 245) (:start . 244)\n  (:id . 72))\n ((:tag . "CD") (:stem . "17/6/2008)[3") (:form . "17/6/2008)[3") (:end . 258)\n  (:start . 246) (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 259) (:start . 258)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 260) (:start . 259)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s9.253) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503017@unknown@formal@none@1@S@I. scapularis (black legged tick) genome project (IGP) data was accessed through http://www.ncbi.nlm.nih.gov/sites/entrez?@(((:tag . "LS") (:stem . "i.") (:form . "I.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "legge") (:form . "legged") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 40)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "project") (:form . "project") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "IGP") (:form . "IGP") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 54) (:start . 53)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 59) (:start . 55)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 63) (:start . 60)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "access") (:form . "accessed") (:end . 72)\n  (:start . 64) (:id . 56))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 80)\n  (:start . 73) (:id . 57))\n ((:tag . "NN") (:stem . "http://www.ncbi.nlm.nih.gov/sites/entrez")\n  (:form . "http://www.ncbi.nlm.nih.gov/sites/entrez") (:end . 121)\n  (:start . 81) (:id . 58))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 122) (:start . 121)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s9.254) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503018@unknown@formal@none@1@S@Db=genomeprj&cmd=ShowDetailView&TermToSearch=16233 (last accessed: 13/6/2008); and 38,276 I. scapularis EST sequences were obtained from the Ixodes scapularis Gene Index (ISGI) at http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=i_scapularis (last accessed: 17/6/2008).@(((:tag . "NNP")\n  (:stem . "Db=genomeprj&cmd=ShowDetailView&TermToSearch=16233")\n  (:form . "Db=genomeprj&cmd=ShowDetailView&TermToSearch=16233") (:end . 50)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 56) (:start . 52)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "access") (:form . "accessed") (:end . 65)\n  (:start . 57) (:id . 45))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 66) (:start . 65)\n  (:id . 46))\n ((:tag . "CD") (:stem . "13/6/2008") (:form . "13/6/2008") (:end . 76)\n  (:start . 67) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 78) (:start . 77)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 50))\n ((:tag . "CD") (:stem . "38,276") (:form . "38,276") (:end . 89)\n  (:start . 83) (:id . 51))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 92) (:start . 90)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 103)\n  (:start . 93) (:id . 53))\n ((:tag . "NNP") (:stem . "EST") (:form . "EST") (:end . 107) (:start . 104)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 117)\n  (:start . 108) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 122) (:start . 118)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 131)\n  (:start . 123) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 136) (:start . 132)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Ixodes") (:form . "Ixodes") (:end . 147)\n  (:start . 141) (:id . 60))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 158)\n  (:start . 148) (:id . 61))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 163) (:start . 159)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Index") (:form . "Index") (:end . 169)\n  (:start . 164) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 171) (:start . 170)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "ISGI") (:form . "ISGI") (:end . 175) (:start . 171)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 66))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 179) (:start . 177)\n  (:id . 67))\n ((:tag . "NNS")\n  (:stem\n   . "http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=i_scapularis")\n  (:form\n   . "http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=i_scapularis")\n  (:end . 255) (:start . 180) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 257) (:start . 256)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 261) (:start . 257)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "access") (:form . "accessed") (:end . 270)\n  (:start . 262) (:id . 71))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 271) (:start . 270)\n  (:id . 72))\n ((:tag . "CD") (:stem . "17/6/2008") (:form . "17/6/2008") (:end . 281)\n  (:start . 272) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 282) (:start . 281)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 283) (:start . 282)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s9.255) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503019@unknown@formal@none@1@S@All other nucleotide and amino acid sequences were obtained from the Entrez nucleotide and protein databases http://www.ncbi.nlm.nih.gov/sites/entrez.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "nucleotide") (:form . "nucleotide") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 45)\n  (:start . 36) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Entrez") (:form . "Entrez") (:end . 75)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "nucleotide") (:form . "nucleotide") (:end . 86)\n  (:start . 76) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 98)\n  (:start . 91) (:id . 56))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 108)\n  (:start . 99) (:id . 57))\n ((:tag . "NN") (:stem . "http://www.ncbi.nlm.nih.gov/sites/entrez")\n  (:form . "http://www.ncbi.nlm.nih.gov/sites/entrez") (:end . 149)\n  (:start . 109) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s9.256) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503020@unknown@formal@none@1@S@Identification of conserved genes in R. microplus@(((:tag . "NN") (:stem . "identification") (:form . "Identification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 27)\n  (:start . 18) (:id . 44))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 33) (:start . 28)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "microplu") (:form . "microplus") (:end . 49)\n  (:start . 40) (:id . 48)))@@@1@7@((:identifiers (:sid . :s9.257) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503021@unknown@formal@none@1@S@Key RNAi pathway-associated proteins from D. melanogaster and C. elegans described previously [28,32,35,36,45,46,50,73,74] were screened against the available tick ESTs (BmiGI2) [3] and I. scapularis genome contig reads obtained from the NCBI whole genome project database (project ID 16233) using BLAST [62].@(((:tag . "NNP") (:stem . "Key") (:form . "Key") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "pathway-associated") (:form . "pathway-associated")\n  (:end . 27) (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 36)\n  (:start . 28) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 41) (:start . 37)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 57)\n  (:start . 45) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "elegan") (:form . "elegans") (:end . 72)\n  (:start . 65) (:id . 51))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 82)\n  (:start . 73) (:id . 52))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 93)\n  (:start . 83) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 95) (:start . 94)\n  (:id . 54))\n ((:tag . "CD") (:stem . "28,32,35,36,45,46,50,73,74")\n  (:form . "28,32,35,36,45,46,50,73,74") (:end . 121) (:start . 95)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 122) (:start . 121)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 127) (:start . 123)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "screen") (:form . "screened") (:end . 136)\n  (:start . 128) (:id . 58))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 144)\n  (:start . 137) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 158)\n  (:start . 149) (:id . 61))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 163) (:start . 159)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "est") (:form . "ESTs") (:end . 168) (:start . 164)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 170) (:start . 169)\n  (:id . 64))\n ((:tag . "NN") (:stem . "bmigi2") (:form . "BmiGI2") (:end . 176)\n  (:start . 170) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 177) (:start . 176)\n  (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 179) (:start . 178)\n  (:id . 67))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 180) (:start . 179)\n  (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 181) (:start . 180)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n  (:id . 70))\n ((:tag . "NN") (:stem . "i.") (:form . "I.") (:end . 188) (:start . 186)\n  (:id . 71))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 199)\n  (:start . 189) (:id . 72))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 206)\n  (:start . 200) (:id . 73))\n ((:tag . "NN") (:stem . "contig") (:form . "contig") (:end . 213)\n  (:start . 207) (:id . 74))\n ((:tag . "NNS") (:stem . "read") (:form . "reads") (:end . 219)\n  (:start . 214) (:id . 75))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 228)\n  (:start . 220) (:id . 76))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 233) (:start . 229)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 237) (:start . 234)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "NCBI") (:form . "NCBI") (:end . 242) (:start . 238)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 248)\n  (:start . 243) (:id . 80))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 255)\n  (:start . 249) (:id . 81))\n ((:tag . "NN") (:stem . "project") (:form . "project") (:end . 263)\n  (:start . 256) (:id . 82))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 272)\n  (:start . 264) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 274) (:start . 273)\n  (:id . 84))\n ((:tag . "NN") (:stem . "project") (:form . "project") (:end . 281)\n  (:start . 274) (:id . 85))\n ((:tag . "NNP") (:stem . "ID") (:form . "ID") (:end . 284) (:start . 282)\n  (:id . 86))\n ((:tag . "CD") (:stem . "16233") (:form . "16233") (:end . 290)\n  (:start . 285) (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 291) (:start . 290)\n  (:id . 88))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 297) (:start . 292)\n  (:id . 89))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 303)\n  (:start . 298) (:id . 90))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 305) (:start . 304)\n  (:id . 91))\n ((:tag . "CD") (:stem . "62") (:form . "62") (:end . 307) (:start . 305)\n  (:id . 92))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 308) (:start . 307)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 309) (:start . 308)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s9.258) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503022@unknown@formal@none@1@S@For the BLAST searches an initial e-value of <1e-05 was set as a threshold.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "search") (:form . "searches") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "e-value") (:form . "e-value") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "CD") (:stem . "<1e-05") (:form . "<1e-05") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 74)\n  (:start . 65) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s9.259) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503023@unknown@formal@none@1@S@The best hits from the R. microplus and I. scapularis sequences where then used as query sequences in a second round of BLAST searches against the D. melanogaster and C. elegans subsets of the NCBI non-redundant protein database.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 35)\n  (:start . 26) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "i.") (:form . "I.") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 53)\n  (:start . 43) (:id . 51))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 88) (:start . 83)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 98)\n  (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 110)\n  (:start . 104) (:id . 61))\n ((:tag . "NN") (:stem . "round") (:form . "round") (:end . 116)\n  (:start . 111) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 63))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 125)\n  (:start . 120) (:id . 64))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 134)\n  (:start . 126) (:id . 65))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 142)\n  (:start . 135) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 149) (:start . 147)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 162) (:start . 150) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 169) (:start . 167)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 177)\n  (:start . 170) (:id . 72))\n ((:tag . "NNS") (:stem . "subset") (:form . "subsets") (:end . 185)\n  (:start . 178) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 188) (:start . 186)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 192) (:start . 189)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "NCBI") (:form . "NCBI") (:end . 197) (:start . 193)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "non-redundant") (:form . "non-redundant")\n  (:end . 211) (:start . 198) (:id . 77))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 219)\n  (:start . 212) (:id . 78))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 228)\n  (:start . 220) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s9.260) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503024@unknown@formal@none@1@S@Results of this reciprocal BLAST search validated the sequence similarity between the key RNAi pathway-associated proteins from D. melanogaster and C. elegans and the two ixodid tick species, sequences which did not return the corresponding RNAi protein were subsequently disregarded.@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "reciprocal") (:form . "reciprocal") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "VBD") (:stem . "validate") (:form . "validated") (:end . 49)\n  (:start . 40) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 73)\n  (:start . 63) (:id . 51))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 81)\n  (:start . 74) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 89) (:start . 86)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "pathway-associated") (:form . "pathway-associated")\n  (:end . 113) (:start . 95) (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 122)\n  (:start . 114) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 127) (:start . 123)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 130) (:start . 128)\n  (:id . 59))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 143)\n  (:start . 131) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 150) (:start . 148)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 158)\n  (:start . 151) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 65))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 170) (:start . 167)\n  (:id . 66))\n ((:tag . "VBD") (:stem . "ixodid") (:form . "ixodid") (:end . 177)\n  (:start . 171) (:id . 67))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 182) (:start . 178)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 190)\n  (:start . 183) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 201)\n  (:start . 192) (:id . 71))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 207)\n  (:start . 202) (:id . 72))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 211) (:start . 208)\n  (:id . 73))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 215) (:start . 212)\n  (:id . 74))\n ((:tag . "VB") (:stem . "return") (:form . "return") (:end . 222)\n  (:start . 216) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 226) (:start . 223)\n  (:id . 76))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 240)\n  (:start . 227) (:id . 77))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 245) (:start . 241)\n  (:id . 78))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 253)\n  (:start . 246) (:id . 79))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 258) (:start . 254)\n  (:id . 80))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 271)\n  (:start . 259) (:id . 81))\n ((:tag . "VBN") (:stem . "disregard") (:form . "disregarded") (:end . 283)\n  (:start . 272) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 284) (:start . 283)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s9.261) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503025@unknown@formal@none@1@S@Further confirmation was obtained by performing searches against the InterPro database using InterProScan (data not shown) [63].@(((:tag . "JJ") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "confirmation") (:form . "confirmation") (:end . 20)\n  (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "perform") (:form . "performing") (:end . 47)\n  (:start . 37) (:id . 47))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 56)\n  (:start . 48) (:id . 48))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 64)\n  (:start . 57) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "InterPro") (:form . "InterPro") (:end . 77)\n  (:start . 69) (:id . 51))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 86)\n  (:start . 78) (:id . 52))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 92) (:start . 87)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "InterProScan") (:form . "InterProScan")\n  (:end . 105) (:start . 93) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 111)\n  (:start . 107) (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 115) (:start . 112)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 121)\n  (:start . 116) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 124) (:start . 123)\n  (:id . 60))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 126) (:start . 124)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 127) (:start . 126)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s9.262) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503026@unknown@formal@none@1@S@All searches were performed with the BLAST default settings.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s9.263) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503027@unknown@formal@none@1@S@Specific approaches for Dicer, Argonautes and RdRP homologues are described below.@(((:tag . "JJ") (:stem . "specific") (:form . "Specific") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 19)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 23) (:start . 20)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 29) (:start . 24)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Argonaute") (:form . "Argonautes") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 61)\n  (:start . 51) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 75)\n  (:start . 66) (:id . 52))\n ((:tag . "RB") (:stem . "below") (:form . "below") (:end . 81) (:start . 76)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s9.264) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503028@unknown@formal@none@1@S@Multiple sequence alignments for the domains typical for proteins of the Dicer family were retrieved from the Pfam website.@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 28)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 32) (:start . 29)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "JJ") (:stem . "typical") (:form . "typical") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 65)\n  (:start . 57) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 78) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 85)\n  (:start . 79) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 90) (:start . 86)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "retrieve") (:form . "retrieved") (:end . 100)\n  (:start . 91) (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 105) (:start . 101)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 114) (:start . 110)\n  (:id . 59))\n ((:tag . "NN") (:stem . "website") (:form . "website") (:end . 122)\n  (:start . 115) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s9.265) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503029@unknown@formal@none@1@S@Specifically these were the alignments for the Helicase conserved C terminal domain (Pfam:PF00271), double-stranded RNA binding domain (Pfam:PF03368), PAZ domain (Pfam:PF02170), RNase3 domain (Pfam:PF00636), and the double-stranded RNA binding motif (Pfam:PF00035).@(((:tag . "RB") (:stem . "specifically") (:form . "Specifically") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 18) (:start . 13)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Helicase") (:form . "Helicase") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 65)\n  (:start . 56) (:id . 50))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 67) (:start . 66)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 76)\n  (:start . 68) (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 83)\n  (:start . 77) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Pfam:PF00271") (:form . "Pfam:PF00271") (:end . 97)\n  (:start . 85) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "double-stranded") (:form . "double-stranded")\n  (:end . 115) (:start . 100) (:id . 58))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 119) (:start . 116)\n  (:id . 59))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 127)\n  (:start . 120) (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 134)\n  (:start . 128) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 136) (:start . 135)\n  (:id . 62))\n ((:tag . "NN") (:stem . "Pfam:PF03368") (:form . "Pfam:PF03368") (:end . 148)\n  (:start . 136) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "PAZ") (:form . "PAZ") (:end . 154) (:start . 151)\n  (:id . 66))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 161)\n  (:start . 155) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 163) (:start . 162)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Pfam:PF02170") (:form . "Pfam:PF02170")\n  (:end . 175) (:start . 163) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 71))\n ((:tag . "NN") (:stem . "rnase3") (:form . "RNase3") (:end . 184)\n  (:start . 178) (:id . 72))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 191)\n  (:start . 185) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 193) (:start . 192)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Pfam:PF00636") (:form . "Pfam:PF00636")\n  (:end . 205) (:start . 193) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 207) (:start . 206)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 211) (:start . 208)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 215) (:start . 212)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "double-stranded") (:form . "double-stranded")\n  (:end . 231) (:start . 216) (:id . 80))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 235) (:start . 232)\n  (:id . 81))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 243)\n  (:start . 236) (:id . 82))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 249)\n  (:start . 244) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 251) (:start . 250)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Pfam:PF00035") (:form . "Pfam:PF00035")\n  (:end . 263) (:start . 251) (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 264) (:start . 263)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s9.266) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503030@unknown@formal@none@1@S@Hidden Markov Models (HMMs) were constructed locally using hmmbuild of the HMMER2 package [64] with default settings.@(((:tag . "NNP") (:stem . "Hidden") (:form . "Hidden") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Markov") (:form . "Markov") (:end . 13)\n  (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "Models") (:form . "Models") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "HMM") (:form . "HMMs") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 44)\n  (:start . 33) (:id . 49))\n ((:tag . "RB") (:stem . "locally") (:form . "locally") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 58) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "hmmbuild") (:form . "hmmbuild") (:end . 67)\n  (:start . 59) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "hmmer2") (:form . "HMMER2") (:end . 81)\n  (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "CD") (:stem . "64") (:form . "64") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 99) (:start . 95)\n  (:id . 60))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 107)\n  (:start . 100) (:id . 61))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 116)\n  (:start . 108) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s9.267) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503031@unknown@formal@none@1@S@The programs estwisedb and genewisedb of the Wise2 package [65] were used to perform searches with each HMM as a query in a local copy of the BmiGI2 database and the I. scapularis sequences obtained from NCBI whole genome sequencing projects.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "estwisedb") (:form . "estwisedb") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "genewisedb") (:form . "genewisedb") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "wise2") (:form . "Wise2") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 58)\n  (:start . 51) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 60) (:start . 59)\n  (:id . 51))\n ((:tag . "CD") (:stem . "65") (:form . "65") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 73) (:start . 69)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . "VB") (:stem . "perform") (:form . "perform") (:end . 84)\n  (:start . 77) (:id . 57))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 93)\n  (:start . 85) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 103) (:start . 99)\n  (:id . 60))\n ((:tag . "NN") (:stem . "hmm") (:form . "HMM") (:end . 107) (:start . 104)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 118)\n  (:start . 113) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 123) (:start . 122)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 129)\n  (:start . 124) (:id . 67))\n ((:tag . "NN") (:stem . "copy") (:form . "copy") (:end . 134) (:start . 130)\n  (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 70))\n ((:tag . "NN") (:stem . "bmigi2") (:form . "BmiGI2") (:end . 148)\n  (:start . 142) (:id . 71))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 157)\n  (:start . 149) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 168) (:start . 166)\n  (:id . 75))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 179)\n  (:start . 169) (:id . 76))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 189)\n  (:start . 180) (:id . 77))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 198)\n  (:start . 190) (:id . 78))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 203) (:start . 199)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "NCBI") (:form . "NCBI") (:end . 208) (:start . 204)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 214)\n  (:start . 209) (:id . 81))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 221)\n  (:start . 215) (:id . 82))\n ((:tag . "NN") (:stem . "sequencing") (:form . "sequencing") (:end . 232)\n  (:start . 222) (:id . 83))\n ((:tag . "NNS") (:stem . "project") (:form . "projects") (:end . 241)\n  (:start . 233) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 242) (:start . 241)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s9.268) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503032@unknown@formal@none@1@S@The best hit sequences from these searches were retrieved from the respective databases and a conceptual translation of encoded open reading frames (ORFs) was performed using the program getorf, part of the EMBOSS package of computational biology tools.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "hit") (:form . "hit") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "retrieve") (:form . "retrieved") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 77)\n  (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 87)\n  (:start . 78) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 93) (:start . 92)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "conceptual") (:form . "conceptual") (:end . 104)\n  (:start . 94) (:id . 57))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 116)\n  (:start . 105) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 127)\n  (:start . 120) (:id . 60))\n ((:tag . "JJ") (:stem . "open") (:form . "open") (:end . 132) (:start . 128)\n  (:id . 61))\n ((:tag . "NN") (:stem . "reading") (:form . "reading") (:end . 140)\n  (:start . 133) (:id . 62))\n ((:tag . "NNS") (:stem . "frame") (:form . "frames") (:end . 147)\n  (:start . 141) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 149) (:start . 148)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "ORF") (:form . "ORFs") (:end . 153) (:start . 149)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 158) (:start . 155)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 168)\n  (:start . 159) (:id . 68))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 174) (:start . 169)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 70))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 186)\n  (:start . 179) (:id . 71))\n ((:tag . "NN") (:stem . "getorf") (:form . "getorf") (:end . 193)\n  (:start . 187) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 194) (:start . 193)\n  (:id . 73))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 199) (:start . 195)\n  (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 202) (:start . 200)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 206) (:start . 203)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "EMBOSS") (:form . "EMBOSS") (:end . 213)\n  (:start . 207) (:id . 77))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 221)\n  (:start . 214) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 224) (:start . 222)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n  (:end . 238) (:start . 225) (:id . 80))\n ((:tag . "NN") (:stem . "biology") (:form . "biology") (:end . 246)\n  (:start . 239) (:id . 81))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 252)\n  (:start . 247) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 253) (:start . 252)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s9.269) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503033@unknown@formal@none@1@S@The ORFs were then used as the query sequence for a blastp search against the NCBI Reference Sequence protein database to verify the validity of the initial search results.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 36) (:start . 31)\n  (:id . 49))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 45)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "blastp") (:form . "blastp") (:end . 58)\n  (:start . 52) (:id . 53))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 65)\n  (:start . 59) (:id . 54))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 73)\n  (:start . 66) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "NCBI") (:form . "NCBI") (:end . 82) (:start . 78)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Reference") (:form . "Reference") (:end . 92)\n  (:start . 83) (:id . 58))\n ((:tag . "NN") (:stem . "sequence") (:form . "Sequence") (:end . 101)\n  (:start . 93) (:id . 59))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 109)\n  (:start . 102) (:id . 60))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 118)\n  (:start . 110) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "VB") (:stem . "verify") (:form . "verify") (:end . 128)\n  (:start . 122) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 64))\n ((:tag . "NN") (:stem . "validity") (:form . "validity") (:end . 141)\n  (:start . 133) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 156)\n  (:start . 149) (:id . 68))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 163)\n  (:start . 157) (:id . 69))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 171)\n  (:start . 164) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s9.270) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503034@unknown@formal@none@1@S@Further confirmation of the search results was achieved by screening the ORFs against the Pfam database using the global search model.@(((:tag . "JJ") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "confirmation") (:form . "confirmation") (:end . 20)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 42)\n  (:start . 35) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "screen") (:form . "screening") (:end . 68)\n  (:start . 59) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 85)\n  (:start . 78) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 103)\n  (:start . 95) (:id . 57))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 109) (:start . 104)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 120)\n  (:start . 114) (:id . 60))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 127)\n  (:start . 121) (:id . 61))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 133)\n  (:start . 128) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s9.271) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503035@unknown@formal@none@1@S@For the prediction of gene models and the identification of the exon/intron structure, the program genewise from the Wise2 package was used to map the detected ORFs to the genomic sequences.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 33)\n  (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 56) (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "exon/intron") (:form . "exon/intron") (:end . 75)\n  (:start . 64) (:id . 53))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 85)\n  (:start . 76) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 98)\n  (:start . 91) (:id . 57))\n ((:tag . "RB") (:stem . "genewise") (:form . "genewise") (:end . 107)\n  (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 112) (:start . 108)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "NN") (:stem . "wise2") (:form . "Wise2") (:end . 122)\n  (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 130)\n  (:start . 123) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 139) (:start . 135)\n  (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 65))\n ((:tag . "VB") (:stem . "map") (:form . "map") (:end . 146) (:start . 143)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 159)\n  (:start . 151) (:id . 68))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 164) (:start . 160)\n  (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 167) (:start . 165)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 171) (:start . 168)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "genomic") (:form . "genomic") (:end . 179)\n  (:start . 172) (:id . 72))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 189)\n  (:start . 180) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s9.272) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503036@unknown@formal@none@1@S@I. scapularis expressed sequence tags from the I. scapularis ISGI2 database were used in blastn searches to verify the validity of the predicted exon/intron structure by genewise.@(((:tag . "LS") (:stem . "i.") (:form . "I.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "NNS") (:stem . "tag") (:form . "tags") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "isgi2") (:form . "ISGI2") (:end . 66) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 75)\n  (:start . 67) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 80) (:start . 76)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 85) (:start . 81)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "NN") (:stem . "blastn") (:form . "blastn") (:end . 95)\n  (:start . 89) (:id . 56))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 104)\n  (:start . 96) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "VB") (:stem . "verify") (:form . "verify") (:end . 114)\n  (:start . 108) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 60))\n ((:tag . "NN") (:stem . "validity") (:form . "validity") (:end . 127)\n  (:start . 119) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 144)\n  (:start . 135) (:id . 64))\n ((:tag . "NN") (:stem . "exon/intron") (:form . "exon/intron") (:end . 156)\n  (:start . 145) (:id . 65))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 166)\n  (:start . 157) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 169) (:start . 167)\n  (:id . 67))\n ((:tag . "NN") (:stem . "genewise") (:form . "genewise") (:end . 178)\n  (:start . 170) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s9.273) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503037@unknown@formal@none@1@S@The sequences of the ORFs were also screened against a local copy of the Pfam database using the program hmmpfam of the HMMER2 package to reveal the sequence structure of the conserved domains.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "screen") (:form . "screened") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "copy") (:form . "copy") (:end . 65) (:start . 61)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 77) (:start . 73)\n  (:id . 56))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 86)\n  (:start . 78) (:id . 57))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 92) (:start . 87)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 104)\n  (:start . 97) (:id . 60))\n ((:tag . "NN") (:stem . "hmmpfam") (:form . "hmmpfam") (:end . 112)\n  (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 63))\n ((:tag . "NN") (:stem . "hmmer2") (:form . "HMMER2") (:end . 126)\n  (:start . 120) (:id . 64))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 134)\n  (:start . 127) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 137) (:start . 135)\n  (:id . 66))\n ((:tag . "VB") (:stem . "reveal") (:form . "reveal") (:end . 144)\n  (:start . 138) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 68))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 157)\n  (:start . 149) (:id . 69))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 167)\n  (:start . 158) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 170) (:start . 168)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 174) (:start . 171)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 184)\n  (:start . 175) (:id . 73))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 192)\n  (:start . 185) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s9.274) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503038@unknown@formal@none@1@S@Multiple sequence alignments of amino acid sequences stored in the Pfam database were obtained for following protein domains and domain families: Domain of unknown function (DUF)1785 (Pfam:PF08699), PAZ domain (Pfam:PF02170) and Piwi (Pfam:PF02171).@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 28)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 37) (:start . 32)\n  (:id . 46))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 52)\n  (:start . 43) (:id . 48))\n ((:tag . "VBN") (:stem . "store") (:form . "stored") (:end . 59)\n  (:start . 53) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 80)\n  (:start . 72) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 85) (:start . 81)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 94)\n  (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 98) (:start . 95)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 108)\n  (:start . 99) (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 116)\n  (:start . 109) (:id . 58))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 124)\n  (:start . 117) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 135)\n  (:start . 129) (:id . 61))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 144)\n  (:start . 136) (:id . 62))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 145) (:start . 144)\n  (:id . 63))\n ((:tag . "NN") (:stem . "domain") (:form . "Domain") (:end . 152)\n  (:start . 146) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "unknown") (:form . "unknown") (:end . 163)\n  (:start . 156) (:id . 66))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 172)\n  (:start . 164) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "DUF)1785") (:form . "DUF)1785") (:end . 182)\n  (:start . 174) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 184) (:start . 183)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Pfam:PF08699") (:form . "Pfam:PF08699")\n  (:end . 196) (:start . 184) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 197) (:start . 196)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 198) (:start . 197)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "PAZ") (:form . "PAZ") (:end . 202) (:start . 199)\n  (:id . 74))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 209)\n  (:start . 203) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 211) (:start . 210)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Pfam:PF02170") (:form . "Pfam:PF02170")\n  (:end . 223) (:start . 211) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 224) (:start . 223)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 228) (:start . 225)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Piwi") (:form . "Piwi") (:end . 233) (:start . 229)\n  (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 235) (:start . 234)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Pfam:PF02171") (:form . "Pfam:PF02171")\n  (:end . 247) (:start . 235) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 248) (:start . 247)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 249) (:start . 248)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s9.275) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503039@unknown@formal@none@1@S@HMMs were built from the multiple sequence alignments using the program hmmbuild with default settings.@(((:tag . "NNP") (:stem . "HMM") (:form . "HMMs") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "build") (:form . "built") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 53)\n  (:start . 43) (:id . 49))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "NN") (:stem . "hmmbuild") (:form . "hmmbuild") (:end . 80)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 85) (:start . 81)\n  (:id . 54))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 102)\n  (:start . 94) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s9.276) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503040@unknown@formal@none@1@S@The BmiGI2 database and I. scapularis sequences were searched with the programs estwisedb and genewisedb using the HMMs as query sequences.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bmigi2") (:form . "BmiGI2") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "i.") (:form . "I.") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "scapularis") (:form . "scapularis") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "search") (:form . "searched") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . "NN") (:stem . "estwisedb") (:form . "estwisedb") (:end . 89)\n  (:start . 80) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "genewisedb") (:form . "genewisedb") (:end . 104)\n  (:start . 94) (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 110) (:start . 105)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "hmm") (:form . "HMMs") (:end . 119) (:start . 115)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 122) (:start . 120)\n  (:id . 60))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 128)\n  (:start . 123) (:id . 61))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 138)\n  (:start . 129) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s9.277) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503041@unknown@formal@none@1@S@The program getorf was used to conceptually translate the ORFs of the best hits.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "getorf") (:form . "getorf") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "RB") (:stem . "conceptually") (:form . "conceptually") (:end . 43)\n  (:start . 31) (:id . 48))\n ((:tag . "VB") (:stem . "translate") (:form . "translate") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s9.278) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503042@unknown@formal@none@1@S@The validity of the initial search results was verified by blastp searches against the NCBI Reference Sequence protein database.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "validity") (:form . "validity") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 42)\n  (:start . 35) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "blastp") (:form . "blastp") (:end . 65)\n  (:start . 59) (:id . 52))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 82)\n  (:start . 75) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "NCBI") (:form . "NCBI") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Reference") (:form . "Reference") (:end . 101)\n  (:start . 92) (:id . 57))\n ((:tag . "NN") (:stem . "sequence") (:form . "Sequence") (:end . 110)\n  (:start . 102) (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 118)\n  (:start . 111) (:id . 59))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 127)\n  (:start . 119) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s9.279) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503043@unknown@formal@none@1@S@Further confirmation of the search results was achieved by screening the ORFs against the Pfam database using the global search model.@(((:tag . "JJ") (:stem . "further") (:form . "Further") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "confirmation") (:form . "confirmation") (:end . 20)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 42)\n  (:start . 35) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "screen") (:form . "screening") (:end . 68)\n  (:start . 59) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 85)\n  (:start . 78) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 103)\n  (:start . 95) (:id . 57))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 109) (:start . 104)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 120)\n  (:start . 114) (:id . 60))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 127)\n  (:start . 121) (:id . 61))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 133)\n  (:start . 128) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s9.280) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503044@unknown@formal@none@1@S@A comparison between known Argonaute proteins from D. melanogaster and C. elegans was performed using the program bl2seq, which uses the BLAST algorithm for a pairwise comparison.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 12)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "argonaute") (:form . "Argonaute") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 50) (:start . 46)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 66)\n  (:start . 54) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 81)\n  (:start . 74) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 95)\n  (:start . 86) (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 101) (:start . 96)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 57))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 113)\n  (:start . 106) (:id . 58))\n ((:tag . "NN") (:stem . "bl2seq") (:form . "bl2seq") (:end . 120)\n  (:start . 114) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 127)\n  (:start . 122) (:id . 61))\n ((:tag . "VBZ") (:stem . "use") (:form . "uses") (:end . 132) (:start . 128)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 63))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 142)\n  (:start . 137) (:id . 64))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 152)\n  (:start . 143) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 156) (:start . 153)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 158) (:start . 157)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "pairwise") (:form . "pairwise") (:end . 167)\n  (:start . 159) (:id . 68))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 178)\n  (:start . 168) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s9.281) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503045@unknown@formal@none@1@S@Multiple sequence alignments of the protein sequences and ORFs were performed using Clustalw [66] with default program settings.@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 28)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 53)\n  (:start . 44) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "orf") (:form . "ORFs") (:end . 62) (:start . 58)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 77)\n  (:start . 68) (:id . 52))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 83) (:start . 78)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Clustalw") (:form . "Clustalw") (:end . 92)\n  (:start . 84) (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 94) (:start . 93)\n  (:id . 55))\n ((:tag . "CD") (:stem . "66") (:form . "66") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 97) (:start . 96)\n  (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 102) (:start . 98)\n  (:id . 58))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 110)\n  (:start . 103) (:id . 59))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 118)\n  (:start . 111) (:id . 60))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 127)\n  (:start . 119) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.282) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503046@unknown@formal@none@1@S@In addition to the Dicer sequences illustrated in Figure 1a, following protein sequences were included in the construction of the phylogenetic tree (Figure 1b): Bos taurus Dicer-1 [GenBank:NP_976235.1] and T. castaneum Dicer-2 [GenBank:NP_001107840.1].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Dicer") (:form . "Dicer") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "VBN") (:stem . "illustrate") (:form . "illustrated") (:end . 46)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 70)\n  (:start . 61) (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 78)\n  (:start . 71) (:id . 54))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 88)\n  (:start . 79) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 102)\n  (:start . 94) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "NN") (:stem . "construction") (:form . "construction") (:end . 122)\n  (:start . 110) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 142)\n  (:start . 130) (:id . 63))\n ((:tag . "NN") (:stem . "tree") (:form . "tree") (:end . 147) (:start . 143)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 149) (:start . 148)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 155)\n  (:start . 149) (:id . 66))\n ((:tag . "NN") (:stem . "1b") (:form . "1b") (:end . 158) (:start . 156)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 68))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 160) (:start . 159)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Bo") (:form . "Bos") (:end . 164) (:start . 161)\n  (:id . 70))\n ((:tag . "NN") (:stem . "taurus") (:form . "taurus") (:end . 171)\n  (:start . 165) (:id . 71))\n ((:tag . "NNP") (:stem . "Dicer-1") (:form . "Dicer-1") (:end . 179)\n  (:start . 172) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 181) (:start . 180)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "GenBank:NP_976235.1")\n  (:form . "GenBank:NP_976235.1") (:end . 200) (:start . 181) (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 201) (:start . 200)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 205) (:start . 202)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "T.") (:form . "T.") (:end . 208) (:start . 206)\n  (:id . 77))\n ((:tag . "NN") (:stem . "castaneum") (:form . "castaneum") (:end . 218)\n  (:start . 209) (:id . 78))\n ((:tag . "NN") (:stem . "dicer-2") (:form . "Dicer-2") (:end . 226)\n  (:start . 219) (:id . 79))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 228) (:start . 227)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "GenBank:NP_001107840.1")\n  (:form . "GenBank:NP_001107840.1") (:end . 250) (:start . 228) (:id . 81))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 251) (:start . 250)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s9.283) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503047@unknown@formal@none@1@S@The phylogenetic trees (Figures 2b and 3b) for Argonaute-1 and Argonaute-2 were constructed using additional sequences from C. elegans [GenBank:NP_510322.2] and [GenBank:NP_871992.1], T. castaneum [GenBank:XP_971295.2] and [GenBank: NP_001107842.1] and B. taurus [GenBank:NP_991363.1] and [GenBank:AAS21301.1].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "tree") (:form . "trees") (:end . 22) (:start . 17)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "2b") (:form . "2b") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "3b") (:form . "3b") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 58)\n  (:start . 47) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "argonaute-2") (:form . "Argonaute-2") (:end . 74)\n  (:start . 63) (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 91)\n  (:start . 80) (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 97) (:start . 92)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 108)\n  (:start . 98) (:id . 58))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 118)\n  (:start . 109) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 123) (:start . 119)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "C.") (:form . "C.") (:end . 126) (:start . 124)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "elegans") (:form . "elegans") (:end . 134)\n  (:start . 127) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 136) (:start . 135)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "GenBank:NP_510322.2")\n  (:form . "GenBank:NP_510322.2") (:end . 155) (:start . 136) (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 156) (:start . 155)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 162) (:start . 161)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "GenBank:NP_871992.1")\n  (:form . "GenBank:NP_871992.1") (:end . 181) (:start . 162) (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 182) (:start . 181)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "T.") (:form . "T.") (:end . 186) (:start . 184)\n  (:id . 71))\n ((:tag . "NN") (:stem . "castaneum") (:form . "castaneum") (:end . 196)\n  (:start . 187) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 198) (:start . 197)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "GenBank:XP_971295.2")\n  (:form . "GenBank:XP_971295.2") (:end . 217) (:start . 198) (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 218) (:start . 217)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 222) (:start . 219)\n  (:id . 76))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 224) (:start . 223)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 231)\n  (:start . 224) (:id . 78))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 232) (:start . 231)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "NP_001107842.1") (:form . "NP_001107842.1")\n  (:end . 247) (:start . 233) (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 248) (:start . 247)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 252) (:start . 249)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "B.") (:form . "B.") (:end . 255) (:start . 253)\n  (:id . 83))\n ((:tag . "NN") (:stem . "taurus") (:form . "taurus") (:end . 262)\n  (:start . 256) (:id . 84))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 264) (:start . 263)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "GenBank:NP_991363.1")\n  (:form . "GenBank:NP_991363.1") (:end . 283) (:start . 264) (:id . 86))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 284) (:start . 283)\n  (:id . 87))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 288) (:start . 285)\n  (:id . 88))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 290) (:start . 289)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "GenBank:AAS21301.1") (:form . "GenBank:AAS21301.1")\n  (:end . 308) (:start . 290) (:id . 90))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 309) (:start . 308)\n  (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 310) (:start . 309)\n  (:id . 92)))@@@1@51@((:identifiers (:sid . :s9.284) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503048@unknown@formal@none@1@S@For both Argonaute-1 and 2 proteins, the phylogenetic trees were based on the alignments of the DUF1785 and PAZ domains.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "argonaute-1") (:form . "Argonaute-1") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 53)\n  (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "tree") (:form . "trees") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 88)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "DUF1785") (:form . "DUF1785") (:end . 103)\n  (:start . 96) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "PAZ") (:form . "PAZ") (:end . 111) (:start . 108)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 119)\n  (:start . 112) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s9.285) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503049@unknown@formal@none@1@S@The phylogenetic tree (Figure 4) for the partial R. microplus RdRP protein (Cat-RdRP) was constructed using additional RdRP domain (Pfam:05183) sequences from the metazoans: C. elegans (Ego-1 [GenBank:NP_492132.1], rrf-1 [GenBank:NP_492131.1] and rrf-3 [GenBank:NP_495713.1]) and I. scapularis ([GenBank:EEC04985.1], [GenBank:EEC05952.1], [GenBank:EEC12509.1], [GenBank:EEC12909.1]); plants: Arabidopsis thaliana [GenBank: NP_172932], Hordeum vulgare [GenBank:ACH53360.1], Nicotiana tabacum [GenBank:CAR47810.1], and Solanum lycopersicum [GenBank:ABI34311.1]; fungi: Aspergillus fumigatus [GenBank:EDP48577.1], Neurospora crassa [GenBank:XP_964248.2] and Schizosaccharomyces pombe [GenBank:NP_593295.1]; and protists: Dictyostelium discoideum [GenBank:XP_636093.1] and Tetrahymena thermophila [GenBank:XP_001026321.1].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . 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5503050@unknown@formal@none@1@S@The conserved RdRP domains were extracted from these sequences and then used for the alignment to the partial R. microplus RdRP domain.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 62)\n  (:start . 53) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "partial") (:form . "partial") (:end . 109)\n  (:start . 102) (:id . 59))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 122)\n  (:start . 113) (:id . 61))\n ((:tag . "NNP") (:stem . "RdRP") (:form . "RdRP") (:end . 127) (:start . 123)\n  (:id . 62))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 134)\n  (:start . 128) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.287) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503051@unknown@formal@none@1@S@The multiple sequence alignments for all 3 studied proteins were visually inspected and the phylogenetic trees were constructed using Geneious 3.8.5 http://www.geneious.com, last accessed on 12/08/08).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 32)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "study") (:form . "studied") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "RB") (:stem . "visually") (:form . "visually") (:end . 73)\n  (:start . 65) (:id . 52))\n ((:tag . "VBN") (:stem . "inspect") (:form . "inspected") (:end . 83)\n  (:start . 74) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 104)\n  (:start . 92) (:id . 56))\n ((:tag . "NNS") (:stem . "tree") (:form . "trees") (:end . 110)\n  (:start . 105) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 115) (:start . 111)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 127)\n  (:start . 116) (:id . 59))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 133) (:start . 128)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "geneious") (:form . "Geneious") (:end . 142)\n  (:start . 134) (:id . 61))\n ((:tag . "CD") (:stem . "3.8.5") (:form . "3.8.5") (:end . 148)\n  (:start . 143) (:id . 62))\n ((:tag . "NN") (:stem . "http://www.geneious.com")\n  (:form . "http://www.geneious.com") (:end . 172) (:start . 149) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 178) (:start . 174)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "access") (:form . "accessed") (:end . 187)\n  (:start . 179) (:id . 66))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 190) (:start . 188)\n  (:id . 67))\n ((:tag . "CD") (:stem . "12/08/08") (:form . "12/08/08") (:end . 199)\n  (:start . 191) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 200) (:start . 199)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s9.288) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503052@unknown@formal@none@1@S@Pairwise distances were calculated based on the BLOSUM62 matrix and the respective trees were constructed using Neighbor-Joining.@(((:tag . "JJ") (:stem . "pairwise") (:form . "Pairwise") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "distance") (:form . "distances") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 34)\n  (:start . 24) (:id . 45))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 40) (:start . 35)\n  (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "NN") (:stem . "blosum62") (:form . "BLOSUM62") (:end . 56)\n  (:start . 48) (:id . 49))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 63)\n  (:start . 57) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "respective") (:form . "respective") (:end . 82)\n  (:start . 72) (:id . 53))\n ((:tag . "NNS") (:stem . "tree") (:form . "trees") (:end . 88) (:start . 83)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 93) (:start . 89)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 105)\n  (:start . 94) (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 111) (:start . 106)\n  (:id . 57))\n ((:tag . "NN") (:stem . "neighbor-joining") (:form . "Neighbor-Joining")\n  (:end . 128) (:start . 112) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s9.289) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503053@unknown@formal@none@1@S@No outgroups were selected and the consensus trees were built using bootstrapping with 5,000 samples.@(((:tag . "DT") (:stem . "no") (:form . "No") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "outgroup") (:form . "outgroups") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "tree") (:form . "trees") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "build") (:form . "built") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "bootstrappe") (:form . "bootstrapping") (:end . 81)\n  (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "CD") (:stem . "5,000") (:form . "5,000") (:end . 92) (:start . 87)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 100)\n  (:start . 93) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s9.290) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503054@unknown@formal@none@1@S@Identification of R. microplus homologues for known Drosophila RNAi viability phenotypes@(((:tag . "NN") (:stem . "identification") (:form . "Identification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 41)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 45) (:start . 42)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 51) (:start . 46)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 62)\n  (:start . 52) (:id . 49))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 67) (:start . 63)\n  (:id . 50))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 77)\n  (:start . 68) (:id . 51))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 88)\n  (:start . 78) (:id . 52)))@@@1@11@((:identifiers (:sid . :s9.291) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503055@unknown@formal@none@1@S@Raw experimental results of the genome wide RNAi screen of D. melanogaster are publicly available at the website http://www.flyrnai.org[67].@(((:tag . "NN") (:stem . "raw") (:form . "Raw") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "screen") (:form . "screen") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 74)\n  (:start . 62) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "RB") (:stem . "publicly") (:form . "publicly") (:end . 87)\n  (:start . 79) (:id . 55))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 97)\n  (:start . 88) (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "NN") (:stem . "website") (:form . "website") (:end . 112)\n  (:start . 105) (:id . 59))\n ((:tag . "CD") (:stem . "http://www.flyrnai.org[67")\n  (:form . "http://www.flyrnai.org[67") (:end . 138) (:start . 113)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 139) (:start . 138)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.292) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503056@unknown@formal@none@1@S@The gene ontology data for the identified RNAi targets were retrieved from http://www.flybase.org[4].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "ontology") (:form . "ontology") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 41)\n  (:start . 31) (:id . 48))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "retrieve") (:form . "retrieved") (:end . 69)\n  (:start . 60) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 74) (:start . 70)\n  (:id . 53))\n ((:tag . "CD") (:stem . "http://www.flybase.org[4")\n  (:form . "http://www.flybase.org[4") (:end . 99) (:start . 75) (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 100) (:start . 99)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s9.293) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503057@unknown@formal@none@1@S@Genes of interest were selected based upon a phenotypic z score > 3 [43].@(((:tag . "NNS") (:stem . "gene") (:form . "Genes") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "phenotypic") (:form . "phenotypic") (:end . 55)\n  (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "SYM") (:stem . ">") (:form . ">") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 69) (:start . 68)\n  (:id . 55))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 71) (:start . 69)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 72) (:start . 71)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s9.294) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503058@unknown@formal@none@1@S@For these genes, corresponding translations were retrieved from FlyBase and used for the subsequent amino acid similarity searches.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 30)\n  (:start . 17) (:id . 46))\n ((:tag . "NNS") (:stem . "translation") (:form . "translations") (:end . 43)\n  (:start . 31) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "retrieve") (:form . "retrieved") (:end . 58)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 63) (:start . 59)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "FlyBase") (:form . "FlyBase") (:end . 71)\n  (:start . 64) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 80) (:start . 76)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 84) (:start . 81)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 99)\n  (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 105)\n  (:start . 100) (:id . 57))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 110) (:start . 106)\n  (:id . 58))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 121)\n  (:start . 111) (:id . 59))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 130)\n  (:start . 122) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s9.295) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503059@unknown@formal@none@1@S@The D. melanogaster cDNA sequences from the selected RNAi targets were used to screen to search the 13,643 of the R. microplus ESTs and TCs for highly conserved genes using blastn [62].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "melanogaster") (:form . "melanogaster") (:end . 19)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "cdna") (:form . "cDNA") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 65)\n  (:start . 58) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 70) (:start . 66)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "VB") (:stem . "screen") (:form . "screen") (:end . 85)\n  (:start . 79) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "VB") (:stem . "search") (:form . "search") (:end . 95)\n  (:start . 89) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "CD") (:stem . "13,643") (:form . "13,643") (:end . 106)\n  (:start . 100) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 116) (:start . 114)\n  (:id . 62))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 126)\n  (:start . 117) (:id . 63))\n ((:tag . "NNPS") (:stem . "EST") (:form . "ESTs") (:end . 131) (:start . 127)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 65))\n ((:tag . "NNPS") (:stem . "TC") (:form . "TCs") (:end . 139) (:start . 136)\n  (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 143) (:start . 140)\n  (:id . 67))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 150)\n  (:start . 144) (:id . 68))\n ((:tag . "JJ") (:stem . "conserved") (:form . "conserved") (:end . 160)\n  (:start . 151) (:id . 69))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 166)\n  (:start . 161) (:id . 70))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 172) (:start . 167)\n  (:id . 71))\n ((:tag . "NN") (:stem . "blastn") (:form . "blastn") (:end . 179)\n  (:start . 173) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 181) (:start . 180)\n  (:id . 73))\n ((:tag . "CD") (:stem . "62") (:form . "62") (:end . 183) (:start . 181)\n  (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 184) (:start . 183)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s9.296) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503060@unknown@formal@none@1@S@Sequences with a similarity of at least 80% and an e-value less than e1-50 were selected, conceptually translated and their putative function was further analyzed by assigning GO terms using InterProScan [63,68,69].@(((:tag . "NNS") (:stem . "sequence") (:form . "Sequences") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "CD") (:stem . "80") (:form . "80") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "NN") (:stem . "e-value") (:form . "e-value") (:end . 58)\n  (:start . 51) (:id . 53))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 63) (:start . 59)\n  (:id . 54))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "NN") (:stem . "e1-50") (:form . "e1-50") (:end . 74) (:start . 69)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 79) (:start . 75)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 88)\n  (:start . 80) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 59))\n ((:tag . "RB") (:stem . "conceptually") (:form . "conceptually") (:end . 102)\n  (:start . 90) (:id . 60))\n ((:tag . "VBN") (:stem . "translate") (:form . "translated") (:end . 113)\n  (:start . 103) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 123)\n  (:start . 118) (:id . 63))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 132)\n  (:start . 124) (:id . 64))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 141)\n  (:start . 133) (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 145) (:start . 142)\n  (:id . 66))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 153)\n  (:start . 146) (:id . 67))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 162)\n  (:start . 154) (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 165) (:start . 163)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "assign") (:form . "assigning") (:end . 175)\n  (:start . 166) (:id . 70))\n ((:tag . "NNP") (:stem . "GO") (:form . "GO") (:end . 178) (:start . 176)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 184)\n  (:start . 179) (:id . 72))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 190) (:start . 185)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "InterProScan") (:form . "InterProScan")\n  (:end . 203) (:start . 191) (:id . 74))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 205) (:start . 204)\n  (:id . 75))\n ((:tag . "CD") (:stem . "63,68,69") (:form . "63,68,69") (:end . 213)\n  (:start . 205) (:id . 76))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 214) (:start . 213)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x9.297.1) (:span 124 132)))\n (:hscopes ((:id . :x9.297.1) (:span 124 141)))\n (:identifiers (:sid . :s9.297) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503061@unknown@formal@none@1@S@Additional Files 2 and 3 describe this selection process and the GO terms utilized respectively.@(((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "File") (:form . "Files") (:end . 16) (:start . 11)\n  (:id . 43))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "describe") (:form . "describe") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 48)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "GO") (:form . "GO") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "utilize") (:form . "utilized") (:end . 82)\n  (:start . 74) (:id . 55))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 95)\n  (:start . 83) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s9.298) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503062@unknown@formal@none@1@S@Tick cell culture and sources of ticks for dsRNA treatment studies@(((:tag . "NN") (:stem . "tick") (:form . "Tick") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "source") (:form . "sources") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 66)\n  (:start . 59) (:id . 52)))@@@1@11@((:identifiers (:sid . :s9.299) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503063@unknown@formal@none@1@S@BME26 was derived in 1985 from R. microplus embryonated eggs in the USA [57] and supplied by Dr. Munderloh (Department of Entomology, University of Minnesota, St. Paul, Minnesota 55108) to the Queensland Department of Primary Industries & Fisheries in Australia.@(((:tag . "NNP") (:stem . "BME26") (:form . "BME26") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "CD") (:stem . "1985") (:form . "1985") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "VBD") (:stem . "embryonate") (:form . "embryonated") (:end . 55)\n  (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "egg") (:form . "eggs") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "USA") (:form . "USA") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "CD") (:stem . "57") (:form . "57") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 76) (:start . 75)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "supply") (:form . "supplied") (:end . 89)\n  (:start . 81) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 92) (:start . 90)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Dr.") (:form . "Dr.") (:end . 96) (:start . 93)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Munderloh") (:form . "Munderloh") (:end . 106)\n  (:start . 97) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Department") (:form . "Department") (:end . 118)\n  (:start . 108) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Entomology") (:form . "Entomology") (:end . 132)\n  (:start . 122) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "University") (:form . "University") (:end . 144)\n  (:start . 134) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Minnesota") (:form . "Minnesota") (:end . 157)\n  (:start . 148) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "St.") (:form . "St.") (:end . 162) (:start . 159)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Paul") (:form . "Paul") (:end . 167) (:start . 163)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Minnesota") (:form . "Minnesota") (:end . 178)\n  (:start . 169) (:id . 75))\n ((:tag . "CD") (:stem . "55108") (:form . "55108") (:end . 184)\n  (:start . 179) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 185) (:start . 184)\n  (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 188) (:start . 186)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 192) (:start . 189)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Queensland") (:form . "Queensland") (:end . 203)\n  (:start . 193) (:id . 80))\n ((:tag . "NNP") (:stem . "Department") (:form . "Department") (:end . 214)\n  (:start . 204) (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 217) (:start . 215)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Primary") (:form . "Primary") (:end . 225)\n  (:start . 218) (:id . 83))\n ((:tag . "NNPS") (:stem . "Industries") (:form . "Industries") (:end . 236)\n  (:start . 226) (:id . 84))\n ((:tag . "CC") (:stem . "&") (:form . "&") (:end . 238) (:start . 237)\n  (:id . 85))\n ((:tag . "NNPS") (:stem . "Fisheries") (:form . "Fisheries") (:end . 248)\n  (:start . 239) (:id . 86))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 251) (:start . 249)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "Australia") (:form . "Australia") (:end . 261)\n  (:start . 252) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 262) (:start . 261)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s9.300) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503064@unknown@formal@none@1@S@Cell culture protocols to maintain and passage the cell line (obtained at passage 55) have been previously described [70].@(((:tag . "NN") (:stem . "cell") (:form . "Cell") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "protocol") (:form . "protocols") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "VB") (:stem . "maintain") (:form . "maintain") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "VB") (:stem . "passage") (:form . "passage") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 70)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "passage") (:form . "passage") (:end . 81)\n  (:start . 74) (:id . 55))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 90) (:start . 86)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 95) (:start . 91)\n  (:id . 59))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 106)\n  (:start . 96) (:id . 60))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 116)\n  (:start . 107) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 120) (:start . 118)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s9.301) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503065@unknown@formal@none@1@S@N strain adult female ticks were obtained from the DPI&F Animal Research Institute tick cell colony [71].@(((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "strain") (:form . "strain") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "female") (:form . "female") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "DPI&F") (:form . "DPI&F") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Animal") (:form . "Animal") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "NNP") (:stem . "Research") (:form . "Research") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . "NNP") (:stem . "Institute") (:form . "Institute") (:end . 82)\n  (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . "NN") (:stem . "colony") (:form . "colony") (:end . 99)\n  (:start . 93) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s9.302) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503066@unknown@formal@none@1@S@DNA and RNA extraction methods@(((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 22)\n  (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 30)\n  (:start . 23) (:id . 46)))@@@1@5@((:identifiers (:sid . :s9.303) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503067@unknown@formal@none@1@S@DNA from BME26 cells was prepared using the QIAamp DNA mini kit (QIAGEN Sciences, MD, USA) – protocol for cultured cells as described by the manufacturer.@(((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "BME26") (:form . "BME26") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "QIAamp") (:form . "QIAamp") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "mini") (:form . "mini") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "QIAGEN") (:form . "QIAGEN") (:end . 71)\n  (:start . 65) (:id . 55))\n ((:tag . "NNPS") (:stem . "Sciences") (:form . "Sciences") (:end . 80)\n  (:start . 72) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "MD") (:form . "MD") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "USA") (:form . "USA") (:end . 89) (:start . 86)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 61))\n ((:tag . "NN") (:stem . "–") (:form . "–") (:end . 92) (:start . 91)\n  (:id . 62))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 101)\n  (:start . 93) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 105) (:start . 102)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 114)\n  (:start . 106) (:id . 65))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 120)\n  (:start . 115) (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 123) (:start . 121)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 133)\n  (:start . 124) (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 136) (:start . 134)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 70))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 153)\n  (:start . 141) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.304) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503068@unknown@formal@none@1@S@RNA for qRT-PCR analysis prepared from BME26 cells, adult tick viscera, and tick eggs was extracted using TRIzol® reagent (Invitrogen, CA, USA) following the manufacturer's instructions.@(((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "bme26") (:form . "BME26") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "viscera") (:form . "viscera") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "egg") (:form . "eggs") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 99)\n  (:start . 90) (:id . 59))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 105) (:start . 100)\n  (:id . 60))\n ((:tag . "NN") (:stem . "trizol®") (:form . "TRIzol®") (:end . 113)\n  (:start . 106) (:id . 61))\n ((:tag . "NN") (:stem . "reagent") (:form . "reagent") (:end . 121)\n  (:start . 114) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 133)\n  (:start . 123) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "CA") (:form . "CA") (:end . 137) (:start . 135)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "USA") (:form . "USA") (:end . 142) (:start . 139)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 153)\n  (:start . 144) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n  (:id . 71))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 170)\n  (:start . 158) (:id . 72))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 172) (:start . 170)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 185)\n  (:start . 173) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s9.305) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503069@unknown@formal@none@1@S@For RNA extractions from larvae, the larvae were first ground in liquid nitrogen using a mortar and pestle prior to TRIzol® reagent extraction following the manufacturer's instruction (Invitrogen, CA, USA).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "extraction") (:form . "extractions") (:end . 19)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "ground") (:form . "ground") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "liquid") (:form . "liquid") (:end . 71)\n  (:start . 65) (:id . 54))\n ((:tag . "NN") (:stem . "nitrogen") (:form . "nitrogen") (:end . 80)\n  (:start . 72) (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 86) (:start . 81)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 88) (:start . 87)\n  (:id . 57))\n ((:tag . "NN") (:stem . "mortar") (:form . "mortar") (:end . 95)\n  (:start . 89) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "pestle") (:form . "pestle") (:end . 106)\n  (:start . 100) (:id . 60))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 112)\n  (:start . 107) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "NN") (:stem . "trizol®") (:form . "TRIzol®") (:end . 123)\n  (:start . 116) (:id . 63))\n ((:tag . "NN") (:stem . "reagent") (:form . "reagent") (:end . 131)\n  (:start . 124) (:id . 64))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 142)\n  (:start . 132) (:id . 65))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 152)\n  (:start . 143) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 67))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 169)\n  (:start . 157) (:id . 68))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 171) (:start . 169)\n  (:id . 69))\n ((:tag . "NN") (:stem . "instruction") (:form . "instruction") (:end . 183)\n  (:start . 172) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 195)\n  (:start . 185) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "CA") (:form . "CA") (:end . 199) (:start . 197)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "USA") (:form . "USA") (:end . 204) (:start . 201)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 205) (:start . 204)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s9.306) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503070@unknown@formal@none@1@S@dsRNA synthesis methods@(((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "synthesis") (:form . "synthesis") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 23)\n  (:start . 16) (:id . 44)))@@@1@3@((:identifiers (:sid . :s9.307) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503071@unknown@formal@none@1@S@Sequences from Anopheles gambiae, D. melanogaster, I. scapularis, and R. microplus (Additional File 4) were aligned using AlignX (Invitrogen Vector NTI, CA, USA) to identify conserved regions for primer design.@(((:tag . "NNP") (:stem . "Sequence") (:form . "Sequences") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Anopheles") (:form . "Anopheles") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "NNP") (:stem . "gambiae") (:form . "gambiae") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster") (:end . 49)\n  (:start . 37) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "I.") (:form . "I.") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "scapularis") (:form . "scapularis") (:end . 64)\n  (:start . 54) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 82)\n  (:start . 73) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 94)\n  (:start . 84) (:id . 57))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 99) (:start . 95)\n  (:id . 58))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 107) (:start . 103)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 115)\n  (:start . 108) (:id . 62))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 121) (:start . 116)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "AlignX") (:form . "AlignX") (:end . 128)\n  (:start . 122) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 140)\n  (:start . 130) (:id . 66))\n ((:tag . "NNP") (:stem . "Vector") (:form . "Vector") (:end . 147)\n  (:start . 141) (:id . 67))\n ((:tag . "NNP") (:stem . "NTI") (:form . "NTI") (:end . 151) (:start . 148)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "CA") (:form . "CA") (:end . 155) (:start . 153)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "USA") (:form . "USA") (:end . 160) (:start . 157)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n  (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 164) (:start . 162)\n  (:id . 74))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 173)\n  (:start . 165) (:id . 75))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 183)\n  (:start . 174) (:id . 76))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 191)\n  (:start . 184) (:id . 77))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 195) (:start . 192)\n  (:id . 78))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 202)\n  (:start . 196) (:id . 79))\n ((:tag . "NN") (:stem . "design") (:form . "design") (:end . 209)\n  (:start . 203) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s9.308) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503072@unknown@formal@none@1@S@Primers were subsequently designed using Invitrogen Vector NTI to amplify the corresponding conserved region in R. microplus (Additional File 5).@(((:tag . "NNS") (:stem . "primer") (:form . "Primers") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 25)\n  (:start . 13) (:id . 44))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 34)\n  (:start . 26) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 40) (:start . 35)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Invitrogen") (:form . "Invitrogen") (:end . 51)\n  (:start . 41) (:id . 47))\n ((:tag . "NNP") (:stem . "Vector") (:form . "Vector") (:end . 58)\n  (:start . 52) (:id . 48))\n ((:tag . "NNP") (:stem . "NTI") (:form . "NTI") (:end . 62) (:start . 59)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "VB") (:stem . "amplify") (:form . "amplify") (:end . 73)\n  (:start . 66) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 91)\n  (:start . 78) (:id . 53))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 101)\n  (:start . 92) (:id . 54))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 108)\n  (:start . 102) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 114) (:start . 112)\n  (:id . 57))\n ((:tag . "CC") (:stem . "microplus") (:form . "microplus") (:end . 124)\n  (:start . 115) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 136)\n  (:start . 126) (:id . 60))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 141) (:start . 137)\n  (:id . 61))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 143) (:start . 142)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.309) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503073@unknown@formal@none@1@S@T7 promoter sequences were added to the 5'-ends of the primers to allow for subsequent RNA transcription as described in the manufacturer's instructions (Ambion MEGAScript RNAi kit, Applied Biosystems, CA, USA).@(((:tag . "NNP") (:stem . "T7") (:form . "T7") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "5'-end") (:form . "5’-ends") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "primer") (:form . "primers") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 86)\n  (:start . 76) (:id . 56))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 90) (:start . 87)\n  (:id . 57))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 104) (:start . 91) (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 117)\n  (:start . 108) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n  (:id . 62))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 137)\n  (:start . 125) (:id . 63))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 139) (:start . 137)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 152)\n  (:start . 140) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Ambion") (:form . "Ambion") (:end . 160)\n  (:start . 154) (:id . 67))\n ((:tag . "NNP") (:stem . "MEGAScript") (:form . "MEGAScript") (:end . 171)\n  (:start . 161) (:id . 68))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 176) (:start . 172)\n  (:id . 69))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 180) (:start . 177)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 181) (:start . 180)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Applied") (:form . "Applied") (:end . 189)\n  (:start . 182) (:id . 72))\n ((:tag . "NNP") (:stem . "Biosystems") (:form . "Biosystems") (:end . 200)\n  (:start . 190) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 201) (:start . 200)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "CA") (:form . "CA") (:end . 204) (:start . 202)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 205) (:start . 204)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "USA") (:form . "USA") (:end . 209) (:start . 206)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 210) (:start . 209)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s9.310) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503074@unknown@formal@none@1@S@PCR products were amplified from 20 ng DNA prepared from BME26 cells as template using 10 pM each primer, 10 pmol dNTPs, HotStart Taq Plus enzyme and the buffer provided by the manufacturer (QIAGEN Sciences, MD, USA) in a 20 µl reaction volume.@(((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "amplify") (:form . "amplified") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "ng") (:form . "ng") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "dna") (:form . 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"and") (:end . 149) (:start . 146)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 71))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 160)\n  (:start . 154) (:id . 72))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 169)\n  (:start . 161) (:id . 73))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 172) (:start . 170)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 176) (:start . 173)\n  (:id . 75))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 189)\n  (:start . 177) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 191) (:start . 190)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "QIAGEN") (:form . "QIAGEN") (:end . 197)\n  (:start . 191) (:id . 78))\n ((:tag . "NNPS") (:stem . "Sciences") (:form . "Sciences") (:end . 206)\n  (:start . 198) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . 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(:form . ".") (:end . 244) (:start . 243)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s9.311) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503075@unknown@formal@none@1@S@The optimal annealing temperature for each assay was determined using gradient PCR and a temperature gradient of 55°C to 70°C in twelve discrete steps in a G-storm GS-1 thermocycler (Geneworks Technologies Pty Ltd, SA, Australia).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "optimal") (:form . "optimal") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBG") (:stem . "anneal") (:form . "annealing") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 33)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 63)\n  (:start . 53) (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 69) (:start . 64)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 78)\n  (:start . 70) (:id . 52))\n ((:tag . "NN") (:stem . "pcr") (:form . "PCR") (:end . 82) (:start . 79)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 100)\n  (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 109)\n  (:start . 101) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "NN") (:stem . "55°c") (:form . "55°C") (:end . 117) (:start . 113)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 120) (:start . 118)\n  (:id . 60))\n ((:tag . "NN") (:stem . "70°c") (:form . "70°C") (:end . 125) (:start . 121)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . "CD") (:stem . "twelve") (:form . "twelve") (:end . 135)\n  (:start . 129) (:id . 63))\n ((:tag . "JJ") (:stem . "discrete") (:form . "discrete") (:end . 144)\n  (:start . 136) (:id . 64))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 150)\n  (:start . 145) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 153) (:start . 151)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 155) (:start . 154)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "g-storm") (:form . "G-storm") (:end . 163)\n  (:start . 156) (:id . 68))\n ((:tag . "NN") (:stem . "gs-1") (:form . "GS-1") (:end . 168) (:start . 164)\n  (:id . 69))\n ((:tag . "NN") (:stem . "thermocycler") (:form . "thermocycler") (:end . 181)\n  (:start . 169) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 183) (:start . 182)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Geneworks") (:form . "Geneworks") (:end . 192)\n  (:start . 183) (:id . 72))\n ((:tag . "NNPS") (:stem . "Technologies") (:form . "Technologies")\n  (:end . 205) (:start . 193) (:id . 73))\n ((:tag . "NNP") (:stem . "Pty") (:form . "Pty") (:end . 209) (:start . 206)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Ltd") (:form . "Ltd") (:end . 213) (:start . 210)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 214) (:start . 213)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "SA") (:form . "SA") (:end . 217) (:start . 215)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 218) (:start . 217)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Australia") (:form . "Australia") (:end . 228)\n  (:start . 219) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 229) (:start . 228)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 230) (:start . 229)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s9.312) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503076@unknown@formal@none@1@S@The PCR thermal profile was as follows: 95°C 2 min, followed by 35 cycles at 95°C 10s, annealing temp 30s, 72°C 1 min (annealing temperatures for each primer pair described in Additional File 5), and a final extension at 72°C 7 min.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "thermal") (:form . "thermal") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . 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"temperature") (:form . "temperatures") (:end . 141)\n  (:start . 129) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 145) (:start . 142)\n  (:id . 72))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 150) (:start . 146)\n  (:id . 73))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 157)\n  (:start . 151) (:id . 74))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 162) (:start . 158)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 172)\n  (:start . 163) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 175) (:start . 173)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 186)\n  (:start . 176) (:id . 78))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 191) (:start . 187)\n  (:id . 79))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 193) (:start . 192)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . 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(:end . 232) (:start . 231)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s9.313) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503077@unknown@formal@none@1@S@The size of the PCR products (Additional File 5) were confirmed by gel electrophoresis using 1.5% Agarose in TAE Buffer (Tris acetate 40 mM, EDTA 2 mM, pH 8.5) after 45 minutes at 90 V.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 40)\n  (:start . 30) (:id . 49))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 47) (:start . 46)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 53) (:start . 49)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 63)\n  (:start . 54) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 66) (:start . 64)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gel") (:form . "gel") (:end . 70) (:start . 67)\n  (:id . 56))\n ((:tag . "NN") (:stem . "electrophoresis") (:form . "electrophoresis")\n  (:end . 86) (:start . 71) (:id . 57))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 92) (:start . 87)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1.5") (:form . "1.5") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 97) (:start . 96)\n  (:id . 60))\n ((:tag . "NN") (:stem . "agarose") (:form . "Agarose") (:end . 105)\n  (:start . 98) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "TAE") (:form . "TAE") (:end . 112) (:start . 109)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Buffer") (:form . "Buffer") (:end . 119)\n  (:start . 113) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Tris") (:form . "Tris") (:end . 125) (:start . 121)\n  (:id . 66))\n ((:tag . "NN") (:stem . "acetate") (:form . "acetate") (:end . 133)\n  (:start . 126) (:id . 67))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 136) (:start . 134)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 139) (:start . 137)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "EDTA") (:form . "EDTA") (:end . 145) (:start . 141)\n  (:id . 71))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 147) (:start . 146)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "mM") (:form . "mM") (:end . 150) (:start . 148)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n  (:id . 74))\n ((:tag . "NN") (:stem . "ph") (:form . "pH") (:end . 154) (:start . 152)\n  (:id . 75))\n ((:tag . "CD") (:stem . "8.5") (:form . "8.5") (:end . 158) (:start . 155)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 77))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 165)\n  (:start . 160) (:id . 78))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 168) (:start . 166)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "minute") (:form . "minutes") (:end . 176)\n  (:start . 169) (:id . 80))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 179) (:start . 177)\n  (:id . 81))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 182) (:start . 180)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "V") (:form . "V") (:end . 184) (:start . 183)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s9.314) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503078@unknown@formal@none@1@S@The PCR products were purified using the QIAquick kit (QIAGEN Sciences, MD, USA) following the manufacturer's protocol.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "QIAquick") (:form . "QIAquick") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "QIAGEN") (:form . "QIAGEN") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "NNPS") (:stem . "Sciences") (:form . "Sciences") (:end . 70)\n  (:start . 62) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "MD") (:form . "MD") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "USA") (:form . "USA") (:end . 79) (:start . 76)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 90)\n  (:start . 81) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 60))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 107)\n  (:start . 95) (:id . 61))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 118)\n  (:start . 110) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s9.315) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503079@unknown@formal@none@1@S@Long dsRNA were synthesized from the purified PCR products (5 pooled 20 µl reactions per gene target) using the MEGAScript RNAi kit as described by the manufacturer (Ambion, Applied Biosystems, CA, USA).@(((:tag . "JJ") (:stem . "long") (:form . "Long") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "synthesize") (:form . "synthesized") (:end . 27)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "purify") (:form . "purified") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "pcr") (:form . "PCR") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "product") (:form . "products") (:end . 58)\n  (:start . 50) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 51))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "pool") (:form . "pooled") (:end . 68) (:start . 62)\n  (:id . 53))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "reaction") (:form . "reactions") (:end . 84)\n  (:start . 75) (:id . 56))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 100)\n  (:start . 94) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 107) (:start . 102)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "MEGAScript") (:form . "MEGAScript") (:end . 122)\n  (:start . 112) (:id . 63))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 127) (:start . 123)\n  (:id . 64))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 131) (:start . 128)\n  (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 134) (:start . 132)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 144)\n  (:start . 135) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 147) (:start . 145)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 69))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 164)\n  (:start . 152) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 166) (:start . 165)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Ambion") (:form . "Ambion") (:end . 172)\n  (:start . 166) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Applied") (:form . "Applied") (:end . 181)\n  (:start . 174) (:id . 74))\n ((:tag . "NNP") (:stem . "Biosystems") (:form . "Biosystems") (:end . 192)\n  (:start . 182) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 193) (:start . 192)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "CA") (:form . "CA") (:end . 196) (:start . 194)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "USA") (:form . "USA") (:end . 201) (:start . 198)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 202) (:start . 201)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s9.316) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503080@unknown@formal@none@1@S@Purified dsRNAs were stored in elution buffer at -70°C until further use.@(((:tag . "VBN") (:stem . "purify") (:form . "Purified") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "dsrna") (:form . "dsRNAs") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "store") (:form . "stored") (:end . 27)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "elution") (:form . "elution") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "buffer") (:form . "buffer") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "-70°c") (:form . "-70°C") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 60) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s9.317) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503081@unknown@formal@none@1@S@Actin (TC12168) and the dsRNA control supplied by the manufacturer (MEGAScript, Ambion, Applied Biosystems, CA, USA) were prepared as tick specific and non-specific dsRNA treatments, respectively.@(((:tag . "NNP") (:stem . "Actin") (:form . "Actin") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "tc12168") (:form . "TC12168") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 29) (:start . 24)\n  (:id . 48))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 37)\n  (:start . 30) (:id . 49))\n ((:tag . "VBN") (:stem . "supply") (:form . "supplied") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 66)\n  (:start . 54) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "MEGAScript") (:form . "MEGAScript") (:end . 78)\n  (:start . 68) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Ambion") (:form . "Ambion") (:end . 86)\n  (:start . 80) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Applied") (:form . "Applied") (:end . 95)\n  (:start . 88) (:id . 59))\n ((:tag . "NNP") (:stem . "Biosystems") (:form . "Biosystems") (:end . 106)\n  (:start . 96) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "CA") (:form . "CA") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "USA") (:form . "USA") (:end . 115) (:start . 112)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 121) (:start . 117)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 130)\n  (:start . 122) (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 133) (:start . 131)\n  (:id . 68))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 138) (:start . 134)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 147)\n  (:start . 139) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 151) (:start . 148)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "non-specific") (:form . "non-specific") (:end . 164)\n  (:start . 152) (:id . 72))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 170)\n  (:start . 165) (:id . 73))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 181)\n  (:start . 171) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 182) (:start . 181)\n  (:id . 75))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 195)\n  (:start . 183) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s9.318) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503082@unknown@formal@none@1@S@Transfection of BME26 tick cells@(((:tag . "NNP") (:stem . "Transfection") (:form . "Transfection") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "BME26") (:form . "BME26") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 32) (:start . 27)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s9.319) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503083@unknown@formal@none@1@S@In vitro transfection methods for the dsRNA treatment of tick cells were modified from D. melanogaster methods originally described by Boutros et al [43].@(((:tag . "FW") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "transfection") (:form . "transfection") (:end . 21)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "modify") (:form . "modified") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 86) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "D.") (:form . "D.") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "melanogaster") (:form . "melanogaster")\n  (:end . 102) (:start . 90) (:id . 57))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 110)\n  (:start . 103) (:id . 58))\n ((:tag . "RB") (:stem . "originally") (:form . "originally") (:end . 121)\n  (:start . 111) (:id . 59))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 131)\n  (:start . 122) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 134) (:start . 132)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Boutros") (:form . "Boutros") (:end . 142)\n  (:start . 135) (:id . 62))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 145) (:start . 143)\n  (:id . 63))\n ((:tag . "FW") (:stem . "al") (:form . "al") (:end . 148) (:start . 146)\n  (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 150) (:start . 149)\n  (:id . 65))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 152) (:start . 150)\n  (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 153) (:start . 152)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s9.320) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503084@unknown@formal@none@1@S@BME26 cells at passage 57 were grown in 96-well plates freshly seeded with 48,000 cells/40 µl per well.@(((:tag . "NNP") (:stem . "BME26") (:form . "BME26") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "passage") (:form . "passage") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "CD") (:stem . "57") (:form . "57") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "grow") (:form . "grown") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "96-well") (:form . "96-well") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "NNS") (:stem . "plate") (:form . "plates") (:end . 54)\n  (:start . 48) (:id . 51))\n ((:tag . "RB") (:stem . "freshly") (:form . "freshly") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "VBN") (:stem . "seed") (:form . "seeded") (:end . 69) (:start . 63)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "CD") (:stem . "48,000") (:form . "48,000") (:end . 81)\n  (:start . 75) (:id . 55))\n ((:tag . "NNS") (:stem . "cells/40") (:form . "cells/40") (:end . 90)\n  (:start . 82) (:id . 56))\n ((:tag . "VBP") (:stem . "µl") (:form . "µl") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s9.321) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503085@unknown@formal@none@1@S@Cells were transfected with 800 ng dsRNA and incubated at 31°C for 60 mins prior to the addition of complete medium (final total well volume of 120 µl).@(((:tag . "NNS") (:stem . "cell") (:form . "Cells") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "transfecte") (:form . "transfected") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "CD") (:stem . "800") (:form . "800") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "ng") (:form . "ng") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 54)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "31°c") (:form . "31°C") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "min") (:form . "mins") (:end . 74) (:start . 70)\n  (:id . 55))\n ((:tag . "RB") (:stem . "prior") (:form . "prior") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 96)\n  (:start . 88) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 108)\n  (:start . 100) (:id . 61))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 115)\n  (:start . 109) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 122)\n  (:start . 117) (:id . 64))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 128)\n  (:start . 123) (:id . 65))\n ((:tag . "NN") (:stem . "well") (:form . "well") (:end . 133) (:start . 129)\n  (:id . 66))\n ((:tag . "NN") (:stem . "volume") (:form . "volume") (:end . 140)\n  (:start . 134) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 68))\n ((:tag . "CD") (:stem . "120") (:form . "120") (:end . 147) (:start . 144)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 150) (:start . 148)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.322) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503086@unknown@formal@none@1@S@Treatments were incubated for 4 days at 31°C and each well was supplemented with 80 µl complete medium at Day 2.@(((:tag . "NNS") (:stem . "treatment") (:form . "Treatments") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "incubate") (:form . "incubated") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "31°c") (:form . "31°C") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "well") (:form . "well") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "supplement") (:form . "supplemented") (:end . 75)\n  (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "CD") (:stem . "80") (:form . "80") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 95)\n  (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 102)\n  (:start . 96) (:id . 59))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 105) (:start . 103)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Day") (:form . "Day") (:end . 109) (:start . 106)\n  (:id . 61))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 111) (:start . 110)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s9.323) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503087@unknown@formal@none@1@S@Each treatment contained 6 replicates to provide 3 replicates for viability assay and 3 for qRT-PCR.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "replicate") (:form . "replicates") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "replicate") (:form . "replicates") (:end . 61)\n  (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 75)\n  (:start . 66) (:id . 52))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 81) (:start . 76)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 99)\n  (:start . 92) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s9.324) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503088@unknown@formal@none@1@S@On Day 4 (96 hrs post treatment), 3 wells were subjected to cell viability testing using the Cell Glow kit as per manufacturer's instructions (Promega Corporation, WI, USA) and 3 wells were subject to RNA extraction for qRT-PCR screening.@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Day") (:form . "Day") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 8) (:start . 7)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 10) (:start . 9)\n  (:id . 45))\n ((:tag . "CD") (:stem . "96") (:form . "96") (:end . 12) (:start . 10)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "hr") (:form . "hrs") (:end . 16) (:start . 13)\n  (:id . 47))\n ((:tag . "IN") (:stem . "post") (:form . "post") (:end . 21) (:start . 17)\n  (:id . 48))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 31)\n  (:start . 22) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 32) (:start . 31)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 51))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 35) (:start . 34)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "well") (:form . "wells") (:end . 41) (:start . 36)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 46) (:start . 42)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "subject") (:form . "subjected") (:end . 56)\n  (:start . 47) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 64) (:start . 60)\n  (:id . 57))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 74)\n  (:start . 65) (:id . 58))\n ((:tag . "NN") (:stem . "testing") (:form . "testing") (:end . 82)\n  (:start . 75) (:id . 59))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 88) (:start . 83)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Cell") (:form . "Cell") (:end . 97) (:start . 93)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Glow") (:form . "Glow") (:end . 102) (:start . 98)\n  (:id . 63))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 106) (:start . 103)\n  (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 109) (:start . 107)\n  (:id . 65))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 113) (:start . 110)\n  (:id . 66))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 126)\n  (:start . 114) (:id . 67))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 128) (:start . 126)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 141)\n  (:start . 129) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Promega") (:form . "Promega") (:end . 150)\n  (:start . 143) (:id . 71))\n ((:tag . "NNP") (:stem . "Corporation") (:form . "Corporation") (:end . 162)\n  (:start . 151) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "WI") (:form . "WI") (:end . 166) (:start . 164)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "USA") (:form . "USA") (:end . 171) (:start . 168)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n  (:id . 78))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 178) (:start . 177)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "well") (:form . "wells") (:end . 184)\n  (:start . 179) (:id . 80))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 189) (:start . 185)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "subject") (:form . "subject") (:end . 197)\n  (:start . 190) (:id . 82))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 200) (:start . 198)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 204) (:start . 201)\n  (:id . 84))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 215)\n  (:start . 205) (:id . 85))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 219) (:start . 216)\n  (:id . 86))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 227)\n  (:start . 220) (:id . 87))\n ((:tag . "NN") (:stem . "screening") (:form . "screening") (:end . 237)\n  (:start . 228) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s9.325) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503089@unknown@formal@none@1@S@Controls included nil treatment (media only) and the dsRNA control from the Ambion MEGAScript RNAi kit (non-specific dsRNA treatment).@(((:tag . "NNP") (:stem . "Control") (:form . "Controls") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "include") (:form . "included") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "nil") (:form . "nil") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 33) (:start . 32)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "medium") (:form . "media") (:end . 38)\n  (:start . 33) (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Ambion") (:form . "Ambion") (:end . 82)\n  (:start . 76) (:id . 56))\n ((:tag . "NNP") (:stem . "MEGAScript") (:form . "MEGAScript") (:end . 93)\n  (:start . 83) (:id . 57))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 102) (:start . 99)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "non-specific") (:form . "non-specific") (:end . 116)\n  (:start . 104) (:id . 61))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 122)\n  (:start . 117) (:id . 62))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 132)\n  (:start . 123) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s9.326) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503090@unknown@formal@none@1@S@Impairment of growth and viability relative to the nil treatment control was statistically determined by calculating inverse z-scores for every treatment [43].@(((:tag . "NN") (:stem . "impairment") (:form . "Impairment") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "viability") (:form . "viability") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 46) (:start . 44)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "nil") (:form . "nil") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 72)\n  (:start . 65) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n  (:end . 90) (:start . 77) (:id . 54))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 101)\n  (:start . 91) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 104) (:start . 102)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "calculate") (:form . "calculating") (:end . 116)\n  (:start . 105) (:id . 57))\n ((:tag . "JJ") (:stem . "inverse") (:form . "inverse") (:end . 124)\n  (:start . 117) (:id . 58))\n ((:tag . "NNS") (:stem . "z-score") (:form . "z-scores") (:end . 133)\n  (:start . 125) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 137) (:start . 134)\n  (:id . 60))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 143)\n  (:start . 138) (:id . 61))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 153)\n  (:start . 144) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 155) (:start . 154)\n  (:id . 63))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 157) (:start . 155)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 158) (:start . 157)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s9.327) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503091@unknown@formal@none@1@S@Injection of R. microplus ticks with dsRNA, monitoring and statistical analysis of mortality and egg output@(((:tag . "NN") (:stem . "injection") (:form . "Injection") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "monitoring") (:form . "monitoring") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 70)\n  (:start . 59) (:id . 52))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "mortality") (:form . "mortality") (:end . 92)\n  (:start . 83) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 107)\n  (:start . 101) (:id . 58)))@@@1@17@((:identifiers (:sid . :s9.328) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503092@unknown@formal@none@1@S@Female adult ticks fed to repletion were collected within 24 hrs from dropping from the bovine host for dsRNA injection.@(((:tag . "JJ") (:stem . "female") (:form . "Female") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "feed") (:form . "fed") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "repletion") (:form . "repletion") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 57)\n  (:start . 51) (:id . 50))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "hr") (:form . "hrs") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "drop") (:form . "dropping") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "bovine") (:form . "bovine") (:end . 94)\n  (:start . 88) (:id . 57))\n ((:tag . "NN") (:stem . "host") (:form . "host") (:end . 99) (:start . 95)\n  (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 103) (:start . 100)\n  (:id . 59))\n ((:tag . "NN") (:stem . "dsrna") (:form . "dsRNA") (:end . 109)\n  (:start . 104) (:id . 60))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 119)\n  (:start . 110) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s9.329) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503093@unknown@formal@none@1@S@Six ticks per treatment (10 Drosophila homologues, no injection control, PBS injection control, tick actin dsRNA and the MEGAScript dsRNA control) were injected with 1–2 × 1012 dsRNA molecules using a micro-injector (World Precision Instruments Inc., Florida, USA) as described previously by Nijhof and colleagues [42], except ticks were first pierced using a 30 G needle rather than 27 G.@(((:tag . "CD") (:stem . "six") (:form . "Six") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "NNP") (:stem . 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"]") (:end . 318) (:start . 317)\n  (:id . 98))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 319) (:start . 318)\n  (:id . 99))\n ((:tag . "IN") (:stem . "except") (:form . "except") (:end . 326)\n  (:start . 320) (:id . 100))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 332)\n  (:start . 327) (:id . 101))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 337) (:start . 333)\n  (:id . 102))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 343)\n  (:start . 338) (:id . 103))\n ((:tag . "VBN") (:stem . "pierce") (:form . "pierced") (:end . 351)\n  (:start . 344) (:id . 104))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 357) (:start . 352)\n  (:id . 105))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 359) (:start . 358)\n  (:id . 106))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 362) (:start . 360)\n  (:id . 107))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 364) (:start . 363)\n  (:id . 108))\n ((:tag . "NN") (:stem . "needle") (:form . "needle") (:end . 371)\n  (:start . 365) (:id . 109))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 378)\n  (:start . 372) (:id . 110))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 383) (:start . 379)\n  (:id . 111))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 386) (:start . 384)\n  (:id . 112))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 388) (:start . 387)\n  (:id . 113))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 389) (:start . 388)\n  (:id . 114)))@@@1@73@((:identifiers (:sid . :s9.330) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503094@unknown@formal@none@1@S@Five out of the 6 ticks per treatment were monitored daily for effects on mortality, egg output and larval hatching rates until all ticks had died [42].@(((:tag . "CD") (:stem . "five") (:form . "Five") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 23) (:start . 18)\n  (:id . 47))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 27) (:start . 24)\n  (:id . 48))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 37)\n  (:start . 28) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "monitor") (:form . "monitored") (:end . 52)\n  (:start . 43) (:id . 51))\n ((:tag . "RB") (:stem . "daily") (:form . "daily") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 70)\n  (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "mortality") (:form . "mortality") (:end . 83)\n  (:start . 74) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 88) (:start . 85)\n  (:id . 58))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 95)\n  (:start . 89) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 106)\n  (:start . 100) (:id . 61))\n ((:tag . "VBG") (:stem . "hatch") (:form . "hatching") (:end . 115)\n  (:start . 107) (:id . 62))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 121)\n  (:start . 116) (:id . 63))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 127)\n  (:start . 122) (:id . 64))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 131) (:start . 128)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 137)\n  (:start . 132) (:id . 66))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 141) (:start . 138)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "die") (:form . "died") (:end . 146) (:start . 142)\n  (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 148) (:start . 147)\n  (:id . 69))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 150) (:start . 148)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 151) (:start . 150)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s9.331) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503095@unknown@formal@none@1@S@Statistical analyses were conducted using GenStat 10 (VSN International).@(((:tag . "JJ") (:stem . "statistical") (:form . "Statistical") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 25) (:start . 21)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "conduct") (:form . "conducted") (:end . 35)\n  (:start . 26) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 41) (:start . 36)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "GenStat") (:form . "GenStat") (:end . 49)\n  (:start . 42) (:id . 47))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 52) (:start . 50)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "VSN") (:form . "VSN") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "International") (:form . "International")\n  (:end . 71) (:start . 58) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s9.332) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503096@unknown@formal@none@1@S@The following variables were subjected to analysis of variance assessing the effect of replicates and treatments: 1. total wt of eggs produced; 2. days ticks survived post injection; 3. days from laying to larval hatch; and 4. percent larvae hatched.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "variable") (:form . "variables") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "subject") (:form . "subjected") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "variance") (:form . "variance") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "VBG") (:stem . "assess") (:form . "assessing") (:end . 72)\n  (:start . 63) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 83)\n  (:start . 77) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "replicate") (:form . "replicates") (:end . 97)\n  (:start . 87) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "treatment") (:form . "treatments") (:end . 112)\n  (:start . 102) (:id . 57))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 113) (:start . 112)\n  (:id . 58))\n ((:tag . "LS") (:stem . "1.") (:form . "1.") (:end . 116) (:start . 114)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 122)\n  (:start . 117) (:id . 60))\n ((:tag . "NN") (:stem . "wt") (:form . "wt") (:end . 125) (:start . 123)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "egg") (:form . "eggs") (:end . 133) (:start . 129)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 142)\n  (:start . 134) (:id . 64))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 143) (:start . 142)\n  (:id . 65))\n ((:tag . "LS") (:stem . "2.") (:form . "2.") (:end . 146) (:start . 144)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 151) (:start . 147)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "tick") (:form . "ticks") (:end . 157)\n  (:start . 152) (:id . 68))\n ((:tag . "VBD") (:stem . "survive") (:form . "survived") (:end . 166)\n  (:start . 158) (:id . 69))\n ((:tag . "NN") (:stem . "post") (:form . "post") (:end . 171) (:start . 167)\n  (:id . 70))\n ((:tag . "NN") (:stem . "injection") (:form . "injection") (:end . 181)\n  (:start . 172) (:id . 71))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 182) (:start . 181)\n  (:id . 72))\n ((:tag . "LS") (:stem . "3.") (:form . "3.") (:end . 185) (:start . 183)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 190) (:start . 186)\n  (:id . 74))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 195) (:start . 191)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "lay") (:form . "laying") (:end . 202)\n  (:start . 196) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 205) (:start . 203)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 212)\n  (:start . 206) (:id . 78))\n ((:tag . "NN") (:stem . "hatch") (:form . "hatch") (:end . 218)\n  (:start . 213) (:id . 79))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 219) (:start . 218)\n  (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 223) (:start . 220)\n  (:id . 81))\n ((:tag . "LS") (:stem . "4.") (:form . "4.") (:end . 226) (:start . 224)\n  (:id . 82))\n ((:tag . "NN") (:stem . "percent") (:form . "percent") (:end . 234)\n  (:start . 227) (:id . 83))\n ((:tag . "NNS") (:stem . "larva") (:form . "larvae") (:end . 241)\n  (:start . 235) (:id . 84))\n ((:tag . "VBN") (:stem . "hatch") (:form . "hatched") (:end . 249)\n  (:start . 242) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 250) (:start . 249)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s9.333) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503097@unknown@formal@none@1@S@A protected least significant difference (LSD) procedure was used to compare treatment means using a significance level of 0.05.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "protected") (:form . "protected") (:end . 11)\n  (:start . 2) (:id . 43))\n ((:tag . "RBS") (:stem . "least") (:form . "least") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 29)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "LSD") (:form . "LSD") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 56)\n  (:start . 47) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 76)\n  (:start . 69) (:id . 54))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 86)\n  (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "mean") (:form . "means") (:end . 92) (:start . 87)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 98) (:start . 93)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 113)\n  (:start . 101) (:id . 59))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 119)\n  (:start . 114) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "CD") (:stem . "0.05") (:form . "0.05") (:end . 127) (:start . 123)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s9.334) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503098@unknown@formal@none@1@S@RNA was extracted from the viscera and from the eggs collected from the 6th replicate tick per treatment for qRT-PCR analysis on days 6 and 14 respectively (see below).@(((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "viscera") (:form . "viscera") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "egg") (:form . "eggs") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "6th") (:form . "6th") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "replicate") (:form . "replicate") (:end . 85)\n  (:start . 76) (:id . 56))\n ((:tag . "VB") (:stem . "tick") (:form . "tick") (:end . 90) (:start . 86)\n  (:id . 57))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 104)\n  (:start . 95) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 108) (:start . 105)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "qRT-PCR") (:form . "qRT-PCR") (:end . 116)\n  (:start . 109) (:id . 61))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 125)\n  (:start . 117) (:id . 62))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 128) (:start . 126)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "day") (:form . "days") (:end . 133) (:start . 129)\n  (:id . 64))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 135) (:start . 134)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 66))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 142) (:start . 140)\n  (:id . 67))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 155)\n  (:start . 143) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n  (:id . 69))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 160) (:start . 157)\n  (:id . 70))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 166)\n  (:start . 161) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s9.335) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503099@unknown@formal@none@1@S@Quantitative RT-PCR gene expression analysis@(((:tag . "JJ") (:stem . "quantitative") (:form . "Quantitative") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 19)\n  (:start . 13) (:id . 43))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 24) (:start . 20)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 35)\n  (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 44)\n  (:start . 36) (:id . 46)))@@@1@5@((:identifiers (:sid . :s9.336) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503100@unknown@formal@none@1@S@Primer sequences, PCR product and annealing temperatures for all targets are described in Additional File 5.@(((:tag . "NNP") (:stem . "Primer") (:form . "Primer") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 16)\n  (:start . 7) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "anneal") (:form . "annealing") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "temperature") (:form . "temperatures") (:end . 56)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 72)\n  (:start . 65) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 86)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Additional") (:form . "Additional") (:end . 100)\n  (:start . 90) (:id . 56))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 105) (:start . 101)\n  (:id . 57))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s9.337) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503101@unknown@formal@none@1@S@cDNA was synthesized using a cDNA synthesis kit (Bioline International, London, UK), and triplicate qPCRs (50 ng per reaction) of BME26 cells was undertaken using SensiMixPlus SYBR kit (Quantace Ltd, Watford, UK) in the Corbett RotorGene 3000 (Corbett, Sydney, Australia) using the following profile: 95°C 10 mins; 40 cycles of 95°C 15 s, 55°C 30 s, 72°C 30 sec, followed by a melt analysis 72–90°C 30 s on the first step, 5 s holds for subsequent steps, according to manufacturer's instructions for SYBR green detection.@(((:tag . "NNP") (:stem . "cDNA") (:form . "cDNA") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "synthesize") (:form . "synthesized") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . 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"detection") (:end . 520)\n  (:start . 511) (:id . 149))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 521) (:start . 520)\n  (:id . 150)))@@@1@109@((:identifiers (:sid . :s9.338) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503102@unknown@formal@none@1@S@All the results corresponded to relative quantification using R. microplus actin (Additional File 5) as an internal control gene using the 2-ΔΔCt method [72].@(((:tag . "PDT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "VBD") (:stem . "correspond") (:form . "corresponded") (:end . 28)\n  (:start . 16) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "quantification") (:form . "quantification")\n  (:end . 55) (:start . 41) (:id . 48))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 61) (:start . 56)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 74)\n  (:start . 65) (:id . 51))\n ((:tag . "NN") (:stem . "actin") (:form . "actin") (:end . 80) (:start . 75)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 92)\n  (:start . 82) (:id . 54))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 97) (:start . 93)\n  (:id . 55))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 99) (:start . 98)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 103) (:start . 101)\n  (:id . 58))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 115)\n  (:start . 107) (:id . 60))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 123)\n  (:start . 116) (:id . 61))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 128) (:start . 124)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 134) (:start . 129)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "2-ΔΔCt") (:form . "2-ΔΔCt") (:end . 145)\n  (:start . 139) (:id . 65))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 152)\n  (:start . 146) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 154) (:start . 153)\n  (:id . 67))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 156) (:start . 154)\n  (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 157) (:start . 156)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s9.339) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503103@unknown@formal@none@1@S@Viscera from the 6th replicate tick of each Drosophila homologue group were homogenized in TRIzol® to extract total RNA.@(((:tag . "NNP") (:stem . "Viscera") (:form . "Viscera") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "6th") (:form . "6th") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "replicate") (:form . "replicate") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "tick") (:form . "tick") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 54)\n  (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "homologue") (:form . "homologue") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 70) (:start . 65)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "homogenize") (:form . "homogenized") (:end . 87)\n  (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "TRIzol®") (:form . "TRIzol®") (:end . 98)\n  (:start . 91) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 57))\n ((:tag . "VB") (:stem . "extract") (:form . "extract") (:end . 109)\n  (:start . 102) (:id . 58))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 115)\n  (:start . 110) (:id . 59))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s9.340) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503104@unknown@formal@none@1@S@The semi quantitative analysis of the samples was undertaken using the QuantiTect SYBR green RT-PCR Kit® (QIAGEN, Australia) as recommended by the manufacturer.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "semi") (:form . "semi") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 21)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "undertake") (:form . "undertaken") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 66) (:start . 61)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "QuantiTect") (:form . "QuantiTect") (:end . 81)\n  (:start . 71) (:id . 53))\n ((:tag . "NNP") (:stem . "SYBR") (:form . "SYBR") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 92) (:start . 87)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 99)\n  (:start . 93) (:id . 56))\n ((:tag . "NNP") (:stem . "Kit®") (:form . "Kit®") (:end . 104) (:start . 100)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "QIAGEN") (:form . "QIAGEN") (:end . 112)\n  (:start . 106) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Australia") (:form . "Australia") (:end . 123)\n  (:start . 114) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "recommend") (:form . "recommended") (:end . 139)\n  (:start . 128) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 142) (:start . 140)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 66))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 159)\n  (:start . 147) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s9.341) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503105@unknown@formal@none@1@S@The expression profiles were normalised against R. microplus actin as above.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "normalise") (:form . "normalised") (:end . 39)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 47)\n  (:start . 40) (:id . 47))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . "NN") (:stem . "actin") (:form . "actin") (:end . 66) (:start . 61)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 75) (:start . 70)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s9.342) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503106@unknown@formal@none@1@S@Reactions contained 125 ng of total RNA, 12.5 µl of 2× QuantiTect SYBR Green RT-PCR Master mix, 10 pmol of each primer, 0.25 µl QuantiTect RT Mix, the final reaction volume was 25 µl.@(((:tag . "NNS") (:stem . "reaction") (:form . "Reactions") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 19)\n  (:start . 10) (:id . 43))\n ((:tag . "CD") (:stem . "125") (:form . "125") (:end . 23) (:start . 20)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ng") (:form . "ng") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "CD") (:stem . "12.5") (:form . "12.5") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "CD") (:stem . "2×") (:form . "2×") (:end . 54) (:start . 52)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "QuantiTect") (:form . "QuantiTect") (:end . 65)\n  (:start . 55) (:id . 54))\n ((:tag . "NNP") (:stem . "SYBR") (:form . "SYBR") (:end . 70) (:start . 66)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Green") (:form . "Green") (:end . 76) (:start . 71)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 83)\n  (:start . 77) (:id . 57))\n ((:tag . "NNP") (:stem . "Master") (:form . "Master") (:end . 90)\n  (:start . 84) (:id . 58))\n ((:tag . "NN") (:stem . "mix") (:form . "mix") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 98) (:start . 96)\n  (:id . 61))\n ((:tag . "NN") (:stem . "pmol") (:form . "pmol") (:end . 103) (:start . 99)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 63))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 111) (:start . 107)\n  (:id . 64))\n ((:tag . "NN") (:stem . "primer") (:form . "primer") (:end . 118)\n  (:start . 112) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 66))\n ((:tag . "CD") (:stem . "0.25") (:form . "0.25") (:end . 124) (:start . 120)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 127) (:start . 125)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "QuantiTect") (:form . "QuantiTect") (:end . 138)\n  (:start . 128) (:id . 69))\n ((:tag . "NNP") (:stem . "RT") (:form . "RT") (:end . 141) (:start . 139)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Mix") (:form . "Mix") (:end . 145) (:start . 142)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 156)\n  (:start . 151) (:id . 74))\n ((:tag . "NN") (:stem . "reaction") (:form . "reaction") (:end . 165)\n  (:start . 157) (:id . 75))\n ((:tag . "NN") (:stem . "volume") (:form . "volume") (:end . 172)\n  (:start . 166) (:id . 76))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 176) (:start . 173)\n  (:id . 77))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 179) (:start . 177)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "µl") (:form . "µl") (:end . 182) (:start . 180)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s9.343) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503107@unknown@formal@none@1@S@RT-PCR reaction were conducted on Rotor-Gene 3000 under the following conditions: reverse transcription 50°C for 30 min, PCR initial activation at 95°C for 15 min, followed by 40 cycles at 94°C, 15 s, 55°C, 30 s and 72°C 30 s.@(((:tag . "NNP") (:stem . "RT-PCR") (:form . "RT-PCR") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "reaction") (:form . "reaction") (:end . 15)\n  (:start . 7) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "conduct") (:form . "conducted") (:end . 30)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Rotor-Gene") (:form . "Rotor-Gene") (:end . 44)\n  (:start . 34) (:id . 47))\n ((:tag . "CD") (:stem . "3000") (:form . "3000") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "following") (:form . "following") (:end . 69)\n  (:start . 60) (:id . 51))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 80)\n  (:start . 70) (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 81) (:start . 80)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 89)\n  (:start . 82) (:id . 54))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 103) (:start . 90) (:id . 55))\n ((:tag . "NN") (:stem . "50°c") (:form . "50°C") (:end . 108) (:start . 104)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 112) (:start . 109)\n  (:id . 57))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 115) (:start . 113)\n  (:id . 58))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 119) (:start . 116)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 124) (:start . 121)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 132)\n  (:start . 125) (:id . 62))\n ((:tag . "NN") (:stem . "activation") (:form . "activation") (:end . 143)\n  (:start . 133) (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 146) (:start . 144)\n  (:id . 64))\n ((:tag . "NN") (:stem . "95°c") (:form . "95°C") (:end . 151) (:start . 147)\n  (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 155) (:start . 152)\n  (:id . 66))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 158) (:start . 156)\n  (:id . 67))\n ((:tag . "NN") (:stem . "min") (:form . "min") (:end . 162) (:start . 159)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 172)\n  (:start . 164) (:id . 70))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 178) (:start . 176)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "cycle") (:form . "cycles") (:end . 185)\n  (:start . 179) (:id . 73))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 188) (:start . 186)\n  (:id . 74))\n ((:tag . "NN") (:stem . "94°c") (:form . "94°C") (:end . 193) (:start . 189)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 194) (:start . 193)\n  (:id . 76))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 197) (:start . 195)\n  (:id . 77))\n ((:tag . "NN") (:stem . "s") (:form . "s") (:end . 199) (:start . 198)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n  (:id . 79))\n ((:tag . "NN") (:stem . "55°c") (:form . "55°C") (:end . 205) (:start . 201)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 206) (:start . 205)\n  (:id . 81))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 209) (:start . 207)\n  (:id . 82))\n ((:tag . "NN") (:stem . "s") (:form . "s") (:end . 211) (:start . 210)\n  (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 215) (:start . 212)\n  (:id . 84))\n ((:tag . "NN") (:stem . "72°c") (:form . "72°C") (:end . 220) (:start . 216)\n  (:id . 85))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 223) (:start . 221)\n  (:id . 86))\n ((:tag . "NN") (:stem . "s") (:form . "s") (:end . 225) (:start . 224)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s9.344) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503108@unknown@formal@none@1@S@Calculation of percent gene expression and knockdown (average of 3 triplicate reactions) was determined by comparative CT method for relative quantification as described above.@(((:tag . "NN") (:stem . "calculation") (:form . "Calculation") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "NN") (:stem . "percent") (:form . "percent") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "knockdown") (:form . "knockdown") (:end . 52)\n  (:start . 43) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "triplicate") (:form . "triplicate") (:end . 77)\n  (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "reaction") (:form . "reactions") (:end . 87)\n  (:start . 78) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 103)\n  (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "comparative") (:form . "comparative") (:end . 118)\n  (:start . 107) (:id . 59))\n ((:tag . "NN") (:stem . "ct") (:form . "CT") (:end . 121) (:start . 119)\n  (:id . 60))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 128)\n  (:start . 122) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 132) (:start . 129)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 141)\n  (:start . 133) (:id . 63))\n ((:tag . "NN") (:stem . "quantification") (:form . "quantification")\n  (:end . 156) (:start . 142) (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 159) (:start . 157)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 169)\n  (:start . 160) (:id . 66))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 175)\n  (:start . 170) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s9.345) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503109@unknown@formal@none@1@S@R. microplus EST Accessions@(((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "EST") (:form . "EST") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Accessions") (:form . "Accessions") (:end . 27)\n  (:start . 17) (:id . 45)))@@@1@4@((:identifiers (:sid . :s9.346) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503110@unknown@formal@none@1@S@GenBank Accessions describing the R. microplus ESTs identified in this study have been appended as Additional File 6.@(((:tag . "NNP") (:stem . "GenBank") (:form . "GenBank") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Accession") (:form . "Accessions") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "VBG") (:stem . "describe") (:form . "describing") (:end . 29)\n  (:start . 19) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "R.") (:form . "R.") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "NN") (:stem . "microplus") (:form . "microplus") (:end . 46)\n  (:start . 37) (:id . 47))\n ((:tag . "NNS") (:stem . "est") (:form . "ESTs") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 62)\n  (:start . 52) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 70) (:start . 66)\n  (:id . 51))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 76) (:start . 71)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 81) (:start . 77)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "append") (:form . "appended") (:end . 95)\n  (:start . 87) (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 98) (:start . 96)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 109)\n  (:start . 99) (:id . 57))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 114) (:start . 110)\n  (:id . 58))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 116) (:start . 115)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s9.347) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503111@unknown@formal@none@1@S@Abbreviations@(((:tag . "NNS") (:stem . "abbreviation") (:form . "Abbreviations")\n  (:end . 13) (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s9.348) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503112@unknown@formal@none@1@S@dsRNA: double-stranded RNA; cDNA: complementary DNA; EST: expressed sequence tags; GO: Gene Ontology; PCR: polymerase chain reaction; RISC: RNA-induced silencing complex; RNAi: RNA interference; siRNA: small interfering RNA;@(((:tag . "NNP") (:stem . "dsRNA") (:form . "dsRNA") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "JJ") (:stem . "double-stranded") (:form . "double-stranded")\n  (:end . 22) (:start . 7) (:id . 44))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "cDNA") (:form . "cDNA") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "complementary") (:form . "complementary")\n  (:end . 47) (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "EST") (:form . "EST") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 67)\n  (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 76)\n  (:start . 68) (:id . 55))\n ((:tag . "NNS") (:stem . "tag") (:form . "tags") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "go") (:form . "GO") (:end . 85) (:start . 83)\n  (:id . 58))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 86) (:start . 85)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 91) (:start . 87)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Ontology") (:form . "Ontology") (:end . 100)\n  (:start . 92) (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 101) (:start . 100)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "PCR") (:form . "PCR") (:end . 105) (:start . 102)\n  (:id . 63))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 106) (:start . 105)\n  (:id . 64))\n ((:tag . "NN") (:stem . "polymerase") (:form . "polymerase") (:end . 117)\n  (:start . 107) (:id . 65))\n ((:tag . "NN") (:stem . "chain") (:form . "chain") (:end . 123)\n  (:start . 118) (:id . 66))\n ((:tag . "NN") (:stem . "reaction") (:form . "reaction") (:end . 132)\n  (:start . 124) (:id . 67))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 133) (:start . 132)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "RISC") (:form . "RISC") (:end . 138) (:start . 134)\n  (:id . 69))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 139) (:start . 138)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "rna-induced") (:form . "RNA-induced") (:end . 151)\n  (:start . 140) (:id . 71))\n ((:tag . "NN") (:stem . "silencing") (:form . "silencing") (:end . 161)\n  (:start . 152) (:id . 72))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 169)\n  (:start . 162) (:id . 73))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 170) (:start . 169)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "RNAi") (:form . "RNAi") (:end . 175) (:start . 171)\n  (:id . 75))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 176) (:start . 175)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 180) (:start . 177)\n  (:id . 77))\n ((:tag . "NN") (:stem . "interference") (:form . "interference") (:end . 193)\n  (:start . 181) (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 194) (:start . 193)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "siRNA") (:form . "siRNA") (:end . 200)\n  (:start . 195) (:id . 80))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 201) (:start . 200)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 207)\n  (:start . 202) (:id . 82))\n ((:tag . "VBG") (:stem . "interfere") (:form . "interfering") (:end . 219)\n  (:start . 208) (:id . 83))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 223) (:start . 220)\n  (:id . 84))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 224) (:start . 223)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s9.349) (:did . :pmc2676286) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503113@unknown@formal@none@1@S@Positional Cues in the Drosophila Nerve Cord: Semaphorins Pattern the Dorso-Ventral Axis@(((:tag . "JJ") (:stem . "positional") (:form . "Positional") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "cue") (:form . "Cues") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 33)\n  (:start . 23) (:id . 46))\n ((:tag . "NNP") (:stem . "Nerve") (:form . "Nerve") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Cord") (:form . "Cord") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Semaphorin") (:form . "Semaphorins") (:end . 57)\n  (:start . 46) (:id . 50))\n ((:tag . "VBP") (:stem . "pattern") (:form . "Pattern") (:end . 65)\n  (:start . 58) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "Dorso-Ventral")\n  (:end . 83) (:start . 70) (:id . 53))\n ((:tag . "NNP") (:stem . "Axis") (:form . "Axis") (:end . 88) (:start . 84)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s10.1) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5503114@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s10.2) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503115@unknown@formal@none@1@S@During the development of neural circuitry, neurons of different kinds establish specific synaptic connections by selecting appropriate targets from large numbers of alternatives.@(((:tag . "IN") (:stem . "during") (:form . "During") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "circuitry") (:form . "circuitry") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "kind") (:form . "kinds") (:end . 70) (:start . 65)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "establish") (:form . "establish") (:end . 80)\n  (:start . 71) (:id . 53))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 98)\n  (:start . 90) (:id . 55))\n ((:tag . "NNS") (:stem . "connection") (:form . "connections") (:end . 110)\n  (:start . 99) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 113) (:start . 111)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "select") (:form . "selecting") (:end . 123)\n  (:start . 114) (:id . 58))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 135)\n  (:start . 124) (:id . 59))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 143)\n  (:start . 136) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 148) (:start . 144)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 154)\n  (:start . 149) (:id . 62))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 162)\n  (:start . 155) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 165) (:start . 163)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "alternative") (:form . "alternatives") (:end . 178)\n  (:start . 166) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.3) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503116@unknown@formal@none@1@S@The range of alternative targets is reduced by well organised patterns of growth, termination, and branching that deliver the terminals of appropriate pre- and postsynaptic partners to restricted volumes of the developing nervous system.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "organise") (:form . "organised") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 80)\n  (:start . 74) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 93)\n  (:start . 82) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 58))\n ((:tag . "NN") (:stem . "branching") (:form . "branching") (:end . 108)\n  (:start . 99) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 113) (:start . 109)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "deliver") (:form . "deliver") (:end . 121)\n  (:start . 114) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 135)\n  (:start . 126) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 150)\n  (:start . 139) (:id . 65))\n ((:tag . "JJ") (:stem . "pre-") (:form . "pre-") (:end . 155) (:start . 151)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 172)\n  (:start . 160) (:id . 68))\n ((:tag . "NNS") (:stem . "partner") (:form . "partners") (:end . 181)\n  (:start . 173) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 184) (:start . 182)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "restricted") (:form . "restricted") (:end . 195)\n  (:start . 185) (:id . 71))\n ((:tag . "NNS") (:stem . "volume") (:form . "volumes") (:end . 203)\n  (:start . 196) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 206) (:start . 204)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 210) (:start . 207)\n  (:id . 74))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 221)\n  (:start . 211) (:id . 75))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 229)\n  (:start . 222) (:id . 76))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 236)\n  (:start . 230) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 237) (:start . 236)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s10.4) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503117@unknown@formal@none@1@S@We use the axons of embryonic Drosophila sensory neurons as a model system in which to study the way in which growing neurons are guided to terminate in specific volumes of the developing nervous system.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "use") (:form . "use") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 29)\n  (:start . 20) (:id . 47))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 40)\n  (:start . 30) (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 74)\n  (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 83) (:start . 78)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "VB") (:stem . "study") (:form . "study") (:end . 92) (:start . 87)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 109)\n  (:start . 104) (:id . 62))\n ((:tag . "VBG") (:stem . "grow") (:form . "growing") (:end . 117)\n  (:start . 110) (:id . 63))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 125)\n  (:start . 118) (:id . 64))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 129) (:start . 126)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "guide") (:form . "guided") (:end . 136)\n  (:start . 130) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n  (:id . 67))\n ((:tag . "VB") (:stem . "terminate") (:form . "terminate") (:end . 149)\n  (:start . 140) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 152) (:start . 150)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 161)\n  (:start . 153) (:id . 70))\n ((:tag . "NNS") (:stem . "volume") (:form . "volumes") (:end . 169)\n  (:start . 162) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 172) (:start . 170)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 176) (:start . 173)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 187)\n  (:start . 177) (:id . 74))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 195)\n  (:start . 188) (:id . 75))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 202)\n  (:start . 196) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s10.5) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503118@unknown@formal@none@1@S@The mediolateral positions of sensory arbors are controlled by the response of Robo receptors to a Slit gradient.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "mediolateral") (:form . "mediolateral") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 26)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . "NNS") (:stem . "arbor") (:form . "arbors") (:end . 44)\n  (:start . 38) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "control") (:form . "controlled") (:end . 59)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 75)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Robo") (:form . "Robo") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 93)\n  (:start . 84) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 98) (:start . 97)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 103) (:start . 99)\n  (:id . 58))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 112)\n  (:start . 104) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.6) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503119@unknown@formal@none@1@S@Here we make a genetic analysis of factors regulating position in the dorso-ventral axis.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "make") (:form . "make") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 22)\n  (:start . 15) (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "VBG") (:stem . "regulate") (:form . "regulating") (:end . 53)\n  (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 83) (:start . 70) (:id . 54))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s10.7) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503120@unknown@formal@none@1@S@We find that dorso-ventral layers of neuropile contain different levels and combinations of Semaphorins.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 26) (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 64)\n  (:start . 55) (:id . 50))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 71)\n  (:start . 65) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 88)\n  (:start . 76) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Semaphorin") (:form . "Semaphorins") (:end . 103)\n  (:start . 92) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s10.8) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503121@unknown@formal@none@1@S@We demonstrate the existence of a central to dorsal and central to ventral gradient of Sema 2a, perpendicular to the Slit gradient.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "existence") (:form . "existence") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 63)\n  (:start . 56) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 74)\n  (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 83)\n  (:start . 75) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 91) (:start . 87)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2a") (:form . "2a") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "perpendicular") (:form . "perpendicular")\n  (:end . 109) (:start . 96) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 121) (:start . 117)\n  (:id . 63))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 130)\n  (:start . 122) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.9) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503122@unknown@formal@none@1@S@We show that a combination of Plexin A (Plex A) and Plexin B (Plex B) receptors specifies the ventral projection of sensory neurons by responding to high concentrations of Semaphorin 1a (Sema 1a) and Semaphorin 2a (Sema 2a).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 26)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Plexin") (:form . "Plexin") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 44) (:start . 40)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 46) (:start . 45)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Plexin") (:form . "Plexin") (:end . 58)\n  (:start . 52) (:id . 55))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 66) (:start . 62)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 68) (:start . 67)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 79)\n  (:start . 70) (:id . 61))\n ((:tag . "VBZ") (:stem . "specify") (:form . "specifies") (:end . 89)\n  (:start . 80) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 101)\n  (:start . 94) (:id . 64))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 112)\n  (:start . 102) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 123)\n  (:start . 116) (:id . 67))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 131)\n  (:start . 124) (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 134) (:start . 132)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "respond") (:form . "responding") (:end . 145)\n  (:start . 135) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 153) (:start . 149)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 168) (:start . 154) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Semaphorin") (:form . "Semaphorin") (:end . 182)\n  (:start . 172) (:id . 75))\n ((:tag . "NNP") (:stem . "1a") (:form . "1a") (:end . 185) (:start . 183)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 187) (:start . 186)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 191) (:start . 187)\n  (:id . 78))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 194) (:start . 192)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 199) (:start . 196)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Semaphorin") (:form . "Semaphorin") (:end . 210)\n  (:start . 200) (:id . 82))\n ((:tag . "NNP") (:stem . "2a") (:form . "2a") (:end . 213) (:start . 211)\n  (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 215) (:start . 214)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 219) (:start . 215)\n  (:id . 85))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 222) (:start . 220)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 223) (:start . 222)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s10.10) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503123@unknown@formal@none@1@S@Together our findings support the idea that axons are delivered to particular regions of the neuropile by their responses to systems of positional cues in each dimension.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "deliver") (:form . "delivered") (:end . 63)\n  (:start . 54) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 77)\n  (:start . 67) (:id . 53))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 85)\n  (:start . 78) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 102)\n  (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 111)\n  (:start . 106) (:id . 59))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 121)\n  (:start . 112) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 124) (:start . 122)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 132)\n  (:start . 125) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 146)\n  (:start . 136) (:id . 64))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 151) (:start . 147)\n  (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n  (:id . 66))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 159) (:start . 155)\n  (:id . 67))\n ((:tag . "NN") (:stem . "dimension") (:form . "dimension") (:end . 169)\n  (:start . 160) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x10.11.1) (:span 34 38)))\n (:hscopes ((:id . :x10.11.1) (:span 34 169)))\n (:identifiers (:sid . :s10.11) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503124@unknown@formal@none@1@S@Author Summary@(((:tag . "NNP") (:stem . "Author") (:form . "Author") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Summary") (:form . "Summary") (:end . 14)\n  (:start . 7) (:id . 43)))@@@1@2@((:identifiers (:sid . :s10.12) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503125@unknown@formal@none@1@S@Axons and dendrites of synaptic partners must be targeted to a common region of the developing neural network so that appropriate connections can be formed.@(((:tag . "NNS") (:stem . "axon") (:form . "Axons") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "partner") (:form . "partners") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "target") (:form . "targeted") (:end . 57)\n  (:start . 49) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 76)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 94)\n  (:start . 84) (:id . 57))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 101)\n  (:start . 95) (:id . 58))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 109)\n  (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 117) (:start . 113)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 129)\n  (:start . 118) (:id . 62))\n ((:tag . "NNS") (:stem . "connection") (:form . "connections") (:end . 141)\n  (:start . 130) (:id . 63))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 145) (:start . 142)\n  (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 148) (:start . 146)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "form") (:form . "formed") (:end . 155)\n  (:start . 149) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s10.13) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503126@unknown@formal@none@1@S@The mechanisms underlying this targeting are incompletely understood.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 40)\n  (:start . 31) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "RB") (:stem . "incompletely") (:form . "incompletely") (:end . 57)\n  (:start . 45) (:id . 48))\n ((:tag . "VBN") (:stem . "understand") (:form . "understood") (:end . 68)\n  (:start . 58) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s10.14) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503127@unknown@formal@none@1@S@We showed previously that a positional cue (Slit) acting in the medio-lateral axis of the Drosophila nerve cord controls the position of sensory terminals independently of their synaptic partners.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "cue") (:form . "cue") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 56) (:start . 50)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 77) (:start . 64) (:id . 55))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 82) (:start . 78)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 100)\n  (:start . 90) (:id . 59))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . "NN") (:stem . "cord") (:form . "cord") (:end . 111) (:start . 107)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "control") (:form . "controls") (:end . 120)\n  (:start . 112) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n  (:id . 63))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 133)\n  (:start . 125) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 144)\n  (:start . 137) (:id . 66))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 154)\n  (:start . 145) (:id . 67))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n  (:end . 168) (:start . 155) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 69))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 177)\n  (:start . 172) (:id . 70))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 186)\n  (:start . 178) (:id . 71))\n ((:tag . "NNS") (:stem . "partner") (:form . "partners") (:end . 195)\n  (:start . 187) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s10.15) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503128@unknown@formal@none@1@S@This work revealed that there might be additional cues operating in a similar fashion in the dorso-ventral axis of the nerve cord.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 49)\n  (:start . 39) (:id . 49))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "operate") (:form . "operating") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 77)\n  (:start . 70) (:id . 54))\n ((:tag . "NN") (:stem . "fashion") (:form . "fashion") (:end . 85)\n  (:start . 78) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 106) (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 111) (:start . 107)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 61))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 124)\n  (:start . 119) (:id . 62))\n ((:tag . "NN") (:stem . "cord") (:form . "cord") (:end . 129) (:start . 125)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x10.16.1) (:span 30 35)))\n (:hscopes ((:id . :x10.16.1) (:span 30 129)))\n (:identifiers (:sid . :s10.16) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503129@unknown@formal@none@1@S@Here we report the discovery of a dorso-ventral system of positional cues, in the form of a gradient of secreted Semaphorin 2a acting at right angles to the Slit gradient, and membrane bound Semaphorin 1a differentially distributed across the neuropile.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "report") (:form . "report") (:end . 14)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "discovery") (:form . "discovery") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 47) (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 54)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 68)\n  (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 100)\n  (:start . 92) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "secrete") (:form . "secreted") (:end . 112)\n  (:start . 104) (:id . 62))\n ((:tag . "NNP") (:stem . "Semaphorin") (:form . "Semaphorin") (:end . 123)\n  (:start . 113) (:id . 63))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 126) (:start . 124)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 133)\n  (:start . 127) (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 136) (:start . 134)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 142)\n  (:start . 137) (:id . 67))\n ((:tag . "NNS") (:stem . "angle") (:form . "angles") (:end . 149)\n  (:start . 143) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 152) (:start . 150)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 161) (:start . 157)\n  (:id . 71))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 170)\n  (:start . 162) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n  (:id . 74))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 184)\n  (:start . 176) (:id . 75))\n ((:tag . "VBD") (:stem . "bind") (:form . "bound") (:end . 190)\n  (:start . 185) (:id . 76))\n ((:tag . "NNP") (:stem . "Semaphorin") (:form . "Semaphorin") (:end . 201)\n  (:start . 191) (:id . 77))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 204) (:start . 202)\n  (:id . 78))\n ((:tag . "RB") (:stem . "differentially") (:form . "differentially")\n  (:end . 219) (:start . 205) (:id . 79))\n ((:tag . "VBN") (:stem . "distribute") (:form . "distributed") (:end . 231)\n  (:start . 220) (:id . 80))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 238)\n  (:start . 232) (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 242) (:start . 239)\n  (:id . 82))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 252)\n  (:start . 243) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 253) (:start . 252)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s10.17) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503130@unknown@formal@none@1@S@The two Semaphorins dictate the termination positions of sensory axons in the dorso-ventral axis.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "semaphorin") (:form . "Semaphorins") (:end . 19)\n  (:start . 8) (:id . 44))\n ((:tag . "VBP") (:stem . "dictate") (:form . "dictate") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 43)\n  (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 53)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 64)\n  (:start . 57) (:id . 50))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 70) (:start . 65)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 91) (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 96) (:start . 92)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s10.18) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503131@unknown@formal@none@1@S@Together with a third signal acting in the antero-posterior axis, Semaphorins and Slit deliver axons to appropriate volumes of the neural network.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 35) (:start . 29)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 59) (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Semaphorin") (:form . "Semaphorins") (:end . 77)\n  (:start . 66) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "slit") (:form . "Slit") (:end . 86) (:start . 82)\n  (:id . 55))\n ((:tag . "NN") (:stem . "deliver") (:form . "deliver") (:end . 94)\n  (:start . 87) (:id . 56))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 100) (:start . 95)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 103) (:start . 101)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 115)\n  (:start . 104) (:id . 59))\n ((:tag . "NNS") (:stem . "volume") (:form . "volumes") (:end . 123)\n  (:start . 116) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 137)\n  (:start . 131) (:id . 63))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 145)\n  (:start . 138) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.19) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503132@unknown@formal@none@1@S@These studies support a model in which axons branch and terminate, independently of synaptic partners, in response to pervasive systems of volumetric positional cues.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "branch") (:form . "branch") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "terminate") (:form . "terminate") (:end . 65)\n  (:start . 56) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n  (:end . 80) (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . "NNS") (:stem . "partner") (:form . "partners") (:end . 101)\n  (:start . 93) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 59))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 114)\n  (:start . 106) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "pervasive") (:form . "pervasive") (:end . 127)\n  (:start . 118) (:id . 62))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 135)\n  (:start . 128) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "volumetric") (:form . "volumetric") (:end . 149)\n  (:start . 139) (:id . 65))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 160)\n  (:start . 150) (:id . 66))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 165) (:start . 161)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s10.20) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503133@unknown@formal@none@1@S@Introduction@(((:tag . "NN") (:stem . "introduction") (:form . "Introduction") (:end . 12)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s10.21) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503134@unknown@formal@none@1@S@During the development of neural circuitry, neurons of different kinds must establish specific synaptic connections by selecting appropriate targets from large numbers of different alternatives.@(((:tag . "IN") (:stem . "during") (:form . "During") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "circuitry") (:form . "circuitry") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "kind") (:form . "kinds") (:end . 70) (:start . 65)\n  (:id . 52))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "VB") (:stem . "establish") (:form . "establish") (:end . 85)\n  (:start . 76) (:id . 54))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 94)\n  (:start . 86) (:id . 55))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 103)\n  (:start . 95) (:id . 56))\n ((:tag . "NNS") (:stem . "connection") (:form . "connections") (:end . 115)\n  (:start . 104) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 118) (:start . 116)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "select") (:form . "selecting") (:end . 128)\n  (:start . 119) (:id . 59))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 140)\n  (:start . 129) (:id . 60))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 148)\n  (:start . 141) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 153) (:start . 149)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 159)\n  (:start . 154) (:id . 63))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 167)\n  (:start . 160) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 170) (:start . 168)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 180)\n  (:start . 171) (:id . 66))\n ((:tag . "NNS") (:stem . "alternative") (:form . "alternatives") (:end . 193)\n  (:start . 181) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s10.22) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503135@unknown@formal@none@1@S@The range of these alternative targets is reduced by well organised patterns of growth, termination, and branching that deliver the terminals of appropriate pre- and postsynaptic partners to restricted regions of the developing nervous system.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 30)\n  (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "organise") (:form . "organised") (:end . 67)\n  (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 76)\n  (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 86)\n  (:start . 80) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 99)\n  (:start . 88) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "branching") (:form . "branching") (:end . 114)\n  (:start . 105) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 119) (:start . 115)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "deliver") (:form . "deliver") (:end . 127)\n  (:start . 120) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 141)\n  (:start . 132) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 156)\n  (:start . 145) (:id . 66))\n ((:tag . "JJ") (:stem . "pre-") (:form . "pre-") (:end . 161) (:start . 157)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 178)\n  (:start . 166) (:id . 69))\n ((:tag . "NNS") (:stem . "partner") (:form . "partners") (:end . 187)\n  (:start . 179) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 190) (:start . 188)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "restricted") (:form . "restricted") (:end . 201)\n  (:start . 191) (:id . 72))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 209)\n  (:start . 202) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 212) (:start . 210)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 216) (:start . 213)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 227)\n  (:start . 217) (:id . 76))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 235)\n  (:start . 228) (:id . 77))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 242)\n  (:start . 236) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s10.23) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503136@unknown@formal@none@1@S@The mechanisms that control the coordinate projection of pre- and postsynaptic neurites to a common region are incompletely understood.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "control") (:form . "control") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "coordinate") (:form . "coordinate") (:end . 42)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 53)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "pre-") (:form . "pre-") (:end . 61) (:start . 57)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 78)\n  (:start . 66) (:id . 52))\n ((:tag . "NNS") (:stem . "neurite") (:form . "neurites") (:end . 87)\n  (:start . 79) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 92) (:start . 91)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 99)\n  (:start . 93) (:id . 56))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 106)\n  (:start . 100) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 110) (:start . 107)\n  (:id . 58))\n ((:tag . "RB") (:stem . "incompletely") (:form . "incompletely") (:end . 123)\n  (:start . 111) (:id . 59))\n ((:tag . "VBN") (:stem . "understand") (:form . "understood") (:end . 134)\n  (:start . 124) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.24) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503137@unknown@formal@none@1@S@Although there has been substantial progress in identifying molecular mechanisms of axon growth and guidance, far less is known about the way in which appropriate target areas are identified, leading to termination and branching [1]–[4].@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "substantial") (:form . "substantial") (:end . 35)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "progress") (:form . "progress") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 59)\n  (:start . 48) (:id . 49))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 69)\n  (:start . 60) (:id . 50))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 80)\n  (:start . 70) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 52))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 88) (:start . 84)\n  (:id . 53))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 95)\n  (:start . 89) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 55))\n ((:tag . "NN") (:stem . "guidance") (:form . "guidance") (:end . 108)\n  (:start . 100) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 57))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 113) (:start . 110)\n  (:id . 58))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 118) (:start . 114)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 121) (:start . 119)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 127)\n  (:start . 122) (:id . 61))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 133)\n  (:start . 128) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 63))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 141) (:start . 138)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 162)\n  (:start . 151) (:id . 67))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 169)\n  (:start . 163) (:id . 68))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 175)\n  (:start . 170) (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 179) (:start . 176)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 190)\n  (:start . 180) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 199)\n  (:start . 192) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 202) (:start . 200)\n  (:id . 74))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 214)\n  (:start . 203) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 218) (:start . 215)\n  (:id . 76))\n ((:tag . "NN") (:stem . "branching") (:form . "branching") (:end . 228)\n  (:start . 219) (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 230) (:start . 229)\n  (:id . 78))\n ((:tag . "CD") (:stem . "1]–[4") (:form . "1]–[4") (:end . 235)\n  (:start . 230) (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 236) (:start . 235)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 237) (:start . 236)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s10.25) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503138@unknown@formal@none@1@S@The extent to which these processes depend on target specific signals as opposed to pervasive guidance cues, to which many different neurons can respond, is far from clear.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "VBP") (:stem . "depend") (:form . "depend") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 61)\n  (:start . 53) (:id . 51))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 69)\n  (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "oppose") (:form . "opposed") (:end . 80)\n  (:start . 73) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "pervasive") (:form . "pervasive") (:end . 93)\n  (:start . 84) (:id . 56))\n ((:tag . "NN") (:stem . "guidance") (:form . "guidance") (:end . 102)\n  (:start . 94) (:id . 57))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 107) (:start . 103)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 117)\n  (:start . 112) (:id . 61))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 122) (:start . 118)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 132)\n  (:start . 123) (:id . 63))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 140)\n  (:start . 133) (:id . 64))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 144) (:start . 141)\n  (:id . 65))\n ((:tag . "VB") (:stem . "respond") (:form . "respond") (:end . 152)\n  (:start . 145) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 156) (:start . 154)\n  (:id . 68))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 160) (:start . 157)\n  (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 165) (:start . 161)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 171)\n  (:start . 166) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x10.26.1) (:span 157 171)))\n (:hscopes ((:id . :x10.26.1) (:span 0 171)))\n (:identifiers (:sid . :s10.26) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503139@unknown@formal@none@1@S@We have used the axons of embryonic Drosophila sensory neurons as a model system in which to study the way in which growing neurons are guided to terminate in a specific region of the developing nervous system.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 35)\n  (:start . 26) (:id . 48))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 46)\n  (:start . 36) (:id . 49))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 62)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 80)\n  (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 89) (:start . 84)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "VB") (:stem . "study") (:form . "study") (:end . 98) (:start . 93)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 115)\n  (:start . 110) (:id . 63))\n ((:tag . "VBG") (:stem . "grow") (:form . "growing") (:end . 123)\n  (:start . 116) (:id . 64))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 131)\n  (:start . 124) (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 135) (:start . 132)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "guide") (:form . "guided") (:end . 142)\n  (:start . 136) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 145) (:start . 143)\n  (:id . 68))\n ((:tag . "VB") (:stem . "terminate") (:form . "terminate") (:end . 155)\n  (:start . 146) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 158) (:start . 156)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 160) (:start . 159)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 169)\n  (:start . 161) (:id . 72))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 176)\n  (:start . 170) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 179) (:start . 177)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 194)\n  (:start . 184) (:id . 76))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 202)\n  (:start . 195) (:id . 77))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 209)\n  (:start . 203) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s10.27) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503140@unknown@formal@none@1@S@These neurons have their cell bodies in the periphery of the embryo, either close to or embedded in the body wall.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 24)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 36) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "periphery") (:form . "periphery") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 67)\n  (:start . 61) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . "JJ") (:stem . "close") (:form . "close") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 84) (:start . 82)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "embed") (:form . "embedded") (:end . 96)\n  (:start . 88) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 61))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . "NN") (:stem . "wall") (:form . "wall") (:end . 113) (:start . 109)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.28) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503141@unknown@formal@none@1@S@Their axons grow into a central ganglion where they terminate in a neuropile that consists of a dense meshwork of interweaving axons and dendrites.@(((:tag . "PRP$") (:stem . "their") (:form . "Their") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "ganglion") (:form . "ganglion") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 76)\n  (:start . 67) (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 90)\n  (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "dense") (:form . "dense") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "meshwork") (:form . "meshwork") (:end . 110)\n  (:start . 102) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "interweave") (:form . "interweaving") (:end . 126)\n  (:start . 114) (:id . 62))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 132)\n  (:start . 127) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 146)\n  (:start . 137) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.29) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503142@unknown@formal@none@1@S@Anatomically the neuropile shows few overt signs of organisation apart from clear regularities such as the commissures that cross the midline and a set of longitudinal axon bundles at stereotyped positions that provide a series of landmarks with respect to which other structures can be mapped [5].@(((:tag . "RB") (:stem . "anatomically") (:form . "Anatomically") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 26)\n  (:start . 17) (:id . 44))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 32) (:start . 27)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "overt") (:form . "overt") (:end . 42) (:start . 37)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "sign") (:form . 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"[") (:end . 295) (:start . 294)\n  (:id . 88))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 296) (:start . 295)\n  (:id . 89))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 297) (:start . 296)\n  (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 298) (:start . 297)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s10.30) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503143@unknown@formal@none@1@S@Functionally however the neuropile is an obviously well-organised structure, with, for example, motor neuron dendrites and the endings of sensory neurons terminating and branching in distinct and characteristic domains.@(((:tag . "RB") (:stem . "functionally") (:form . "Functionally") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 20)\n  (:start . 13) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 44))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "RB") (:stem . "obviously") (:form . "obviously") (:end . 50)\n  (:start . 41) (:id . 48))\n ((:tag . "JJ") (:stem . "well-organised") (:form . "well-organised")\n  (:end . 65) (:start . 51) (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 75)\n  (:start . 66) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 81) (:start . 77)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 86) (:start . 83)\n  (:id . 54))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 94)\n  (:start . 87) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "motor") (:form . "motor") (:end . 101) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 108)\n  (:start . 102) (:id . 58))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 118)\n  (:start . 109) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "ending") (:form . "endings") (:end . 134)\n  (:start . 127) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 145)\n  (:start . 138) (:id . 64))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 153)\n  (:start . 146) (:id . 65))\n ((:tag . "VBG") (:stem . "terminate") (:form . "terminating") (:end . 165)\n  (:start . 154) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 169) (:start . 166)\n  (:id . 67))\n ((:tag . "NN") (:stem . "branching") (:form . "branching") (:end . 179)\n  (:start . 170) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 182) (:start . 180)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 191)\n  (:start . 183) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 195) (:start . 192)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 210) (:start . 196) (:id . 72))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 218)\n  (:start . 211) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s10.31) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503144@unknown@formal@none@1@S@Thus it is clear that there must be cues operating in the neuropile that deliver terminals to these specific destinations within the forming network.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 40) (:start . 36)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "operate") (:form . "operating") (:end . 50)\n  (:start . 41) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 67)\n  (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "deliver") (:form . "deliver") (:end . 80)\n  (:start . 73) (:id . 56))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 90)\n  (:start . 81) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 99) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 108)\n  (:start . 100) (:id . 60))\n ((:tag . "NNS") (:stem . "destination") (:form . "destinations") (:end . 121)\n  (:start . 109) (:id . 61))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 128)\n  (:start . 122) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 140)\n  (:start . 133) (:id . 64))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 148)\n  (:start . 141) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x10.32.1) (:span 28 32)))\n (:hscopes ((:id . :x10.32.1) (:span 28 148)))\n (:identifiers (:sid . :s10.32) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503145@unknown@formal@none@1@S@In the case of the sensory neurons, it is clear that specific types of neurons serving particular modalities terminate in well ordered and characteristically different parts of the neuropile.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 26)\n  (:start . 19) (:id . 47))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 34)\n  (:start . 27) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 47) (:start . 42)\n  (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 52) (:start . 48)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 61)\n  (:start . 53) (:id . 54))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 67) (:start . 62)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 78)\n  (:start . 71) (:id . 57))\n ((:tag . "VBG") (:stem . "serve") (:form . "serving") (:end . 86)\n  (:start . 79) (:id . 58))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 97)\n  (:start . 87) (:id . 59))\n ((:tag . "NNS") (:stem . "modality") (:form . "modalities") (:end . 108)\n  (:start . 98) (:id . 60))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 118)\n  (:start . 109) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 126) (:start . 122)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "order") (:form . "ordered") (:end . 134)\n  (:start . 127) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n  (:id . 65))\n ((:tag . "RB") (:stem . "characteristically") (:form . "characteristically")\n  (:end . 157) (:start . 139) (:id . 66))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 167)\n  (:start . 158) (:id . 67))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 173)\n  (:start . 168) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 180) (:start . 177)\n  (:id . 70))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 190)\n  (:start . 181) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.33) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503146@unknown@formal@none@1@S@These termination zones together with the overall structure of the neuropile are shown in diagrammatic form in Figure 1.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 17)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "zone") (:form . "zones") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 59)\n  (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 76)\n  (:start . 67) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 80) (:start . 77)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 86) (:start . 81)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "diagrammatic") (:form . "diagrammatic") (:end . 102)\n  (:start . 90) (:id . 56))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 107) (:start . 103)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 117)\n  (:start . 111) (:id . 59))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.34) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503147@unknown@formal@none@1@S@Because the sensory neurons provide us with an accessible set of cells whose terminals grow to different parts of the forming neuropile, we can readily use these neurons to investigate the guidance mechanisms that operate to determine these distinctive patterns of growth and termination.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "accessible") (:form . "accessible") (:end . 57)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 76) (:start . 71)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 86)\n  (:start . 77) (:id . 55))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 104)\n  (:start . 95) (:id . 58))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 110)\n  (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 125)\n  (:start . 118) (:id . 62))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 135)\n  (:start . 126) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 139) (:start . 137)\n  (:id . 65))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 143) (:start . 140)\n  (:id . 66))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 151)\n  (:start . 144) (:id . 67))\n ((:tag . "VB") (:stem . "use") (:form . "use") (:end . 155) (:start . 152)\n  (:id . 68))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 161)\n  (:start . 156) (:id . 69))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 169)\n  (:start . 162) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 172) (:start . 170)\n  (:id . 71))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 184)\n  (:start . 173) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n  (:id . 73))\n ((:tag . "NN") (:stem . "guidance") (:form . "guidance") (:end . 197)\n  (:start . 189) (:id . 74))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 208)\n  (:start . 198) (:id . 75))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 213) (:start . 209)\n  (:id . 76))\n ((:tag . "VBP") (:stem . "operate") (:form . "operate") (:end . 221)\n  (:start . 214) (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 224) (:start . 222)\n  (:id . 78))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 234)\n  (:start . 225) (:id . 79))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 240)\n  (:start . 235) (:id . 80))\n ((:tag . "JJ") (:stem . "distinctive") (:form . "distinctive") (:end . 252)\n  (:start . 241) (:id . 81))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 261)\n  (:start . 253) (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 264) (:start . 262)\n  (:id . 83))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 271)\n  (:start . 265) (:id . 84))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 275) (:start . 272)\n  (:id . 85))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 287)\n  (:start . 276) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 288) (:start . 287)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s10.35) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503148@unknown@formal@none@1@S@Different neuron classes project to different medio-lateral domains and to different dorso-ventral layers of neuropile.@(((:tag . "JJ") (:stem . "different") (:form . "Different") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 16)\n  (:start . 10) (:id . 43))\n ((:tag . "VBZ") (:stem . "class") (:form . "classes") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "NN") (:stem . "project") (:form . "project") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 45)\n  (:start . 36) (:id . 47))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 59) (:start . 46) (:id . 48))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 67)\n  (:start . 60) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 84)\n  (:start . 75) (:id . 52))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 98) (:start . 85) (:id . 53))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 105)\n  (:start . 99) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 55))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 118)\n  (:start . 109) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.36) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503149@unknown@formal@none@1@S@We previously showed that Slit secreted at the midline and acting through its Robo receptors constitutes a repellent gradient to which sensory neurons respond by terminating and branching at specific positions in the medio-lateral axis of the neuropile [6].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 20) (:start . 14)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "secrete") (:form . "secreted") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 65) (:start . 59)\n  (:id . 52))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 73)\n  (:start . 66) (:id . 53))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 77) (:start . 74)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Robo") (:form . "Robo") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 92)\n  (:start . 83) (:id . 56))\n ((:tag . "VBZ") (:stem . "constitute") (:form . "constitutes") (:end . 104)\n  (:start . 93) (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 106) (:start . 105)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "repellent") (:form . "repellent") (:end . 116)\n  (:start . 107) (:id . 59))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 125)\n  (:start . 117) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 128) (:start . 126)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 134)\n  (:start . 129) (:id . 62))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 142)\n  (:start . 135) (:id . 63))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 150)\n  (:start . 143) (:id . 64))\n ((:tag . "VBP") (:stem . "respond") (:form . "respond") (:end . 158)\n  (:start . 151) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 161) (:start . 159)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "terminate") (:form . "terminating") (:end . 173)\n  (:start . 162) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 177) (:start . 174)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "branch") (:form . "branching") (:end . 187)\n  (:start . 178) (:id . 69))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 190) (:start . 188)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 199)\n  (:start . 191) (:id . 71))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 209)\n  (:start . 200) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 212) (:start . 210)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 216) (:start . 213)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 230) (:start . 217) (:id . 75))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 235) (:start . 231)\n  (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 238) (:start . 236)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 242) (:start . 239)\n  (:id . 78))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 252)\n  (:start . 243) (:id . 79))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 254) (:start . 253)\n  (:id . 80))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 255) (:start . 254)\n  (:id . 81))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 256) (:start . 255)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s10.37) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503150@unknown@formal@none@1@S@Expression of a particular Robo receptor by a sensory axon is necessary and sufficient to determine the distance from the midline at which that axon will terminate.@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "NNP") (:stem . "Robo") (:form . "Robo") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 71)\n  (:start . 62) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 86)\n  (:start . 76) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 99)\n  (:start . 90) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 112)\n  (:start . 104) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 117) (:start . 113)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 61))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 129)\n  (:start . 122) (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 138)\n  (:start . 133) (:id . 64))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 143) (:start . 139)\n  (:id . 65))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 148) (:start . 144)\n  (:id . 66))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 153) (:start . 149)\n  (:id . 67))\n ((:tag . "VB") (:stem . "terminate") (:form . "terminate") (:end . 163)\n  (:start . 154) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.38) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503151@unknown@formal@none@1@S@Thus, in the medio-lateral axis at least, the position at which an axon terminates within the forming neuropile is determined not by some putative signals from its postsynaptic target, but by the presynaptic neuron's response to a pervasive cue secreted from the midline.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 26) (:start . 13) (:id . 46))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 54)\n  (:start . 46) (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 63) (:start . 58)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 66) (:start . 64)\n  (:id . 55))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 71) (:start . 67)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "terminate") (:form . "terminates") (:end . 82)\n  (:start . 72) (:id . 57))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 89)\n  (:start . 83) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 101)\n  (:start . 94) (:id . 60))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 111)\n  (:start . 102) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 125)\n  (:start . 115) (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 129) (:start . 126)\n  (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 137) (:start . 133)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 146)\n  (:start . 138) (:id . 67))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 154)\n  (:start . 147) (:id . 68))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 159) (:start . 155)\n  (:id . 69))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 163) (:start . 160)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 176)\n  (:start . 164) (:id . 71))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 183)\n  (:start . 177) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 73))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 188) (:start . 185)\n  (:id . 74))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 191) (:start . 189)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 195) (:start . 192)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "presynaptic") (:form . "presynaptic") (:end . 207)\n  (:start . 196) (:id . 77))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 214)\n  (:start . 208) (:id . 78))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 216) (:start . 214)\n  (:id . 79))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 225)\n  (:start . 217) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 228) (:start . 226)\n  (:id . 81))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 230) (:start . 229)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "pervasive") (:form . "pervasive") (:end . 240)\n  (:start . 231) (:id . 83))\n ((:tag . "NN") (:stem . "cue") (:form . "cue") (:end . 244) (:start . 241)\n  (:id . 84))\n ((:tag . "VBN") (:stem . "secrete") (:form . "secreted") (:end . 253)\n  (:start . 245) (:id . 85))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 258) (:start . 254)\n  (:id . 86))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 262) (:start . 259)\n  (:id . 87))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 270)\n  (:start . 263) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 271) (:start . 270)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s10.39) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503152@unknown@formal@none@1@S@However, the neuropile is a 3-D structure and there must therefore be additional cues that determine the dorso-ventral and antero-posterior termination domains for each axonal and dendritic arbor.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "3-d") (:form . "3-D") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 41)\n  (:start . 32) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 80)\n  (:start . 70) (:id . 55))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 90) (:start . 86)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "determine") (:form . "determine") (:end . 100)\n  (:start . 91) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 118) (:start . 105) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 139) (:start . 123) (:id . 62))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 151)\n  (:start . 140) (:id . 63))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 159)\n  (:start . 152) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 163) (:start . 160)\n  (:id . 65))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 168) (:start . 164)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 175)\n  (:start . 169) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "dendritic") (:form . "dendritic") (:end . 189)\n  (:start . 180) (:id . 69))\n ((:tag . "NN") (:stem . "arbor") (:form . "arbor") (:end . 195)\n  (:start . 190) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x10.40.1) (:span 52 56)))\n (:hscopes ((:id . :x10.40.1) (:span 52 195)))\n (:identifiers (:sid . :s10.40) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503153@unknown@formal@none@1@S@Our previous study provided evidence for at least one further signal that operates to determine positions in the dorso-ventral axis.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "provide") (:form . "provided") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 36)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "operate") (:form . "operates") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 95)\n  (:start . 86) (:id . 56))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 105)\n  (:start . 96) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 126) (:start . 113) (:id . 60))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 131) (:start . 127)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s10.41) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503154@unknown@formal@none@1@S@Sensory terminals that are shifted experimentally along the medio-lateral axis of the neuropile maintain their characteristic dorso-ventral location in their new position, suggesting that the factor that determines this position may be a “dorso-ventral” patterning cue that is present at different positions in the medio-lateral axis.@(((:tag . "JJ") (:stem . "sensory") (:form . "Sensory") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "shift") (:form . "shifted") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n  (:end . 49) (:start . 35) (:id . 47))\n ((:tag . "IN") (:stem . "along") (:form . 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"”") (:end . 253) (:start . 252)\n  (:id . 78))\n ((:tag . "NN") (:stem . "patterning") (:form . "patterning") (:end . 264)\n  (:start . 254) (:id . 79))\n ((:tag . "NN") (:stem . "cue") (:form . "cue") (:end . 268) (:start . 265)\n  (:id . 80))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 273) (:start . 269)\n  (:id . 81))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 276) (:start . 274)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 284)\n  (:start . 277) (:id . 83))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 287) (:start . 285)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 297)\n  (:start . 288) (:id . 85))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 307)\n  (:start . 298) (:id . 86))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 310) (:start . 308)\n  (:id . 87))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 314) (:start . 311)\n  (:id . 88))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 328) (:start . 315) (:id . 89))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 333) (:start . 329)\n  (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 334) (:start . 333)\n  (:id . 91)))@@@1@50@((:hcues ((:id . :x10.42.1) (:span 229 232))\n  ((:id . :x10.42.2) (:span 172 182)))\n (:hscopes ((:id . :x10.42.1) (:span 229 333))\n  ((:id . :x10.42.2) (:span 172 333)))\n (:identifiers (:sid . :s10.42) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503155@unknown@formal@none@1@S@This additional finding led us to propose a general model for the cues that delineate domains within a neuropile in which presynaptic axons and their postsynaptic partners terminate and form connections [6].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "VBD") (:stem . "lead") (:form . "led") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "VB") (:stem . "propose") (:form . "propose") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 51)\n  (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 75) (:start . 71)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "delineate") (:form . "delineate") (:end . 85)\n  (:start . 76) (:id . 56))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 93)\n  (:start . 86) (:id . 57))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 100)\n  (:start . 94) (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 112)\n  (:start . 103) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 121)\n  (:start . 116) (:id . 62))\n ((:tag . "JJ") (:stem . "presynaptic") (:form . "presynaptic") (:end . 133)\n  (:start . 122) (:id . 63))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 139)\n  (:start . 134) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 65))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 149)\n  (:start . 144) (:id . 66))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 162)\n  (:start . 150) (:id . 67))\n ((:tag . "NNS") (:stem . "partner") (:form . "partners") (:end . 171)\n  (:start . 163) (:id . 68))\n ((:tag . "NN") (:stem . "terminate") (:form . "terminate") (:end . 181)\n  (:start . 172) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n  (:id . 70))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 190) (:start . 186)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "connection") (:form . "connections") (:end . 202)\n  (:start . 191) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 204) (:start . 203)\n  (:id . 73))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 205) (:start . 204)\n  (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 206) (:start . 205)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s10.43) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503156@unknown@formal@none@1@S@In this model, termination sites depend on the response of axons to a system of positional cues that dictate the behaviour and final location of many, perhaps all terminals within a developing network of pre- and postsynaptic neurons.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 26)\n  (:start . 15) (:id . 46))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "depend") (:form . "depend") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 64) (:start . 59)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 69) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 76)\n  (:start . 70) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 90)\n  (:start . 80) (:id . 58))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 95) (:start . 91)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "dictate") (:form . "dictate") (:end . 108)\n  (:start . 101) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 62))\n ((:tag . "NN") (:stem . "behaviour") (:form . "behaviour") (:end . 122)\n  (:start . 113) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 132)\n  (:start . 127) (:id . 65))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 141)\n  (:start . 133) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 149) (:start . 145)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 69))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 158)\n  (:start . 151) (:id . 70))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 162) (:start . 159)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 172)\n  (:start . 163) (:id . 72))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 179)\n  (:start . 173) (:id . 73))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 181) (:start . 180)\n  (:id . 74))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 192)\n  (:start . 182) (:id . 75))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 200)\n  (:start . 193) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 203) (:start . 201)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "pre-") (:form . "pre-") (:end . 208) (:start . 204)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 212) (:start . 209)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 225)\n  (:start . 213) (:id . 80))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 233)\n  (:start . 226) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x10.44.1) (:span 151 158)))\n (:hscopes ((:id . :x10.44.1) (:span 151 162)))\n (:identifiers (:sid . :s10.44) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503157@unknown@formal@none@1@S@Specific locations are given not by the target, but by the set of receptors for these positional cues that each neuron expresses.@(((:tag . "JJ") (:stem . "specific") (:form . "Specific") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "location") (:form . "locations") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 28) (:start . 23)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 75)\n  (:start . 66) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n  (:id . 57))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 85) (:start . 80)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 96)\n  (:start . 86) (:id . 59))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 101) (:start . 97)\n  (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 106) (:start . 102)\n  (:id . 61))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 111) (:start . 107)\n  (:id . 62))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 118)\n  (:start . 112) (:id . 63))\n ((:tag . "VBZ") (:stem . "express") (:form . "expresses") (:end . 128)\n  (:start . 119) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.45) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503158@unknown@formal@none@1@S@Here, we test and augment this model by using a genetic screen to identify cues and their receptors that guide terminating axons in the dorso-ventral axis of the neuropile.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 13) (:start . 9)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 17) (:start . 14)\n  (:id . 46))\n ((:tag . "VB") (:stem . "augment") (:form . "augment") (:end . 25)\n  (:start . 18) (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 30) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 36) (:start . 31)\n  (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 45) (:start . 40)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 55)\n  (:start . 48) (:id . 53))\n ((:tag . "NN") (:stem . "screen") (:form . "screen") (:end . 62)\n  (:start . 56) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 74)\n  (:start . 66) (:id . 56))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 79) (:start . 75)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 89)\n  (:start . 84) (:id . 59))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 99)\n  (:start . 90) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 104) (:start . 100)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "guide") (:form . "guide") (:end . 110)\n  (:start . 105) (:id . 62))\n ((:tag . "VBG") (:stem . "terminate") (:form . "terminating") (:end . 122)\n  (:start . 111) (:id . 63))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 128)\n  (:start . 123) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 131) (:start . 129)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 135) (:start . 132)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 149) (:start . 136) (:id . 67))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 154) (:start . 150)\n  (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 157) (:start . 155)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 70))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 171)\n  (:start . 162) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.46) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503159@unknown@formal@none@1@S@We find that dorso-ventral layers of neuropile contain different levels and combinations of semaphorins.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 26) (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 64)\n  (:start . 55) (:id . 50))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 71)\n  (:start . 65) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 88)\n  (:start . 76) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "semaphorin") (:form . "semaphorins") (:end . 103)\n  (:start . 92) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s10.47) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503160@unknown@formal@none@1@S@We demonstrate the existence of a central to dorsal and central to ventral gradient of Sema 2a, perpendicular to the Slit gradient.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "existence") (:form . "existence") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 63)\n  (:start . 56) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 74)\n  (:start . 67) (:id . 54))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 83)\n  (:start . 75) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 91) (:start . 87)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2a") (:form . "2a") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "perpendicular") (:form . "perpendicular")\n  (:end . 109) (:start . 96) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 121) (:start . 117)\n  (:id . 63))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 130)\n  (:start . 122) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.48) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503161@unknown@formal@none@1@S@We show that a combination of Plexin A (Plex A) and Plexin B (Plex B) receptors specifies the ventral projection of sensory neurons by responding to high concentrations of Semaphorin 1a (Sema 1a) and Semaphorin 2a (Sema 2a).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 26)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Plexin") (:form . "Plexin") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 44) (:start . 40)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 46) (:start . 45)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Plexin") (:form . "Plexin") (:end . 58)\n  (:start . 52) (:id . 55))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 66) (:start . 62)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 68) (:start . 67)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 79)\n  (:start . 70) (:id . 61))\n ((:tag . "VBZ") (:stem . "specify") (:form . "specifies") (:end . 89)\n  (:start . 80) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 101)\n  (:start . 94) (:id . 64))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 112)\n  (:start . 102) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 123)\n  (:start . 116) (:id . 67))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 131)\n  (:start . 124) (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 134) (:start . 132)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "respond") (:form . "responding") (:end . 145)\n  (:start . 135) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 153) (:start . 149)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "concentration") (:form . "concentrations")\n  (:end . 168) (:start . 154) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Semaphorin") (:form . "Semaphorin") (:end . 182)\n  (:start . 172) (:id . 75))\n ((:tag . "NNP") (:stem . "1a") (:form . "1a") (:end . 185) (:start . 183)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 187) (:start . 186)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 191) (:start . 187)\n  (:id . 78))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 194) (:start . 192)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 199) (:start . 196)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Semaphorin") (:form . "Semaphorin") (:end . 210)\n  (:start . 200) (:id . 82))\n ((:tag . "NNP") (:stem . "2a") (:form . "2a") (:end . 213) (:start . 211)\n  (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 215) (:start . 214)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 219) (:start . 215)\n  (:id . 85))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 222) (:start . 220)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 223) (:start . 222)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s10.49) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503162@unknown@formal@none@1@S@These signals together with the Slit/Robo system acting in the medio-lateral axis limit the arborisations of sensory axons to specific termination domains within the neuropile.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Slit/Robo") (:form . "Slit/Robo") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 48)\n  (:start . 42) (:id . 48))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 55) (:start . 49)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 76) (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 81) (:start . 77)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "limit") (:form . "limit") (:end . 87) (:start . 82)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "arborisation") (:form . "arborisations")\n  (:end . 105) (:start . 92) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 116)\n  (:start . 109) (:id . 58))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 122)\n  (:start . 117) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 125) (:start . 123)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 134)\n  (:start . 126) (:id . 61))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 146)\n  (:start . 135) (:id . 62))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 154)\n  (:start . 147) (:id . 63))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 161)\n  (:start . 155) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 65))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 175)\n  (:start . 166) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s10.50) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503163@unknown@formal@none@1@S@Since these are the domains within which specific functional sets of connections will be formed, the terminating sensory axons, by responding to pervasive positional cues, are able to lay out part of the characteristic functional architecture of the forming network.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "connection") (:form . "connections") (:end . 80)\n  (:start . 69) (:id . 53))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 85) (:start . 81)\n  (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "form") (:form . "formed") (:end . 95) (:start . 89)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "terminate") (:form . "terminating") (:end . 112)\n  (:start . 101) (:id . 59))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 120)\n  (:start . 113) (:id . 60))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 126)\n  (:start . 121) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 130) (:start . 128)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "respond") (:form . "responding") (:end . 141)\n  (:start . 131) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "pervasive") (:form . "pervasive") (:end . 154)\n  (:start . 145) (:id . 66))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 165)\n  (:start . 155) (:id . 67))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 170) (:start . 166)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 175) (:start . 172)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 180) (:start . 176)\n  (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 183) (:start . 181)\n  (:id . 72))\n ((:tag . "VB") (:stem . "lay") (:form . "lay") (:end . 187) (:start . 184)\n  (:id . 73))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 191) (:start . 188)\n  (:id . 74))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 196) (:start . 192)\n  (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 199) (:start . 197)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 218) (:start . 204) (:id . 78))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 229)\n  (:start . 219) (:id . 79))\n ((:tag . "NN") (:stem . "architecture") (:form . "architecture") (:end . 242)\n  (:start . 230) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 245) (:start . 243)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 249) (:start . 246)\n  (:id . 82))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 257)\n  (:start . 250) (:id . 83))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 265)\n  (:start . 258) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 266) (:start . 265)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s10.51) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503164@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s10.52) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503165@unknown@formal@none@1@S@The Drosophila Embryonic Neuropile Can Be Divided into Four Dorso-Ventral Layers, Which Are Likely to Have Distinct Functions in Information Processing@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Embryonic") (:form . "Embryonic") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "NNP") (:stem . "Neuropile") (:form . "Neuropile") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . "NNP") (:stem . "Can") (:form . "Can") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Be") (:form . "Be") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Divided") (:form . "Divided") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "CD") (:stem . "four") (:form . "Four") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "Dorso-Ventral")\n  (:end . 73) (:start . 60) (:id . 51))\n ((:tag . "NNPS") (:stem . "Layer") (:form . "Layers") (:end . 80)\n  (:start . 74) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "Which") (:end . 87) (:start . 82)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "Are") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "RB") (:stem . "likely") (:form . "Likely") (:end . 98)\n  (:start . 92) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 57))\n ((:tag . "VB") (:stem . "have") (:form . "Have") (:end . 106) (:start . 102)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "distinct") (:form . "Distinct") (:end . 115)\n  (:start . 107) (:id . 59))\n ((:tag . "NNPS") (:stem . "Function") (:form . "Functions") (:end . 125)\n  (:start . 116) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Information") (:form . "Information") (:end . 140)\n  (:start . 129) (:id . 62))\n ((:tag . "NNP") (:stem . "Processing") (:form . "Processing") (:end . 151)\n  (:start . 141) (:id . 63)))@@@1@22@((:hcues ((:id . :x10.53.1) (:span 92 98)))\n (:hscopes ((:id . :x10.53.1) (:span 82 151)))\n (:identifiers (:sid . :s10.53) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503166@unknown@formal@none@1@S@Previous studies have shown that the axons of sensory neurons project to distinct medio-lateral, dorso-ventral, and antero-posterior domains in the neuropile in correlation with their modality and dendritic morphology [7]–[9].@(((:tag . "JJ") (:stem . "previous") (:form . "Previous") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "VBP") (:stem . "project") (:form . "project") (:end . 69)\n  (:start . 62) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 95) (:start . 82) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 110) (:start . 97) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 132) (:start . 116) (:id . 60))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 140)\n  (:start . 133) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 143) (:start . 141)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n  (:id . 63))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 157)\n  (:start . 148) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 160) (:start . 158)\n  (:id . 65))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 172)\n  (:start . 161) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 177) (:start . 173)\n  (:id . 67))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 183)\n  (:start . 178) (:id . 68))\n ((:tag . "NN") (:stem . "modality") (:form . "modality") (:end . 192)\n  (:start . 184) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 196) (:start . 193)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "dendritic") (:form . "dendritic") (:end . 206)\n  (:start . 197) (:id . 71))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 217)\n  (:start . 207) (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 219) (:start . 218)\n  (:id . 73))\n ((:tag . "CD") (:stem . "7]–[9") (:form . "7]–[9") (:end . 224)\n  (:start . 219) (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 225) (:start . 224)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s10.54) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503167@unknown@formal@none@1@S@We have extended these studies using Fasciclin II (Fas II) positive tracts as reference points (Figure 1A) [6],[10].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "extend") (:form . "extended") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Fasciclin") (:form . "Fasciclin") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 67)\n  (:start . 59) (:id . 54))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 74)\n  (:start . 68) (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 87)\n  (:start . 78) (:id . 57))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 94)\n  (:start . 88) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 102)\n  (:start . 96) (:id . 60))\n ((:tag . "NN") (:stem . "1a") (:form . "1A") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 108) (:start . 107)\n  (:id . 63))\n ((:tag . "CD") (:stem . "6],[10") (:form . "6],[10") (:end . 114)\n  (:start . 108) (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 115) (:start . 114)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.55) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503168@unknown@formal@none@1@S@We divide the neuropile into three medio-lateral domains and four dorso-ventral layers (Figure 1C).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "divide") (:form . "divide") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 48) (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 56)\n  (:start . 49) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 79) (:start . 66) (:id . 52))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 86)\n  (:start . 80) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 94)\n  (:start . 88) (:id . 55))\n ((:tag . "NN") (:stem . "1c") (:form . "1C") (:end . 97) (:start . 95)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.56) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503169@unknown@formal@none@1@S@With the exception of the chordotonal (ch) neurons, sensory axons terminate in the medial domain of the neuropile.@(((:tag . "IN") (:stem . "with") (:form . "With") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "exception") (:form . "exception") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "chordotonal") (:form . "chordotonal") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "ch") (:form . "ch") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 50)\n  (:start . 43) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 59)\n  (:start . 52) (:id . 53))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 75)\n  (:start . 66) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 89)\n  (:start . 83) (:id . 58))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 96)\n  (:start . 90) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 61))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 113)\n  (:start . 104) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.57) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503170@unknown@formal@none@1@S@Ch axons terminate and branch in the intermediate domain.@(((:tag . "NNP") (:stem . "Ch") (:form . "Ch") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "terminate") (:form . "terminate") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "branch") (:form . "branch") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 49)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s10.58) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503171@unknown@formal@none@1@S@There is very little sensory input to the dorsal-most layer (layer 1) where motor neurons establish their dendritic arbors.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "little") (:form . "little") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dorsal-most") (:form . "dorsal-most") (:end . 53)\n  (:start . 42) (:id . 50))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 66) (:start . 61)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 55))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 75) (:start . 70)\n  (:id . 56))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 81) (:start . 76)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 89)\n  (:start . 82) (:id . 58))\n ((:tag . "VBP") (:stem . "establish") (:form . "establish") (:end . 99)\n  (:start . 90) (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 105)\n  (:start . 100) (:id . 60))\n ((:tag . "JJ") (:stem . "dendritic") (:form . "dendritic") (:end . 115)\n  (:start . 106) (:id . 61))\n ((:tag . "NNS") (:stem . "arbor") (:form . "arbors") (:end . 122)\n  (:start . 116) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.59) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503172@unknown@formal@none@1@S@The proprioceptive dorsal bipolar dendritic (dbd) and class I md (multidendritic) neurons terminate in the upper central layer (layer 2) [6],[9],[11].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "proprioceptive") (:form . "proprioceptive")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 25)\n  (:start . 19) (:id . 44))\n ((:tag . "JJ") (:stem . "bipolar") (:form . "bipolar") (:end . 33)\n  (:start . 26) (:id . 45))\n ((:tag . "JJ") (:stem . "dendritic") (:form . "dendritic") (:end . 43)\n  (:start . 34) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dbd") (:form . "dbd") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "CD") (:stem . "i") (:form . "I") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "multidendritic") (:form . "multidendritic")\n  (:end . 80) (:start . 66) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 89)\n  (:start . 82) (:id . 57))\n ((:tag . "VB") (:stem . "terminate") (:form . "terminate") (:end . 99)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 112)\n  (:start . 107) (:id . 61))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 120)\n  (:start . 113) (:id . 62))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 126)\n  (:start . 121) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 133)\n  (:start . 128) (:id . 65))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 135) (:start . 134)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 138) (:start . 137)\n  (:id . 68))\n ((:tag . "CD") (:stem . "6],[9],[11") (:form . "6],[9],[11") (:end . 148)\n  (:start . 138) (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 149) (:start . 148)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s10.60) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503173@unknown@formal@none@1@S@The ch neurons terminate in the lower central layer (layer 3) [6], whereas nociceptive class IV md neurons terminate in the ventral-most layer (layer 4).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "ch") (:form . "ch") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 51) (:start . 46)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 64) (:start . 63)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 65) (:start . 64)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 58))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 74)\n  (:start . 67) (:id . 59))\n ((:tag . "JJ") (:stem . "nociceptive") (:form . "nociceptive") (:end . 86)\n  (:start . 75) (:id . 60))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 92) (:start . 87)\n  (:id . 61))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 95) (:start . 93)\n  (:id . 62))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 98) (:start . 96)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 106)\n  (:start . 99) (:id . 64))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 116)\n  (:start . 107) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "ventral-most") (:form . "ventral-most") (:end . 136)\n  (:start . 124) (:id . 68))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 142)\n  (:start . 137) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 144) (:start . 143)\n  (:id . 70))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 149)\n  (:start . 144) (:id . 71))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 151) (:start . 150)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s10.61) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503174@unknown@formal@none@1@S@Class IV md neurons can be identified with ppkEGFP, which labels one intersegmental nerve (ISN) and two segmental nerve (SN) neurons in each hemisegment [9],[12].@(((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 37)\n  (:start . 27) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "ppkEGFP") (:form . "ppkEGFP") (:end . 50)\n  (:start . 43) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 57) (:start . 52)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "label") (:form . "labels") (:end . 64)\n  (:start . 58) (:id . 53))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "intersegmental") (:form . "intersegmental")\n  (:end . 83) (:start . 69) (:id . 55))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 89) (:start . 84)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "ISN") (:form . "ISN") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 60))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 103) (:start . 100)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "segmental") (:form . "segmental") (:end . 113)\n  (:start . 104) (:id . 62))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 119)\n  (:start . 114) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 123) (:start . 121)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 132)\n  (:start . 125) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 68))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 140) (:start . 136)\n  (:id . 69))\n ((:tag . "NN") (:stem . "hemisegment") (:form . "hemisegment") (:end . 152)\n  (:start . 141) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 154) (:start . 153)\n  (:id . 71))\n ((:tag . "CD") (:stem . "9],[12") (:form . "9],[12") (:end . 160)\n  (:start . 154) (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 161) (:start . 160)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s10.62) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503175@unknown@formal@none@1@S@The position of termination in the neuropile does not correlate with the nerve route by which the sensory neurons reach the neuropile (see Figure S1).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 27)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "VB") (:stem . "correlate") (:form . "correlate") (:end . 63)\n  (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 78) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "route") (:form . "route") (:end . 84) (:start . 79)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 105)\n  (:start . 98) (:id . 59))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 113)\n  (:start . 106) (:id . 60))\n ((:tag . "VBP") (:stem . "reach") (:form . "reach") (:end . 119)\n  (:start . 114) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 62))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 133)\n  (:start . 124) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 64))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 138) (:start . 135)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 145)\n  (:start . 139) (:id . 66))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 148) (:start . 146)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.63) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503176@unknown@formal@none@1@S@Sensory axons whose cell bodies are located ventrally in the body wall travel in the SN, whereas axons whose cell bodies are located dorsally or laterally in the body wall travel in the ISN [13].@(((:tag . "JJ") (:stem . "sensory") (:form . "Sensory") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 31) (:start . 25)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "wall") (:form . "wall") (:end . 70) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "travel") (:form . "travel") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 58))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 96)\n  (:start . 89) (:id . 59))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 102) (:start . 97)\n  (:id . 60))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 108)\n  (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 113) (:start . 109)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 120)\n  (:start . 114) (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 124) (:start . 121)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 132)\n  (:start . 125) (:id . 65))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 141)\n  (:start . 133) (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 144) (:start . 142)\n  (:id . 67))\n ((:tag . "RB") (:stem . "laterally") (:form . "laterally") (:end . 154)\n  (:start . 145) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 157) (:start . 155)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 70))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 166) (:start . 162)\n  (:id . 71))\n ((:tag . "NN") (:stem . "wall") (:form . "wall") (:end . 171) (:start . 167)\n  (:id . 72))\n ((:tag . "NN") (:stem . "travel") (:form . "travel") (:end . 178)\n  (:start . 172) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 181) (:start . 179)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "ISN") (:form . "ISN") (:end . 189) (:start . 186)\n  (:id . 76))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 191) (:start . 190)\n  (:id . 77))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 193) (:start . 191)\n  (:id . 78))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 194) (:start . 193)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s10.64) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503177@unknown@formal@none@1@S@Sensory axons running in the SN and ISN terminate in layers 2, 3, or 4, in correlation with their modality and dendritic morphology [9],[11].@(((:tag . "JJ") (:stem . "sensory") (:form . "Sensory") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "run") (:form . "running") (:end . 21) (:start . 14)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "ISN") (:form . "ISN") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 49)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 64) (:start . 63)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 68) (:start . 66)\n  (:id . 57))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 70) (:start . 69)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 60))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 86)\n  (:start . 75) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 91) (:start . 87)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 97)\n  (:start . 92) (:id . 63))\n ((:tag . "NN") (:stem . "modality") (:form . "modality") (:end . 106)\n  (:start . 98) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "dendritic") (:form . "dendritic") (:end . 120)\n  (:start . 111) (:id . 66))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 131)\n  (:start . 121) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 133) (:start . 132)\n  (:id . 68))\n ((:tag . "CD") (:stem . "9],[11") (:form . "9],[11") (:end . 139)\n  (:start . 133) (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 140) (:start . 139)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s10.65) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503178@unknown@formal@none@1@S@Since each of the three modality-specific sensory termination domains contains some neurons that have travelled through the SN, and others that have travelled through the ISN, differences in axon routing to the neuropile cannot account for differences in termination within the neuropile.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "modality-specific") (:form . "modality-specific")\n  (:end . 41) (:start . 24) (:id . 47))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 61)\n  (:start . 50) (:id . 49))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 69)\n  (:start . 62) (:id . 50))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 78)\n  (:start . 70) (:id . 51))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 83) (:start . 79)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 91)\n  (:start . 84) (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 96) (:start . 92)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 101) (:start . 97)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "travel") (:form . "travelled") (:end . 111)\n  (:start . 102) (:id . 56))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 119)\n  (:start . 112) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 126) (:start . 124)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 138)\n  (:start . 132) (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 143) (:start . 139)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 148) (:start . 144)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "travel") (:form . "travelled") (:end . 158)\n  (:start . 149) (:id . 65))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 166)\n  (:start . 159) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "ISN") (:form . "ISN") (:end . 174) (:start . 171)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 187)\n  (:start . 176) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 190) (:start . 188)\n  (:id . 71))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 195) (:start . 191)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "rout") (:form . "routing") (:end . 203)\n  (:start . 196) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 206) (:start . 204)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 210) (:start . 207)\n  (:id . 75))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 220)\n  (:start . 211) (:id . 76))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 227)\n  (:start . 221) (:id . 77))\n ((:tag . "VB") (:stem . "account") (:form . "account") (:end . 235)\n  (:start . 228) (:id . 78))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 239) (:start . 236)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 251)\n  (:start . 240) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 254) (:start . 252)\n  (:id . 81))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 266)\n  (:start . 255) (:id . 82))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 273)\n  (:start . 267) (:id . 83))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 277) (:start . 274)\n  (:id . 84))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 287)\n  (:start . 278) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 288) (:start . 287)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s10.66) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503179@unknown@formal@none@1@S@Expressing plex B or plex A in Sensory Neurons Shifts Their Terminals away from Central and Dorsal Layers of the Ventral Nerve Cord@(((:tag . "VBG") (:stem . "express") (:form . "Expressing") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "b") (:form . "B") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sensory") (:form . "Sensory") (:end . 38)\n  (:start . 31) (:id . 49))\n ((:tag . "NNPS") (:stem . "Neurons") (:form . "Neurons") (:end . 46)\n  (:start . 39) (:id . 50))\n ((:tag . "NNP") (:stem . "Shift") (:form . "Shifts") (:end . 53)\n  (:start . 47) (:id . 51))\n ((:tag . "PRP$") (:stem . "their") (:form . "Their") (:end . 59)\n  (:start . 54) (:id . 52))\n ((:tag . "NNPS") (:stem . "Terminal") (:form . "Terminals") (:end . 69)\n  (:start . 60) (:id . 53))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Central") (:form . "Central") (:end . 87)\n  (:start . 80) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 98)\n  (:start . 92) (:id . 58))\n ((:tag . "NNPS") (:stem . "Layers") (:form . "Layers") (:end . 105)\n  (:start . 99) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Ventral") (:form . "Ventral") (:end . 120)\n  (:start . 113) (:id . 62))\n ((:tag . "NNP") (:stem . "Nerve") (:form . "Nerve") (:end . 126)\n  (:start . 121) (:id . 63))\n ((:tag . "NNP") (:stem . "Cord") (:form . "Cord") (:end . 131) (:start . 127)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.67) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503180@unknown@formal@none@1@S@To investigate mechanisms that confine sensory projections of different modalities to different dorso-ventral layers of the neuropile, we carried out a gain-of-function screen for trans-membrane proteins, which, when expressed selectively in sensory neurons, shift sensory terminals with respect to Fas II tracts.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "confine") (:form . "confine") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 46)\n  (:start . 39) (:id . 47))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 58)\n  (:start . 47) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 71)\n  (:start . 62) (:id . 50))\n ((:tag . "NNS") (:stem . "modality") (:form . "modalities") (:end . 82)\n  (:start . 72) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 85) (:start . 83)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 95)\n  (:start . 86) (:id . 53))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 109) (:start . 96) (:id . 54))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 116)\n  (:start . 110) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 57))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 133)\n  (:start . 124) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 137) (:start . 135)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "carry") (:form . "carried") (:end . 145)\n  (:start . 138) (:id . 61))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 149) (:start . 146)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 151) (:start . 150)\n  (:id . 63))\n ((:tag . "NN") (:stem . "gain-of-function") (:form . "gain-of-function")\n  (:end . 168) (:start . 152) (:id . 64))\n ((:tag . "NN") (:stem . "screen") (:form . "screen") (:end . 175)\n  (:start . 169) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 179) (:start . 176)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "trans-membrane") (:form . "trans-membrane")\n  (:end . 194) (:start . 180) (:id . 67))\n ((:tag . "NNS") (:stem . "protein") (:form . 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",") (:end . 258) (:start . 257)\n  (:id . 78))\n ((:tag . "VB") (:stem . "shift") (:form . "shift") (:end . 264)\n  (:start . 259) (:id . 79))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 272)\n  (:start . 265) (:id . 80))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 282)\n  (:start . 273) (:id . 81))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 287) (:start . 283)\n  (:id . 82))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 295)\n  (:start . 288) (:id . 83))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 298) (:start . 296)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 302) (:start . 299)\n  (:id . 85))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 305) (:start . 303)\n  (:id . 86))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 312)\n  (:start . 306) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") 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5503181@unknown@formal@none@1@S@We used PO163GAL4, UAS-n-synaptobrevin-GFP flies to target gene expression selectively to sensory neurons and simultaneously to visualise their terminals (Figure 2A) [14].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "po163gal4") (:form . "PO163GAL4") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "UAS-n-synaptobrevin-GFP")\n  (:form . "UAS-n-synaptobrevin-GFP") (:end . 42) (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "fly") (:form . "flies") (:end . 48) (:start . 43)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 48))\n ((:tag . "VB") (:stem . "target") (:form . "target") (:end . 58)\n  (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 63) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 74)\n  (:start . 64) (:id . 51))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 86)\n  (:start . 75) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 97)\n  (:start . 90) (:id . 54))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 105)\n  (:start . 98) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 56))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n  (:end . 124) (:start . 110) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 127) (:start . 125)\n  (:id . 58))\n ((:tag . "VB") (:stem . "visualise") (:form . "visualise") (:end . 137)\n  (:start . 128) (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 143)\n  (:start . 138) (:id . 60))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 153)\n  (:start . 144) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 161)\n  (:start . 155) (:id . 63))\n ((:tag . "NN") (:stem . "2a") (:form . "2A") (:end . 164) (:start . 162)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 167) (:start . 166)\n  (:id . 66))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 169) (:start . 167)\n  (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 170) (:start . 169)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.69) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503182@unknown@formal@none@1@S@As a test of our method, we confirmed that expressing the Robo 3 receptor for Slit in sensory neurons shifts their terminals away from the medial domain of neuropile (Figure 2B) [6].@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 9) (:start . 5)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 23)\n  (:start . 17) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 27) (:start . 25)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 37)\n  (:start . 28) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 42) (:start . 38)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 53)\n  (:start . 43) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Robo") (:form . "Robo") (:end . 62) (:start . 58)\n  (:id . 54))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 64) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 73)\n  (:start . 65) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 82) (:start . 78)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 93)\n  (:start . 86) (:id . 60))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 101)\n  (:start . 94) (:id . 61))\n ((:tag . "VBZ") (:stem . "shift") (:form . "shifts") (:end . 108)\n  (:start . 102) (:id . 62))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 114)\n  (:start . 109) (:id . 63))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 124)\n  (:start . 115) (:id . 64))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 129) (:start . 125)\n  (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 134) (:start . 130)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 145)\n  (:start . 139) (:id . 68))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 152)\n  (:start . 146) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 70))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 165)\n  (:start . 156) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 173)\n  (:start . 167) (:id . 73))\n ((:tag . "NN") (:stem . "2b") (:form . "2B") (:end . 176) (:start . 174)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 177) (:start . 176)\n  (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 179) (:start . 178)\n  (:id . 76))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 180) (:start . 179)\n  (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 181) (:start . 180)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s10.70) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503183@unknown@formal@none@1@S@Effects of altering levels of receptors for Slit, Sema 2a, or Sema 1a in sensory neurons and the distribution of cues in neuropile.@(((:tag . "NNPS") (:stem . "Effect") (:form . "Effects") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "alter") (:form . "altering") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 61) (:start . 59)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 66) (:start . 62)\n  (:id . 55))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 69) (:start . 67)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 80)\n  (:start . 73) (:id . 58))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 88)\n  (:start . 81) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 61))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 109)\n  (:start . 97) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 117) (:start . 113)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n  (:id . 65))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 130)\n  (:start . 121) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s10.71) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503184@unknown@formal@none@1@S@We screened 418 lines with UAS inserts in front of trans-membrane protein coding genes (see Materials and Methods and Table S1 for detailed results of the screen) by systematically expressing them in sensory neurons and analysing the pattern of sensory terminals in abdominal segments (A1–A7) at 21-h after egg laying (AEL).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "screen") (:form . "screened") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "418") (:form . "418") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "UAS") (:form . "UAS") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "insert") (:form . "inserts") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "front") (:form . "front") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "trans-membrane") (:form . "trans-membrane")\n  (:end . 65) (:start . 51) (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 73)\n  (:start . 66) (:id . 53))\n ((:tag . "NN") (:stem . "coding") (:form . "coding") (:end . 80)\n  (:start . 74) (:id . 54))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 86) (:start . 81)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 91) (:start . 88)\n  (:id . 57))\n ((:tag . "NNPS") (:stem . "Material") (:form . 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"(") (:end . 286) (:start . 285)\n  (:id . 88))\n ((:tag . "NN") (:stem . "a1–a7") (:form . "A1–A7") (:end . 291)\n  (:start . 286) (:id . 89))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 292) (:start . 291)\n  (:id . 90))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 295) (:start . 293)\n  (:id . 91))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 300) (:start . 296)\n  (:id . 92))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 306)\n  (:start . 301) (:id . 93))\n ((:tag . "NN") (:stem . "egg") (:form . "egg") (:end . 310) (:start . 307)\n  (:id . 94))\n ((:tag . "NN") (:stem . "laying") (:form . "laying") (:end . 317)\n  (:start . 311) (:id . 95))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 319) (:start . 318)\n  (:id . 96))\n ((:tag . "NNP") (:stem . "AEL") (:form . "AEL") (:end . 322) (:start . 319)\n  (:id . 97))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 323) (:start . 322)\n  (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 324) (:start . 323)\n  (:id . 99)))@@@1@58@((:identifiers (:sid . :s10.72) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503185@unknown@formal@none@1@S@We identified 11 genes (2.6%) that change the pattern of sensory terminals, without altering the number of neurons or preventing sensory axons from reaching the central nervous system (CNS) (Table S1).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "CD") (:stem . "2.6") (:form . "2.6") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "change") (:form . "change") (:end . 41)\n  (:start . 35) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 52))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 53)\n  (:start . 46) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 64)\n  (:start . 57) (:id . 55))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 74)\n  (:start . 65) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 83)\n  (:start . 76) (:id . 58))\n ((:tag . "VBG") (:stem . "alter") (:form . "altering") (:end . 92)\n  (:start . 84) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 60))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 103)\n  (:start . 97) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 114)\n  (:start . 107) (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 117) (:start . 115)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "prevent") (:form . "preventing") (:end . 128)\n  (:start . 118) (:id . 65))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 136)\n  (:start . 129) (:id . 66))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 142)\n  (:start . 137) (:id . 67))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 147) (:start . 143)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "reach") (:form . "reaching") (:end . 156)\n  (:start . 148) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 160) (:start . 157)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 168)\n  (:start . 161) (:id . 71))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 176)\n  (:start . 169) (:id . 72))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 183)\n  (:start . 177) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "CNS") (:form . "CNS") (:end . 188) (:start . 185)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 191) (:start . 190)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 196)\n  (:start . 191) (:id . 78))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 199) (:start . 197)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 200) (:start . 199)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s10.73) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503186@unknown@formal@none@1@S@Of the 11 genes expressed, two produced obvious shifts along the dorso-ventral axis.@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 15) (:start . 10)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 25)\n  (:start . 16) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 39)\n  (:start . 31) (:id . 49))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "NNS") (:stem . "shift") (:form . "shifts") (:end . 54)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 78) (:start . 65) (:id . 54))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s10.74) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503187@unknown@formal@none@1@S@Both belong to the same family: plex B and A.@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "belong") (:form . "belong") (:end . 11)\n  (:start . 5) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 36) (:start . 32)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 44) (:start . 43)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s10.75) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503188@unknown@formal@none@1@S@If plex B is expressed in all sensory neurons, sensory terminals are excluded from layer 2 (Figure 2C).@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 9) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 22)\n  (:start . 13) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 37)\n  (:start . 30) (:id . 49))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 45)\n  (:start . 38) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 54)\n  (:start . 47) (:id . 52))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 64)\n  (:start . 55) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 77)\n  (:start . 69) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 82) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 88) (:start . 83)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 98)\n  (:start . 92) (:id . 60))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 101) (:start . 99)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.76) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503189@unknown@formal@none@1@S@If plex A is expressed, terminals are excluded from the intermediate regions of layer 3 and from layer 1 (Figure 2D).@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 9) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 22)\n  (:start . 13) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 33)\n  (:start . 24) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 68)\n  (:start . 56) (:id . 53))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 76)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 96) (:start . 92)\n  (:id . 59))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 102) (:start . 97)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 104) (:start . 103)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 112)\n  (:start . 106) (:id . 63))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 115) (:start . 113)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.77) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503190@unknown@formal@none@1@S@We also co-expressed Robo3 and Plex B in sensory neurons and found that this produces a “combination” of Robo 3 and Plex B expression phenotypes.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "co-expresse") (:form . "co-expressed") (:end . 20)\n  (:start . 8) (:id . 44))\n ((:tag . "NNP") (:stem . "Robo3") (:form . "Robo3") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 66) (:start . 61)\n  (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "produce") (:form . "produces") (:end . 85)\n  (:start . 77) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 89) (:start . 88)\n  (:id . 58))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 100)\n  (:start . 89) (:id . 59))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 101) (:start . 100)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Robo") (:form . "Robo") (:end . 109) (:start . 105)\n  (:id . 62))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 111) (:start . 110)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 120) (:start . 116)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 122) (:start . 121)\n  (:id . 66))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 133)\n  (:start . 123) (:id . 67))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 144)\n  (:start . 134) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.78) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503191@unknown@formal@none@1@S@In these embryos sensory terminals are now mostly confined to the lateral-most portion of layers 3 and 4 (Figure 2E).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "RB") (:stem . "mostly") (:form . "mostly") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "VBN") (:stem . "confine") (:form . "confined") (:end . 58)\n  (:start . 50) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "lateral-most") (:form . "lateral-most") (:end . 78)\n  (:start . 66) (:id . 53))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 86)\n  (:start . 79) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 96)\n  (:start . 90) (:id . 56))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 98) (:start . 97)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 112)\n  (:start . 106) (:id . 61))\n ((:tag . "NN") (:stem . "2e") (:form . "2E") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.79) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503192@unknown@formal@none@1@S@Sema 2a and Sema 1a Are Expressed in Central and Dorsal Layers of the Ventral Nerve Cord@(((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "2a") (:form . "2a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "Are") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "express") (:form . "Expressed") (:end . 33)\n  (:start . 24) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Central") (:form . "Central") (:end . 44)\n  (:start . 37) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 55)\n  (:start . 49) (:id . 52))\n ((:tag . "NNPS") (:stem . "Layers") (:form . "Layers") (:end . 62)\n  (:start . 56) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Ventral") (:form . "Ventral") (:end . 77)\n  (:start . 70) (:id . 56))\n ((:tag . "NNP") (:stem . "Nerve") (:form . "Nerve") (:end . 83) (:start . 78)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Cord") (:form . "Cord") (:end . 88) (:start . 84)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.80) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503193@unknown@formal@none@1@S@The Plexins are receptors for the Semaphorins (Semas), a diverse family of secreted and membrane-associated proteins [15]–[19].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNPS") (:stem . "Plexin") (:form . "Plexins") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Semaphorin") (:form . "Semaphorins") (:end . 45)\n  (:start . 34) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Semas") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 64)\n  (:start . 57) (:id . 54))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 71)\n  (:start . 65) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "secrete") (:form . "secreted") (:end . 83)\n  (:start . 75) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "membrane-associated")\n  (:form . "membrane-associated") (:end . 107) (:start . 88) (:id . 59))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 116)\n  (:start . 108) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "CD") (:stem . "15]–[19") (:form . "15]–[19") (:end . 125)\n  (:start . 118) (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 126) (:start . 125)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.81) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503194@unknown@formal@none@1@S@In Drosophila there are two Plexins (A and B) and five Semas: 1a, 1b, and 5c (transmembrane) and 2a and 2b (secreted).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "plexin") (:form . "Plexins") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 53))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 54) (:start . 50)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Semas") (:form . "Semas") (:end . 60) (:start . 55)\n  (:id . 55))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 61) (:start . 60)\n  (:id . 56))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 64) (:start . 62)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 58))\n ((:tag . "NN") (:stem . "1b") (:form . "1b") (:end . 68) (:start . 66)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 61))\n ((:tag . "NN") (:stem . "5c") (:form . "5c") (:end . 76) (:start . 74)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 63))\n ((:tag . "NN") (:stem . "transmembrane") (:form . "transmembrane")\n  (:end . 91) (:start . 78) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 66))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 99) (:start . 97)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 68))\n ((:tag . "NN") (:stem . "2b") (:form . "2b") (:end . 106) (:start . 104)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "secrete") (:form . "secreted") (:end . 116)\n  (:start . 108) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 117) (:start . 116)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s10.82) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503195@unknown@formal@none@1@S@Plex B binds Sema 2a and mediates the Sema 2a-dependent repulsion of motor and sensory axons in the periphery and the fasciculation of longitudinal tracts in the ventral nerve cord (VNC) [20],[21].@(((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "bind") (:form . "binds") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "mediate") (:form . "mediates") (:end . 33)\n  (:start . 25) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "2a-dependent") (:form . "2a-dependent") (:end . 55)\n  (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "repulsion") (:form . "repulsion") (:end . 65)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 86)\n  (:start . 79) (:id . 56))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "periphery") (:form . "periphery") (:end . 109)\n  (:start . 100) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "NN") (:stem . "fasciculation") (:form . "fasciculation")\n  (:end . 131) (:start . 118) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "longitudinal") (:form . "longitudinal") (:end . 147)\n  (:start . 135) (:id . 65))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 154)\n  (:start . 148) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 157) (:start . 155)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 169)\n  (:start . 162) (:id . 69))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 175)\n  (:start . 170) (:id . 70))\n ((:tag . "NN") (:stem . "cord") (:form . "cord") (:end . 180) (:start . 176)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 182) (:start . 181)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 185) (:start . 182)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 186) (:start . 185)\n  (:id . 74))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 188) (:start . 187)\n  (:id . 75))\n ((:tag . "CD") (:stem . "20],[21") (:form . "20],[21") (:end . 195)\n  (:start . 188) (:id . 76))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 196) (:start . 195)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s10.83) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503196@unknown@formal@none@1@S@Plex A binds strongly to Sema 1a and Sema 1b and mediates the Sema-dependent repulsion of embryonic motor axons in the periphery and the repulsion of adult olfactory receptor axons by Sema 1a in the antennal lobes [22]–[24].@(((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "bind") (:form . "binds") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "1b") (:form . "1b") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "mediate") (:form . "mediates") (:end . 57)\n  (:start . 49) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "sema-dependent") (:form . "Sema-dependent")\n  (:end . 76) (:start . 62) (:id . 55))\n ((:tag . "NN") (:stem . "repulsion") (:form . "repulsion") (:end . 86)\n  (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 99)\n  (:start . 90) (:id . 58))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 105)\n  (:start . 100) (:id . 59))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 111)\n  (:start . 106) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 62))\n ((:tag . "NN") (:stem . "periphery") (:form . "periphery") (:end . 128)\n  (:start . 119) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 65))\n ((:tag . "NN") (:stem . "repulsion") (:form . "repulsion") (:end . 146)\n  (:start . 137) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 155)\n  (:start . 150) (:id . 68))\n ((:tag . "JJ") (:stem . "olfactory") (:form . "olfactory") (:end . 165)\n  (:start . 156) (:id . 69))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 174)\n  (:start . 166) (:id . 70))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 180)\n  (:start . 175) (:id . 71))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 183) (:start . 181)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 188) (:start . 184)\n  (:id . 73))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 191) (:start . 189)\n  (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 194) (:start . 192)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 198) (:start . 195)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "antennal") (:form . "antennal") (:end . 207)\n  (:start . 199) (:id . 77))\n ((:tag . "NNS") (:stem . "lobe") (:form . "lobes") (:end . 213)\n  (:start . 208) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 215) (:start . 214)\n  (:id . 79))\n ((:tag . "CD") (:stem . "22]–[24") (:form . "22]–[24") (:end . 222)\n  (:start . 215) (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 223) (:start . 222)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s10.84) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503197@unknown@formal@none@1@S@The Plexin overexpression phenotypes suggested that their Sema ligands might act as cues to position the terminals of neurons along the dorso-ventral axis of the forming neuropile.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Plexin") (:form . "Plexin") (:end . 10)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 25) (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 36)\n  (:start . 26) (:id . 45))\n ((:tag . "VBD") (:stem . "suggest") (:form . "suggested") (:end . 46)\n  (:start . 37) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 51) (:start . 47)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 57)\n  (:start . 52) (:id . 48))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 62) (:start . 58)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "ligand") (:form . "ligands") (:end . 70)\n  (:start . 63) (:id . 50))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 76) (:start . 71)\n  (:id . 51))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 80) (:start . 77)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 83) (:start . 81)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 88) (:start . 84)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "VB") (:stem . "position") (:form . "position") (:end . 100)\n  (:start . 92) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 114)\n  (:start . 105) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 125)\n  (:start . 118) (:id . 60))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 131)\n  (:start . 126) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 135) (:start . 132)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 149) (:start . 136) (:id . 63))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 154) (:start . 150)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 157) (:start . 155)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 169)\n  (:start . 162) (:id . 67))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 179)\n  (:start . 170) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x10.85.1) (:span 71 76)) ((:id . :x10.85.2) (:span 37 46)))\n (:hscopes ((:id . :x10.85.1) (:span 71 179))\n  ((:id . :x10.85.2) (:span 37 179)))\n (:identifiers (:sid . :s10.85) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503198@unknown@formal@none@1@S@We therefore used antibody labelling to analyse the expression of Semas 2a and 1a in the CNS at different stages of embryogenesis: prior to sensory axon ingrowth (11-h AEL), at stages when sensory axons form their terminal arbors (13-h AEL), and several hours after sensory axons have completed their terminal arbors (21-h AEL).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "labelling") (:form . "labelling") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "VB") (:stem . "analyse") (:form . 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"at") (:form . "at") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 105)\n  (:start . 96) (:id . 60))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 112)\n  (:start . 106) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 129) (:start . 116) (:id . 63))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 136)\n  (:start . 131) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 147)\n  (:start . 140) (:id . 67))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 152) (:start . 148)\n  (:id . 68))\n ((:tag . "NN") (:stem . "ingrowth") (:form . 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"(") (:end . 318) (:start . 317)\n  (:id . 100))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 322) (:start . 318)\n  (:id . 101))\n ((:tag . "NNP") (:stem . "AEL") (:form . "AEL") (:end . 326) (:start . 323)\n  (:id . 102))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 327) (:start . 326)\n  (:id . 103))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 328) (:start . 327)\n  (:id . 104)))@@@1@63@((:identifiers (:sid . :s10.86) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503199@unknown@formal@none@1@S@Sema 2a expression first becomes detectable at 11 h as the outgrowth of sensory axons begins, persists strongly until 16 h, but has disappeared by 21 h, when the embryo is mature and ready to hatch.@(((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "become") (:form . "becomes") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 46) (:start . 44)\n  (:id . 48))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "outgrowth") (:form . "outgrowth") (:end . 68)\n  (:start . 59) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 79)\n  (:start . 72) (:id . 55))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "begin") (:form . "begins") (:end . 92)\n  (:start . 86) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "persist") (:form . "persists") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 111)\n  (:start . 103) (:id . 60))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 117)\n  (:start . 112) (:id . 61))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 120) (:start . 118)\n  (:id . 62))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 64))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 127) (:start . 124)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 131) (:start . 128)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "disappear") (:form . "disappeared") (:end . 143)\n  (:start . 132) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 146) (:start . 144)\n  (:id . 68))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 149) (:start . 147)\n  (:id . 69))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 151) (:start . 150)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 71))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 157) (:start . 153)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 73))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 168)\n  (:start . 162) (:id . 74))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 171) (:start . 169)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "mature") (:form . "mature") (:end . 178)\n  (:start . 172) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 182) (:start . 179)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "ready") (:form . "ready") (:end . 188)\n  (:start . 183) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 191) (:start . 189)\n  (:id . 79))\n ((:tag . "VB") (:stem . "hatch") (:form . "hatch") (:end . 197)\n  (:start . 192) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s10.87) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503200@unknown@formal@none@1@S@At 13 h, when sensory axons are forming their terminal arbors, the highest levels of Sema 2a are in layer 2 in the centre of the neuropile (Figure 2F and 2H).@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 45))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 13) (:start . 9)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 21)\n  (:start . 14) (:id . 47))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 27) (:start . 22)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 31) (:start . 28)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 39)\n  (:start . 32) (:id . 50))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 45)\n  (:start . 40) (:id . 51))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 54)\n  (:start . 46) (:id . 52))\n ((:tag . "NNS") (:stem . "arbor") (:form . "arbors") (:end . 61)\n  (:start . 55) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 74)\n  (:start . 67) (:id . 56))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 81)\n  (:start . 75) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 89) (:start . 85)\n  (:id . 59))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 92) (:start . 90)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 96) (:start . 93)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 62))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 105)\n  (:start . 100) (:id . 63))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 107) (:start . 106)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 66))\n ((:tag . "NN") (:stem . "centre") (:form . "centre") (:end . 121)\n  (:start . 115) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n  (:id . 69))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 138)\n  (:start . 129) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 146)\n  (:start . 140) (:id . 72))\n ((:tag . "NN") (:stem . "2f") (:form . "2F") (:end . 149) (:start . 147)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 153) (:start . 150)\n  (:id . 74))\n ((:tag . "NN") (:stem . "2h") (:form . "2H") (:end . 156) (:start . 154)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s10.88) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503201@unknown@formal@none@1@S@Strikingly, the protein forms gradients of expression in the neuropile that extend dorsally and ventrally from layer 2 (Figure 2L), at right angles to the mediolateral gradient of Slit (Figure 2F, 2G, 2J, and 2K).@(((:tag . "RB") (:stem . "strikingly") (:form . "Strikingly") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "VBZ") (:stem . "form") (:form . "forms") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "gradient") (:form . "gradients") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 53)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 70)\n  (:start . 61) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "extend") (:form . "extend") (:end . 82)\n  (:start . 76) (:id . 54))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 91)\n  (:start . 83) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 56))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 105)\n  (:start . 96) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 110) (:start . 106)\n  (:id . 58))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 116)\n  (:start . 111) (:id . 59))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 118) (:start . 117)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 126)\n  (:start . 120) (:id . 62))\n ((:tag . "NN") (:stem . "2l") (:form . "2L") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 134) (:start . 132)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 140)\n  (:start . 135) (:id . 67))\n ((:tag . "NNS") (:stem . "angle") (:form . "angles") (:end . 147)\n  (:start . 141) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 150) (:start . 148)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "mediolateral") (:form . "mediolateral") (:end . 167)\n  (:start . 155) (:id . 71))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 176)\n  (:start . 168) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 179) (:start . 177)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 184) (:start . 180)\n  (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 186) (:start . 185)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 192)\n  (:start . 186) (:id . 76))\n ((:tag . "NN") (:stem . "2f") (:form . "2F") (:end . 195) (:start . 193)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n  (:id . 78))\n ((:tag . "NN") (:stem . "2g") (:form . "2G") (:end . 199) (:start . 197)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n  (:id . 80))\n ((:tag . "NN") (:stem . "2j") (:form . "2J") (:end . 203) (:start . 201)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 204) (:start . 203)\n  (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 208) (:start . 205)\n  (:id . 83))\n ((:tag . "NN") (:stem . "2k") (:form . "2K") (:end . 211) (:start . 209)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 212) (:start . 211)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s10.89) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503202@unknown@formal@none@1@S@There is no detectable expression in layer 4.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 22)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 33)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s10.90) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503203@unknown@formal@none@1@S@Our experiments show that the effect of overexpressing Plex B in sensory neurons is to shift their terminals away from regions with high Sema 2a levels.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "overexpresse") (:form . "overexpressing")\n  (:end . 54) (:start . 40) (:id . 49))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 61) (:start . 60)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 80)\n  (:start . 73) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 83) (:start . 81)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . "VB") (:stem . "shift") (:form . "shift") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 98)\n  (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 108)\n  (:start . 99) (:id . 59))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 113) (:start . 109)\n  (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 118) (:start . 114)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 126)\n  (:start . 119) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 131) (:start . 127)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 136) (:start . 132)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 141) (:start . 137)\n  (:id . 65))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 144) (:start . 142)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 151)\n  (:start . 145) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s10.91) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503204@unknown@formal@none@1@S@This effect is still detectable at 21 h when there is no Sema 2a expression and we conclude that misplaced terminals do not compensate by delayed growth into central neuropile (Figure 2C).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 50) (:start . 45)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 64) (:start . 62)\n  (:id . 55))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 75)\n  (:start . 65) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 82) (:start . 80)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 91)\n  (:start . 83) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 96) (:start . 92)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "misplace") (:form . "misplaced") (:end . 106)\n  (:start . 97) (:id . 61))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 116)\n  (:start . 107) (:id . 62))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 119) (:start . 117)\n  (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 123) (:start . 120)\n  (:id . 64))\n ((:tag . "VB") (:stem . "compensate") (:form . "compensate") (:end . 134)\n  (:start . 124) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 137) (:start . 135)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "delay") (:form . "delayed") (:end . 145)\n  (:start . 138) (:id . 67))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 152)\n  (:start . 146) (:id . 68))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 157) (:start . 153)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 165)\n  (:start . 158) (:id . 70))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 175)\n  (:start . 166) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 177) (:start . 176)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 183)\n  (:start . 177) (:id . 73))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 186) (:start . 184)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s10.92) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503205@unknown@formal@none@1@S@Sema 1a expression is present at 10-h AEL, before sensory axons have entered the neuropile and persists throughout embryogenesis (unpublished data).@(((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "10-h") (:form . "10-h") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "AEL") (:form . "AEL") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "IN") (:stem . "before") (:form . "before") (:end . 49)\n  (:start . 43) (:id . 51))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 63) (:start . 58)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "enter") (:form . "entered") (:end . 76)\n  (:start . 69) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 90)\n  (:start . 81) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "persist") (:form . "persists") (:end . 103)\n  (:start . 95) (:id . 59))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 114)\n  (:start . 104) (:id . 60))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 128) (:start . 115) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "unpublished") (:form . "unpublished") (:end . 141)\n  (:start . 130) (:id . 63))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 146)\n  (:start . 142) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.93) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503206@unknown@formal@none@1@S@By 13 h the highest levels of Sema 1a are in the lateral and intermediate portions of layers 1 and 3, at lower levels in layer 2, and not detectable in layer 4 (Figure 2F and 2I).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 45))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 19)\n  (:start . 12) (:id . 46))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 26)\n  (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 34) (:start . 30)\n  (:id . 49))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 37) (:start . 35)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 41) (:start . 38)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 56)\n  (:start . 49) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 73)\n  (:start . 61) (:id . 56))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 82)\n  (:start . 74) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 92)\n  (:start . 86) (:id . 59))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 94) (:start . 93)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 61))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 100) (:start . 99)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 104) (:start . 102)\n  (:id . 64))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 110) (:start . 105)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 117)\n  (:start . 111) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n  (:id . 67))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 126)\n  (:start . 121) (:id . 68))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 128) (:start . 127)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 71))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 137) (:start . 134)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 148)\n  (:start . 138) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 151) (:start . 149)\n  (:id . 74))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 157)\n  (:start . 152) (:id . 75))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 159) (:start . 158)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 161) (:start . 160)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 167)\n  (:start . 161) (:id . 78))\n ((:tag . "NN") (:stem . "2f") (:form . "2F") (:end . 170) (:start . 168)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 174) (:start . 171)\n  (:id . 80))\n ((:tag . "NN") (:stem . "2i") (:form . "2I") (:end . 177) (:start . 175)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 178) (:start . 177)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s10.94) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503207@unknown@formal@none@1@S@In addition to differences in the levels of Sema 1a expression in different dorso-ventral layers of the neuropile, we also find an apparent decrease in concentration from intermediate (high) to medial (low) in layers 1 and 3.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 62)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 75)\n  (:start . 66) (:id . 54))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 89) (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 96)\n  (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 113)\n  (:start . 104) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 117) (:start . 115)\n  (:id . 61))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 122) (:start . 118)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 127) (:start . 123)\n  (:id . 63))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 130) (:start . 128)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "apparent") (:form . "apparent") (:end . 139)\n  (:start . 131) (:id . 65))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 148)\n  (:start . 140) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 151) (:start . 149)\n  (:id . 67))\n ((:tag . "NN") (:stem . "concentration") (:form . "concentration")\n  (:end . 165) (:start . 152) (:id . 68))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 170) (:start . 166)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 183)\n  (:start . 171) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 189) (:start . 185)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n  (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 193) (:start . 191)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 200)\n  (:start . 194) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 202) (:start . 201)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 205) (:start . 202)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 209) (:start . 207)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 216)\n  (:start . 210) (:id . 80))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 218) (:start . 217)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 222) (:start . 219)\n  (:id . 82))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 224) (:start . 223)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s10.95) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503208@unknown@formal@none@1@S@At 21 h Sema 1a is still strong in intermediate portions of layers 1 and 3.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 12) (:start . 8)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 47))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 24) (:start . 19)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "strong") (:form . "strong") (:end . 31)\n  (:start . 25) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 47)\n  (:start . 35) (:id . 51))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 56)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 66)\n  (:start . 60) (:id . 54))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 74) (:start . 73)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.96) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503209@unknown@formal@none@1@S@The effect of overexpressing Plex A is to exclude sensory terminals from these high levels of Sema 1a expression (Figure 2D).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "overexpresse") (:form . "overexpressing")\n  (:end . 28) (:start . 14) (:id . 45))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 49)\n  (:start . 42) (:id . 50))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 57)\n  (:start . 50) (:id . 51))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 67)\n  (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 78) (:start . 73)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 90)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 112)\n  (:start . 102) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 120)\n  (:start . 114) (:id . 62))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 123) (:start . 121)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.97) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503210@unknown@formal@none@1@S@We also analyzed the distributions of Sema 1a and Sema 2a in the antero-posterior axis, at the time of sensory axon ingrowth into the CNS, and found they appear uniform (Figure S2A and S2B).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "analyze") (:form . "analyzed") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 34) (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 81) (:start . 65) (:id . 55))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 99) (:start . 95)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 110)\n  (:start . 103) (:id . 62))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 115) (:start . 111)\n  (:id . 63))\n ((:tag . "NN") (:stem . "ingrowth") (:form . "ingrowth") (:end . 124)\n  (:start . 116) (:id . 64))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 129) (:start . 125)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "NN") (:stem . "cns") (:form . "CNS") (:end . 137) (:start . 134)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 148)\n  (:start . 143) (:id . 70))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 153) (:start . 149)\n  (:id . 71))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 160)\n  (:start . 154) (:id . 72))\n ((:tag . "JJ") (:stem . "uniform") (:form . "uniform") (:end . 168)\n  (:start . 161) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 170) (:start . 169)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 176)\n  (:start . 170) (:id . 75))\n ((:tag . "NNP") (:stem . "S2A") (:form . "S2A") (:end . 180) (:start . 177)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 184) (:start . 181)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "S2B") (:form . "S2B") (:end . 188) (:start . 185)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s10.98) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503211@unknown@formal@none@1@S@To confirm that Sema 2a and Sema 1a act as the ligands for Plex B and Plex A in our experiments, we tested the sema 2a and sema 1a dependence of the Plex B and Plex A overexpression phenotypes in sensory neurons.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "confirm") (:form . "confirm") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "act") (:form . "act") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 42) (:start . 40)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "ligand") (:form . "ligands") (:end . 54)\n  (:start . 47) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 58) (:start . 55)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 63) (:start . 59)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 65) (:start . 64)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 74) (:start . 70)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 76) (:start . 75)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 83) (:start . 80)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 95)\n  (:start . 84) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 63))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 99) (:start . 97)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 106)\n  (:start . 100) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 66))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 115) (:start . 111)\n  (:id . 67))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 118) (:start . 116)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 69))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 127) (:start . 123)\n  (:id . 70))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 130) (:start . 128)\n  (:id . 71))\n ((:tag . "NN") (:stem . "dependence") (:form . "dependence") (:end . 141)\n  (:start . 131) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 153) (:start . 149)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 155) (:start . 154)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 164) (:start . 160)\n  (:id . 78))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 166) (:start . 165)\n  (:id . 79))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 181) (:start . 167) (:id . 80))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 192)\n  (:start . 182) (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 195) (:start . 193)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 203)\n  (:start . 196) (:id . 83))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 211)\n  (:start . 204) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s10.99) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503212@unknown@formal@none@1@S@We analysed patterns of sensory terminals in sema 2a03021 loss of function embryos [25] and in embryos in which plex B was overexpressed in sensory neurons in a sema 2a03021 background.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "CD") (:stem . "2a03021") (:form . "2a03021") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 82)\n  (:start . 75) (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 102)\n  (:start . 95) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 111)\n  (:start . 106) (:id . 62))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 116) (:start . 112)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 118) (:start . 117)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 122) (:start . 119)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 136) (:start . 123) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 139) (:start . 137)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 147)\n  (:start . 140) (:id . 68))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 155)\n  (:start . 148) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 158) (:start . 156)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 160) (:start . 159)\n  (:id . 71))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 165) (:start . 161)\n  (:id . 72))\n ((:tag . "CD") (:stem . "2a03021") (:form . "2a03021") (:end . 173)\n  (:start . 166) (:id . 73))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 184)\n  (:start . 174) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s10.100) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503213@unknown@formal@none@1@S@In sema 2a03021 embryos we find ectopic sensory terminals in layer 2 (Figure 3A).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "2a03021") (:form . "2a03021") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 76)\n  (:start . 70) (:id . 55))\n ((:tag . "NN") (:stem . "3a") (:form . "3A") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.101) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503214@unknown@formal@none@1@S@Overexpression of Plex B in sensory neurons in a sema 2a03021 background fails to exclude sensory terminals from central and dorsal neuropile (compare Figures 2C and 3B).@(((:tag . "NNP") (:stem . "Overexpression") (:form . "Overexpression")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "CD") (:stem . "2a03021") (:form . "2a03021") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 72)\n  (:start . 62) (:id . 53))\n ((:tag . "VBZ") (:stem . "fail") (:form . "fails") (:end . 78) (:start . 73)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 107)\n  (:start . 98) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 112) (:start . 108)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 120)\n  (:start . 113) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 131)\n  (:start . 125) (:id . 62))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 141)\n  (:start . 132) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 64))\n ((:tag . "NN") (:stem . "compare") (:form . "compare") (:end . 150)\n  (:start . 143) (:id . 65))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 158)\n  (:start . 151) (:id . 66))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 161) (:start . 159)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 68))\n ((:tag . "NN") (:stem . "3b") (:form . "3B") (:end . 168) (:start . 166)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s10.102) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503215@unknown@formal@none@1@S@The pattern of sensory terminals in these embryos is similar to their pattern in sema 2a03021 mutants (compare Figure 3A and 3B).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 69)\n  (:start . 64) (:id . 53))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 77)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "CD") (:stem . "2a03021") (:form . "2a03021") (:end . 93)\n  (:start . 86) (:id . 57))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 101)\n  (:start . 94) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 110)\n  (:start . 103) (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 117)\n  (:start . 111) (:id . 61))\n ((:tag . "NN") (:stem . "3a") (:form . "3A") (:end . 120) (:start . 118)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 63))\n ((:tag . "NN") (:stem . "3b") (:form . "3B") (:end . 127) (:start . 125)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.103) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503216@unknown@formal@none@1@S@We conclude that Sema 2a is the functional ligand for Plex B in this system.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 42)\n  (:start . 32) (:id . 49))\n ((:tag . "NN") (:stem . "ligand") (:form . "ligand") (:end . 49)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 75)\n  (:start . 69) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.104) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503217@unknown@formal@none@1@S@sema 2a and sema 1a mutations suppress the phenotypes of Plex B and Plex A overexpression in sensory neurons.@(((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 29)\n  (:start . 20) (:id . 47))\n ((:tag . "VBP") (:stem . "suppress") (:form . "suppress") (:end . 38)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 53)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 89) (:start . 75) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 100)\n  (:start . 93) (:id . 59))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 108)\n  (:start . 101) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.105) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503218@unknown@formal@none@1@S@We recombined the UAS-plex A-HA [24] transgene with the sema 1aP1 [26] mutation to express Plex A in a sema 1a mutant background.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "recombine") (:form . "recombined") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "UAS-plex") (:form . "UAS-plex") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "NNP") (:stem . "A-HA") (:form . "A-HA") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "NN") (:stem . "transgene") (:form . "transgene") (:end . 46)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 60) (:start . 56)\n  (:id . 53))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 69) (:start . 67)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 70) (:start . 69)\n  (:id . 57))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 79)\n  (:start . 71) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 82) (:start . 80)\n  (:id . 59))\n ((:tag . "VB") (:stem . "express") (:form . "express") (:end . 90)\n  (:start . 83) (:id . 60))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 95) (:start . 91)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 97) (:start . 96)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 102) (:start . 101)\n  (:id . 64))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 107) (:start . 103)\n  (:id . 65))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 110) (:start . 108)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 117)\n  (:start . 111) (:id . 67))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 128)\n  (:start . 118) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.106) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503219@unknown@formal@none@1@S@We analysed patterns of sensory terminals in sema 1aP1 mutant embryos and in embryos in which Plex A was overexpressed in sensory neurons in a sema 1aP1 background.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 61)\n  (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 69)\n  (:start . 62) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "overexpresse") (:form . "overexpressed")\n  (:end . 118) (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 129)\n  (:start . 122) (:id . 63))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 137)\n  (:start . 130) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 142) (:start . 141)\n  (:id . 66))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 147) (:start . 143)\n  (:id . 67))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 152) (:start . 148)\n  (:id . 68))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 163)\n  (:start . 153) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s10.107) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503220@unknown@formal@none@1@S@In sema 1aP1 embryos, we found ectopic sensory terminals in layers 1 and 3 (Figure 3C).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 30) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 38)\n  (:start . 31) (:id . 49))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 46)\n  (:start . 39) (:id . 50))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 56)\n  (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 82)\n  (:start . 76) (:id . 58))\n ((:tag . "NN") (:stem . "3c") (:form . "3C") (:end . 85) (:start . 83)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.108) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503221@unknown@formal@none@1@S@Overexpression of Plex A in sensory neurons in a sema 1aP1 background failed to exclude them from layers 1 and 3 (compare Figures 2D and 3D).@(((:tag . "NNP") (:stem . "Overexpression") (:form . "Overexpression")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 76) (:start . 70)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 87)\n  (:start . 80) (:id . 56))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 92) (:start . 88)\n  (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 97) (:start . 93)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 104)\n  (:start . 98) (:id . 59))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 112) (:start . 111)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 63))\n ((:tag . "NN") (:stem . "compare") (:form . "compare") (:end . 121)\n  (:start . 114) (:id . 64))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 129)\n  (:start . 122) (:id . 65))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 132) (:start . 130)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n  (:id . 67))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 139) (:start . 137)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s10.109) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503222@unknown@formal@none@1@S@The pattern of sensory terminals in these embryos is strikingly similar to their pattern in sema 1aP1 mutants (compare Figure 3C and 3D).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "RB") (:stem . "strikingly") (:form . "strikingly") (:end . 63)\n  (:start . 53) (:id . 51))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 80)\n  (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 88)\n  (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 109)\n  (:start . 102) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 118)\n  (:start . 111) (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 125)\n  (:start . 119) (:id . 62))\n ((:tag . "NN") (:stem . "3c") (:form . "3C") (:end . 128) (:start . 126)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 64))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s10.110) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503223@unknown@formal@none@1@S@We conclude that Sema 1a is the functional ligand for Plex A in this system.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 42)\n  (:start . 32) (:id . 49))\n ((:tag . "NN") (:stem . "ligand") (:form . "ligand") (:end . 49)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 75)\n  (:start . 69) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.111) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503224@unknown@formal@none@1@S@We were able to identify potential cellular sources of the transmembrane Semaphorin Sema 1a by looking for neuronal populations that project to layers 1 and 3 (Figure S3).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "source") (:form . "sources") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "transmembrane") (:form . "transmembrane")\n  (:end . 72) (:start . 59) (:id . 52))\n ((:tag . "NNP") (:stem . "Semaphorin") (:form . "Semaphorin") (:end . 83)\n  (:start . 73) (:id . 53))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 88) (:start . 84)\n  (:id . 54))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "look") (:form . "looking") (:end . 102)\n  (:start . 95) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 106) (:start . 103)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 115)\n  (:start . 107) (:id . 59))\n ((:tag . "NNS") (:stem . "population") (:form . "populations") (:end . 127)\n  (:start . 116) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 132) (:start . 128)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "project") (:form . "project") (:end . 140)\n  (:start . 133) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 150)\n  (:start . 144) (:id . 64))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 66))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 158) (:start . 157)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 166)\n  (:start . 160) (:id . 69))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 169) (:start . 167)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.112) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503225@unknown@formal@none@1@S@One such population are the motorneurons, most of which project dendrites to layer 1 (Figures 1 and S3A).@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "motorneuron") (:form . "motorneurons") (:end . 40)\n  (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 55) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "project") (:form . "project") (:end . 63)\n  (:start . 56) (:id . 52))\n ((:tag . "VBZ") (:stem . "dendrite") (:form . "dendrites") (:end . 73)\n  (:start . 64) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 82) (:start . 77)\n  (:id . 55))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 93)\n  (:start . 86) (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "S3A") (:form . "S3A") (:end . 103) (:start . 100)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.113) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503226@unknown@formal@none@1@S@Using the OK371-GAL4 we targeted the expression of the cell death gene reaper and of the CD8GFP reporter (OK371-GAL4, UASCD8GFP;UAS-reaper) to the motor neurons [27].@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "ok371-gal4") (:form . "OK371-GAL4") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "target") (:form . "targeted") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 65) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 70) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "reaper") (:form . "reaper") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "CD8GFP") (:form . "CD8GFP") (:end . 95)\n  (:start . 89) (:id . 58))\n ((:tag . "NN") (:stem . "reporter") (:form . "reporter") (:end . 104)\n  (:start . 96) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "OK371-GAL4") (:form . "OK371-GAL4") (:end . 116)\n  (:start . 106) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "UASCD8GFP;UAS-reaper")\n  (:form . "UASCD8GFP;UAS-reaper") (:end . 138) (:start . 118) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 66))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 152)\n  (:start . 147) (:id . 67))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 160)\n  (:start . 153) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 162) (:start . 161)\n  (:id . 69))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 164) (:start . 162)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 165) (:start . 164)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.114) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503227@unknown@formal@none@1@S@This resulted in the death of most motor neurons by the early first instar larval stage (as judged both by the onset of larval paralysis and by the loss of GFP signal) (Figure S3C).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "death") (:form . "death") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 61) (:start . 56)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "instar") (:form . "instar") (:end . 74)\n  (:start . 68) (:id . 55))\n ((:tag . "NN") (:stem . "larval") (:form . "larval") (:end . 81)\n  (:start . 75) (:id . 56))\n ((:tag . "NN") (:stem . "stage") (:form . "stage") (:end . 87) (:start . 82)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "judge") (:form . "judged") (:end . 98)\n  (:start . 92) (:id . 60))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 103) (:start . 99)\n  (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "NN") (:stem . "onset") (:form . "onset") (:end . 116)\n  (:start . 111) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "larval") (:form . "larval") (:end . 126)\n  (:start . 120) (:id . 66))\n ((:tag . "NN") (:stem . "paralysis") (:form . "paralysis") (:end . 136)\n  (:start . 127) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 143) (:start . 141)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n  (:id . 70))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 152) (:start . 148)\n  (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 159) (:start . 156)\n  (:id . 73))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 166)\n  (:start . 160) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 175)\n  (:start . 169) (:id . 77))\n ((:tag . "NNP") (:stem . "S3C") (:form . "S3C") (:end . 179) (:start . 176)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s10.115) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503228@unknown@formal@none@1@S@Immunofluorescence visualisation of Sema 1a shows a significant reduction in Sema 1a levels in layer 1 in animals that lack motor neurons, compared to animals with intact motor neurons (Figure S3B, S3D, and S3E).@(((:tag . "NNP") (:stem . "Immunofluorescence") (:form . "Immunofluorescence")\n  (:end . 18) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "visualisation") (:form . "visualisation")\n  (:end . 32) (:start . 19) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 40) (:start . 36)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 43) (:start . 41)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 49) (:start . 44)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 63)\n  (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 73)\n  (:start . 64) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 81) (:start . 77)\n  (:id . 52))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 84) (:start . 82)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 91)\n  (:start . 85) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n  (:id . 55))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 100) (:start . 95)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 102) (:start . 101)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 113)\n  (:start . 106) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 118) (:start . 114)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "lack") (:form . "lack") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 129)\n  (:start . 124) (:id . 62))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 137)\n  (:start . 130) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 147)\n  (:start . 139) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 150) (:start . 148)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "animal") (:form . "animals") (:end . 158)\n  (:start . 151) (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 163) (:start . 159)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "intact") (:form . "intact") (:end . 170)\n  (:start . 164) (:id . 69))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 176)\n  (:start . 171) (:id . 70))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 184)\n  (:start . 177) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 186) (:start . 185)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 192)\n  (:start . 186) (:id . 73))\n ((:tag . "NNP") (:stem . "S3B") (:form . "S3B") (:end . 196) (:start . 193)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "S3D") (:form . "S3D") (:end . 201) (:start . 198)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 202) (:start . 201)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 206) (:start . 203)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "S3E") (:form . "S3E") (:end . 210) (:start . 207)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 211) (:start . 210)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s10.116) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503229@unknown@formal@none@1@S@We conclude that the motorneuron dendrites are likely to be a source of Sema 1a in the dorsal neuropile.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "motorneuron") (:form . "motorneuron") (:end . 32)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 68)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 93)\n  (:start . 87) (:id . 59))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 103)\n  (:start . 94) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x10.117.1) (:span 47 53)))\n (:hscopes ((:id . :x10.117.1) (:span 17 103)))\n (:identifiers (:sid . :s10.117) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503230@unknown@formal@none@1@S@Another cell population that projects to layer 1, as well as to layer 3, are the GABAergic interneurons (Figure S3F).@(((:tag . "DT") (:stem . "another") (:form . "Another") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "population") (:form . "population") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "project") (:form . "projects") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 46) (:start . 41)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 69) (:start . 64)\n  (:id . 55))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 76) (:start . 73)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "gabaergic") (:form . "GABAergic") (:end . 90)\n  (:start . 81) (:id . 60))\n ((:tag . "NNS") (:stem . "interneuron") (:form . "interneurons") (:end . 103)\n  (:start . 91) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 111)\n  (:start . 105) (:id . 63))\n ((:tag . "NNP") (:stem . "S3F") (:form . "S3F") (:end . 115) (:start . 112)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.118) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503231@unknown@formal@none@1@S@We used GADGAL4 [28],[29] to visualise and kill both the motor neurons and the GABAergic interneurons and found that this resulted in nearly complete loss of Sema 1a staining from both layers 1 and 3 (Figure S3G, n=10 embryos).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "GADGAL4") (:form . "GADGAL4") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "CD") (:stem . "28],[29") (:form . "28],[29") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "VB") (:stem . "visualise") (:form . "visualise") (:end . 38)\n  (:start . 29) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "VB") (:stem . "kill") (:form . "kill") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 52) (:start . 48)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 62) (:start . 57)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 70)\n  (:start . 63) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "gabaergic") (:form . "GABAergic") (:end . 88)\n  (:start . 79) (:id . 58))\n ((:tag . "NNS") (:stem . "interneuron") (:form . "interneurons") (:end . 101)\n  (:start . 89) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 111)\n  (:start . 106) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n  (:id . 62))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 121) (:start . 117)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 130)\n  (:start . 122) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 133) (:start . 131)\n  (:id . 65))\n ((:tag . "RB") (:stem . "nearly") (:form . "nearly") (:end . 140)\n  (:start . 134) (:id . 66))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 149)\n  (:start . 141) (:id . 67))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 154) (:start . 150)\n  (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 157) (:start . 155)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 162) (:start . 158)\n  (:id . 70))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 165) (:start . 163)\n  (:id . 71))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 174)\n  (:start . 166) (:id . 72))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 179) (:start . 175)\n  (:id . 73))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 184) (:start . 180)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 191)\n  (:start . 185) (:id . 75))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 193) (:start . 192)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 197) (:start . 194)\n  (:id . 77))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 199) (:start . 198)\n  (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 201) (:start . 200)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 207)\n  (:start . 201) (:id . 80))\n ((:tag . "NNP") (:stem . "S3G") (:form . "S3G") (:end . 211) (:start . 208)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 212) (:start . 211)\n  (:id . 82))\n ((:tag . "CD") (:stem . "n=10") (:form . "n=10") (:end . 217) (:start . 213)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 225)\n  (:start . 218) (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 226) (:start . 225)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s10.119) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503232@unknown@formal@none@1@S@We conclude that the GABAergic interneurons are likely to be a significant source of Sema 1a in layer 1 and also in layer 3.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "gabaergic") (:form . "GABAergic") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "interneuron") (:form . "interneurons") (:end . 43)\n  (:start . 31) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 54)\n  (:start . 48) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 74)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 81)\n  (:start . 75) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 61))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 112) (:start . 108)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 63))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 121)\n  (:start . 116) (:id . 64))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 123) (:start . 122)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x10.120.1) (:span 48 54)))\n (:hscopes ((:id . :x10.120.1) (:span 17 123)))\n (:identifiers (:sid . :s10.120) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503233@unknown@formal@none@1@S@We have so far been unable to identify cellular populations that project exclusively to layer 2, but since the expression is continuous across the midline (see Figure S2A), at least some midline cells could be involved.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "unable") (:form . "unable") (:end . 26)\n  (:start . 20) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 38)\n  (:start . 30) (:id . 49))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 47)\n  (:start . 39) (:id . 50))\n ((:tag . "NNS") (:stem . "population") (:form . "populations") (:end . 59)\n  (:start . 48) (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "project") (:form . "project") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "RB") (:stem . "exclusively") (:form . "exclusively") (:end . 84)\n  (:start . 73) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 93) (:start . 88)\n  (:id . 56))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 100) (:start . 97)\n  (:id . 59))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 121)\n  (:start . 111) (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "continuous") (:form . "continuous") (:end . 135)\n  (:start . 125) (:id . 64))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 142)\n  (:start . 136) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 66))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 154)\n  (:start . 147) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 68))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 159) (:start . 156)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 166)\n  (:start . 160) (:id . 70))\n ((:tag . "NNP") (:stem . "S2A") (:form . "S2A") (:end . 170) (:start . 167)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 171) (:start . 170)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 73))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 175) (:start . 173)\n  (:id . 74))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 181)\n  (:start . 176) (:id . 75))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 186) (:start . 182)\n  (:id . 76))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 194)\n  (:start . 187) (:id . 77))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 200)\n  (:start . 195) (:id . 78))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 206)\n  (:start . 201) (:id . 79))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 209) (:start . 207)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 218)\n  (:start . 210) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x10.121.1) (:span 201 206)))\n (:hscopes ((:id . :x10.121.1) (:span 173 218)))\n (:identifiers (:sid . :s10.121) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503234@unknown@formal@none@1@S@One possibility is that the recently described extensions of midline glial cells, the gliopodia [30], might provide a vehicle by which high levels of Sema 2a are deployed across the developing neuropile.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "extension") (:form . "extensions") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 68)\n  (:start . 61) (:id . 51))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 80) (:start . 75)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gliopodia") (:form . "gliopodia") (:end . 95)\n  (:start . 86) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 97) (:start . 96)\n  (:id . 57))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 60))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 107)\n  (:start . 102) (:id . 61))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 115)\n  (:start . 108) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . "NN") (:stem . "vehicle") (:form . "vehicle") (:end . 125)\n  (:start . 118) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 128) (:start . 126)\n  (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 134)\n  (:start . 129) (:id . 66))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 139) (:start . 135)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 146)\n  (:start . 140) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 154) (:start . 150)\n  (:id . 70))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 157) (:start . 155)\n  (:id . 71))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 161) (:start . 158)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "deploy") (:form . "deployed") (:end . 170)\n  (:start . 162) (:id . 73))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 177)\n  (:start . 171) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 181) (:start . 178)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 192)\n  (:start . 182) (:id . 76))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 202)\n  (:start . 193) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x10.122.1) (:span 102 107))\n  ((:id . :x10.122.2) (:span 4 15)))\n (:hscopes ((:id . :x10.122.1) (:span 102 202))\n  ((:id . :x10.122.2) (:span 4 202)))\n (:identifiers (:sid . :s10.122) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503235@unknown@formal@none@1@S@Interestingly these extensions of the glial cells have a limited life span, becoming much reduced late in embryogenesis and we find that Sema 2a expression also declines in these late stages.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 19) (:start . 14)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "extension") (:form . "extensions") (:end . 30)\n  (:start . 20) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 43) (:start . 38)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 49) (:start . 44)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 64)\n  (:start . 57) (:id . 51))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 69) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "span") (:form . "span") (:end . 74) (:start . 70)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "become") (:form . "becoming") (:end . 84)\n  (:start . 76) (:id . 55))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . "RB") (:stem . "late") (:form . "late") (:end . 102) (:start . 98)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 59))\n ((:tag . "NN") (:stem . "embryogenesis") (:form . "embryogenesis")\n  (:end . 119) (:start . 106) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 61))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 126) (:start . 124)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 131) (:start . 127)\n  (:id . 63))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 136) (:start . 132)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 141) (:start . 137)\n  (:id . 65))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 144) (:start . 142)\n  (:id . 66))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 155)\n  (:start . 145) (:id . 67))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 160) (:start . 156)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "decline") (:form . "declines") (:end . 169)\n  (:start . 161) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 172) (:start . 170)\n  (:id . 70))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 178)\n  (:start . 173) (:id . 71))\n ((:tag . "JJ") (:stem . "late") (:form . "late") (:end . 183) (:start . 179)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "stage") (:form . "stages") (:end . 190)\n  (:start . 184) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s10.123) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503236@unknown@formal@none@1@S@The VNC of embryos that lack midline glial cells (for example in single minded mutants; [31]) are too fragile and disorganized to allow analysis of levels of Sema 2a along the dorso-ventral axis.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 18)\n  (:start . 11) (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "lack") (:form . "lack") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "midline") (:form . "midline") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 61)\n  (:start . 54) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 71)\n  (:start . 65) (:id . 55))\n ((:tag . "JJ") (:stem . "minded") (:form . "minded") (:end . 78)\n  (:start . 72) (:id . 56))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 86)\n  (:start . 79) (:id . 57))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 89) (:start . 88)\n  (:id . 59))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 91) (:start . 89)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 92) (:start . 91)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 97) (:start . 94)\n  (:id . 63))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 101) (:start . 98)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "fragile") (:form . "fragile") (:end . 109)\n  (:start . 102) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "disorganized") (:form . "disorganized") (:end . 126)\n  (:start . 114) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 129) (:start . 127)\n  (:id . 68))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 135)\n  (:start . 130) (:id . 69))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 144)\n  (:start . 136) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 147) (:start . 145)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 154)\n  (:start . 148) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 157) (:start . 155)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 162) (:start . 158)\n  (:id . 74))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 165) (:start . 163)\n  (:id . 75))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 171)\n  (:start . 166) (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 175) (:start . 172)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 189) (:start . 176) (:id . 78))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 194) (:start . 190)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s10.124) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503237@unknown@formal@none@1@S@Instead we restored Sema 2a expression in the midline glial cells using the single mindedGAL4 line [31], in an otherwise sema 2a mutant background (sema 2a, UAS-sema 2a;single-mindedGAL4) (see Figure S4A–S4C for details of these experiments).@(((:tag . "RB") (:stem . "instead") (:form . "Instead") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "restore") (:form . "restored") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "JJ") (:stem . "glial") (:form . "glial") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 65) (:start . 60)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 82)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "mindedgal4") (:form . "mindedGAL4") (:end . 93)\n  (:start . 83) (:id . 56))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 98) (:start . 94)\n  (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 107) (:start . 105)\n  (:id . 62))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 110) (:start . 108)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "otherwise") (:form . "otherwise") (:end . 120)\n  (:start . 111) (:id . 64))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 125) (:start . 121)\n  (:id . 65))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 128) (:start . 126)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 135)\n  (:start . 129) (:id . 67))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 146)\n  (:start . 136) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 69))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 152) (:start . 148)\n  (:id . 70))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 155) (:start . 153)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "UAS-sema") (:form . "UAS-sema") (:end . 165)\n  (:start . 157) (:id . 73))\n ((:tag . "CD") (:stem . "2a;single-mindedGAL4")\n  (:form . "2a;single-mindedGAL4") (:end . 186) (:start . 166) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n  (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n  (:id . 76))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 192) (:start . 189)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 199)\n  (:start . 193) (:id . 78))\n ((:tag . "NNP") (:stem . "S4A–S4C") (:form . "S4A–S4C") (:end . 207)\n  (:start . 200) (:id . 79))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 211) (:start . 208)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 219)\n  (:start . 212) (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 222) (:start . 220)\n  (:id . 82))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 228)\n  (:start . 223) (:id . 83))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 240)\n  (:start . 229) (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 241) (:start . 240)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 242) (:start . 241)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s10.125) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503238@unknown@formal@none@1@S@We were able to restore Sema 2a expression in the neuropile (Figure S4B), in layers 1, 2, and 3 (Figure S4C), but in a pattern that appeared broader than the endogenous stripe in layer 2.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VB") (:stem . "restore") (:form . "restore") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 42)\n  (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 59)\n  (:start . 50) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 67)\n  (:start . 61) (:id . 54))\n ((:tag . "NNP") (:stem . "S4B") (:form . "S4B") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 83)\n  (:start . 77) (:id . 59))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 85) (:start . 84)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 61))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 88) (:start . 87)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 64))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 95) (:start . 94)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 103)\n  (:start . 97) (:id . 67))\n ((:tag . "NNP") (:stem . "S4C") (:form . "S4C") (:end . 107) (:start . 104)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 70))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 113) (:start . 110)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 116) (:start . 114)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 118) (:start . 117)\n  (:id . 73))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 126)\n  (:start . 119) (:id . 74))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 131) (:start . 127)\n  (:id . 75))\n ((:tag . "VBD") (:stem . "appear") (:form . "appeared") (:end . 140)\n  (:start . 132) (:id . 76))\n ((:tag . "JJR") (:stem . "broad") (:form . "broader") (:end . 148)\n  (:start . 141) (:id . 77))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 153) (:start . 149)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 168)\n  (:start . 158) (:id . 80))\n ((:tag . "NN") (:stem . "stripe") (:form . "stripe") (:end . 175)\n  (:start . 169) (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 178) (:start . 176)\n  (:id . 82))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 184)\n  (:start . 179) (:id . 83))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 186) (:start . 185)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s10.126) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503239@unknown@formal@none@1@S@Thus a source of the Sema 2a gradients could potentially be a subset of the midline cells, although we cannot exclude the possibility that some other cells are the endogenous source of this cue in the CNS.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "gradient") (:form . "gradients") (:end . 38)\n  (:start . 29) (:id . 49))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 44) (:start . 39)\n  (:id . 50))\n ((:tag . "RB") (:stem . "potentially") (:form . "potentially") (:end . 56)\n  (:start . 45) (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 68)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 83)\n  (:start . 76) (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 89) (:start . 84)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 59))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 99)\n  (:start . 91) (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 102) (:start . 100)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "cannot") (:form . "cannot") (:end . 109)\n  (:start . 103) (:id . 62))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 117)\n  (:start . 110) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 64))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 133)\n  (:start . 122) (:id . 65))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 138) (:start . 134)\n  (:id . 66))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 143) (:start . 139)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 149)\n  (:start . 144) (:id . 68))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 155)\n  (:start . 150) (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 159) (:start . 156)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 174)\n  (:start . 164) (:id . 72))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 181)\n  (:start . 175) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n  (:id . 74))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 189) (:start . 185)\n  (:id . 75))\n ((:tag . "NN") (:stem . "cue") (:form . "cue") (:end . 193) (:start . 190)\n  (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 196) (:start . 194)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 200) (:start . 197)\n  (:id . 78))\n ((:tag . "NN") (:stem . "cns") (:form . "CNS") (:end . 204) (:start . 201)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x10.127.1) (:span 103 133))\n  ((:id . :x10.127.2) (:span 45 56)) ((:id . :x10.127.3) (:span 39 44)))\n (:hscopes ((:id . :x10.127.1) (:span 103 204))\n  ((:id . :x10.127.2) (:span 45 89)) ((:id . :x10.127.3) (:span 39 89)))\n (:identifiers (:sid . :s10.127) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503240@unknown@formal@none@1@S@Ventrally Projecting Sensory Neurons Terminate in Regions of Low Sema 1a and Low Sema 2a Expression Levels@(((:tag . "RB") (:stem . "ventrally") (:form . "Ventrally") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBG") (:stem . "project") (:form . "Projecting") (:end . 20)\n  (:start . 10) (:id . 43))\n ((:tag . "NNP") (:stem . "Sensory") (:form . "Sensory") (:end . 28)\n  (:start . 21) (:id . 44))\n ((:tag . "NNPS") (:stem . "Neurons") (:form . "Neurons") (:end . 36)\n  (:start . 29) (:id . 45))\n ((:tag . "NNP") (:stem . "Terminate") (:form . "Terminate") (:end . 46)\n  (:start . 37) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 47))\n ((:tag . "NNPS") (:stem . "Region") (:form . "Regions") (:end . 57)\n  (:start . 50) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Low") (:form . "Low") (:end . 64) (:start . 61)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "1a") (:form . "1a") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Low") (:form . "Low") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "2a") (:form . "2a") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Expression") (:form . "Expression") (:end . 99)\n  (:start . 89) (:id . 57))\n ((:tag . "NNPS") (:stem . "Levels") (:form . "Levels") (:end . 106)\n  (:start . 100) (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.128) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503241@unknown@formal@none@1@S@To investigate the role of the Sema/Plexin system in determining the position at which axons terminate within the layered structure of the neuropile we decided to focus our experiments on a single class of sensory cells with well defined terminal branches, the nociceptive class IV md neurons.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "investigate") (:form . "investigate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sema/Plexin") (:form . "Sema/Plexin") (:end . 42)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "determine") (:form . "determining") (:end . 64)\n  (:start . 53) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 86) (:start . 81)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 92) (:start . 87)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 102)\n  (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 109)\n  (:start . 103) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "layered") (:form . "layered") (:end . 121)\n  (:start . 114) (:id . 60))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 131)\n  (:start . 122) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 63))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 148)\n  (:start . 139) (:id . 64))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 151) (:start . 149)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "decide") (:form . "decided") (:end . 159)\n  (:start . 152) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 162) (:start . 160)\n  (:id . 67))\n ((:tag . "VB") (:stem . "focus") (:form . "focus") (:end . 168)\n  (:start . 163) (:id . 68))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 172) (:start . 169)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 184)\n  (:start . 173) (:id . 70))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 187) (:start . 185)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 189) (:start . 188)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 196)\n  (:start . 190) (:id . 73))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 202)\n  (:start . 197) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 213)\n  (:start . 206) (:id . 76))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 219)\n  (:start . 214) (:id . 77))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 224) (:start . 220)\n  (:id . 78))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 229) (:start . 225)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 237)\n  (:start . 230) (:id . 80))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 246)\n  (:start . 238) (:id . 81))\n ((:tag . "NNS") (:stem . "branch") (:form . "branches") (:end . 255)\n  (:start . 247) (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 256) (:start . 255)\n  (:id . 83))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 260) (:start . 257)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "nociceptive") (:form . "nociceptive") (:end . 272)\n  (:start . 261) (:id . 85))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 278)\n  (:start . 273) (:id . 86))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 281) (:start . 279)\n  (:id . 87))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 284) (:start . 282)\n  (:id . 88))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 292)\n  (:start . 285) (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 293) (:start . 292)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s10.129) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503242@unknown@formal@none@1@S@Class IV md neurons can be identified with ppkEGFP [9],[12], which labels one ISN and two SN neurons in each hemisegment.@(((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 37)\n  (:start . 27) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "ppkegfp") (:form . "ppkEGFP") (:end . 50)\n  (:start . 43) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "CD") (:stem . "9],[12") (:form . "9],[12") (:end . 58)\n  (:start . 52) (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 66) (:start . 61)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "label") (:form . "labels") (:end . 73)\n  (:start . 67) (:id . 56))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "NN") (:stem . "isn") (:form . "ISN") (:end . 81) (:start . 78)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 59))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 89) (:start . 86)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 92) (:start . 90)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 100)\n  (:start . 93) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 63))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 108) (:start . 104)\n  (:id . 64))\n ((:tag . "NN") (:stem . "hemisegment") (:form . "hemisegment") (:end . 120)\n  (:start . 109) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.130) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503243@unknown@formal@none@1@S@The axons of these cells terminate medially in the ventral-most part of the neuropile, layer 4 (Figure 1C), where they branch asymmetrically in the antero-posterior axis (Figure S7A).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "RB") (:stem . "medially") (:form . "medially") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "ventral-most") (:form . "ventral-most") (:end . 63)\n  (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 85)\n  (:start . 76) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 102)\n  (:start . 96) (:id . 60))\n ((:tag . "NN") (:stem . "1c") (:form . "1C") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 63))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 113)\n  (:start . 108) (:id . 64))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 118) (:start . 114)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "branch") (:form . "branch") (:end . 125)\n  (:start . 119) (:id . 66))\n ((:tag . "RB") (:stem . "asymmetrically") (:form . "asymmetrically")\n  (:end . 140) (:start . 126) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 143) (:start . 141)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 164) (:start . 148) (:id . 70))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 169) (:start . 165)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 171) (:start . 170)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 177)\n  (:start . 171) (:id . 73))\n ((:tag . "NNP") (:stem . "S7A") (:form . "S7A") (:end . 181) (:start . 178)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 182) (:start . 181)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s10.131) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503244@unknown@formal@none@1@S@By examining the location of these ppkEGFP-expressing axons with respect to Sema expression we confirmed that at 13-h AEL these axons terminate in a region of low Sema 2a (Figure 4A) and just below regions of high Sema 1a expression levels (Figure 4B).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "examine") (:form . "examining") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "ppkegfp-expressing") (:form . "ppkEGFP-expressing")\n  (:end . 53) (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 59) (:start . 54)\n  (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 64) (:start . 60)\n  (:id . 50))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 72)\n  (:start . 65) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 75) (:start . 73)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 80) (:start . 76)\n  (:id . 53))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 91)\n  (:start . 81) (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 94) (:start . 92)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 104)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 109) (:start . 105)\n  (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "13-h") (:form . "13-h") (:end . 117) (:start . 113)\n  (:id . 59))\n ((:tag . "NN") (:stem . "ael") (:form . "AEL") (:end . 121) (:start . 118)\n  (:id . 60))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 127)\n  (:start . 122) (:id . 61))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 133)\n  (:start . 128) (:id . 62))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 143)\n  (:start . 134) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 148) (:start . 147)\n  (:id . 65))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 155)\n  (:start . 149) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 162) (:start . 159)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 167) (:start . 163)\n  (:id . 69))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 170) (:start . 168)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 71))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 178)\n  (:start . 172) (:id . 72))\n ((:tag . "NN") (:stem . "4a") (:form . "4A") (:end . 181) (:start . 179)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 182) (:start . 181)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 186) (:start . 183)\n  (:id . 75))\n ((:tag . "RB") (:stem . "just") (:form . "just") (:end . 191) (:start . 187)\n  (:id . 76))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 197)\n  (:start . 192) (:id . 77))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 205)\n  (:start . 198) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 208) (:start . 206)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 213) (:start . 209)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 218) (:start . 214)\n  (:id . 81))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 221) (:start . 219)\n  (:id . 82))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 232)\n  (:start . 222) (:id . 83))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 239)\n  (:start . 233) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 241) (:start . 240)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 247)\n  (:start . 241) (:id . 86))\n ((:tag . "NN") (:stem . "4b") (:form . "4B") (:end . 250) (:start . 248)\n  (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 251) (:start . 250)\n  (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s10.132) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503245@unknown@formal@none@1@S@At 21-h AEL the class IV terminals remain in a region with low Sema 1a expression (Figure 4C).@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "AEL") (:form . "AEL") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 21) (:start . 16)\n  (:id . 46))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 34)\n  (:start . 25) (:id . 48))\n ((:tag . "VBP") (:stem . "remain") (:form . "remain") (:end . 41)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 53)\n  (:start . 47) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 58) (:start . 54)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 67) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 70) (:start . 68)\n  (:id . 56))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 81)\n  (:start . 71) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 89)\n  (:start . 83) (:id . 59))\n ((:tag . "NN") (:stem . "4c") (:form . "4C") (:end . 92) (:start . 90)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s10.133) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503246@unknown@formal@none@1@S@Class IV md neurons terminate in a neuropile region with low levels of Sema 1a and Sema 2a.@(((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 29)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "neuropile") (:form . "neuropile") (:end . 44)\n  (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 67)\n  (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 75) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 87) (:start . 83)\n  (:id . 58))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.134) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503247@unknown@formal@none@1@S@sema 1a and sema 2a Are Required to Exclude Ventrally Projecting Class IV md Neurons from Dorsal and Central Neuropile@(((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "Are") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "require") (:form . "Required") (:end . 32)\n  (:start . 24) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "VB") (:stem . "exclude") (:form . "Exclude") (:end . 43)\n  (:start . 36) (:id . 50))\n ((:tag . "RB") (:stem . "ventrally") (:form . "Ventrally") (:end . 53)\n  (:start . 44) (:id . 51))\n ((:tag . "VBG") (:stem . "project") (:form . "Projecting") (:end . 64)\n  (:start . 54) (:id . 52))\n ((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "neuron") (:form . "Neurons") (:end . 84)\n  (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 89) (:start . 85)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 96)\n  (:start . 90) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Central") (:form . "Central") (:end . 108)\n  (:start . 101) (:id . 60))\n ((:tag . "NNP") (:stem . "Neuropile") (:form . "Neuropile") (:end . 118)\n  (:start . 109) (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.135) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503248@unknown@formal@none@1@S@We now asked whether sema 1a and sema 2a are required to confine class IV projections to layer 4.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "ask") (:form . "asked") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 44) (:start . 41)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 53)\n  (:start . 45) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "VB") (:stem . "confine") (:form . "confine") (:end . 64)\n  (:start . 57) (:id . 54))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 70) (:start . 65)\n  (:id . 55))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 85)\n  (:start . 74) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 94) (:start . 89)\n  (:id . 59))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x10.136.1) (:span 13 20)))\n (:hscopes ((:id . :x10.136.1) (:span 13 96)))\n (:identifiers (:sid . :s10.136) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503249@unknown@formal@none@1@S@In embryos mutant for sema 1aP1 [26], sema 2a03021 [25], and in sema 1aP1, sema 2a03021 double mutants, the class IV axons have aberrant patterns of termination and/or growth in the dorso-ventral axis (compare Figure 5A with 5B, 5C and 5D; see also Figure S6 for details of the effects of these mutations on the dorso-ventral position of Fas II tracts).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "(") (:stem . "[") (:form . 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"DT") (:stem . "the") (:form . "the") (:end . 277) (:start . 274)\n  (:id . 101))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 285)\n  (:start . 278) (:id . 102))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 288) (:start . 286)\n  (:id . 103))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 294)\n  (:start . 289) (:id . 104))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 304)\n  (:start . 295) (:id . 105))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 307) (:start . 305)\n  (:id . 106))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 311) (:start . 308)\n  (:id . 107))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 325) (:start . 312) (:id . 108))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 334)\n  (:start . 326) (:id . 109))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 337) (:start . 335)\n  (:id . 110))\n ((:tag . "NNP") (:stem . 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5503250@unknown@formal@none@1@S@We make a distinction between growth and termination phenotypes of class IV axons (For details of this distinction and examples of different kinds of growth and termination phenotypes see Figure S5).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "make") (:form . "make") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 9) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "distinction") (:form . "distinction") (:end . 21)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 52)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 63)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "For") (:end . 86) (:start . 83)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 94)\n  (:start . 87) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "distinction") (:form . "distinction") (:end . 114)\n  (:start . 103) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 127)\n  (:start . 119) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 140)\n  (:start . 131) (:id . 64))\n ((:tag . "NNS") (:stem . "kind") (:form . "kinds") (:end . 146)\n  (:start . 141) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 66))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 156)\n  (:start . 150) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 68))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 172)\n  (:start . 161) (:id . 69))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 183)\n  (:start . 173) (:id . 70))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 187) (:start . 184)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 194)\n  (:start . 188) (:id . 72))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 197) (:start . 195)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 198) (:start . 197)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s10.138) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503251@unknown@formal@none@1@S@sema 1a and sema 2a are required to exclude Class IV axons from dorsal and central neuropile.@(((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 32)\n  (:start . 24) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 43)\n  (:start . 36) (:id . 50))\n ((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 49) (:start . 44)\n  (:id . 51))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 52) (:start . 50)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 58) (:start . 53)\n  (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 63) (:start . 59)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 70)\n  (:start . 64) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 82)\n  (:start . 75) (:id . 57))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 92)\n  (:start . 83) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s10.139) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503252@unknown@formal@none@1@S@We found a significant increase in the percentage of hemisegments with aberrant terminals in sema 1aP1, sema 2a03021, and sema 1aP1, sema 2a03021 double mutants with respect to sema 1aP1/+ controls (Figure 5A–5H).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 22)\n  (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 49)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 65)\n  (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 70) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 89)\n  (:start . 80) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 102) (:start . 98)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . "CD") (:stem . "2a03021") (:form . "2a03021") (:end . 116)\n  (:start . 109) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 126) (:start . 122)\n  (:id . 63))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 131) (:start . 127)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 65))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 137) (:start . 133)\n  (:id . 66))\n ((:tag . "CD") (:stem . "2a03021") (:form . "2a03021") (:end . 145)\n  (:start . 138) (:id . 67))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 152)\n  (:start . 146) (:id . 68))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 160)\n  (:start . 153) (:id . 69))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 165) (:start . 161)\n  (:id . 70))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 173)\n  (:start . 166) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 176) (:start . 174)\n  (:id . 72))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 181) (:start . 177)\n  (:id . 73))\n ((:tag . "NN") (:stem . "1ap1/+") (:form . "1aP1/+") (:end . 188)\n  (:start . 182) (:id . 74))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 197)\n  (:start . 189) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 199) (:start . 198)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 205)\n  (:start . 199) (:id . 77))\n ((:tag . "NNP") (:stem . "5A–5H") (:form . "5A–5H") (:end . 211)\n  (:start . 206) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 212) (:start . 211)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s10.140) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503253@unknown@formal@none@1@S@Moreover, the percentage of hemisegments with aberrant termination in sema 1aP1, sema 2a03021 double mutants, was significantly higher than in either sema 1aP1 or sema 2a0302 single mutants (Figure 5E).@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 40)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 66)\n  (:start . 55) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 79) (:start . 75)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "CD") (:stem . "2a03021") (:form . "2a03021") (:end . 93)\n  (:start . 86) (:id . 56))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 100)\n  (:start . 94) (:id . 57))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 108)\n  (:start . 101) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 113) (:start . 110)\n  (:id . 60))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 127) (:start . 114) (:id . 61))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 134)\n  (:start . 128) (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 139) (:start . 135)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 149)\n  (:start . 143) (:id . 65))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 154) (:start . 150)\n  (:id . 66))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 159) (:start . 155)\n  (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 162) (:start . 160)\n  (:id . 68))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 167) (:start . 163)\n  (:id . 69))\n ((:tag . "CD") (:stem . "2a0302") (:form . "2a0302") (:end . 174)\n  (:start . 168) (:id . 70))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 181)\n  (:start . 175) (:id . 71))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 189)\n  (:start . 182) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 191) (:start . 190)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 197)\n  (:start . 191) (:id . 74))\n ((:tag . "NN") (:stem . "5e") (:form . "5E") (:end . 200) (:start . 198)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 201) (:start . 200)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s10.141) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503254@unknown@formal@none@1@S@We found that in sema 1aP1 mutants aberrant class IV axons tend to terminate in layer 1 more often than in layer 2 (Figure 5F).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 34)\n  (:start . 27) (:id . 48))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 43)\n  (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "tend") (:form . "tend") (:end . 63) (:start . 59)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "VB") (:stem . "terminate") (:form . "terminate") (:end . 76)\n  (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 85) (:start . 80)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 92) (:start . 88)\n  (:id . 59))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 98) (:start . 93)\n  (:id . 60))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 103) (:start . 99)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 112)\n  (:start . 107) (:id . 63))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 114) (:start . 113)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 122)\n  (:start . 116) (:id . 66))\n ((:tag . "NN") (:stem . "5f") (:form . "5F") (:end . 125) (:start . 123)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.142) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503255@unknown@formal@none@1@S@Conversely, in 2a03021 mutants, we found that aberrant class IV axons tend to terminate in layer 2 more often than in layer 1 (Figure 5G).@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "CD") (:stem . "2a03021") (:form . "2a03021") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "tend") (:form . "tend") (:end . 74) (:start . 70)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "VB") (:stem . "terminate") (:form . "terminate") (:end . 87)\n  (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 96) (:start . 91)\n  (:id . 59))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 98) (:start . 97)\n  (:id . 60))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 103) (:start . 99)\n  (:id . 61))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 109)\n  (:start . 104) (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 114) (:start . 110)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n  (:id . 64))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 123)\n  (:start . 118) (:id . 65))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 125) (:start . 124)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 133)\n  (:start . 127) (:id . 68))\n ((:tag . "NN") (:stem . "5g") (:form . "5G") (:end . 136) (:start . 134)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s10.143) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503256@unknown@formal@none@1@S@In sema 1aP1, sema 2a03021 double mutants (Figure 5H) class IV axons terminate with roughly equal probability in layers 1, 2, or 3.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 18) (:start . 14)\n  (:id . 46))\n ((:tag . "CD") (:stem . "2a03021") (:form . "2a03021") (:end . 26)\n  (:start . 19) (:id . 47))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 49)\n  (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "5h") (:form . "5H") (:end . 52) (:start . 50)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 53) (:start . 52)\n  (:id . 53))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 59) (:start . 54)\n  (:id . 54))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 62) (:start . 60)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 68) (:start . 63)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 78)\n  (:start . 69) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 83) (:start . 79)\n  (:id . 58))\n ((:tag . "RB") (:stem . "roughly") (:form . "roughly") (:end . 91)\n  (:start . 84) (:id . 59))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 97) (:start . 92)\n  (:id . 60))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 109)\n  (:start . 98) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 119)\n  (:start . 113) (:id . 63))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 65))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 124) (:start . 123)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 128) (:start . 126)\n  (:id . 68))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 130) (:start . 129)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s10.144) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503257@unknown@formal@none@1@S@Sema 1a appears to play a more important role in preventing termination in layer 1, followed by layer 3, and a minor role in preventing termination in layer 2.@(((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "1a") (:form . "1a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 30) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 40)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "prevent") (:form . "preventing") (:end . 59)\n  (:start . 49) (:id . 52))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 71)\n  (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 80) (:start . 75)\n  (:id . 55))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 92)\n  (:start . 84) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 101) (:start . 96)\n  (:id . 60))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 110) (:start . 109)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "minor") (:form . "minor") (:end . 116)\n  (:start . 111) (:id . 65))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 121) (:start . 117)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 124) (:start . 122)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "prevent") (:form . "preventing") (:end . 135)\n  (:start . 125) (:id . 68))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 147)\n  (:start . 136) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n  (:id . 70))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 156)\n  (:start . 151) (:id . 71))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 158) (:start . 157)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x10.145.1) (:span 8 15)))\n (:hscopes ((:id . :x10.145.1) (:span 0 158)))\n (:identifiers (:sid . :s10.145) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503258@unknown@formal@none@1@S@Sema 2a appears to play a more important role in preventing termination in layer 2, and a minor role in preventing termination in layers 1 and 3.@(((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "2a") (:form . "2a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 30) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 40)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "prevent") (:form . "preventing") (:end . 59)\n  (:start . 49) (:id . 52))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 71)\n  (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 80) (:start . 75)\n  (:id . 55))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 89) (:start . 88)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "minor") (:form . "minor") (:end . 95) (:start . 90)\n  (:id . 60))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 100) (:start . 96)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "prevent") (:form . "preventing") (:end . 114)\n  (:start . 104) (:id . 63))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 126)\n  (:start . 115) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 136)\n  (:start . 130) (:id . 66))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 138) (:start . 137)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 68))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 144) (:start . 143)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x10.146.1) (:span 8 15)))\n (:hscopes ((:id . :x10.146.1) (:span 0 144)))\n (:identifiers (:sid . :s10.146) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503259@unknown@formal@none@1@S@Our results suggest that Sema 1a and Sema 2a are instructive for termination of class IV axons along the dorso-ventral axis.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "instructive") (:form . "instructive") (:end . 60)\n  (:start . 49) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 76)\n  (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 94) (:start . 89)\n  (:id . 58))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 100) (:start . 95)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 118) (:start . 105) (:id . 61))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 123) (:start . 119)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x10.147.1) (:span 12 19)))\n (:hscopes ((:id . :x10.147.1) (:span 12 123)))\n (:identifiers (:sid . :s10.147) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503260@unknown@formal@none@1@S@We also assessed the potential roles of Sema 1a and Sema 2a in controlling the termination of class IV axons in the antero-posterior axis by analysing their projections in a top-down view of the neuropile in wild type and in sema 1a, sema 2a double mutants (Figure S7).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "assess") (:form . "assessed") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sema") (:form . 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"NNP") (:stem . "S7") (:form . "S7") (:end . 267) (:start . 265)\n  (:id . 91))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 268) (:start . 267)\n  (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 269) (:start . 268)\n  (:id . 93)))@@@1@52@((:hcues ((:id . :x10.148.1) (:span 21 30)))\n (:hscopes ((:id . :x10.148.1) (:span 21 137)))\n (:identifiers (:sid . :s10.148) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503261@unknown@formal@none@1@S@We chose the sema 1a, sema 2a double mutant for this analysis, because it exhibited the strongest phenotypes in the dorso-ventral axis.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 26) (:start . 22)\n  (:id . 48))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 29) (:start . 27)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 36)\n  (:start . 30) (:id . 50))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 43)\n  (:start . 37) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 52) (:start . 48)\n  (:id . 53))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 61)\n  (:start . 53) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 70)\n  (:start . 63) (:id . 56))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 73) (:start . 71)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "exhibit") (:form . "exhibited") (:end . 83)\n  (:start . 74) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 59))\n ((:tag . "JJS") (:stem . "strong") (:form . "strongest") (:end . 97)\n  (:start . 88) (:id . 60))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 108)\n  (:start . 98) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 129) (:start . 116) (:id . 64))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 134) (:start . 130)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.149) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503262@unknown@formal@none@1@S@Wild-type class IV axons grow asymmetrically, within their normal ventral and medial termination domain, forming thicker terminal in the anterior than in the posterior portion of the segment (Figure S7A).@(((:tag . "JJ") (:stem . "wild-type") (:form . "Wild-type") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "RB") (:stem . "asymmetrically") (:form . "asymmetrically")\n  (:end . 44) (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 52)\n  (:start . 46) (:id . 49))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 58)\n  (:start . 53) (:id . 50))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 65)\n  (:start . 59) (:id . 51))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 73)\n  (:start . 66) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 84)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 96)\n  (:start . 85) (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 103)\n  (:start . 97) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 112)\n  (:start . 105) (:id . 58))\n ((:tag . "JJR") (:stem . "thick") (:form . "thicker") (:end . 120)\n  (:start . 113) (:id . 59))\n ((:tag . "NN") (:stem . "terminal") (:form . "terminal") (:end . 129)\n  (:start . 121) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 145)\n  (:start . 137) (:id . 63))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 150) (:start . 146)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 153) (:start . 151)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 167)\n  (:start . 158) (:id . 67))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 175)\n  (:start . 168) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 178) (:start . 176)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 182) (:start . 179)\n  (:id . 70))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 190)\n  (:start . 183) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 192) (:start . 191)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 198)\n  (:start . 192) (:id . 73))\n ((:tag . "NNP") (:stem . "S7A") (:form . "S7A") (:end . 202) (:start . 199)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 203) (:start . 202)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s10.150) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503263@unknown@formal@none@1@S@We did not observe a significant loss of this asymmetry in the sema 1a, sema 2a double mutant compared to wild type (Figure S7B and S7C).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "VB") (:stem . "observe") (:form . "observe") (:end . 18)\n  (:start . 11) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 32)\n  (:start . 21) (:id . 47))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "asymmetry") (:form . "asymmetry") (:end . 55)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 76) (:start . 72)\n  (:id . 57))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 79) (:start . 77)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 86)\n  (:start . 80) (:id . 59))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 93)\n  (:start . 87) (:id . 60))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 102)\n  (:start . 94) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 110) (:start . 106)\n  (:id . 63))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 115) (:start . 111)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 123)\n  (:start . 117) (:id . 66))\n ((:tag . "NNP") (:stem . "S7B") (:form . "S7B") (:end . 127) (:start . 124)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "S7C") (:form . "S7C") (:end . 135) (:start . 132)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s10.151) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503264@unknown@formal@none@1@S@In top down view, class IV terminals do appear disorganized compared to wild type, but we assume this disorganization is a consequence of the major defects in growth and termination in the dorsoventral axis.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "down") (:form . "down") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "view") (:form . "view") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 23) (:start . 18)\n  (:id . 47))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 26) (:start . 24)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 36)\n  (:start . 27) (:id . 49))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 46)\n  (:start . 40) (:id . 51))\n ((:tag . "VBN") (:stem . "disorganize") (:form . "disorganized") (:end . 59)\n  (:start . 47) (:id . 52))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 89) (:start . 87)\n  (:id . 59))\n ((:tag . "VB") (:stem . "assume") (:form . "assume") (:end . 96)\n  (:start . 90) (:id . 60))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 101) (:start . 97)\n  (:id . 61))\n ((:tag . "NN") (:stem . "disorganization") (:form . "disorganization")\n  (:end . 117) (:start . 102) (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 120) (:start . 118)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 122) (:start . 121)\n  (:id . 64))\n ((:tag . "NN") (:stem . "consequence") (:form . "consequence") (:end . 134)\n  (:start . 123) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 147)\n  (:start . 142) (:id . 68))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 155)\n  (:start . 148) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 158) (:start . 156)\n  (:id . 70))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 165)\n  (:start . 159) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 169) (:start . 166)\n  (:id . 72))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 181)\n  (:start . 170) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 184) (:start . 182)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "dorsoventral") (:form . "dorsoventral") (:end . 201)\n  (:start . 189) (:id . 76))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 206) (:start . 202)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x10.152.1) (:span 90 96)))\n (:hscopes ((:id . :x10.152.1) (:span 90 206)))\n (:identifiers (:sid . :s10.152) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503265@unknown@formal@none@1@S@Thus Sema 1a and Sema 2a do not appear to play a major role in confining class IV terminals to the anterior portion of the segment.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 31) (:start . 28)\n  (:id . 49))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 38)\n  (:start . 32) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 51))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 46) (:start . 42)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 54) (:start . 49)\n  (:id . 54))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 59) (:start . 55)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "confine") (:form . "confining") (:end . 72)\n  (:start . 63) (:id . 57))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 78) (:start . 73)\n  (:id . 58))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 81) (:start . 79)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 91)\n  (:start . 82) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 107)\n  (:start . 99) (:id . 63))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 115)\n  (:start . 108) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 66))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 130)\n  (:start . 123) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x10.153.1) (:span 32 38)))\n (:hscopes ((:id . :x10.153.1) (:span 5 130)))\n (:identifiers (:sid . :s10.153) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503266@unknown@formal@none@1@S@Consistent with this idea is also our finding that the distributions of Sema 1a and Sema 2a appear uniform in the antero-posterior axis, at the time of sensory axon ingrowth into the CNS (Figure S2A and S2B).@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "finding") (:form . "finding") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 68) (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 98)\n  (:start . 92) (:id . 59))\n ((:tag . "NN") (:stem . "uniform") (:form . "uniform") (:end . 106)\n  (:start . 99) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 109) (:start . 107)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 130) (:start . 114) (:id . 63))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 135) (:start . 131)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 139) (:start . 137)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 67))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 148) (:start . 144)\n  (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 159)\n  (:start . 152) (:id . 70))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 164) (:start . 160)\n  (:id . 71))\n ((:tag . "NN") (:stem . "ingrowth") (:form . "ingrowth") (:end . 173)\n  (:start . 165) (:id . 72))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 178) (:start . 174)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 182) (:start . 179)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "CNS") (:form . "CNS") (:end . 186) (:start . 183)\n  (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 188) (:start . 187)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 194)\n  (:start . 188) (:id . 77))\n ((:tag . "NNP") (:stem . "S2A") (:form . "S2A") (:end . 198) (:start . 195)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 202) (:start . 199)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "S2B") (:form . "S2B") (:end . 206) (:start . 203)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 207) (:start . 206)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s10.154) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503267@unknown@formal@none@1@S@sema 1a Is Required Non-Cell-Autonomously to Exclude Class IV Axons from Dorsal Neuropile@(((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "require") (:form . "Required") (:end . 19)\n  (:start . 11) (:id . 45))\n ((:tag . "RB") (:stem . "non-cell-autonomously")\n  (:form . "Non-Cell-Autonomously") (:end . 41) (:start . 20) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "VB") (:stem . "exclude") (:form . "Exclude") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 58) (:start . 53)\n  (:id . 49))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "NNPS") (:stem . "Axon") (:form . "Axons") (:end . 67) (:start . 62)\n  (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 79)\n  (:start . 73) (:id . 53))\n ((:tag . "NNP") (:stem . "Neuropile") (:form . "Neuropile") (:end . 89)\n  (:start . 80) (:id . 54)))@@@1@13@((:identifiers (:sid . :s10.155) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503268@unknown@formal@none@1@S@In some cases membrane-bound Sema 1a acts as a receptor [18],[32].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "membrane-bound") (:form . "membrane-bound")\n  (:end . 28) (:start . 14) (:id . 45))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "act") (:form . "acts") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "CD") (:stem . "18],[32") (:form . "18],[32") (:end . 64)\n  (:start . 57) (:id . 53))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.156) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503269@unknown@formal@none@1@S@Thus, rather than a requirement to act as a cue, the class IV mutant phenotypes could reflect a cell-autonomous requirement for Sema 1a in the sensory neurons themselves.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 12) (:start . 6)\n  (:id . 44))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "requirement") (:form . "requirement") (:end . 31)\n  (:start . 20) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cue") (:form . "cue") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 54))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 58) (:start . 53)\n  (:id . 55))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 61) (:start . 59)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 68)\n  (:start . 62) (:id . 57))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 79)\n  (:start . 69) (:id . 58))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 85) (:start . 80)\n  (:id . 59))\n ((:tag . "VB") (:stem . "reflect") (:form . "reflect") (:end . 93)\n  (:start . 86) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 95) (:start . 94)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "cell-autonomous") (:form . "cell-autonomous")\n  (:end . 111) (:start . 96) (:id . 62))\n ((:tag . "NN") (:stem . "requirement") (:form . "requirement") (:end . 123)\n  (:start . 112) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 132) (:start . 128)\n  (:id . 65))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 135) (:start . 133)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 138) (:start . 136)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 150)\n  (:start . 143) (:id . 69))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 158)\n  (:start . 151) (:id . 70))\n ((:tag . "PRP") (:stem . "themselves") (:form . "themselves") (:end . 169)\n  (:start . 159) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x10.157.1) (:span 80 85)))\n (:hscopes ((:id . :x10.157.1) (:span 80 169)))\n (:identifiers (:sid . :s10.157) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503270@unknown@formal@none@1@S@To resolve this, we performed two kinds of rescue experiments.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "resolve") (:form . "resolve") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "perform") (:form . "performed") (:end . 29)\n  (:start . 20) (:id . 47))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "kind") (:form . "kinds") (:end . 39) (:start . 34)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 49)\n  (:start . 43) (:id . 51))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 61)\n  (:start . 50) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s10.158) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503271@unknown@formal@none@1@S@First, we restored sema 1a expression to sensory neurons in sema 1aP1mutant embryos using PO163GAL4.@(((:tag . "RB") (:stem . "first") (:form . "First") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "restore") (:form . "restored") (:end . 18)\n  (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 37)\n  (:start . 27) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "1ap1mutant") (:form . "1aP1mutant") (:end . 75)\n  (:start . 65) (:id . 54))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 83)\n  (:start . 76) (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 89) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "po163gal4") (:form . "PO163GAL4") (:end . 99)\n  (:start . 90) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.159) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503272@unknown@formal@none@1@S@Antibody labelling confirms that Sema 1a is successfully targeted to embryonic sensory terminals using this driver (compare Figure 6A, 6C, and 6E) and shows that in the mutant a large fraction of Sema 1a-expressing sensory neurons aberrantly project to the dorsal part of the neuropile (Figure 6E).@(((:tag . "NN") (:stem . "antibody") (:form . "Antibody") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "labelling") (:form . "labelling") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "VBZ") (:stem . "confirm") (:form . "confirms") (:end . 27)\n  (:start . 19) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "RB") (:stem . "successfully") (:form . "successfully") (:end . 56)\n  (:start . 44) (:id . 49))\n ((:tag . "VBN") (:stem . "target") (:form . "targeted") (:end . 65)\n  (:start . 57) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 78)\n  (:start . 69) (:id . 52))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 86)\n  (:start . 79) (:id . 53))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 96)\n  (:start . 87) (:id . 54))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 102) (:start . 97)\n  (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 107) (:start . 103)\n  (:id . 56))\n ((:tag . "NN") (:stem . "driver") (:form . "driver") (:end . 114)\n  (:start . 108) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 58))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 123)\n  (:start . 116) (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 130)\n  (:start . 124) (:id . 60))\n ((:tag . "NN") (:stem . "6a") (:form . "6A") (:end . 133) (:start . 131)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 62))\n ((:tag . "NN") (:stem . "6c") (:form . "6C") (:end . 137) (:start . 135)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 65))\n ((:tag . "NN") (:stem . "6e") (:form . "6E") (:end . 145) (:start . 143)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 156)\n  (:start . 151) (:id . 69))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 161) (:start . 157)\n  (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 164) (:start . 162)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 72))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 175)\n  (:start . 169) (:id . 73))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 177) (:start . 176)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 183)\n  (:start . 178) (:id . 75))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 192)\n  (:start . 184) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 195) (:start . 193)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 200) (:start . 196)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "1a-expressing") (:form . "1a-expressing")\n  (:end . 214) (:start . 201) (:id . 79))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 222)\n  (:start . 215) (:id . 80))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 230)\n  (:start . 223) (:id . 81))\n ((:tag . "RB") (:stem . "aberrantly") (:form . "aberrantly") (:end . 241)\n  (:start . 231) (:id . 82))\n ((:tag . "VBP") (:stem . "project") (:form . "project") (:end . 249)\n  (:start . 242) (:id . 83))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 252) (:start . 250)\n  (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 256) (:start . 253)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 263)\n  (:start . 257) (:id . 86))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 268) (:start . 264)\n  (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 271) (:start . 269)\n  (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 275) (:start . 272)\n  (:id . 89))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 285)\n  (:start . 276) (:id . 90))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 287) (:start . 286)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 293)\n  (:start . 287) (:id . 92))\n ((:tag . "NN") (:stem . "6e") (:form . "6E") (:end . 296) (:start . 294)\n  (:id . 93))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 297) (:start . 296)\n  (:id . 94))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 298) (:start . 297)\n  (:id . 95)))@@@1@54@((:identifiers (:sid . :s10.160) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503273@unknown@formal@none@1@S@We then analysed specifically the projections of class IV neurons in embryos where sema 1a expression had been restored to sensory neurons in the sema 1aP1 mutant background (compare Figure 6B, 6D, and 6F).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 29)\n  (:start . 17) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 45)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 54) (:start . 49)\n  (:id . 49))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 65)\n  (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 82) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 101)\n  (:start . 91) (:id . 57))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 105) (:start . 102)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 110) (:start . 106)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "restore") (:form . "restored") (:end . 119)\n  (:start . 111) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 130)\n  (:start . 123) (:id . 62))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 138)\n  (:start . 131) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 65))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 150) (:start . 146)\n  (:id . 66))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 155) (:start . 151)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 162)\n  (:start . 156) (:id . 68))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 173)\n  (:start . 163) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 175) (:start . 174)\n  (:id . 70))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 182)\n  (:start . 175) (:id . 71))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 189)\n  (:start . 183) (:id . 72))\n ((:tag . "NN") (:stem . "6b") (:form . "6B") (:end . 192) (:start . 190)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 193) (:start . 192)\n  (:id . 74))\n ((:tag . "NN") (:stem . "6d") (:form . "6D") (:end . 196) (:start . 194)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 201) (:start . 198)\n  (:id . 77))\n ((:tag . "NN") (:stem . "6f") (:form . "6F") (:end . 204) (:start . 202)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 205) (:start . 204)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s10.161) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503274@unknown@formal@none@1@S@There was no rescue of the dorsal termination phenotype of class IV axons in these embryos.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 45)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 64) (:start . 59)\n  (:id . 52))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 82) (:start . 77)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 90)\n  (:start . 83) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.162) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503275@unknown@formal@none@1@S@Quantification revealed no significant reduction in dorsal termination of class IV axons, compared to sema 1aP1 mutants (Figure 6I).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 23)\n  (:start . 15) (:id . 43))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 26) (:start . 24)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 38)\n  (:start . 27) (:id . 45))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 48)\n  (:start . 39) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 58)\n  (:start . 52) (:id . 48))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 70)\n  (:start . 59) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 50))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 79) (:start . 74)\n  (:id . 51))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 82) (:start . 80)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 88) (:start . 83)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 98)\n  (:start . 90) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 56))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 106) (:start . 102)\n  (:id . 57))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 111) (:start . 107)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 119)\n  (:start . 112) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 127)\n  (:start . 121) (:id . 61))\n ((:tag . "NN") (:stem . "6i") (:form . "6I") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.163) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503276@unknown@formal@none@1@S@Thus, sema 1a is not required in class IV neurons themselves to exclude their terminals from dorsal neuropile.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 20) (:start . 17)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 29)\n  (:start . 21) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 49))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 38) (:start . 33)\n  (:id . 50))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 41) (:start . 39)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 49)\n  (:start . 42) (:id . 52))\n ((:tag . "PRP") (:stem . "themselves") (:form . "themselves") (:end . 60)\n  (:start . 50) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 71)\n  (:start . 64) (:id . 55))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 77)\n  (:start . 72) (:id . 56))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 87)\n  (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 99)\n  (:start . 93) (:id . 59))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 109)\n  (:start . 100) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.164) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503277@unknown@formal@none@1@S@sema 1a is required non-cell autonomously in dorsal neuropile for the ventral projection of Class IV axons.@(((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 19)\n  (:start . 11) (:id . 45))\n ((:tag . "JJ") (:stem . "non-cell") (:form . "non-cell") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "RB") (:stem . "autonomously") (:form . "autonomously") (:end . 41)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 61)\n  (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 88)\n  (:start . 78) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 97) (:start . 92)\n  (:id . 56))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 106)\n  (:start . 101) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s10.165) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503278@unknown@formal@none@1@S@In a second set of experiments, we selectively restored Sema 1a to dorsal neuropile in an otherwise sema 1aP1 mutant background, by using HB9GAL4 to drive its expression in a subset of motor neurons [33].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 11) (:start . 5)\n  (:id . 44))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 30)\n  (:start . 19) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 46)\n  (:start . 35) (:id . 50))\n ((:tag . "VBD") (:stem . "restore") (:form . "restored") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 73)\n  (:start . 67) (:id . 55))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 83)\n  (:start . 74) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "otherwise") (:form . "otherwise") (:end . 99)\n  (:start . 90) (:id . 59))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 104) (:start . 100)\n  (:id . 60))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 109) (:start . 105)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 116)\n  (:start . 110) (:id . 62))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 127)\n  (:start . 117) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 131) (:start . 129)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 137) (:start . 132)\n  (:id . 66))\n ((:tag . "NN") (:stem . "hb9gal4") (:form . "HB9GAL4") (:end . 145)\n  (:start . 138) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 68))\n ((:tag . "VB") (:stem . "drive") (:form . "drive") (:end . 154)\n  (:start . 149) (:id . 69))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 158) (:start . 155)\n  (:id . 70))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 169)\n  (:start . 159) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 172) (:start . 170)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 174) (:start . 173)\n  (:id . 73))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 181)\n  (:start . 175) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n  (:id . 75))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 190)\n  (:start . 185) (:id . 76))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 198)\n  (:start . 191) (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 200) (:start . 199)\n  (:id . 78))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 202) (:start . 200)\n  (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 203) (:start . 202)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s10.166) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503279@unknown@formal@none@1@S@We used the HB9GAL4 line for this rescue experiment, because it is expressed before sensory neurons grow into the neuropile, unlike GADGAL4 or OK371GAL4, which are expressed later.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "hb9gal4") (:form . "HB9GAL4") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 40)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 51)\n  (:start . 41) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 60)\n  (:start . 53) (:id . 52))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 76)\n  (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "before") (:form . "before") (:end . 83)\n  (:start . 77) (:id . 56))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 91)\n  (:start . 84) (:id . 57))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 99)\n  (:start . 92) (:id . 58))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 104) (:start . 100)\n  (:id . 59))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 61))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 123)\n  (:start . 114) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . "IN") (:stem . "unlike") (:form . "unlike") (:end . 131)\n  (:start . 125) (:id . 64))\n ((:tag . "NN") (:stem . "gadgal4") (:form . "GADGAL4") (:end . 139)\n  (:start . 132) (:id . 65))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 142) (:start . 140)\n  (:id . 66))\n ((:tag . "NN") (:stem . "ok371gal4") (:form . "OK371GAL4") (:end . 152)\n  (:start . 143) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 159)\n  (:start . 154) (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 163) (:start . 160)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 173)\n  (:start . 164) (:id . 71))\n ((:tag . "RB") (:stem . "later") (:form . "later") (:end . 179)\n  (:start . 174) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s10.167) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503280@unknown@formal@none@1@S@We confirmed that Sema 1a is selectively present in dorsal neuropile in these experiments (compare Figure 6A, 6C, and 6G), and we observed a significant reduction in the dorsal termination of class IV axons compared to sema 1aP1 mutants (Figure 6H and 6I).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 40)\n  (:start . 29) (:id . 48))\n ((:tag . "JJ") (:stem . "present") (:form . 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"axons") (:end . 206)\n  (:start . 201) (:id . 80))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 215)\n  (:start . 207) (:id . 81))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 218) (:start . 216)\n  (:id . 82))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 223) (:start . 219)\n  (:id . 83))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 228) (:start . 224)\n  (:id . 84))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 236)\n  (:start . 229) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 238) (:start . 237)\n  (:id . 86))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 244)\n  (:start . 238) (:id . 87))\n ((:tag . "NN") (:stem . "6h") (:form . "6H") (:end . 247) (:start . 245)\n  (:id . 88))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 251) (:start . 248)\n  (:id . 89))\n ((:tag . "NN") (:stem . "6i") (:form . "6I") (:end . 254) (:start . 252)\n  (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 255) (:start . 254)\n  (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 256) (:start . 255)\n  (:id . 92)))@@@1@51@((:identifiers (:sid . :s10.168) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503281@unknown@formal@none@1@S@Thus in an otherwise mutant background, the mutant phenotype of class IV axons can be partially rescued by expressing sema1a dorsally in the dendrites of motor neurons.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 20)\n  (:start . 11) (:id . 45))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 60)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 78) (:start . 73)\n  (:id . 55))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 95)\n  (:start . 86) (:id . 58))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 103)\n  (:start . 96) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 106) (:start . 104)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 117)\n  (:start . 107) (:id . 61))\n ((:tag . "NN") (:stem . "sema1a") (:form . "sema1a") (:end . 124)\n  (:start . 118) (:id . 62))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 133)\n  (:start . 125) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 150)\n  (:start . 141) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 153) (:start . 151)\n  (:id . 67))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 159)\n  (:start . 154) (:id . 68))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 167)\n  (:start . 160) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s10.169) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503282@unknown@formal@none@1@S@We also asked whether restoration of Sema 2a expression in the midline glial cells using the single mindedGAL4 line in an otherwise sema 2a mutant background (sema 2a, UAS-sema 2a;single-mindedGAL4, ppkeGFP) rescues the sema 2a mutant phenotype of class IV axons (see Figure S4 for details of these experiments).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "ask") (:form . "asked") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "restoration") (:form . "restoration") (:end . 33)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sema") (:form . 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5503283@unknown@formal@none@1@S@We observed a significant reduction in the aberrant termination of class IV axons in layer 2 compared to sema 2a mutant embryos (Figure S4D and S4E).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 25)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 63)\n  (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 90) (:start . 85)\n  (:id . 56))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 92) (:start . 91)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 101)\n  (:start . 93) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n  (:id . 59))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "CD") (:stem . "2a") (:form . "2a") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 119)\n  (:start . 113) (:id . 62))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 127)\n  (:start . 120) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 135)\n  (:start . 129) (:id . 65))\n ((:tag . "NNP") (:stem . "S4D") (:form . "S4D") (:end . 139) (:start . 136)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "S4E") (:form . "S4E") (:end . 147) (:start . 144)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s10.171) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503284@unknown@formal@none@1@S@plex A and plex B Are Both Required to Exclude Class IV Terminals from Regions with High Sema 1a and Sema 2a Expression Levels@(((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "Are") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "CC") (:stem . "both") (:form . "Both") (:end . 26) (:start . 22)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "require") (:form . "Required") (:end . 35)\n  (:start . 27) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . "VB") (:stem . "exclude") (:form . "Exclude") (:end . 46)\n  (:start . 39) (:id . 51))\n ((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 52) (:start . 47)\n  (:id . 52))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 55) (:start . 53)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "terminal") (:form . "Terminals") (:end . 65)\n  (:start . 56) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 70) (:start . 66)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "region") (:form . "Regions") (:end . 78)\n  (:start . 71) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "high") (:form . "High") (:end . 88) (:start . 84)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 93) (:start . 89)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "1a") (:form . "1a") (:end . 96) (:start . 94)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 105) (:start . 101)\n  (:id . 62))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 108) (:start . 106)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Expression") (:form . "Expression") (:end . 119)\n  (:start . 109) (:id . 64))\n ((:tag . "NNPS") (:stem . "Level") (:form . "Levels") (:end . 126)\n  (:start . 120) (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.172) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503285@unknown@formal@none@1@S@The experiments we describe suggest that both Sema 1a and Sema 2a are required as cues to confine class IV sensory axons to ventral neuropile.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 35)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 78)\n  (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "VB") (:stem . "confine") (:form . "confine") (:end . 97)\n  (:start . 90) (:id . 59))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 103) (:start . 98)\n  (:id . 60))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 114)\n  (:start . 107) (:id . 62))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 120)\n  (:start . 115) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 131)\n  (:start . 124) (:id . 65))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 141)\n  (:start . 132) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x10.173.1) (:span 28 35)))\n (:hscopes ((:id . :x10.173.1) (:span 28 141)))\n (:identifiers (:sid . :s10.173) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503286@unknown@formal@none@1@S@We also find that expressing either plex A or plex B in sensory neurons is sufficient to shift their terminals away from regions with high levels of Sema 1a and 2a.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "b") (:form . "B") (:end . 52) (:start . 51)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 63)\n  (:start . 56) (:id . 54))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 71)\n  (:start . 64) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 85)\n  (:start . 75) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "VB") (:stem . "shift") (:form . "shift") (:end . 94) (:start . 89)\n  (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 100)\n  (:start . 95) (:id . 60))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 110)\n  (:start . 101) (:id . 61))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 115) (:start . 111)\n  (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 120) (:start . 116)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 128)\n  (:start . 121) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 133) (:start . 129)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 138) (:start . 134)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 145)\n  (:start . 139) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 153) (:start . 149)\n  (:id . 69))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 156) (:start . 154)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 71))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 163) (:start . 161)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s10.174) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503287@unknown@formal@none@1@S@Thus, a combination of Plexins could be required in ventrally projecting sensory neurons to exclude them from dorsal and central neuropile.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 19)\n  (:start . 8) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Plexin") (:form . "Plexins") (:end . 30)\n  (:start . 23) (:id . 47))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 61)\n  (:start . 52) (:id . 52))\n ((:tag . "VBG") (:stem . "project") (:form . "projecting") (:end . 72)\n  (:start . 62) (:id . 53))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 80)\n  (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 88)\n  (:start . 81) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 99)\n  (:start . 92) (:id . 57))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 104) (:start . 100)\n  (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 109) (:start . 105)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 116)\n  (:start . 110) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 128)\n  (:start . 121) (:id . 62))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 138)\n  (:start . 129) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x10.175.1) (:span 31 36)))\n (:hscopes ((:id . :x10.175.1) (:span 6 138)))\n (:identifiers (:sid . :s10.175) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503288@unknown@formal@none@1@S@By in situ hybridization we confirmed previous reports [20] that ch, dbd, and class I–IV md neurons express plex B at the time that sensory axons grow into and terminate in the VNC (Figure S8D).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "FW") (:stem . "situ") (:form . "situ") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "hybridization") (:form . "hybridization")\n  (:end . 24) (:start . 11) (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 37)\n  (:start . 28) (:id . 47))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 56) (:start . 55)\n  (:id . 50))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "ch") (:form . "ch") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "NN") (:stem . "dbd") (:form . "dbd") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 58))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 83) (:start . 78)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "I–IV") (:form . "I–IV") (:end . 88) (:start . 84)\n  (:id . 60))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 91) (:start . 89)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 99)\n  (:start . 92) (:id . 62))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 107)\n  (:start . 100) (:id . 63))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 112) (:start . 108)\n  (:id . 64))\n ((:tag . "NN") (:stem . "b") (:form . "B") (:end . 114) (:start . 113)\n  (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 117) (:start . 115)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 67))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 126) (:start . 122)\n  (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 131) (:start . 127)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 139)\n  (:start . 132) (:id . 70))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 145)\n  (:start . 140) (:id . 71))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 150) (:start . 146)\n  (:id . 72))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 155) (:start . 151)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 74))\n ((:tag . "VB") (:stem . "terminate") (:form . "terminate") (:end . 169)\n  (:start . 160) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 172) (:start . 170)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 176) (:start . 173)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 180) (:start . 177)\n  (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 182) (:start . 181)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 188)\n  (:start . 182) (:id . 80))\n ((:tag . "NNP") (:stem . "S8D") (:form . "S8D") (:end . 192) (:start . 189)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 193) (:start . 192)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s10.176) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503289@unknown@formal@none@1@S@By double labelling with anti-Plex A and anti-horseradish peroxidase we confirmed that Plex A is expressed in sensory neuron cell bodies at 13-h AEL (Figure S8A), and by double labelling with anti-Plex A and anti-GFP showed that Plex A is strongly expressed in the ppk-expressing class IV neurons (Figure S8B).@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "labelling") (:form . "labelling") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "anti-plex") (:form . "anti-Plex") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . 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5503290@unknown@formal@none@1@S@Unfortunately, none of these experiments allows us to draw quantitative conclusions about levels of expression in different cells.@(((:tag . "RB") (:stem . "unfortunately") (:form . "Unfortunately")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "none") (:form . "none") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 40)\n  (:start . 29) (:id . 47))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 47)\n  (:start . 41) (:id . 48))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "VB") (:stem . "draw") (:form . "draw") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 71)\n  (:start . 59) (:id . 52))\n ((:tag . "NNS") (:stem . "conclusion") (:form . "conclusions") (:end . 83)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 89) (:start . 84)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 96)\n  (:start . 90) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 56))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 110)\n  (:start . 100) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 123)\n  (:start . 114) (:id . 59))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 129)\n  (:start . 124) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.178) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503291@unknown@formal@none@1@S@High background levels also prevented a reliable analysis of Plex A expression along the dorso-ventral axis of the CNS.@(((:tag . "JJ") (:stem . "high") (:form . "High") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 22)\n  (:start . 16) (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "prevent") (:form . "prevented") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 39) (:start . 38)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "reliable") (:form . "reliable") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 78)\n  (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 84) (:start . 79)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 102) (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 107) (:start . 103)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cns") (:form . "CNS") (:end . 118) (:start . 115)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.179) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503292@unknown@formal@none@1@S@However antibody labelling against Plex A does reveal expression in the neuropile at 13-h AEL (Figure S8C).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "labelling") (:form . "labelling") (:end . 26)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 34)\n  (:start . 27) (:id . 45))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 41) (:start . 40)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "VB") (:stem . "reveal") (:form . "reveal") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 64)\n  (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 81)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "13-h") (:form . "13-h") (:end . 89) (:start . 85)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AEL") (:form . "AEL") (:end . 93) (:start . 90)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 101)\n  (:start . 95) (:id . 58))\n ((:tag . "NNP") (:stem . "S8C") (:form . "S8C") (:end . 105) (:start . 102)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.180) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503293@unknown@formal@none@1@S@To show whether both Plexins are required to exclude the ventrally projecting sensory neurons from central and/or dorsal neuropile, we analysed the projection pattern of class IV axons in plex A and B mutants.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "show") (:form . "show") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NNPS") (:stem . "Plexin") (:form . "Plexins") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 66)\n  (:start . 57) (:id . 52))\n ((:tag . "VBG") (:stem . "project") (:form . "projecting") (:end . 77)\n  (:start . 67) (:id . 53))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 85)\n  (:start . 78) (:id . 54))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 98) (:start . 94)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 106)\n  (:start . 99) (:id . 57))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 113)\n  (:start . 107) (:id . 58))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 120)\n  (:start . 114) (:id . 59))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 130)\n  (:start . 121) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 61))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 134) (:start . 132)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 143)\n  (:start . 135) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n  (:id . 64))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 158)\n  (:start . 148) (:id . 65))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 166)\n  (:start . 159) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 169) (:start . 167)\n  (:id . 67))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 175)\n  (:start . 170) (:id . 68))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 178) (:start . 176)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 184)\n  (:start . 179) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 187) (:start . 185)\n  (:id . 71))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 192) (:start . 188)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 194) (:start . 193)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 198) (:start . 195)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 200) (:start . 199)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 208)\n  (:start . 201) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x10.181.1) (:span 8 15)))\n (:hscopes ((:id . :x10.181.1) (:span 8 130)))\n (:identifiers (:sid . :s10.181) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503294@unknown@formal@none@1@S@In plex ADf(4)C3 mutants, class IV axons project aberrantly to central and/or dorsal neuropile (Figure 7A and 7B).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "ADf(4)C3") (:form . "ADf(4)C3") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "project") (:form . "project") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "RB") (:stem . "aberrantly") (:form . "aberrantly") (:end . 59)\n  (:start . 49) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 84)\n  (:start . 78) (:id . 55))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 102)\n  (:start . 96) (:id . 58))\n ((:tag . "NN") (:stem . "7a") (:form . "7A") (:end . 105) (:start . 103)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . "NN") (:stem . "7b") (:form . "7B") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.182) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503295@unknown@formal@none@1@S@Quantification reveals significantly more terminals in dorsal and central neuropile, compared to wild type (Figure 7G).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 22)\n  (:start . 15) (:id . 43))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 36) (:start . 23) (:id . 44))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 41) (:start . 37)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 51)\n  (:start . 42) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 61)\n  (:start . 55) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 73)\n  (:start . 66) (:id . 50))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 83)\n  (:start . 74) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 93)\n  (:start . 85) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 96) (:start . 94)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 101) (:start . 97)\n  (:id . 55))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 106) (:start . 102)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 114)\n  (:start . 108) (:id . 58))\n ((:tag . "NN") (:stem . "7g") (:form . "7G") (:end . 117) (:start . 115)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.183) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503296@unknown@formal@none@1@S@Plex A and Plex B are required in sensory neurons for the ventral termination of Class IV axons.@(((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 30)\n  (:start . 22) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 41)\n  (:start . 34) (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 49)\n  (:start . 42) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 65)\n  (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 77)\n  (:start . 66) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 86) (:start . 81)\n  (:id . 57))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 95) (:start . 90)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.184) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503297@unknown@formal@none@1@S@In plex BKG00878 mutants class IV axons also project to dorsal or central neuropile (Figures 7D and 7E).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "bkg00878") (:form . "BKG00878") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "project") (:form . "project") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 73)\n  (:start . 66) (:id . 54))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 83)\n  (:start . 74) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "7d") (:form . "7D") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "7e") (:form . "7E") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s10.185) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503298@unknown@formal@none@1@S@Quantification reveals significantly more terminals in dorsal and central neuropile compared to wild type (Figure 7G).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 22)\n  (:start . 15) (:id . 43))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 36) (:start . 23) (:id . 44))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 41) (:start . 37)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 51)\n  (:start . 42) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 61)\n  (:start . 55) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 73)\n  (:start . 66) (:id . 50))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 83)\n  (:start . 74) (:id . 51))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 92)\n  (:start . 84) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 100) (:start . 96)\n  (:id . 54))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 105) (:start . 101)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 113)\n  (:start . 107) (:id . 57))\n ((:tag . "NN") (:stem . "7g") (:form . "7G") (:end . 116) (:start . 114)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 117) (:start . 116)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.186) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503299@unknown@formal@none@1@S@We also quantified the proportion of terminals in each of the different layers of the neuropile (Figure 7H and 7I).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "quantify") (:form . "quantified") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 33)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 71)\n  (:start . 62) (:id . 53))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 78)\n  (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 95)\n  (:start . 86) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 103)\n  (:start . 97) (:id . 59))\n ((:tag . "NN") (:stem . "7h") (:form . "7H") (:end . 106) (:start . 104)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "NN") (:stem . "7i") (:form . "7I") (:end . 113) (:start . 111)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.187) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503300@unknown@formal@none@1@S@We found that in plex B mutants Class IV axons terminate with roughly equal probability in layers 1, 2, or 3.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 31)\n  (:start . 24) (:id . 48))\n ((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 46) (:start . 41)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 56)\n  (:start . 47) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "RB") (:stem . "roughly") (:form . "roughly") (:end . 69)\n  (:start . 62) (:id . 54))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 75) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 87)\n  (:start . 76) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 97)\n  (:start . 91) (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 62))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 106) (:start . 104)\n  (:id . 63))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 108) (:start . 107)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.188) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503301@unknown@formal@none@1@S@This suggests that Plex B may normally have a role in preventing termination in layers with high levels of Sema 2a or Sema 1a and may therefore be a functional receptor for both ligands.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 38)\n  (:start . 30) (:id . 48))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "prevent") (:form . "preventing") (:end . 64)\n  (:start . 54) (:id . 53))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 76)\n  (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 86)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 91) (:start . 87)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 96) (:start . 92)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 103)\n  (:start . 97) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 111) (:start . 107)\n  (:id . 61))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 117) (:start . 115)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 122) (:start . 118)\n  (:id . 64))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 125) (:start . 123)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 66))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 133) (:start . 130)\n  (:id . 67))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 143)\n  (:start . 134) (:id . 68))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 146) (:start . 144)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 148) (:start . 147)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 159)\n  (:start . 149) (:id . 71))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 168)\n  (:start . 160) (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 172) (:start . 169)\n  (:id . 73))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 177) (:start . 173)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "ligand") (:form . "ligands") (:end . 185)\n  (:start . 178) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x10.189.1) (:span 130 133))\n  ((:id . :x10.189.2) (:span 26 29)) ((:id . :x10.189.3) (:span 5 13)))\n (:hscopes ((:id . :x10.189.1) (:span 130 185))\n  ((:id . :x10.189.2) (:span 26 125)) ((:id . :x10.189.3) (:span 5 185)))\n (:identifiers (:sid . :s10.189) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503302@unknown@formal@none@1@S@We also observed that embryos transheterozygous for plex B and either sema 1a (sema 1a/+; plex B/+), sema 2a (sema 2a/+; plex B/+), or plex A (plex B/plex A) all exhibit class IV termination phenotypes, indicating a genetic interaction between these mutations (unpublished data).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "JJ") (:stem . "transheterozygous") (:form . "transheterozygous")\n  (:end . 47) (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 51) (:start . 48)\n  (:id . 48))\n ((:tag . 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"IN") (:stem . "between") (:form . "between") (:end . 243)\n  (:start . 236) (:id . 92))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 249)\n  (:start . 244) (:id . 93))\n ((:tag . "NNS") (:stem . "mutation") (:form . "mutations") (:end . 259)\n  (:start . 250) (:id . 94))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 261) (:start . 260)\n  (:id . 95))\n ((:tag . "JJ") (:stem . "unpublished") (:form . "unpublished") (:end . 272)\n  (:start . 261) (:id . 96))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 277)\n  (:start . 273) (:id . 97))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 278) (:start . 277)\n  (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 279) (:start . 278)\n  (:id . 99)))@@@1@58@((:hcues ((:id . :x10.190.1) (:span 203 213))\n  ((:id . :x10.190.2) (:span 63 69 132 134)))\n (:hscopes ((:id . :x10.190.1) (:span 203 259))\n  ((:id . :x10.190.2) (:span 63 157)))\n (:identifiers (:sid . :s10.190) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503303@unknown@formal@none@1@S@To further test whether Plex B functions to prevent termination in regions with high Sema 1a levels we analysed the patterns of sensory terminals that overexpress Plex B in a sema 1a mutant (Figure S9).@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "function") (:form . "functions") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 51)\n  (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 63)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 74)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 99)\n  (:start . 93) (:id . 58))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 111)\n  (:start . 103) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 135)\n  (:start . 128) (:id . 64))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 145)\n  (:start . 136) (:id . 65))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 150) (:start . 146)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "overexpres") (:form . "overexpress") (:end . 162)\n  (:start . 151) (:id . 67))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 167) (:start . 163)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 169) (:start . 168)\n  (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 172) (:start . 170)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 174) (:start . 173)\n  (:id . 71))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 179) (:start . 175)\n  (:id . 72))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 182) (:start . 180)\n  (:id . 73))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 189)\n  (:start . 183) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 191) (:start . 190)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 197)\n  (:start . 191) (:id . 76))\n ((:tag . "NNP") (:stem . "S9") (:form . "S9") (:end . 200) (:start . 198)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 201) (:start . 200)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 202) (:start . 201)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x10.191.1) (:span 16 23)))\n (:hscopes ((:id . :x10.191.1) (:span 16 99)))\n (:identifiers (:sid . :s10.191) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503304@unknown@formal@none@1@S@In these embryos we observed a striking expansion of sensory terminals into the intermediate region of layer 1 that normally contains highest Sema 1a levels within this layer (compare Figure S9A and S9B).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "striking") (:form . "striking") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 70)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 92)\n  (:start . 80) (:id . 55))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 99)\n  (:start . 93) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 57))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 108)\n  (:start . 103) (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 110) (:start . 109)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 115) (:start . 111)\n  (:id . 60))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 124)\n  (:start . 116) (:id . 61))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 133)\n  (:start . 125) (:id . 62))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 141)\n  (:start . 134) (:id . 63))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 146) (:start . 142)\n  (:id . 64))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 149) (:start . 147)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 156)\n  (:start . 150) (:id . 66))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 163)\n  (:start . 157) (:id . 67))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 168) (:start . 164)\n  (:id . 68))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 174)\n  (:start . 169) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n  (:id . 70))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 183)\n  (:start . 176) (:id . 71))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 190)\n  (:start . 184) (:id . 72))\n ((:tag . "NNP") (:stem . "S9A") (:form . "S9A") (:end . 194) (:start . 191)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 198) (:start . 195)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "S9B") (:form . "S9B") (:end . 202) (:start . 199)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 203) (:start . 202)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s10.192) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503305@unknown@formal@none@1@S@In a wild-type background Plex B-overexpressing sensory terminals remain confined in the most medial portion of layer 1, even though they become excluded from layer 2 (Figures 2C, S9A).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 14)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "b-overexpressing") (:form . "B-overexpressing")\n  (:end . 47) (:start . 31) (:id . 47))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 55)\n  (:start . 48) (:id . 48))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 65)\n  (:start . 56) (:id . 49))\n ((:tag . "VBP") (:stem . "remain") (:form . "remain") (:end . 72)\n  (:start . 66) (:id . 50))\n ((:tag . "VBN") (:stem . "confine") (:form . "confined") (:end . 81)\n  (:start . 73) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 53))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 93) (:start . 89)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 100)\n  (:start . 94) (:id . 55))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 108)\n  (:start . 101) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 57))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 117)\n  (:start . 112) (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 119) (:start . 118)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 60))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 125) (:start . 121)\n  (:id . 61))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 132)\n  (:start . 126) (:id . 62))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 137) (:start . 133)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "become") (:form . "become") (:end . 144)\n  (:start . 138) (:id . 64))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 153)\n  (:start . 145) (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 158) (:start . 154)\n  (:id . 66))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 164)\n  (:start . 159) (:id . 67))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 166) (:start . 165)\n  (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 168) (:start . 167)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 175)\n  (:start . 168) (:id . 70))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 178) (:start . 176)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 179) (:start . 178)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "S9A") (:form . "S9A") (:end . 183) (:start . 180)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s10.193) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503306@unknown@formal@none@1@S@A similar expansion is also observed in plex ADf(4)C3 mutants, indicating that Plex A function is required to prevent termination in regions with highest levels of Sema 1a (Figure S9C).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "ADf(4)C3") (:form . "ADf(4)C3") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 73)\n  (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 94)\n  (:start . 86) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 106)\n  (:start . 98) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 109) (:start . 107)\n  (:id . 60))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 117)\n  (:start . 110) (:id . 61))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 129)\n  (:start . 118) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 140)\n  (:start . 133) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 145) (:start . 141)\n  (:id . 65))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 153)\n  (:start . 146) (:id . 66))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 160)\n  (:start . 154) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 168) (:start . 164)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "1a") (:form . "1a") (:end . 171) (:start . 169)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 173) (:start . 172)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 179)\n  (:start . 173) (:id . 72))\n ((:tag . "NNP") (:stem . "S9C") (:form . "S9C") (:end . 183) (:start . 180)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x10.194.1) (:span 63 78)))\n (:hscopes ((:id . :x10.194.1) (:span 63 171)))\n (:identifiers (:sid . :s10.194) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503307@unknown@formal@none@1@S@Interestingly, we found that in the absence of plex A, Plex B overexpression in sensory neurons is sufficient to prevent their expansion into regions with highest Sema 1a levels (in PO163GAL4, UAS-plex B; plex ADf(4)C3 embryos) (Figure S9D).@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 59) (:start . 55)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 61) (:start . 60)\n  (:id . 55))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 76) (:start . 62) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 87)\n  (:start . 80) (:id . 58))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 95)\n  (:start . 88) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 98) (:start . 96)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 109)\n  (:start . 99) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 120)\n  (:start . 113) (:id . 63))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 126)\n  (:start . 121) (:id . 64))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 136)\n  (:start . 127) (:id . 65))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 141) (:start . 137)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 149)\n  (:start . 142) (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 154) (:start . 150)\n  (:id . 68))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 162)\n  (:start . 155) (:id . 69))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 167) (:start . 163)\n  (:id . 70))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 170) (:start . 168)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 177)\n  (:start . 171) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 179) (:start . 178)\n  (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 181) (:start . 179)\n  (:id . 74))\n ((:tag . "NN") (:stem . "po163gal4") (:form . "PO163GAL4") (:end . 191)\n  (:start . 182) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 192) (:start . 191)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "UAS-plex") (:form . "UAS-plex") (:end . 201)\n  (:start . 193) (:id . 77))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 203) (:start . 202)\n  (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 204) (:start . 203)\n  (:id . 79))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 209) (:start . 205)\n  (:id . 80))\n ((:tag . "CD") (:stem . "ADf(4)C3") (:form . "ADf(4)C3") (:end . 218)\n  (:start . 210) (:id . 81))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 226)\n  (:start . 219) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 227) (:start . 226)\n  (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 229) (:start . 228)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 235)\n  (:start . 229) (:id . 85))\n ((:tag . "NNP") (:stem . "S9D") (:form . "S9D") (:end . 239) (:start . 236)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 240) (:start . 239)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 241) (:start . 240)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s10.195) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503308@unknown@formal@none@1@S@Rescuing plex A and plex B in Sensory Neurons Alone Is Sufficient to Prevent the Aberrant Projection of Class IV Neurons to Dorsal and Central Neuropile@(((:tag . "VBG") (:stem . "rescue") (:form . "Rescuing") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "b") (:form . "B") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sensory") (:form . "Sensory") (:end . 37)\n  (:start . 30) (:id . 49))\n ((:tag . "NNP") (:stem . "Neurons") (:form . "Neurons") (:end . 45)\n  (:start . 38) (:id . 50))\n ((:tag . "NNP") (:stem . "Alone") (:form . "Alone") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "Sufficient") (:end . 65)\n  (:start . 55) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "VB") (:stem . "prevent") (:form . "Prevent") (:end . 76)\n  (:start . 69) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "Aberrant") (:end . 89)\n  (:start . 81) (:id . 57))\n ((:tag . "NN") (:stem . "projection") (:form . "Projection") (:end . 100)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 109)\n  (:start . 104) (:id . 60))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "NNPS") (:stem . "Neuron") (:form . "Neurons") (:end . 120)\n  (:start . 113) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 123) (:start . 121)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 130)\n  (:start . 124) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Central") (:form . "Central") (:end . 142)\n  (:start . 135) (:id . 66))\n ((:tag . "NNP") (:stem . "Neuropile") (:form . "Neuropile") (:end . 152)\n  (:start . 143) (:id . 67)))@@@1@26@((:identifiers (:sid . :s10.196) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503309@unknown@formal@none@1@S@To exclude (a) the possibility that plex A and B are required in the central targets of sensory neurons, in which case the mutant phenotypes might be a result of aberrations in normal target directed growth and (b) the possibility that Plex A and B are acting as guidance cues we restored their expression selectively to sensory neurons using the P0163 GAL4 driver.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 47))\n ((:tag . "NN") (:stem . "possibility") (:form . 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5503310@unknown@formal@none@1@S@Restoration of Plex B expression selectively in sensory neurons in a plex BKG00878 mutant background, rescues the phenotype of class IV md neurons (Figure 7E).@(((:tag . "NNP") (:stem . "Restoration") (:form . "Restoration") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 44)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 63)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "bkg00878") (:form . "BKG00878") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 89)\n  (:start . 83) (:id . 55))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 100)\n  (:start . 90) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "rescue") (:form . "rescues") (:end . 109)\n  (:start . 102) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 59))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 123)\n  (:start . 114) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 61))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 132)\n  (:start . 127) (:id . 62))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 135) (:start . 133)\n  (:id . 63))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 138) (:start . 136)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 146)\n  (:start . 139) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 154)\n  (:start . 148) (:id . 67))\n ((:tag . "NN") (:stem . "7e") (:form . "7E") (:end . 157) (:start . 155)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s10.198) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503311@unknown@formal@none@1@S@Quantification reveals significantly fewer aberrant class IV terminals in plex B-rescue embryos as compared to plex B mutants (Figure 7G).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 22)\n  (:start . 15) (:id . 43))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 36) (:start . 23) (:id . 44))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 42) (:start . 37)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 51)\n  (:start . 43) (:id . 46))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 57) (:start . 52)\n  (:id . 47))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 60) (:start . 58)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 70)\n  (:start . 61) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 50))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 78) (:start . 74)\n  (:id . 51))\n ((:tag . "NN") (:stem . "b-rescue") (:form . "B-rescue") (:end . 87)\n  (:start . 79) (:id . 52))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 95)\n  (:start . 88) (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 98) (:start . 96)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 107)\n  (:start . 99) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 56))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 115) (:start . 111)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 117) (:start . 116)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 125)\n  (:start . 118) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 133)\n  (:start . 127) (:id . 61))\n ((:tag . "NN") (:stem . "7g") (:form . "7G") (:end . 136) (:start . 134)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.199) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503312@unknown@formal@none@1@S@The Fas II tracts continued to exhibit mutant phenotypes in these experiments, as would be expected if the rest of the neuropile, other than the sensory neurons, remained mutant (Figure S10).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 17)\n  (:start . 11) (:id . 45))\n ((:tag . "VBD") (:stem . "continue") (:form . "continued") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "VB") (:stem . "exhibit") (:form . "exhibit") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 65) (:start . 60)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 77)\n  (:start . 66) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 87) (:start . 82)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 99)\n  (:start . 91) (:id . 58))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . "NN") (:stem . "rest") (:form . "rest") (:end . 111) (:start . 107)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 63))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 128)\n  (:start . 119) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 135)\n  (:start . 130) (:id . 66))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 140) (:start . 136)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 152)\n  (:start . 145) (:id . 69))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 160)\n  (:start . 153) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "remain") (:form . "remained") (:end . 170)\n  (:start . 162) (:id . 72))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 177)\n  (:start . 171) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 179) (:start . 178)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 185)\n  (:start . 179) (:id . 75))\n ((:tag . "NNP") (:stem . "S10") (:form . "S10") (:end . 189) (:start . 186)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s10.200) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503313@unknown@formal@none@1@S@Likewise, restoration of Plex A expression in sensory neurons in a plex ADf(4)C3 mutant background, rescued the phenotype of class IV md neurons (Figures 7C).@(((:tag . "RB") (:stem . "likewise") (:form . "Likewise") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "restoration") (:form . "restoration") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "ADf(4)C3") (:form . "ADf(4)C3") (:end . 80)\n  (:start . 72) (:id . 55))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 87)\n  (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 98)\n  (:start . 88) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "rescue") (:form . "rescued") (:end . 107)\n  (:start . 100) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 60))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 121)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 62))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 130)\n  (:start . 125) (:id . 63))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 133) (:start . 131)\n  (:id . 64))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 136) (:start . 134)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 144)\n  (:start . 137) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 153)\n  (:start . 146) (:id . 68))\n ((:tag . "NN") (:stem . "7c") (:form . "7C") (:end . 156) (:start . 154)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s10.201) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503314@unknown@formal@none@1@S@Quantification reveals significantly fewer aberrant class IV terminals in plex A-rescue embryos compared to plex A mutants (Figure 7G).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 22)\n  (:start . 15) (:id . 43))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 36) (:start . 23) (:id . 44))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 42) (:start . 37)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 51)\n  (:start . 43) (:id . 46))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 57) (:start . 52)\n  (:id . 47))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 60) (:start . 58)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 70)\n  (:start . 61) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 50))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 78) (:start . 74)\n  (:id . 51))\n ((:tag . "NN") (:stem . "a-rescue") (:form . "A-rescue") (:end . 87)\n  (:start . 79) (:id . 52))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 95)\n  (:start . 88) (:id . 53))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 104)\n  (:start . 96) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 107) (:start . 105)\n  (:id . 55))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 112) (:start . 108)\n  (:id . 56))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 114) (:start . 113)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 122)\n  (:start . 115) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 130)\n  (:start . 124) (:id . 60))\n ((:tag . "NN") (:stem . "7g") (:form . "7G") (:end . 133) (:start . 131)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.202) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503315@unknown@formal@none@1@S@We conclude that both plex A and plex B are required in sensory neurons for the appropriate targeting of class IV axons to the ventral neuropile.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "conclude") (:form . "conclude") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 39) (:start . 38)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 52)\n  (:start . 44) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 63)\n  (:start . 56) (:id . 54))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 71)\n  (:start . 64) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 91)\n  (:start . 80) (:id . 58))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 101)\n  (:start . 92) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 110)\n  (:start . 105) (:id . 61))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 113) (:start . 111)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 119)\n  (:start . 114) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 122) (:start . 120)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 134)\n  (:start . 127) (:id . 66))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 144)\n  (:start . 135) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s10.203) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503316@unknown@formal@none@1@S@Discussion@(((:tag . "NN") (:stem . "discussion") (:form . "Discussion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s10.204) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503317@unknown@formal@none@1@S@In the work we report here, we have addressed the general issue of how neuronal termination is regulated within a complex meshwork of differentiating axons and dendrites.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "report") (:form . "report") (:end . 21)\n  (:start . 15) (:id . 46))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 35) (:start . 31)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "address") (:form . "addressed") (:end . 45)\n  (:start . 36) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 57)\n  (:start . 50) (:id . 53))\n ((:tag . "NN") (:stem . "issue") (:form . "issue") (:end . 63) (:start . 58)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 55))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 70) (:start . 67)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 79)\n  (:start . 71) (:id . 57))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 91)\n  (:start . 80) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 94) (:start . 92)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 104)\n  (:start . 95) (:id . 60))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 111)\n  (:start . 105) (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 121)\n  (:start . 114) (:id . 63))\n ((:tag . "NN") (:stem . "meshwork") (:form . "meshwork") (:end . 130)\n  (:start . 122) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "differentiate") (:form . "differentiating")\n  (:end . 149) (:start . 134) (:id . 66))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 155)\n  (:start . 150) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 169)\n  (:start . 160) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s10.205) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503318@unknown@formal@none@1@S@Connections are formed within a central neuropile from which cell bodies are excluded.@(((:tag . "NNP") (:stem . "Connection") (:form . "Connections") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "form") (:form . "formed") (:end . 22) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 29)\n  (:start . 23) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 49)\n  (:start . 40) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 60) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 72) (:start . 66)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 85)\n  (:start . 77) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.206) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503319@unknown@formal@none@1@S@As first noted by Cajal [34], removing cell bodies to the periphery, while multiple connections are formed within a central core, maximises the economy with which the network is wired together.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "note") (:form . "noted") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Cajal") (:form . "Cajal") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 28) (:start . 27)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "remove") (:form . "removing") (:end . 38)\n  (:start . 30) (:id . 51))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 43) (:start . 39)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 50) (:start . 44)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 53) (:start . 51)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 55))\n ((:tag . "NN") (:stem . "periphery") (:form . "periphery") (:end . 67)\n  (:start . 58) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 57))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 74) (:start . 69)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 83)\n  (:start . 75) (:id . 59))\n ((:tag . "NNS") (:stem . "connection") (:form . "connections") (:end . 95)\n  (:start . 84) (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 99) (:start . 96)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "form") (:form . "formed") (:end . 106)\n  (:start . 100) (:id . 62))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 113)\n  (:start . 107) (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 123)\n  (:start . 116) (:id . 65))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 128) (:start . 124)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "maximise") (:form . "maximises") (:end . 139)\n  (:start . 130) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 69))\n ((:tag . "NN") (:stem . "economy") (:form . "economy") (:end . 151)\n  (:start . 144) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 156) (:start . 152)\n  (:id . 71))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 162)\n  (:start . 157) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 73))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 174)\n  (:start . 167) (:id . 74))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 177) (:start . 175)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "wire") (:form . "wired") (:end . 183)\n  (:start . 178) (:id . 76))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 192)\n  (:start . 184) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s10.207) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503320@unknown@formal@none@1@S@As a consequence of this organisation the processes of neurons of all kinds—motor, sensory, and interneurons—grow into a common volume of the nervous system within which connections will be formed.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "consequence") (:form . "consequence") (:end . 16)\n  (:start . 5) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "organisation") (:form . "organisation") (:end . 37)\n  (:start . 25) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 62)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "kinds") (:form . "kinds") (:end . 75) (:start . 70)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "—") (:form . "—") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "sensory") (:form . "sensory") (:end . 90)\n  (:start . 83) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "interneurons") (:form . "interneurons")\n  (:end . 108) (:start . 96) (:id . 61))\n ((:tag . "PRP") (:stem . "—") (:form . "—") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 113) (:start . 109)\n  (:id . 63))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 118) (:start . 114)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 120) (:start . 119)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 127)\n  (:start . 121) (:id . 66))\n ((:tag . "NN") (:stem . "volume") (:form . "volume") (:end . 134)\n  (:start . 128) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 149)\n  (:start . 142) (:id . 70))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 156)\n  (:start . 150) (:id . 71))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 163)\n  (:start . 157) (:id . 72))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 169)\n  (:start . 164) (:id . 73))\n ((:tag . "NNS") (:stem . "connection") (:form . "connections") (:end . 181)\n  (:start . 170) (:id . 74))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 186) (:start . 182)\n  (:id . 75))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 189) (:start . 187)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "form") (:form . "formed") (:end . 196)\n  (:start . 190) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s10.208) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503321@unknown@formal@none@1@S@This growth is patterned and consistent, so that the forming network is partitioned into different domains within which limited subsets of neurons terminate and form characteristic arborisations.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "pattern") (:form . "patterned") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 39)\n  (:start . 29) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 60)\n  (:start . 53) (:id . 52))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "partition") (:form . "partitioned") (:end . 83)\n  (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 98)\n  (:start . 89) (:id . 57))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 106)\n  (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 113)\n  (:start . 107) (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 119)\n  (:start . 114) (:id . 60))\n ((:tag . "JJ") (:stem . "limited") (:form . "limited") (:end . 127)\n  (:start . 120) (:id . 61))\n ((:tag . "NNS") (:stem . "subset") (:form . "subsets") (:end . 135)\n  (:start . 128) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 146)\n  (:start . 139) (:id . 64))\n ((:tag . "VB") (:stem . "terminate") (:form . "terminate") (:end . 156)\n  (:start . 147) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 66))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 165) (:start . 161)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 180) (:start . 166) (:id . 68))\n ((:tag . "NNS") (:stem . "arborisation") (:form . "arborisations")\n  (:end . 194) (:start . 181) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s10.209) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503322@unknown@formal@none@1@S@In the VNC of Drosophila embryo, for example, motor neurons place their dendrites in the most dorsal domain of the neuropile where they arborise to form a myotopic map that represents centrally the distribution of innervated muscles in the periphery [35].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "FW") (:stem . "drosophila") (:form . "Drosophila") (:end . 24)\n  (:start . 14) (:id . 46))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 44)\n  (:start . 37) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 51) (:start . 46)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 59)\n  (:start . 52) (:id . 53))\n ((:tag . "VBP") (:stem . "place") (:form . "place") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 71)\n  (:start . 66) (:id . 55))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 81)\n  (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 58))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 93) (:start . 89)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 100)\n  (:start . 94) (:id . 60))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 107)\n  (:start . 101) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 63))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 124)\n  (:start . 115) (:id . 64))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 130)\n  (:start . 125) (:id . 65))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 135) (:start . 131)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "arborise") (:form . "arborise") (:end . 144)\n  (:start . 136) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 147) (:start . 145)\n  (:id . 68))\n ((:tag . "VB") (:stem . "form") (:form . "form") (:end . 152) (:start . 148)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 154) (:start . 153)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "myotopic") (:form . "myotopic") (:end . 163)\n  (:start . 155) (:id . 71))\n ((:tag . "NN") (:stem . "map") (:form . "map") (:end . 167) (:start . 164)\n  (:id . 72))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 172) (:start . 168)\n  (:id . 73))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 183)\n  (:start . 173) (:id . 74))\n ((:tag . "RB") (:stem . "centrally") (:form . "centrally") (:end . 193)\n  (:start . 184) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n  (:id . 76))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 210)\n  (:start . 198) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 213) (:start . 211)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "innervated") (:form . "innervated") (:end . 224)\n  (:start . 214) (:id . 79))\n ((:tag . "NNS") (:stem . "muscle") (:form . "muscles") (:end . 232)\n  (:start . 225) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 235) (:start . 233)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 239) (:start . 236)\n  (:id . 82))\n ((:tag . "NN") (:stem . "periphery") (:form . "periphery") (:end . 249)\n  (:start . 240) (:id . 83))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 251) (:start . 250)\n  (:id . 84))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 253) (:start . 251)\n  (:id . 85))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 254) (:start . 253)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 255) (:start . 254)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s10.210) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503323@unknown@formal@none@1@S@While these dendritic maps are forming dorsally, the axons of sensory neurons are growing into the same neuropile and terminating in other characteristic and consistent domains.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "dendritic") (:form . "dendritic") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "map") (:form . "maps") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 47)\n  (:start . 39) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 58) (:start . 53)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 69)\n  (:start . 62) (:id . 53))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 77)\n  (:start . 70) (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "grow") (:form . "growing") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 94) (:start . 90)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 103) (:start . 99)\n  (:id . 59))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 113)\n  (:start . 104) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 117) (:start . 114)\n  (:id . 61))\n ((:tag . "NN") (:stem . "terminating") (:form . "terminating") (:end . 129)\n  (:start . 118) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 138)\n  (:start . 133) (:id . 64))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 153) (:start . 139) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 168)\n  (:start . 158) (:id . 67))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 176)\n  (:start . 169) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.211) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503324@unknown@formal@none@1@S@Here too, each modality is targeted to a particular volume of the neuropile where the terminals form a characteristic pattern of arborisations [7].@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 14) (:start . 10)\n  (:id . 45))\n ((:tag . "NN") (:stem . "modality") (:form . "modality") (:end . 23)\n  (:start . 15) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "target") (:form . "targeted") (:end . 35)\n  (:start . 27) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 51)\n  (:start . 41) (:id . 51))\n ((:tag . "NN") (:stem . "volume") (:form . "volume") (:end . 58)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 75)\n  (:start . 66) (:id . 55))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 95)\n  (:start . 86) (:id . 58))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 117) (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 125)\n  (:start . 118) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "arborisation") (:form . "arborisations")\n  (:end . 142) (:start . 129) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 144) (:start . 143)\n  (:id . 65))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 145) (:start . 144)\n  (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 146) (:start . 145)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s10.212) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503325@unknown@formal@none@1@S@In a system in which neither the axonal nor dendritic terminals are constrained by the cell bodies or by the position of entry of the main dendrite or axon trunk into the neuropile, we envisage that connectivity develops in stages with an initial phase in which growing axons and dendrites are both delivered to appropriate volumes of the neuropile, followed by a phase of targeted connection between appropriate pre- and postsynaptic partners.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 11) (:start . 5)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 20) (:start . 15)\n  (:id . 46))\n ((:tag . "CC") (:stem . "neither") (:form . 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(:end . 444) (:start . 443)\n  (:id . 116)))@@@1@75@((:hcues ((:id . :x10.213.1) (:span 185 193)))\n (:hscopes ((:id . :x10.213.1) (:span 185 443)))\n (:identifiers (:sid . :s10.213) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503326@unknown@formal@none@1@S@A pattern of growth of this kind would resemble that seen in the developing olfactory system of the adult fly where coarse targeting to particular regions of the antennal lobe is followed by precise recognition and matching between axons and dendrites [36],[37].@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "kind") (:form . "kind") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 38) (:start . 33)\n  (:id . 49))\n ((:tag . "VB") (:stem . "resemble") (:form . "resemble") (:end . 47)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 75)\n  (:start . 65) (:id . 55))\n ((:tag . "JJ") (:stem . "olfactory") (:form . "olfactory") (:end . 85)\n  (:start . 76) (:id . 56))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 92)\n  (:start . 86) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "adult") (:form . "adult") (:end . 105)\n  (:start . 100) (:id . 60))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 109) (:start . 106)\n  (:id . 61))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 115)\n  (:start . 110) (:id . 62))\n ((:tag . "NN") (:stem . "coarse") (:form . "coarse") (:end . 122)\n  (:start . 116) (:id . 63))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 132)\n  (:start . 123) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 146)\n  (:start . 136) (:id . 66))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 154)\n  (:start . 147) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 157) (:start . 155)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "antennal") (:form . "antennal") (:end . 170)\n  (:start . 162) (:id . 70))\n ((:tag . "NN") (:stem . "lobe") (:form . "lobe") (:end . 175) (:start . 171)\n  (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 178) (:start . 176)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 187)\n  (:start . 179) (:id . 73))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 190) (:start . 188)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "precise") (:form . "precise") (:end . 198)\n  (:start . 191) (:id . 75))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 210)\n  (:start . 199) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 214) (:start . 211)\n  (:id . 77))\n ((:tag . "NN") (:stem . "matching") (:form . "matching") (:end . 223)\n  (:start . 215) (:id . 78))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 231)\n  (:start . 224) (:id . 79))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 237)\n  (:start . 232) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 241) (:start . 238)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 251)\n  (:start . 242) (:id . 82))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 253) (:start . 252)\n  (:id . 83))\n ((:tag . "CD") (:stem . "36],[37") (:form . "36],[37") (:end . 260)\n  (:start . 253) (:id . 84))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 261) (:start . 260)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 262) (:start . 261)\n  (:id . 86)))@@@1@45@((:hcues ((:id . :x10.214.1) (:span 33 38)))\n (:hscopes ((:id . :x10.214.1) (:span 33 109)))\n (:identifiers (:sid . :s10.214) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503327@unknown@formal@none@1@S@Alternatively it may be that the mechanisms that pattern the growth of fibres representing a single modality such as olfaction are different from those required to organise the distribution of terminals within a highly heterogeneous network such as that seen in the VNC.@(((:tag . "RB") (:stem . "alternatively") (:form . "Alternatively")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 16) (:start . 14)\n  (:id . 43))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "pattern") (:form . "pattern") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 67)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "fibre") (:form . "fibres") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "VBG") (:stem . "represent") (:form . "representing") (:end . 90)\n  (:start . 78) (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 92) (:start . 91)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 99)\n  (:start . 93) (:id . 57))\n ((:tag . "NN") (:stem . "modality") (:form . "modality") (:end . 108)\n  (:start . 100) (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 113) (:start . 109)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "NN") (:stem . "olfaction") (:form . "olfaction") (:end . 126)\n  (:start . 117) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 130) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 140)\n  (:start . 131) (:id . 63))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 145) (:start . 141)\n  (:id . 64))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 151)\n  (:start . 146) (:id . 65))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 160)\n  (:start . 152) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 163) (:start . 161)\n  (:id . 67))\n ((:tag . "VB") (:stem . "organise") (:form . "organise") (:end . 172)\n  (:start . 164) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 176) (:start . 173)\n  (:id . 69))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 189)\n  (:start . 177) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 192) (:start . 190)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 202)\n  (:start . 193) (:id . 72))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 209)\n  (:start . 203) (:id . 73))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 211) (:start . 210)\n  (:id . 74))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 218)\n  (:start . 212) (:id . 75))\n ((:tag . "JJ") (:stem . "heterogeneous") (:form . "heterogeneous")\n  (:end . 232) (:start . 219) (:id . 76))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 240)\n  (:start . 233) (:id . 77))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 245) (:start . 241)\n  (:id . 78))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 248) (:start . 246)\n  (:id . 79))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 253) (:start . 249)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 258) (:start . 254)\n  (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 261) (:start . 259)\n  (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 265) (:start . 262)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 269) (:start . 266)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x10.215.1) (:span 17 20)))\n (:hscopes ((:id . :x10.215.1) (:span 17 269)))\n (:identifiers (:sid . :s10.215) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503328@unknown@formal@none@1@S@In our view the initial delivery and restriction of fibres to particular subvolumes of the VNC neuropile is likely to be by individual growth responses to generalised systems of cues that operate to pattern the network as it develops.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "view") (:form . "view") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "delivery") (:form . "delivery") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "restriction") (:form . "restriction") (:end . 48)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "fibre") (:form . "fibres") (:end . 58)\n  (:start . 52) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 72)\n  (:start . 62) (:id . 53))\n ((:tag . "NNS") (:stem . "subvolume") (:form . "subvolumes") (:end . 83)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 94) (:start . 91)\n  (:id . 57))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 104)\n  (:start . 95) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 114)\n  (:start . 108) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n  (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 120) (:start . 118)\n  (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 123) (:start . 121)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 134)\n  (:start . 124) (:id . 64))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 141)\n  (:start . 135) (:id . 65))\n ((:tag . "NNS") (:stem . "response") (:form . "responses") (:end . 151)\n  (:start . 142) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "generalise") (:form . "generalised") (:end . 166)\n  (:start . 155) (:id . 68))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 174)\n  (:start . 167) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 177) (:start . 175)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 182) (:start . 178)\n  (:id . 71))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 187) (:start . 183)\n  (:id . 72))\n ((:tag . "VBP") (:stem . "operate") (:form . "operate") (:end . 195)\n  (:start . 188) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 198) (:start . 196)\n  (:id . 74))\n ((:tag . "VB") (:stem . "pattern") (:form . "pattern") (:end . 206)\n  (:start . 199) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 210) (:start . 207)\n  (:id . 76))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 218)\n  (:start . 211) (:id . 77))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 221) (:start . 219)\n  (:id . 78))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 224) (:start . 222)\n  (:id . 79))\n ((:tag . "VBZ") (:stem . "develop") (:form . "develops") (:end . 233)\n  (:start . 225) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x10.216.1) (:span 108 114)))\n (:hscopes ((:id . :x10.216.1) (:span 12 233)))\n (:identifiers (:sid . :s10.216) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503329@unknown@formal@none@1@S@In a previous paper we were able to demonstrate the operation of one such cue, Slit, which, acting through its Robo receptors dictates the different positions in the mediolateral axis at which specific sensory axons will terminate and arborise.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 13)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "paper") (:form . "paper") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "VB") (:stem . "demonstrate") (:form . "demonstrate") (:end . 47)\n  (:start . 36) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "operation") (:form . "operation") (:end . 61)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 73) (:start . 69)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cue") (:form . "cue") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 83) (:start . 79)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 90) (:start . 85)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 98) (:start . 92)\n  (:id . 62))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 106)\n  (:start . 99) (:id . 63))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 110) (:start . 107)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Robo") (:form . "Robo") (:end . 115) (:start . 111)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 125)\n  (:start . 116) (:id . 66))\n ((:tag . "VBZ") (:stem . "dictate") (:form . "dictates") (:end . 134)\n  (:start . 126) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 148)\n  (:start . 139) (:id . 69))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 158)\n  (:start . 149) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 161) (:start . 159)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "mediolateral") (:form . "mediolateral") (:end . 178)\n  (:start . 166) (:id . 73))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 183) (:start . 179)\n  (:id . 74))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 186) (:start . 184)\n  (:id . 75))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 192)\n  (:start . 187) (:id . 76))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 201)\n  (:start . 193) (:id . 77))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 209)\n  (:start . 202) (:id . 78))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 215)\n  (:start . 210) (:id . 79))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 220) (:start . 216)\n  (:id . 80))\n ((:tag . "VB") (:stem . "terminate") (:form . "terminate") (:end . 230)\n  (:start . 221) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 234) (:start . 231)\n  (:id . 82))\n ((:tag . "VB") (:stem . "arborise") (:form . "arborise") (:end . 243)\n  (:start . 235) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s10.217) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503330@unknown@formal@none@1@S@Here we have shown that membrane bound and secreted Semas acting through their receptors the Plexins restrict growing axons and their terminals to particular dorso-ventral layers of the forming neuropile.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "VBD") (:stem . "bind") (:form . "bound") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "secrete") (:form . "secreted") (:end . 51)\n  (:start . 43) (:id . 50))\n ((:tag . "NNP") (:stem . "Semas") (:form . "Semas") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 64) (:start . 58)\n  (:id . 52))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 78)\n  (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 88)\n  (:start . 79) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "plexin") (:form . "Plexins") (:end . 100)\n  (:start . 93) (:id . 57))\n ((:tag . "NN") (:stem . "restrict") (:form . "restrict") (:end . 109)\n  (:start . 101) (:id . 58))\n ((:tag . "VBG") (:stem . "grow") (:form . "growing") (:end . 117)\n  (:start . 110) (:id . 59))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 123)\n  (:start . 118) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 61))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 133)\n  (:start . 128) (:id . 62))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 143)\n  (:start . 134) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 146) (:start . 144)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 157)\n  (:start . 147) (:id . 65))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 171) (:start . 158) (:id . 66))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 178)\n  (:start . 172) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 181) (:start . 179)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 193)\n  (:start . 186) (:id . 70))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 203)\n  (:start . 194) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.218) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503331@unknown@formal@none@1@S@Evidence for Sema/Plexin Signalling Acting in the Dorso-Ventral Axis of the Neuropile@(((:tag . "NN") (:stem . "evidence") (:form . "Evidence") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Sema/Plexin") (:form . "Sema/Plexin") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "NNP") (:stem . "Signalling") (:form . "Signalling") (:end . 35)\n  (:start . 25) (:id . 45))\n ((:tag . "NNP") (:stem . "Acting") (:form . "Acting") (:end . 42)\n  (:start . 36) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "Dorso-Ventral")\n  (:end . 63) (:start . 50) (:id . 49))\n ((:tag . "NNP") (:stem . "Axis") (:form . "Axis") (:end . 68) (:start . 64)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Neuropile") (:form . "Neuropile") (:end . 85)\n  (:start . 76) (:id . 53)))@@@1@12@((:identifiers (:sid . :s10.219) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503332@unknown@formal@none@1@S@Our initial approach of using a misexpression screen targeted to all sensory axons was sufficient to reveal the existence of the Semas as putative cues in the dorso-ventral axis by showing that there were generalised redistributions of sensory endings in this axis when the cells concerned were forced to express either of the two Sema receptors, Plex A or Plex B.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "misexpression") (:form . "misexpression")\n  (:end . 45) (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "screen") (:form . "screen") (:end . 52)\n  (:start . 46) (:id . 49))\n ((:tag . "VBN") (:stem . "target") (:form . "targeted") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 82) (:start . 77)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 97)\n  (:start . 87) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "VB") (:stem . "reveal") (:form . "reveal") (:end . 107)\n  (:start . 101) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "NN") (:stem . "existence") (:form . "existence") (:end . 121)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Semas") (:form . "Semas") (:end . 134)\n  (:start . 129) (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 146)\n  (:start . 138) (:id . 65))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 151) (:start . 147)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . 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",") (:end . 346) (:start . 345)\n  (:id . 98))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 351) (:start . 347)\n  (:id . 99))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 353) (:start . 352)\n  (:id . 100))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 356) (:start . 354)\n  (:id . 101))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 361) (:start . 357)\n  (:id . 102))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 363) (:start . 362)\n  (:id . 103))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 364) (:start . 363)\n  (:id . 104)))@@@1@63@((:hcues ((:id . :x10.220.1) (:span 138 146)))\n (:hscopes ((:id . :x10.220.1) (:span 138 177)))\n (:identifiers (:sid . :s10.220) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503333@unknown@formal@none@1@S@These shifts were readily detectable when the nervous system was viewed in a plane at right angles to the neuraxis.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "shift") (:form . "shifts") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 36)\n  (:start . 26) (:id . 46))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 60)\n  (:start . 54) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "view") (:form . "viewed") (:end . 71) (:start . 65)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "plane") (:form . "plane") (:end . 82) (:start . 77)\n  (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 91) (:start . 86)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "angle") (:form . "angles") (:end . 98)\n  (:start . 92) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "neuraxis") (:form . "neuraxis") (:end . 114)\n  (:start . 106) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s10.221) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503334@unknown@formal@none@1@S@Viewing the nervous system in this plane also reveals the largely complementary patterns of expression for the two Semas.@(((:tag . "VBG") (:stem . "view") (:form . "Viewing") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "plane") (:form . "plane") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "JJ") (:stem . "complementary") (:form . "complementary")\n  (:end . 79) (:start . 66) (:id . 53))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 88)\n  (:start . 80) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 102)\n  (:start . 92) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 106) (:start . 103)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 114) (:start . 111)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Semas") (:form . "Semas") (:end . 120)\n  (:start . 115) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.222) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503335@unknown@formal@none@1@S@The membrane bound Sema 1a is distributed in an alternating pattern across the neuropile with high levels in both layers 1 and 3.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "bind") (:form . "bound") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "distribute") (:form . "distributed") (:end . 41)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "alternate") (:form . "alternating") (:end . 59)\n  (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 67)\n  (:start . 60) (:id . 52))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 74)\n  (:start . 68) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 88)\n  (:start . 79) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 98) (:start . 94)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 105)\n  (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 113) (:start . 109)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 120)\n  (:start . 114) (:id . 61))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 63))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.223) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503336@unknown@formal@none@1@S@The secreted Sema, Sema 2a, on the other hand, is expressed at high levels in a central strip that extends across the midline and in gradients that decline ventrally and dorsally orthogonal to the Slit gradient (Figure 2).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "secrete") (:form . "secreted") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "CD") (:stem . "2a") (:form . "2a") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 40) (:start . 35)\n  (:id . 51))\n ((:tag . "NN") (:stem . "hand") (:form . "hand") (:end . 45) (:start . 41)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 59)\n  (:start . 50) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 62) (:start . 60)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 67) (:start . 63)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 74)\n  (:start . 68) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 79) (:start . 78)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 87)\n  (:start . 80) (:id . 61))\n ((:tag . "NN") (:stem . "strip") (:form . "strip") (:end . 93) (:start . 88)\n  (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 98) (:start . 94)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "extend") (:form . "extends") (:end . 106)\n  (:start . 99) (:id . 64))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 113)\n  (:start . 107) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 66))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 125)\n  (:start . 118) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 132) (:start . 130)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "gradient") (:form . "gradients") (:end . 142)\n  (:start . 133) (:id . 70))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 147) (:start . 143)\n  (:id . 71))\n ((:tag . "VBP") (:stem . "decline") (:form . "decline") (:end . 155)\n  (:start . 148) (:id . 72))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 165)\n  (:start . 156) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 169) (:start . 166)\n  (:id . 74))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 178)\n  (:start . 170) (:id . 75))\n ((:tag . "JJ") (:stem . "orthogonal") (:form . "orthogonal") (:end . 189)\n  (:start . 179) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 192) (:start . 190)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 201) (:start . 197)\n  (:id . 79))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 210)\n  (:start . 202) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 212) (:start . 211)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 218)\n  (:start . 212) (:id . 82))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 220) (:start . 219)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s10.224) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503337@unknown@formal@none@1@S@A gradient of Sema 2a has also been described in the embryonic limb of the grasshopper [38].@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 30) (:start . 26)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 35) (:start . 31)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 45)\n  (:start . 36) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 62)\n  (:start . 53) (:id . 53))\n ((:tag . "NN") (:stem . "limb") (:form . "limb") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 56))\n ((:tag . "NN") (:stem . "grasshopper") (:form . "grasshopper") (:end . 86)\n  (:start . 75) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 88) (:start . 87)\n  (:id . 58))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 91) (:start . 90)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.225) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503338@unknown@formal@none@1@S@There it contributes to the polarized growth of pioneer sensory axons away from the region of highest Sema 2a expression at the tip.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "contribute") (:form . "contributes") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "polarize") (:form . "polarized") (:end . 37)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "pioneer") (:form . "pioneer") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 63)\n  (:start . 56) (:id . 51))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 74) (:start . 70)\n  (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 90)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 101)\n  (:start . 94) (:id . 58))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 109) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 120)\n  (:start . 110) (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . "NN") (:stem . "tip") (:form . "tip") (:end . 131) (:start . 128)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.226) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503339@unknown@formal@none@1@S@In the developing Drosophila embryo selective overexpression of the putative receptors for Sema 1a and Sema 2a in sensory neurons acts in a predictable fashion to exclude sensory axons and terminals from those regions where the ligands are highly expressed: overexpression of Plex A excludes projections from high levels of Sema 1a expression in layers 1 and 3.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 35)\n  (:start . 29) (:id . 46))\n ((:tag . "JJ") (:stem . "selective") (:form . "selective") (:end . 45)\n  (:start . 36) (:id . 47))\n ((:tag . "NN") (:stem . 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5503340@unknown@formal@none@1@S@Overexpression of Plex B shifts sensory terminals further away from the central layer of the neuropile.@(((:tag . "NNP") (:stem . "Overexpression") (:form . "Overexpression")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "shift") (:form . "shifts") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 49)\n  (:start . 40) (:id . 48))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . "RB") (:stem . "away") (:form . "away") (:end . 62) (:start . 58)\n  (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 79)\n  (:start . 72) (:id . 53))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 85) (:start . 80)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 102)\n  (:start . 93) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.228) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503341@unknown@formal@none@1@S@These findings suggest that Sema 2a and Sema 1a provide guidance cues to the growth cones of sensory neurons that express Plex A and Plex B.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "guidance") (:form . "guidance") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 83)\n  (:start . 77) (:id . 56))\n ((:tag . "NNS") (:stem . "cone") (:form . "cones") (:end . 89) (:start . 84)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 100)\n  (:start . 93) (:id . 59))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 108)\n  (:start . 101) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 121)\n  (:start . 114) (:id . 62))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 126) (:start . 122)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 137) (:start . 133)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 139) (:start . 138)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x10.229.1) (:span 15 22)))\n (:hscopes ((:id . :x10.229.1) (:span 15 139)))\n (:identifiers (:sid . :s10.229) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503342@unknown@formal@none@1@S@It is consistent with this idea that in the absence of Sema 1a, Plex A overexpression in sensory neurons does not exclude their terminals from regions that normally contain high Sema 1a levels.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 16)\n  (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 51)\n  (:start . 44) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 59) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 68) (:start . 64)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 70) (:start . 69)\n  (:id . 57))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 85) (:start . 71) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 96)\n  (:start . 89) (:id . 60))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 104)\n  (:start . 97) (:id . 61))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 109) (:start . 105)\n  (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 113) (:start . 110)\n  (:id . 63))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 121)\n  (:start . 114) (:id . 64))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 127)\n  (:start . 122) (:id . 65))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 137)\n  (:start . 128) (:id . 66))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 142) (:start . 138)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 150)\n  (:start . 143) (:id . 68))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 155) (:start . 151)\n  (:id . 69))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 164)\n  (:start . 156) (:id . 70))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 172)\n  (:start . 165) (:id . 71))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 177) (:start . 173)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 182) (:start . 178)\n  (:id . 73))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 185) (:start . 183)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 192)\n  (:start . 186) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s10.230) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503343@unknown@formal@none@1@S@Similarly, in the absence of Sema 2a, Plex B overexpression in sensory neurons does not exclude their terminals from the central layer of the neuropile.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 42) (:start . 38)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 44) (:start . 43)\n  (:id . 52))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 59) (:start . 45) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 70)\n  (:start . 63) (:id . 55))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 78)\n  (:start . 71) (:id . 56))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 95)\n  (:start . 88) (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 101)\n  (:start . 96) (:id . 60))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 111)\n  (:start . 102) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 116) (:start . 112)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 128)\n  (:start . 121) (:id . 64))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 134)\n  (:start . 129) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 67))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 151)\n  (:start . 142) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.231) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503344@unknown@formal@none@1@S@The manipulations of the pattern of sensory terminals in the dorso-ventral axis found with Plexin overexpression are analogous to the manipulations in the medio-lateral axis that are found with Robo3 misexpression.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "manipulation") (:form . "manipulations")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 74) (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 79) (:start . 75)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 85) (:start . 80)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Plexin") (:form . "Plexin") (:end . 97)\n  (:start . 91) (:id . 56))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 112) (:start . 98) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 116) (:start . 113)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "analogous") (:form . "analogous") (:end . 126)\n  (:start . 117) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 129) (:start . 127)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "manipulation") (:form . "manipulations")\n  (:end . 147) (:start . 134) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 168) (:start . 155) (:id . 65))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 173) (:start . 169)\n  (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 178) (:start . 174)\n  (:id . 67))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 182) (:start . 179)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 188)\n  (:start . 183) (:id . 69))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 193) (:start . 189)\n  (:id . 70))\n ((:tag . "NN") (:stem . "robo3") (:form . "Robo3") (:end . 199)\n  (:start . 194) (:id . 71))\n ((:tag . "NN") (:stem . "misexpression") (:form . "misexpression")\n  (:end . 213) (:start . 200) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s10.232) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503345@unknown@formal@none@1@S@In both dimensions the position at which sensory neurons form their terminals is determined by their expression of receptors for positional cues.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "dimension") (:form . "dimensions") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 67)\n  (:start . 62) (:id . 52))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 77)\n  (:start . 68) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 91)\n  (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 100)\n  (:start . 95) (:id . 57))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 111)\n  (:start . 101) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 124)\n  (:start . 115) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 128) (:start . 125)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 139)\n  (:start . 129) (:id . 62))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 144) (:start . 140)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.233) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503346@unknown@formal@none@1@S@Sema/Plexin Signalling Guides Termination in the Dorso-Ventral Axis@(((:tag . "NNP") (:stem . "Sema/Plexin") (:form . "Sema/Plexin") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Signalling") (:form . "Signalling") (:end . 22)\n  (:start . 12) (:id . 43))\n ((:tag . "VBZ") (:stem . "guide") (:form . "Guides") (:end . 29)\n  (:start . 23) (:id . 44))\n ((:tag . "NN") (:stem . "termination") (:form . "Termination") (:end . 41)\n  (:start . 30) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "Dorso-Ventral")\n  (:end . 62) (:start . 49) (:id . 48))\n ((:tag . "NNP") (:stem . "Axis") (:form . "Axis") (:end . 67) (:start . 63)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s10.234) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503347@unknown@formal@none@1@S@The most ventrally located sensory terminals, the ppk-expressing md neurons are derived from axons that actually enter the nervous system dorsally and grow downwards, skirting alternative neuropile regions before turning inwards to reach their characteristic medial, ventral domain of termination.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 44)\n  (:start . 35) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "ppk-expressing") (:form . "ppk-expressing")\n  (:end . 64) (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 75)\n  (:start . 68) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 79) (:start . 76)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 87)\n  (:start . 80) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 92) (:start . 88)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 98) (:start . 93)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 103) (:start . 99)\n  (:id . 57))\n ((:tag . "RB") (:stem . "actually") (:form . "actually") (:end . 112)\n  (:start . 104) (:id . 58))\n ((:tag . "VBP") (:stem . "enter") (:form . "enter") (:end . 118)\n  (:start . 113) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "nervous") (:form . "nervous") (:end . 130)\n  (:start . 123) (:id . 61))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 137)\n  (:start . 131) (:id . 62))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 146)\n  (:start . 138) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 64))\n ((:tag . "VB") (:stem . "grow") (:form . "grow") (:end . 155) (:start . 151)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "downward") (:form . "downwards") (:end . 165)\n  (:start . 156) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "skirt") (:form . "skirting") (:end . 175)\n  (:start . 167) (:id . 68))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 187)\n  (:start . 176) (:id . 69))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 197)\n  (:start . 188) (:id . 70))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 205)\n  (:start . 198) (:id . 71))\n ((:tag . "IN") (:stem . "before") (:form . "before") (:end . 212)\n  (:start . 206) (:id . 72))\n ((:tag . "VBG") (:stem . "turn") (:form . "turning") (:end . 220)\n  (:start . 213) (:id . 73))\n ((:tag . "NNS") (:stem . "inward") (:form . "inwards") (:end . 228)\n  (:start . 221) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 231) (:start . 229)\n  (:id . 75))\n ((:tag . "VB") (:stem . "reach") (:form . "reach") (:end . 237)\n  (:start . 232) (:id . 76))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 243)\n  (:start . 238) (:id . 77))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 258) (:start . 244) (:id . 78))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 265)\n  (:start . 259) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 266) (:start . 265)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 274)\n  (:start . 267) (:id . 81))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 281)\n  (:start . 275) (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 284) (:start . 282)\n  (:id . 83))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 296)\n  (:start . 285) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 297) (:start . 296)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s10.235) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503348@unknown@formal@none@1@S@A consequence of Sema signalling is that these ventrally targeted axons are excluded from more dorsal regions of the neuropile and channelled instead through a limited lateral region where the expression of both proteins is low, so that their inward migration towards the midline is blocked until they reach the most ventral region.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "consequence") (:form . "consequence") (:end . 13)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "signalling") (:form . "signalling") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . 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5503349@unknown@formal@none@1@S@In the absence of either of the Semas or their Plexin receptors, ppk-expressing axons aberrantly enter and terminate in more dorsal regions of the neuropile.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Semas") (:form . "Semas") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 46)\n  (:start . 41) (:id . 51))\n ((:tag . "NNP") (:stem . "Plexin") (:form . "Plexin") (:end . 53)\n  (:start . 47) (:id . 52))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 63)\n  (:start . 54) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "ppk-expressing") (:form . "ppk-expressing")\n  (:end . 79) (:start . 65) (:id . 55))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "RB") (:stem . "aberrantly") (:form . "aberrantly") (:end . 96)\n  (:start . 86) (:id . 57))\n ((:tag . "VB") (:stem . "enter") (:form . "enter") (:end . 102) (:start . 97)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "VB") (:stem . "terminate") (:form . "terminate") (:end . 116)\n  (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 124) (:start . 120)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 131)\n  (:start . 125) (:id . 63))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 139)\n  (:start . 132) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 66))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 156)\n  (:start . 147) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s10.237) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503350@unknown@formal@none@1@S@This suggests that the growth cones of these cells are attracted towards to midline (we assume by Netrins) [39] as soon as they enter the CNS, but that entry and termination in the more dorsal region of the neuropile is prevented by high levels of Sema 1a in layer 1.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "cone") (:form . "cones") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . 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5503351@unknown@formal@none@1@S@In vertebrates genetic studies show that proprioceptive axons are excluded from the superficial dorsal horn by Sema 6D/6C signalling mediated by Plex A1.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "proprioceptive") (:form . "proprioceptive")\n  (:end . 55) (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 61) (:start . 56)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 65) (:start . 62)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 74)\n  (:start . 66) (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 79) (:start . 75)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "superficial") (:form . "superficial") (:end . 95)\n  (:start . 84) (:id . 54))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 102)\n  (:start . 96) (:id . 55))\n ((:tag . "NN") (:stem . "horn") (:form . "horn") (:end . 107) (:start . 103)\n  (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 110) (:start . 108)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 115) (:start . 111)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "6D/6C") (:form . "6D/6C") (:end . 121)\n  (:start . 116) (:id . 59))\n ((:tag . "NN") (:stem . "signalling") (:form . "signalling") (:end . 132)\n  (:start . 122) (:id . 60))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 141)\n  (:start . 133) (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 144) (:start . 142)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 149) (:start . 145)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "A1") (:form . "A1") (:end . 152) (:start . 150)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.239) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503352@unknown@formal@none@1@S@Loss of Plex A1 allows proprioceptive collaterals to invade the superficial dorsal horn although most succeed in projecting through it to their normal more ventral target zones [19].@(((:tag . "NN") (:stem . "loss") (:form . "Loss") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "A1") (:form . "A1") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 22)\n  (:start . 16) (:id . 46))\n ((:tag . "JJ") (:stem . "proprioceptive") (:form . "proprioceptive")\n  (:end . 37) (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "collateral") (:form . "collaterals") (:end . 49)\n  (:start . 38) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "VB") (:stem . "invade") (:form . "invade") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "superficial") (:form . "superficial") (:end . 75)\n  (:start . 64) (:id . 52))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 82)\n  (:start . 76) (:id . 53))\n ((:tag . "NN") (:stem . "horn") (:form . "horn") (:end . 87) (:start . 83)\n  (:id . 54))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 96)\n  (:start . 88) (:id . 55))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 101) (:start . 97)\n  (:id . 56))\n ((:tag . "VB") (:stem . "succeed") (:form . "succeed") (:end . 109)\n  (:start . 102) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "project") (:form . "projecting") (:end . 123)\n  (:start . 113) (:id . 59))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 131)\n  (:start . 124) (:id . 60))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 134) (:start . 132)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 137) (:start . 135)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 143)\n  (:start . 138) (:id . 63))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 150)\n  (:start . 144) (:id . 64))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 155) (:start . 151)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 163)\n  (:start . 156) (:id . 66))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 170)\n  (:start . 164) (:id . 67))\n ((:tag . "NNS") (:stem . "zone") (:form . "zones") (:end . 176)\n  (:start . 171) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 178) (:start . 177)\n  (:id . 69))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 180) (:start . 178)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 181) (:start . 180)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.240) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503353@unknown@formal@none@1@S@In an analogous (though not topologically equivalent) fashion, ventrally projecting afferents in Drosophila require Sema signalling through Plex A for their proper exclusion from the most dorsal neuropile.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "analogous") (:form . "analogous") (:end . 15)\n  (:start . 6) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "RB") (:stem . "topologically") (:form . "topologically")\n  (:end . 41) (:start . 28) (:id . 48))\n ((:tag . "JJ") (:stem . "equivalent") (:form . "equivalent") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "fashion") (:form . "fashion") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 72)\n  (:start . 63) (:id . 53))\n ((:tag . "VBG") (:stem . "project") (:form . "projecting") (:end . 83)\n  (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "afferent") (:form . "afferents") (:end . 93)\n  (:start . 84) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Drosophila") (:form . "Drosophila") (:end . 107)\n  (:start . 97) (:id . 57))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 115)\n  (:start . 108) (:id . 58))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 120) (:start . 116)\n  (:id . 59))\n ((:tag . "NN") (:stem . "signalling") (:form . "signalling") (:end . 131)\n  (:start . 121) (:id . 60))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 139)\n  (:start . 132) (:id . 61))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 144) (:start . 140)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 146) (:start . 145)\n  (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 150) (:start . 147)\n  (:id . 64))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 156)\n  (:start . 151) (:id . 65))\n ((:tag . "JJ") (:stem . "proper") (:form . "proper") (:end . 163)\n  (:start . 157) (:id . 66))\n ((:tag . "NN") (:stem . "exclusion") (:form . "exclusion") (:end . 173)\n  (:start . 164) (:id . 67))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 178) (:start . 174)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 182) (:start . 179)\n  (:id . 69))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 187) (:start . 183)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 194)\n  (:start . 188) (:id . 71))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 204)\n  (:start . 195) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s10.241) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503354@unknown@formal@none@1@S@Loss of plex A appears to affect class IV terminals less strongly than loss of sema 1a.@(((:tag . "NN") (:stem . "loss") (:form . "Loss") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 22)\n  (:start . 15) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 32)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 38) (:start . 33)\n  (:id . 49))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 51)\n  (:start . 42) (:id . 51))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 65)\n  (:start . 57) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 75) (:start . 71)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 86) (:start . 84)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x10.242.1) (:span 15 22)))\n (:hscopes ((:id . :x10.242.1) (:span 0 86)))\n (:identifiers (:sid . :s10.242) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503355@unknown@formal@none@1@S@One explanation could be that Plex B might also function as a receptor for Sema 1a in this system.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "explanation") (:form . "explanation") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 56)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 70)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 79) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n  (:id . 58))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 90) (:start . 86)\n  (:id . 59))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 97)\n  (:start . 91) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x10.243.1) (:span 37 42)) ((:id . :x10.243.2) (:span 16 21)))\n (:hscopes ((:id . :x10.243.1) (:span 37 97))\n  ((:id . :x10.243.2) (:span 16 97)))\n (:identifiers (:sid . :s10.243) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503356@unknown@formal@none@1@S@Our observation that in plex B mutants class IV axons aberrantly terminate in layers 1, 2, or 3 supports this possibility.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "RB") (:stem . "aberrantly") (:form . "aberrantly") (:end . 64)\n  (:start . 54) (:id . 52))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 74)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 84)\n  (:start . 78) (:id . 55))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 86) (:start . 85)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 89) (:start . 88)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 59))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 95) (:start . 94)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "support") (:form . "supports") (:end . 104)\n  (:start . 96) (:id . 62))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 109) (:start . 105)\n  (:id . 63))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 121)\n  (:start . 110) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.244) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503357@unknown@formal@none@1@S@We also find that Plex B overexpression in sensory neurons in plex A mutant embryos, prevents aberrant expansion of sensory terminals into intermediate portion of layer 1, which contains very high levels of Sema 1a (Figure S9).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "find") (:form . "find") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 24) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 39) (:start . 25) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 50)\n  (:start . 43) (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 58)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 83)\n  (:start . 76) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "prevent") (:form . "prevents") (:end . 93)\n  (:start . 85) (:id . 58))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 112)\n  (:start . 103) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 123)\n  (:start . 116) (:id . 62))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 133)\n  (:start . 124) (:id . 63))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 138) (:start . 134)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 151)\n  (:start . 139) (:id . 65))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 159)\n  (:start . 152) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 162) (:start . 160)\n  (:id . 67))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 168)\n  (:start . 163) (:id . 68))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 170) (:start . 169)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 70))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 177)\n  (:start . 172) (:id . 71))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 186)\n  (:start . 178) (:id . 72))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 191) (:start . 187)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 196) (:start . 192)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 203)\n  (:start . 197) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 206) (:start . 204)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 211) (:start . 207)\n  (:id . 77))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 214) (:start . 212)\n  (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 216) (:start . 215)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 222)\n  (:start . 216) (:id . 80))\n ((:tag . "NNP") (:stem . "S9") (:form . "S9") (:end . 225) (:start . 223)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 226) (:start . 225)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s10.245) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503358@unknown@formal@none@1@S@Such an expansion occurs in both plex A and sema 1a mutant embryos.@(((:tag . "PDT") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 48) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 58)\n  (:start . 52) (:id . 53))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 66)\n  (:start . 59) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.246) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503359@unknown@formal@none@1@S@High levels of Plex B signalling thus appear to be able to substitute for the absence of Plex A signalling and prevent expansion into regions with high Sema 1a levels.@(((:tag . "JJ") (:stem . "high") (:form . "High") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "signalling") (:form . "signalling") (:end . 32)\n  (:start . 22) (:id . 47))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "VB") (:stem . "substitute") (:form . "substitute") (:end . 69)\n  (:start . 59) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 85)\n  (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 93) (:start . 89)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "NN") (:stem . "signalling") (:form . "signalling") (:end . 106)\n  (:start . 96) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 62))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 118)\n  (:start . 111) (:id . 63))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 128)\n  (:start . 119) (:id . 64))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 133) (:start . 129)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 141)\n  (:start . 134) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 146) (:start . 142)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 151) (:start . 147)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 156) (:start . 152)\n  (:id . 69))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 159) (:start . 157)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 166)\n  (:start . 160) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x10.247.1) (:span 38 44)))\n (:hscopes ((:id . :x10.247.1) (:span 0 166)))\n (:identifiers (:sid . :s10.247) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503360@unknown@formal@none@1@S@These findings could be explained if Plex B were to function as a lower affinity receptor for Sema 1a, as well as a high affinity receptor for Sema 2a.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "explain") (:form . "explained") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 60)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 71) (:start . 66)\n  (:id . 55))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 80)\n  (:start . 72) (:id . 56))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 89)\n  (:start . 81) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 101) (:start . 99)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 105) (:start . 103)\n  (:id . 62))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 110) (:start . 106)\n  (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 113) (:start . 111)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 120) (:start . 116)\n  (:id . 66))\n ((:tag . "NN") (:stem . "affinity") (:form . "affinity") (:end . 129)\n  (:start . 121) (:id . 67))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 138)\n  (:start . 130) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 142) (:start . 139)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 147) (:start . 143)\n  (:id . 70))\n ((:tag . "CD") (:stem . "2a") (:form . "2a") (:end . 150) (:start . 148)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x10.248.1) (:span 15 20)))\n (:hscopes ((:id . :x10.248.1) (:span 0 150)))\n (:identifiers (:sid . :s10.248) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503361@unknown@formal@none@1@S@Sema 1a and Sema 2a are unlikely to be the only cues that operate in the dorso-ventral axis.@(((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "1a") (:form . "1a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 32)\n  (:start . 24) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 47) (:start . 43)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 52) (:start . 48)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 57) (:start . 53)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "operate") (:form . "operate") (:end . 65)\n  (:start . 58) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 86) (:start . 73) (:id . 58))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 91) (:start . 87)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x10.249.1) (:span 24 32)))\n (:hscopes ((:id . :x10.249.1) (:span 0 91)))\n (:identifiers (:sid . :s10.249) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503362@unknown@formal@none@1@S@The incomplete penetrance of the termination phenotype in the sema 1a, sema 2a double mutant suggests that additional factors may operate to control the ventral targeting of class IV axons.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "incomplete") (:form . "incomplete") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "penetrance") (:form . "penetrance") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 44)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 54)\n  (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 85)\n  (:start . 79) (:id . 56))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 92)\n  (:start . 86) (:id . 57))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 101)\n  (:start . 93) (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 117)\n  (:start . 107) (:id . 60))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 125)\n  (:start . 118) (:id . 61))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "VB") (:stem . "operate") (:form . "operate") (:end . 137)\n  (:start . 130) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 140) (:start . 138)\n  (:id . 64))\n ((:tag . "VB") (:stem . "control") (:form . "control") (:end . 148)\n  (:start . 141) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 160)\n  (:start . 153) (:id . 67))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 170)\n  (:start . 161) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 69))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 179)\n  (:start . 174) (:id . 70))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 182) (:start . 180)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 188)\n  (:start . 183) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x10.250.1) (:span 126 129))\n  ((:id . :x10.250.2) (:span 93 101)))\n (:hscopes ((:id . :x10.250.1) (:span 126 188))\n  ((:id . :x10.250.2) (:span 93 188)))\n (:identifiers (:sid . :s10.250) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503363@unknown@formal@none@1@S@There may be long range ventral attractants or local substrate bound attractive cues for these axons in the neuropile.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "attractant") (:form . "attractants") (:end . 43)\n  (:start . 32) (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "substrate") (:form . "substrate") (:end . 62)\n  (:start . 53) (:id . 51))\n ((:tag . "VBD") (:stem . "bind") (:form . "bound") (:end . 68) (:start . 63)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "attractive") (:form . "attractive") (:end . 79)\n  (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 84) (:start . 80)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 88) (:start . 85)\n  (:id . 55))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 94) (:start . 89)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 100) (:start . 95)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 117)\n  (:start . 108) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x10.251.1) (:span 6 9)))\n (:hscopes ((:id . :x10.251.1) (:span 6 117)))\n (:identifiers (:sid . :s10.251) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503364@unknown@formal@none@1@S@It is also likely that dorsally and centrally located sensory and interneuron terminals, as well as dendrites of motor neurons may require additional signals to exclude them from ventral neuropile.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 17)\n  (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "RB") (:stem . "centrally") (:form . "centrally") (:end . 45)\n  (:start . 36) (:id . 49))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "interneuron") (:form . "interneuron") (:end . 77)\n  (:start . 66) (:id . 53))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 87)\n  (:start . 78) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 109)\n  (:start . 100) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 118)\n  (:start . 113) (:id . 61))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 126)\n  (:start . 119) (:id . 62))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "VB") (:stem . "require") (:form . "require") (:end . 138)\n  (:start . 131) (:id . 64))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 149)\n  (:start . 139) (:id . 65))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 157)\n  (:start . 150) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 160) (:start . 158)\n  (:id . 67))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 168)\n  (:start . 161) (:id . 68))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 173) (:start . 169)\n  (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 178) (:start . 174)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 186)\n  (:start . 179) (:id . 71))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 196)\n  (:start . 187) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x10.252.1) (:span 127 130))\n  ((:id . :x10.252.2) (:span 11 17)))\n (:hscopes ((:id . :x10.252.1) (:span 127 196))\n  ((:id . :x10.252.2) (:span 11 196)))\n (:identifiers (:sid . :s10.252) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503365@unknown@formal@none@1@S@Such signals could be the other Semas.@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Semas") (:form . "Semas") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 38) (:start . 37)\n  (:id . 49)))@@@1@8@((:hcues ((:id . :x10.253.1) (:span 13 18)))\n (:hscopes ((:id . :x10.253.1) (:span 13 37)))\n (:identifiers (:sid . :s10.253) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503366@unknown@formal@none@1@S@Alternatively, by analogy with the optic tectum, where Wnt signalling drives dorsal projections and Ephrins dictate ventral projections, it is possible that some other signalling system may operate with Semas to confine dorsally projecting neurons to dorsal neuropile [3],[40],[41].@(((:tag . "RB") (:stem . "alternatively") (:form . "Alternatively")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "analogy") (:form . "analogy") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "optic") (:form . "optic") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "tectum") (:form . "tectum") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Wnt") (:form . "Wnt") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "signalling") (:form . "signalling") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . "VBZ") (:stem . "drive") (:form . "drives") (:end . 76)\n  (:start . 70) (:id . 54))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 83)\n  (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 95)\n  (:start . 84) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "ephrin") (:form . "Ephrins") (:end . 107)\n  (:start . 100) (:id . 58))\n ((:tag . "VBP") (:stem . "dictate") (:form . "dictate") (:end . 115)\n  (:start . 108) (:id . 59))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 123)\n  (:start . 116) (:id . 60))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 135)\n  (:start . 124) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 62))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 139) (:start . 137)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 151)\n  (:start . 143) (:id . 65))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 156) (:start . 152)\n  (:id . 66))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 161) (:start . 157)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 167)\n  (:start . 162) (:id . 68))\n ((:tag . "NN") (:stem . "signalling") (:form . "signalling") (:end . 178)\n  (:start . 168) (:id . 69))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 185)\n  (:start . 179) (:id . 70))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 189) (:start . 186)\n  (:id . 71))\n ((:tag . "VB") (:stem . "operate") (:form . "operate") (:end . 197)\n  (:start . 190) (:id . 72))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 202) (:start . 198)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Semas") (:form . "Semas") (:end . 208)\n  (:start . 203) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 211) (:start . 209)\n  (:id . 75))\n ((:tag . "VB") (:stem . "confine") (:form . "confine") (:end . 219)\n  (:start . 212) (:id . 76))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 228)\n  (:start . 220) (:id . 77))\n ((:tag . "VBG") (:stem . "project") (:form . "projecting") (:end . 239)\n  (:start . 229) (:id . 78))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 247)\n  (:start . 240) (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 250) (:start . 248)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 257)\n  (:start . 251) (:id . 81))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 267)\n  (:start . 258) (:id . 82))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 269) (:start . 268)\n  (:id . 83))\n ((:tag . "CD") (:stem . "3],[40],[41") (:form . "3],[40],[41") (:end . 280)\n  (:start . 269) (:id . 84))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 281) (:start . 280)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 282) (:start . 281)\n  (:id . 86)))@@@1@45@((:hcues ((:id . :x10.254.1) (:span 186 189))\n  ((:id . :x10.254.2) (:span 143 151)))\n (:hscopes ((:id . :x10.254.1) (:span 186 267))\n  ((:id . :x10.254.2) (:span 143 267)))\n (:identifiers (:sid . :s10.254) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503367@unknown@formal@none@1@S@Type-Specific Repulsion in the VNC@(((:tag . "JJ") (:stem . "type-specific") (:form . "Type-Specific")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "repulsion") (:form . "Repulsion") (:end . 23)\n  (:start . 14) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 34) (:start . 31)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s10.255) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503368@unknown@formal@none@1@S@In the fly antennal lobe, during the formation of the olfactory map, Sema 1a expression on the surfaces of antennal olfactory receptor neuron (ORN) axons excludes Plex A expressing maxillary palp ORN axons from inappropriate glomeruli [22],[23].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "fly") (:form . "fly") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "antennal") (:form . "antennal") (:end . 19)\n  (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "lobe") (:form . "lobe") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 32)\n  (:start . 26) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 46)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "olfactory") (:form . "olfactory") (:end . 63)\n  (:start . 54) (:id . 53))\n ((:tag . "NN") (:stem . "map") (:form . "map") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 73) (:start . 69)\n  (:id . 56))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 76) (:start . 74)\n  (:id . 57))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 87)\n  (:start . 77) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "surface") (:form . "surfaces") (:end . 103)\n  (:start . 95) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "antennal") (:form . "antennal") (:end . 115)\n  (:start . 107) (:id . 63))\n ((:tag . "JJ") (:stem . "olfactory") (:form . "olfactory") (:end . 125)\n  (:start . 116) (:id . 64))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 134)\n  (:start . 126) (:id . 65))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 141)\n  (:start . 135) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "ORN") (:form . "ORN") (:end . 146) (:start . 143)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 153)\n  (:start . 148) (:id . 70))\n ((:tag . "VBZ") (:stem . "exclude") (:form . "excludes") (:end . 162)\n  (:start . 154) (:id . 71))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 167) (:start . 163)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 169) (:start . 168)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 180)\n  (:start . 170) (:id . 74))\n ((:tag . "JJ") (:stem . "maxillary") (:form . "maxillary") (:end . 190)\n  (:start . 181) (:id . 75))\n ((:tag . "NN") (:stem . "palp") (:form . "palp") (:end . 195) (:start . 191)\n  (:id . 76))\n ((:tag . "NN") (:stem . "orn") (:form . "ORN") (:end . 199) (:start . 196)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 205)\n  (:start . 200) (:id . 78))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 210) (:start . 206)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "inappropriate") (:form . "inappropriate")\n  (:end . 224) (:start . 211) (:id . 80))\n ((:tag . "NNS") (:stem . "glomerulus") (:form . "glomeruli") (:end . 234)\n  (:start . 225) (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 236) (:start . 235)\n  (:id . 82))\n ((:tag . "CD") (:stem . "22],[23") (:form . "22],[23") (:end . 243)\n  (:start . 236) (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 244) (:start . 243)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 245) (:start . 244)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s10.256) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503369@unknown@formal@none@1@S@Our findings suggest that much of the Sema 1a expression in the neuropile of the VNC is on the surfaces of motor neuron dendrites and on the projections of the GABAergic interneurons.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "much") (:form . "much") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 56)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 73)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "surface") (:form . "surfaces") (:end . 103)\n  (:start . 95) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 112)\n  (:start . 107) (:id . 63))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 119)\n  (:start . 113) (:id . 64))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 129)\n  (:start . 120) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 136) (:start . 134)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 152)\n  (:start . 141) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "gabaergic") (:form . "GABAergic") (:end . 169)\n  (:start . 160) (:id . 72))\n ((:tag . "NNS") (:stem . "interneuron") (:form . "interneurons") (:end . 182)\n  (:start . 170) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x10.257.1) (:span 13 20)))\n (:hscopes ((:id . :x10.257.1) (:span 13 182)))\n (:identifiers (:sid . :s10.257) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503370@unknown@formal@none@1@S@Thus, there appear to be two kinds of positional cues in the neuropile.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "kind") (:form . "kinds") (:end . 34) (:start . 29)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 48)\n  (:start . 38) (:id . 51))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 70)\n  (:start . 61) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x10.258.1) (:span 12 18)))\n (:hscopes ((:id . :x10.258.1) (:span 12 70)))\n (:identifiers (:sid . :s10.258) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503371@unknown@formal@none@1@S@Slit and Sema 2a are examples of secreted and possibly glia-mediated positional cues.@(((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "2a") (:form . "2a") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "secrete") (:form . "secreted") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "RB") (:stem . "possibly") (:form . "possibly") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . "JJ") (:stem . "glia-mediated") (:form . "glia-mediated")\n  (:end . 68) (:start . 55) (:id . 52))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 79)\n  (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 84) (:start . 80)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n  (:id . 55)))@@@1@14@((:hcues ((:id . :x10.259.1) (:span 46 54)))\n (:hscopes ((:id . :x10.259.1) (:span 46 68)))\n (:identifiers (:sid . :s10.259) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503372@unknown@formal@none@1@S@Sema 1a on the other hand is presented on membranes of particular neuronal classes (GABAergic interneurons and motorneurons) and is a repellent for the axons of at least one other type of neuron (class IV md neurons).@(((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 20) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "hand") (:form . "hand") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 38)\n  (:start . 29) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "membrane") (:form . "membranes") (:end . 51)\n  (:start . 42) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 65)\n  (:start . 55) (:id . 53))\n ((:tag . "JJ") (:stem . "neuronal") (:form . "neuronal") (:end . 74)\n  (:start . 66) (:id . 54))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 82)\n  (:start . 75) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "gabaergic") (:form . "GABAergic") (:end . 93)\n  (:start . 84) (:id . 57))\n ((:tag . "NNS") (:stem . "interneuron") (:form . "interneurons") (:end . 106)\n  (:start . 94) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "motorneuron") (:form . "motorneurons") (:end . 123)\n  (:start . 111) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 131) (:start . 129)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "NN") (:stem . "repellent") (:form . "repellent") (:end . 143)\n  (:start . 134) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 147) (:start . 144)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 157)\n  (:start . 152) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n  (:id . 69))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 163) (:start . 161)\n  (:id . 70))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 169)\n  (:start . 164) (:id . 71))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 173) (:start . 170)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 179)\n  (:start . 174) (:id . 73))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 184) (:start . 180)\n  (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n  (:id . 75))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 194)\n  (:start . 188) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 196) (:start . 195)\n  (:id . 77))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 201)\n  (:start . 196) (:id . 78))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 204) (:start . 202)\n  (:id . 79))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 207) (:start . 205)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 215)\n  (:start . 208) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 216) (:start . 215)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s10.260) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503373@unknown@formal@none@1@S@Thus, the presentation of repellent molecules on the surfaces of subsets of neurons can act to exclude specific classes of axons from particular regions of the neuropile.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "presentation") (:form . "presentation") (:end . 22)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "repellent") (:form . "repellent") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "molecule") (:form . "molecules") (:end . 45)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "surface") (:form . "surfaces") (:end . 61)\n  (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "subset") (:form . "subsets") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 83)\n  (:start . 76) (:id . 55))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 91) (:start . 88)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 102)\n  (:start . 95) (:id . 59))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 111)\n  (:start . 103) (:id . 60))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 119)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 128)\n  (:start . 123) (:id . 63))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 133) (:start . 129)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 144)\n  (:start . 134) (:id . 65))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 152)\n  (:start . 145) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 68))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 169)\n  (:start . 160) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x10.261.1) (:span 84 87)))\n (:hscopes ((:id . :x10.261.1) (:span 84 169)))\n (:identifiers (:sid . :s10.261) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503374@unknown@formal@none@1@S@Positional Cues Subdivide the Neuropile into Different Termination Domains within Which Connections Form@(((:tag . "JJ") (:stem . "positional") (:form . "Positional") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "cue") (:form . "Cues") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "subdivide") (:form . "Subdivide") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "neuropile") (:form . "Neuropile") (:end . 39)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 44) (:start . 40)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "different") (:form . "Different") (:end . 54)\n  (:start . 45) (:id . 48))\n ((:tag . "NN") (:stem . "termination") (:form . "Termination") (:end . 66)\n  (:start . 55) (:id . 49))\n ((:tag . "NNS") (:stem . "domain") (:form . "Domains") (:end . 74)\n  (:start . 67) (:id . 50))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 81)\n  (:start . 75) (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "Which") (:end . 87) (:start . 82)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Connection") (:form . "Connections") (:end . 99)\n  (:start . 88) (:id . 53))\n ((:tag . "VBP") (:stem . "form") (:form . "Form") (:end . 104) (:start . 100)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s10.262) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503375@unknown@formal@none@1@S@Theoretical models for gradient-guided axonal growth and targeting during the formation of 2-D neural maps, such as the retinotopic projections, require at least one gradient in each of the two—not necessarily Cartesian—dimensions [42].@(((:tag . "JJ") (:stem . "theoretical") (:form . "Theoretical") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 18)\n  (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "gradient-guided") (:form . "gradient-guided")\n  (:end . 38) (:start . 23) (:id . 45))\n ((:tag . "JJ") (:stem . "axonal") (:form . "axonal") (:end . 45)\n  (:start . 39) (:id . 46))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 52)\n  (:start . 46) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "target") (:form . "targeting") (:end . 66)\n  (:start . 57) (:id . 49))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 73)\n  (:start . 67) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 51))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 87)\n  (:start . 78) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 53))\n ((:tag . "NN") (:stem . "2-d") (:form . "2-D") (:end . 94) (:start . 91)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 101)\n  (:start . 95) (:id . 55))\n ((:tag . "NNS") (:stem . "map") (:form . "maps") (:end . 106) (:start . 102)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 112) (:start . 108)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 115) (:start . 113)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "retinotopic") (:form . "retinotopic") (:end . 131)\n  (:start . 120) (:id . 61))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 143)\n  (:start . 132) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 152)\n  (:start . 145) (:id . 64))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 155) (:start . 153)\n  (:id . 65))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 161)\n  (:start . 156) (:id . 66))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 165) (:start . 162)\n  (:id . 67))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 174)\n  (:start . 166) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 177) (:start . 175)\n  (:id . 69))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 182) (:start . 178)\n  (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 185) (:start . 183)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 189) (:start . 186)\n  (:id . 72))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 193) (:start . 190)\n  (:id . 73))\n ((:tag . "NN") (:stem . "—") (:form . "—") (:end . 194) (:start . 193)\n  (:id . 74))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 197) (:start . 194)\n  (:id . 75))\n ((:tag . "RB") (:stem . "necessarily") (:form . "necessarily") (:end . 209)\n  (:start . 198) (:id . 76))\n ((:tag . "JJ") (:stem . "Cartesian") (:form . "Cartesian") (:end . 219)\n  (:start . 210) (:id . 77))\n ((:tag . "JJ") (:stem . "—") (:form . "—") (:end . 220) (:start . 219)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "dimensions") (:form . "dimensions") (:end . 230)\n  (:start . 220) (:id . 79))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 232) (:start . 231)\n  (:id . 80))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 234) (:start . 232)\n  (:id . 81))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 235) (:start . 234)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 236) (:start . 235)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s10.263) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503376@unknown@formal@none@1@S@These ideas have been borne out by experimental findings.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "idea") (:form . "ideas") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "bear") (:form . "borne") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 47)\n  (:start . 35) (:id . 49))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s10.264) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503377@unknown@formal@none@1@S@Gradients of attractants and repellents in one dimension have been implicated in providing positional information for terminating sensory axons during the formation of both continuous and discrete neural maps [18],[43],[44].@(((:tag . "NNS") (:stem . "gradient") (:form . "Gradients") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "attractant") (:form . "attractants") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "repellent") (:form . "repellents") (:end . 39)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "dimension") (:form . "dimension") (:end . 56)\n  (:start . 47) (:id . 49))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 61) (:start . 57)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 77)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "provide") (:form . "providing") (:end . 90)\n  (:start . 81) (:id . 54))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 101)\n  (:start . 91) (:id . 55))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 113)\n  (:start . 102) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 117) (:start . 114)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "terminate") (:form . "terminating") (:end . 129)\n  (:start . 118) (:id . 58))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 137)\n  (:start . 130) (:id . 59))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 143)\n  (:start . 138) (:id . 60))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 150)\n  (:start . 144) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 62))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 164)\n  (:start . 155) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 167) (:start . 165)\n  (:id . 64))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 172) (:start . 168)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "continuous") (:form . "continuous") (:end . 183)\n  (:start . 173) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 187) (:start . 184)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "discrete") (:form . "discrete") (:end . 196)\n  (:start . 188) (:id . 68))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 203)\n  (:start . 197) (:id . 69))\n ((:tag . "NNS") (:stem . "map") (:form . "maps") (:end . 208) (:start . 204)\n  (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 210) (:start . 209)\n  (:id . 71))\n ((:tag . "CD") (:stem . "18],[43],[44") (:form . "18],[43],[44") (:end . 222)\n  (:start . 210) (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 223) (:start . 222)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s10.265) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503378@unknown@formal@none@1@S@Furthermore, a recent study has shown that two orthogonal systems of graded cues operate to specify position of termination along each axis of a somatotopic map in the optic tectum.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "orthogonal") (:form . "orthogonal") (:end . 57)\n  (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "grade") (:form . "graded") (:end . 75)\n  (:start . 69) (:id . 54))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "operate") (:form . "operate") (:end . 88)\n  (:start . 81) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "VB") (:stem . "specify") (:form . "specify") (:end . 99)\n  (:start . 92) (:id . 58))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 108)\n  (:start . 100) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 123)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 129)\n  (:start . 124) (:id . 62))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 134) (:start . 130)\n  (:id . 63))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 139) (:start . 135)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 144) (:start . 143)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "somatotopic") (:form . "somatotopic") (:end . 156)\n  (:start . 145) (:id . 67))\n ((:tag . "NN") (:stem . "map") (:form . "map") (:end . 160) (:start . 157)\n  (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 163) (:start . 161)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "optic") (:form . "optic") (:end . 173)\n  (:start . 168) (:id . 71))\n ((:tag . "NN") (:stem . "tectum") (:form . "tectum") (:end . 180)\n  (:start . 174) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s10.266) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503379@unknown@formal@none@1@S@Our findings address the larger issue of how termination of distinct neuron classes is regulated within a complex meshwork of differentiating axons and dendrites.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "finding") (:form . "findings") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "address") (:form . "address") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "issue") (:form . "issue") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 56)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 68)\n  (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 75)\n  (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 83)\n  (:start . 76) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 96)\n  (:start . 87) (:id . 56))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 103)\n  (:start . 97) (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 113)\n  (:start . 106) (:id . 59))\n ((:tag . "NN") (:stem . "meshwork") (:form . "meshwork") (:end . 122)\n  (:start . 114) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "differentiate") (:form . "differentiating")\n  (:end . 141) (:start . 126) (:id . 62))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 147)\n  (:start . 142) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 151) (:start . 148)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 161)\n  (:start . 152) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.267) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503380@unknown@formal@none@1@S@They suggest that similar mechanisms that are used for the establishment of neural maps, only involving generalized positional cues in each dimension, control targeting of many different classes of neurons to specific termination domains within a complex neuropile.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 36)\n  (:start . 26) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "establishment") (:form . "establishment")\n  (:end . 72) (:start . 59) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "neural") (:form . "neural") (:end . 82)\n  (:start . 76) (:id . 54))\n ((:tag . "NNS") (:stem . "map") (:form . "maps") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 93) (:start . 89)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "involve") (:form . "involving") (:end . 103)\n  (:start . 94) (:id . 58))\n ((:tag . "VBN") (:stem . "generalize") (:form . "generalized") (:end . 115)\n  (:start . 104) (:id . 59))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 126)\n  (:start . 116) (:id . 60))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 131) (:start . 127)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n  (:id . 62))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 139) (:start . 135)\n  (:id . 63))\n ((:tag . "NN") (:stem . "dimension") (:form . "dimension") (:end . 149)\n  (:start . 140) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "control") (:form . "control") (:end . 158)\n  (:start . 151) (:id . 66))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 168)\n  (:start . 159) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 176) (:start . 172)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 186)\n  (:start . 177) (:id . 70))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 194)\n  (:start . 187) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 197) (:start . 195)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 205)\n  (:start . 198) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 208) (:start . 206)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 217)\n  (:start . 209) (:id . 75))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 229)\n  (:start . 218) (:id . 76))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 237)\n  (:start . 230) (:id . 77))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 244)\n  (:start . 238) (:id . 78))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 246) (:start . 245)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 254)\n  (:start . 247) (:id . 80))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 264)\n  (:start . 255) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x10.268.1) (:span 5 12)))\n (:hscopes ((:id . :x10.268.1) (:span 5 264)))\n (:identifiers (:sid . :s10.268) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503381@unknown@formal@none@1@S@Although the evidence we provide here suggests that positional cues can specify particular domains for the termination of sensory neurons, we do not suppose that the control of termination and branching by a pervasive system of positional cues would necessarily be sufficient to allow connections to form selectively and specifically between appropriate pre- and postsynaptic partners.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . 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5503382@unknown@formal@none@1@S@What such a system does provide is a framework of signals that could regulate simultaneously the growth of axons and dendrites of many different neurons and induce their termination and branching in appropriate parts of the developing network.@(((:tag . "WP") (:stem . "what") (:form . "What") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "PDT") (:stem . "such") (:form . "such") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 46)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "VB") (:stem . "regulate") (:form . "regulate") (:end . 77)\n  (:start . 69) (:id . 55))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n  (:end . 92) (:start . 78) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 112)\n  (:start . 107) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 126)\n  (:start . 117) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 134) (:start . 130)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 144)\n  (:start . 135) (:id . 65))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 152)\n  (:start . 145) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 67))\n ((:tag . "VBP") (:stem . "induce") (:form . "induce") (:end . 163)\n  (:start . 157) (:id . 68))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 169)\n  (:start . 164) (:id . 69))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 181)\n  (:start . 170) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n  (:id . 71))\n ((:tag . "NN") (:stem . "branching") (:form . "branching") (:end . 195)\n  (:start . 186) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 198) (:start . 196)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 210)\n  (:start . 199) (:id . 74))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 216)\n  (:start . 211) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 219) (:start . 217)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 223) (:start . 220)\n  (:id . 77))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 234)\n  (:start . 224) (:id . 78))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 242)\n  (:start . 235) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x10.270.1) (:span 63 68)))\n (:hscopes ((:id . :x10.270.1) (:span 63 242)))\n (:identifiers (:sid . :s10.270) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503383@unknown@formal@none@1@S@Within these restricted regions it is likely that further, localised mechanisms, including competitive interactions, patterns of activity, and target derived cues might all be required to control synaptogenesis and determine the emergence of precise patterns of connectivity within a termination domain.@(((:tag . "IN") (:stem . "within") (:form . "Within") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "restricted") (:form . "restricted") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 31)\n  (:start . 24) (:id . 45))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "likely") (:form . 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(:end . 303) (:start . 302)\n  (:id . 87)))@@@1@46@((:hcues ((:id . :x10.271.1) (:span 163 168))\n  ((:id . :x10.271.2) (:span 38 44)))\n (:hscopes ((:id . :x10.271.1) (:span 50 302))\n  ((:id . :x10.271.2) (:span 38 302)))\n (:identifiers (:sid . :s10.271) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503384@unknown@formal@none@1@S@Coordinate Positioning of Pre- and Postsynaptic Terminals by the Same Cues?@(((:tag . "NNP") (:stem . "Coordinate") (:form . "Coordinate") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Positioning") (:form . "Positioning") (:end . 22)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Pre-") (:form . "Pre-") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "Postsynaptic") (:end . 47)\n  (:start . 35) (:id . 47))\n ((:tag . "NNS") (:stem . "terminal") (:form . "Terminals") (:end . 57)\n  (:start . 48) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 60) (:start . 58)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Same") (:form . "Same") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . "NNPS") (:stem . "Cue") (:form . "Cues") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 75) (:start . 74)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s10.272) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503385@unknown@formal@none@1@S@If the pattern of sensory axon termination within the neuropile is controlled by a system of positional cues, most likely, in three dimensions, it may well be that the location of their postsynaptic dendrites is determined in a similar fashion.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 42)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 63)\n  (:start . 54) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "control") (:form . "controlled") (:end . 77)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 89)\n  (:start . 83) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 103)\n  (:start . 93) (:id . 58))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 60))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 114) (:start . 110)\n  (:id . 61))\n ((:tag . "RB") (:stem . "likely") (:form . "likely") (:end . 121)\n  (:start . 115) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 125) (:start . 123)\n  (:id . 64))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 131)\n  (:start . 126) (:id . 65))\n ((:tag . "NNS") (:stem . "dimension") (:form . "dimensions") (:end . 142)\n  (:start . 132) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 146) (:start . 144)\n  (:id . 68))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 150) (:start . 147)\n  (:id . 69))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 155) (:start . 151)\n  (:id . 70))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 158) (:start . 156)\n  (:id . 71))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 163) (:start . 159)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 73))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 176)\n  (:start . 168) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 179) (:start . 177)\n  (:id . 75))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 185)\n  (:start . 180) (:id . 76))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 198)\n  (:start . 186) (:id . 77))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 208)\n  (:start . 199) (:id . 78))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 211) (:start . 209)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 222)\n  (:start . 212) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 225) (:start . 223)\n  (:id . 81))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 227) (:start . 226)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 235)\n  (:start . 228) (:id . 83))\n ((:tag . "NN") (:stem . "fashion") (:form . "fashion") (:end . 243)\n  (:start . 236) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x10.273.1) (:span 147 150))\n  ((:id . :x10.273.2) (:span 115 121)))\n (:hscopes ((:id . :x10.273.1) (:span 147 243))\n  ((:id . :x10.273.2) (:span 110 142)))\n (:identifiers (:sid . :s10.273) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503386@unknown@formal@none@1@S@If this were the case, the matched expression of receptors for the same system of signals by pre- and postsynaptic neurites would guide them to a common volume as a prelude to the formation of synaptic connections between them.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "match") (:form . "matched") (:end . 34)\n  (:start . 27) (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 45)\n  (:start . 35) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 58)\n  (:start . 49) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 71) (:start . 67)\n  (:id . 55))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 78)\n  (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 89)\n  (:start . 82) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "pre-") (:form . "pre-") (:end . 97) (:start . 93)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 114)\n  (:start . 102) (:id . 62))\n ((:tag . "NNS") (:stem . "neurite") (:form . "neurites") (:end . 123)\n  (:start . 115) (:id . 63))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 129)\n  (:start . 124) (:id . 64))\n ((:tag . "VB") (:stem . "guide") (:form . "guide") (:end . 135)\n  (:start . 130) (:id . 65))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 140) (:start . 136)\n  (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 145) (:start . 144)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 152)\n  (:start . 146) (:id . 69))\n ((:tag . "NN") (:stem . "volume") (:form . "volume") (:end . 159)\n  (:start . 153) (:id . 70))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 162) (:start . 160)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 164) (:start . 163)\n  (:id . 72))\n ((:tag . "NN") (:stem . "prelude") (:form . "prelude") (:end . 172)\n  (:start . 165) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 175) (:start . 173)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 75))\n ((:tag . "NN") (:stem . "formation") (:form . "formation") (:end . 189)\n  (:start . 180) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 192) (:start . 190)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "synaptic") (:form . "synaptic") (:end . 201)\n  (:start . 193) (:id . 78))\n ((:tag . "NNS") (:stem . "connection") (:form . "connections") (:end . 213)\n  (:start . 202) (:id . 79))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 221)\n  (:start . 214) (:id . 80))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 226) (:start . 222)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s10.274) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503387@unknown@formal@none@1@S@Recent studies that show that developing motor neuron dendrites respond to some of the same cues as terminating sensory axons provide indirect evidence for common systems of positional cues leading to the coordinate targeting of presynaptic axons and postsynaptic dendrites [45],[46].@(((:tag . "JJ") (:stem . "recent") (:form . "Recent") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "JJ") (:stem . "motor") (:form . "motor") (:end . 46) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 63)\n  (:start . 54) (:id . 50))\n ((:tag . "VBP") (:stem . "respond") (:form . "respond") (:end . 71)\n  (:start . 64) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 79) (:start . 75)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "terminate") (:form . "terminating") (:end . 111)\n  (:start . 100) (:id . 59))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 119)\n  (:start . 112) (:id . 60))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 125)\n  (:start . 120) (:id . 61))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 133)\n  (:start . 126) (:id . 62))\n ((:tag . "JJ") (:stem . "indirect") (:form . "indirect") (:end . 142)\n  (:start . 134) (:id . 63))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 151)\n  (:start . 143) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 155) (:start . 152)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 162)\n  (:start . 156) (:id . 66))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 170)\n  (:start . 163) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 184)\n  (:start . 174) (:id . 69))\n ((:tag . "NNS") (:stem . "cue") (:form . "cues") (:end . 189) (:start . 185)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "lead") (:form . "leading") (:end . 197)\n  (:start . 190) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 200) (:start . 198)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 204) (:start . 201)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "coordinate") (:form . "coordinate") (:end . 215)\n  (:start . 205) (:id . 74))\n ((:tag . "NN") (:stem . "targeting") (:form . "targeting") (:end . 225)\n  (:start . 216) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 228) (:start . 226)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "presynaptic") (:form . "presynaptic") (:end . 240)\n  (:start . 229) (:id . 77))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 246)\n  (:start . 241) (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 250) (:start . 247)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 263)\n  (:start . 251) (:id . 80))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 273)\n  (:start . 264) (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 275) (:start . 274)\n  (:id . 82))\n ((:tag . "CD") (:stem . "45],[46") (:form . "45],[46") (:end . 282)\n  (:start . 275) (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 283) (:start . 282)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 284) (:start . 283)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s10.275) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503388@unknown@formal@none@1@S@A direct test of this hypothesis, however, must await the identification of the postsynaptic interneurons with which developing sensory neurons form connections.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 32)\n  (:start . 22) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "VB") (:stem . "await") (:form . "await") (:end . 53) (:start . 48)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 72) (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 92)\n  (:start . 80) (:id . 57))\n ((:tag . "NNS") (:stem . "interneuron") (:form . "interneurons") (:end . 105)\n  (:start . 93) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 110) (:start . 106)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 116)\n  (:start . 111) (:id . 60))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 127)\n  (:start . 117) (:id . 61))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 135)\n  (:start . 128) (:id . 62))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 143)\n  (:start . 136) (:id . 63))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 148) (:start . 144)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "connection") (:form . "connections") (:end . 160)\n  (:start . 149) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.276) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503389@unknown@formal@none@1@S@It will then be possible to make a direct investigation of the molecular mechanisms that control the termination and branching of pre- and postsynaptic endings and thereby lay out a ground plan for connectivity within the developing neuropile.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VB") (:stem . "make") (:form . "make") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 41)\n  (:start . 35) (:id . 50))\n ((:tag . "NN") (:stem . "investigation") (:form . "investigation")\n  (:end . 55) (:start . 42) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 72)\n  (:start . 63) (:id . 54))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 83)\n  (:start . 73) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "control") (:form . "control") (:end . 96)\n  (:start . 89) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 112)\n  (:start . 101) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "NN") (:stem . "branching") (:form . "branching") (:end . 126)\n  (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "pre-") (:form . "pre-") (:end . 134) (:start . 130)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "postsynaptic") (:form . "postsynaptic") (:end . 151)\n  (:start . 139) (:id . 65))\n ((:tag . "NNS") (:stem . "ending") (:form . "endings") (:end . 159)\n  (:start . 152) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 163) (:start . 160)\n  (:id . 67))\n ((:tag . "RB") (:stem . "thereby") (:form . "thereby") (:end . 171)\n  (:start . 164) (:id . 68))\n ((:tag . "VBD") (:stem . "lie") (:form . "lay") (:end . 175) (:start . 172)\n  (:id . 69))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 179) (:start . 176)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 181) (:start . 180)\n  (:id . 71))\n ((:tag . "NN") (:stem . "ground") (:form . "ground") (:end . 188)\n  (:start . 182) (:id . 72))\n ((:tag . "NN") (:stem . "plan") (:form . "plan") (:end . 193) (:start . 189)\n  (:id . 73))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 197) (:start . 194)\n  (:id . 74))\n ((:tag . "NN") (:stem . "connectivity") (:form . "connectivity") (:end . 210)\n  (:start . 198) (:id . 75))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 217)\n  (:start . 211) (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 221) (:start . 218)\n  (:id . 77))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 232)\n  (:start . 222) (:id . 78))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 242)\n  (:start . 233) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x10.277.1) (:span 16 24)))\n (:hscopes ((:id . :x10.277.1) (:span 16 242)))\n (:identifiers (:sid . :s10.277) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503390@unknown@formal@none@1@S@Materials and Methods@(((:tag . "NNPS") (:stem . "Material") (:form . "Materials") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 21)\n  (:start . 14) (:id . 44)))@@@1@3@((:identifiers (:sid . :s10.278) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503391@unknown@formal@none@1@S@Fly Stocks@(((:tag . "RB") (:stem . "fly") (:form . "Fly") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "stock") (:form . "Stocks") (:end . 10) (:start . 4)\n  (:id . 43)))@@@1@2@((:identifiers (:sid . :s10.279) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503392@unknown@formal@none@1@S@For mutant analyses sema 2a03021 [25], sema 1aP1 [26], plex ADf(4)C3 [47], and plex BKG00878 [21],[48] were crossed into the ppkEGFP [9] stock.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "CD") (:stem . "2a03021") (:form . "2a03021") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 43) (:start . 39)\n  (:id . 51))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 48) (:start . 44)\n  (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 50) (:start . 49)\n  (:id . 53))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 52) (:start . 50)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 53) (:start . 52)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 56))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 59) (:start . 55)\n  (:id . 57))\n ((:tag . "NN") (:stem . "ADf(4)C3") (:form . "ADf(4)C3") (:end . 68)\n  (:start . 60) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 70) (:start . 69)\n  (:id . 59))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 72) (:start . 70)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 73) (:start . 72)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 63))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 83) (:start . 79)\n  (:id . 64))\n ((:tag . "NN") (:stem . "bkg00878") (:form . "BKG00878") (:end . 92)\n  (:start . 84) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 94) (:start . 93)\n  (:id . 66))\n ((:tag . "CD") (:stem . "21],[48") (:form . "21],[48") (:end . 101)\n  (:start . 94) (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 102) (:start . 101)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 107) (:start . 103)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "cross") (:form . "crossed") (:end . 115)\n  (:start . 108) (:id . 70))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 120) (:start . 116)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n  (:id . 72))\n ((:tag . "NN") (:stem . "ppkegfp") (:form . "ppkEGFP") (:end . 132)\n  (:start . 125) (:id . 73))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 134) (:start . 133)\n  (:id . 74))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 135) (:start . 134)\n  (:id . 75))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 136) (:start . 135)\n  (:id . 76))\n ((:tag . "NN") (:stem . "stock") (:form . "stock") (:end . 142)\n  (:start . 137) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s10.280) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503393@unknown@formal@none@1@S@Stocks were made using GFP balancers [49].@(((:tag . "NNS") (:stem . "stock") (:form . "Stocks") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "balancer") (:form . "balancers") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "CD") (:stem . "49") (:form . "49") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s10.281) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503394@unknown@formal@none@1@S@Homozygous mutant embryos were identified by lack of GFP.@(((:tag . "JJ") (:stem . "homozygous") (:form . "Homozygous") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 17)\n  (:start . 11) (:id . 43))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 25)\n  (:start . 18) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 41)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 57) (:start . 56)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s10.282) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503395@unknown@formal@none@1@S@For misexpression we used the following stocks: UAS-robo3 [50],[51] inserts on second and third chromosome, UAS-plexB [21] and UAS-plexA-HA [47], UAS-robo2 [51], UAS-ephrin [52],[53], UAS-eph [52], UAS-unc5 [54], UAS-frazzled [55], UAS-drl-DN [56], UAS-comm [57], UAS-robo, 410 EP-lines from the Rorth collection [58],[59].@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "misexpression") (:form . "misexpression")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 20) (:start . 18)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "stock") (:form . "stocks") (:end . 46)\n  (:start . 40) (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "uas-robo3") (:form . "UAS-robo3") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 59) (:start . 58)\n  (:id . 51))\n ((:tag . "CD") (:stem . "50],[51") (:form . "50],[51") (:end . 66)\n  (:start . 59) (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "insert") (:form . "inserts") (:end . 75)\n  (:start . 68) (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 85)\n  (:start . 79) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 95) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "chromosome") (:form . "chromosome") (:end . 106)\n  (:start . 96) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "UAS-plexB") (:form . "UAS-plexB") (:end . 117)\n  (:start . 108) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 119) (:start . 118)\n  (:id . 62))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 121) (:start . 119)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 122) (:start . 121)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "UAS-plexA-HA") (:form . "UAS-plexA-HA")\n  (:end . 139) (:start . 127) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 141) (:start . 140)\n  (:id . 67))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 143) (:start . 141)\n  (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 144) (:start . 143)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "UAS-robo2") (:form . "UAS-robo2") (:end . 155)\n  (:start . 146) (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 157) (:start . 156)\n  (:id . 72))\n ((:tag . "CD") (:stem . "51") (:form . "51") (:end . 159) (:start . 157)\n  (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 160) (:start . 159)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "UAS-ephrin") (:form . "UAS-ephrin") (:end . 172)\n  (:start . 162) (:id . 76))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 174) (:start . 173)\n  (:id . 77))\n ((:tag . "CD") (:stem . "52],[53") (:form . "52],[53") (:end . 181)\n  (:start . 174) (:id . 78))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 182) (:start . 181)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "UAS-eph") (:form . "UAS-eph") (:end . 191)\n  (:start . 184) (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 193) (:start . 192)\n  (:id . 82))\n ((:tag . "CD") (:stem . "52") (:form . "52") (:end . 195) (:start . 193)\n  (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 196) (:start . 195)\n  (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 197) (:start . 196)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "UAS-unc5") (:form . "UAS-unc5") (:end . 206)\n  (:start . 198) (:id . 86))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 208) (:start . 207)\n  (:id . 87))\n ((:tag . "CD") (:stem . "54") (:form . "54") (:end . 210) (:start . 208)\n  (:id . 88))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 211) (:start . 210)\n  (:id . 89))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 212) (:start . 211)\n  (:id . 90))\n ((:tag . "JJ") (:stem . "uas-frazzled") (:form . "UAS-frazzled") (:end . 225)\n  (:start . 213) (:id . 91))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 227) (:start . 226)\n  (:id . 92))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 229) (:start . 227)\n  (:id . 93))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 230) (:start . 229)\n  (:id . 94))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 231) (:start . 230)\n  (:id . 95))\n ((:tag . "NNP") (:stem . "UAS-drl-DN") (:form . "UAS-drl-DN") (:end . 242)\n  (:start . 232) (:id . 96))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 244) (:start . 243)\n  (:id . 97))\n ((:tag . "CD") (:stem . "56") (:form . "56") (:end . 246) (:start . 244)\n  (:id . 98))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 247) (:start . 246)\n  (:id . 99))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 248) (:start . 247)\n  (:id . 100))\n ((:tag . "NNP") (:stem . "UAS-comm") (:form . "UAS-comm") (:end . 257)\n  (:start . 249) (:id . 101))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 259) (:start . 258)\n  (:id . 102))\n ((:tag . "CD") (:stem . "57") (:form . "57") (:end . 261) (:start . 259)\n  (:id . 103))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 262) (:start . 261)\n  (:id . 104))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 263) (:start . 262)\n  (:id . 105))\n ((:tag . "NNP") (:stem . "UAS-robo") (:form . "UAS-robo") (:end . 272)\n  (:start . 264) (:id . 106))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 273) (:start . 272)\n  (:id . 107))\n ((:tag . "CD") (:stem . "410") (:form . "410") (:end . 277) (:start . 274)\n  (:id . 108))\n ((:tag . "NNS") (:stem . "ep-line") (:form . "EP-lines") (:end . 286)\n  (:start . 278) (:id . 109))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 291) (:start . 287)\n  (:id . 110))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 295) (:start . 292)\n  (:id . 111))\n ((:tag . "NNP") (:stem . "Rorth") (:form . "Rorth") (:end . 301)\n  (:start . 296) (:id . 112))\n ((:tag . "NN") (:stem . "collection") (:form . "collection") (:end . 312)\n  (:start . 302) (:id . 113))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 314) (:start . 313)\n  (:id . 114))\n ((:tag . "CD") (:stem . "58],[59") (:form . "58],[59") (:end . 321)\n  (:start . 314) (:id . 115))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 322) (:start . 321)\n  (:id . 116))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 323) (:start . 322)\n  (:id . 117)))@@@1@76@((:identifiers (:sid . :s10.283) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503396@unknown@formal@none@1@S@For the misexpression screen the UAS-lines were crossed into the PO163GAL4, UAS-n-syb-GFP stock [14],[60].@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "misexpression") (:form . "misexpression")\n  (:end . 21) (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "screen") (:form . "screen") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "uas-line") (:form . "UAS-lines") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "cross") (:form . "crossed") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "po163gal4") (:form . "PO163GAL4") (:end . 74)\n  (:start . 65) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "UAS-n-syb-GFP") (:form . "UAS-n-syb-GFP")\n  (:end . 89) (:start . 76) (:id . 54))\n ((:tag . "NN") (:stem . "stock") (:form . "stock") (:end . 95) (:start . 90)\n  (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 97) (:start . 96)\n  (:id . 56))\n ((:tag . "CD") (:stem . "14],[60") (:form . "14],[60") (:end . 104)\n  (:start . 97) (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s10.284) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503397@unknown@formal@none@1@S@For rescue experiments the following embryos were analysed: UAS-sema 1a, sema 1aP1; PO163GAL4, ppkEGFP [26], UAS-sema 1a, sema 1aP1; HB9GAL4, ppkEGFP; UAS-plexA-HA/+; PO163GAL4, ppkEGFP/+; plex ADf(4)C3, and UAS-plex B/PO163GAL4, ppkEGFP; plex BKG00878.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 44)\n  (:start . 37) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "analyse") (:form . "analysed") (:end . 58)\n  (:start . 50) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 59) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "UAS-sema") (:form . "UAS-sema") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "PO163GAL4") (:form . "PO163GAL4") (:end . 93)\n  (:start . 84) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "ppkEGFP") (:form . "ppkEGFP") (:end . 102)\n  (:start . 95) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 107) (:start . 106)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "UAS-sema") (:form . "UAS-sema") (:end . 117)\n  (:start . 109) (:id . 64))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 120) (:start . 118)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 66))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 126) (:start . 122)\n  (:id . 67))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 131) (:start . 127)\n  (:id . 68))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 132) (:start . 131)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "HB9GAL4") (:form . "HB9GAL4") (:end . 140)\n  (:start . 133) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "ppkEGFP") (:form . "ppkEGFP") (:end . 149)\n  (:start . 142) (:id . 72))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 150) (:start . 149)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "uas-plexa-ha/+") (:form . "UAS-plexA-HA/+")\n  (:end . 165) (:start . 151) (:id . 74))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 166) (:start . 165)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "PO163GAL4") (:form . "PO163GAL4") (:end . 176)\n  (:start . 167) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "ppkEGFP/+") (:form . "ppkEGFP/+") (:end . 187)\n  (:start . 178) (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 188) (:start . 187)\n  (:id . 79))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 193) (:start . 189)\n  (:id . 80))\n ((:tag . "NN") (:stem . "ADf(4)C3") (:form . "ADf(4)C3") (:end . 202)\n  (:start . 194) (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 203) (:start . 202)\n  (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 207) (:start . 204)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "UAS-plex") (:form . "UAS-plex") (:end . 216)\n  (:start . 208) (:id . 84))\n ((:tag . "NNP") (:stem . "B/PO163GAL4") (:form . "B/PO163GAL4") (:end . 228)\n  (:start . 217) (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 229) (:start . 228)\n  (:id . 86))\n ((:tag . "NNP") (:stem . "ppkEGFP") (:form . "ppkEGFP") (:end . 237)\n  (:start . 230) (:id . 87))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 238) (:start . 237)\n  (:id . 88))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 243) (:start . 239)\n  (:id . 89))\n ((:tag . "NN") (:stem . "bkg00878") (:form . "BKG00878") (:end . 252)\n  (:start . 244) (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 253) (:start . 252)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s10.285) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503398@unknown@formal@none@1@S@We also used OK371GAL4 (gift of M.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ok371gal4") (:form . "OK371GAL4") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gift") (:form . "gift") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 33) (:start . 32)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 34) (:start . 33)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s10.286) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503399@unknown@formal@none@1@S@Landgraf), GADGAL4 [29], single mindedGAL4 [31], UAS-reaper [27] and wnt5D7 stocks [56].@(((:tag . "NNP") (:stem . "Landgraf") (:form . "Landgraf") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "GADGAL4") (:form . "GADGAL4") (:end . 18)\n  (:start . 11) (:id . 45))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 22) (:start . 20)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 23) (:start . 22)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 31)\n  (:start . 25) (:id . 50))\n ((:tag . "NN") (:stem . "mindedgal4") (:form . "mindedGAL4") (:end . 42)\n  (:start . 32) (:id . 51))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 44) (:start . 43)\n  (:id . 52))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 46) (:start . 44)\n  (:id . 53))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 47) (:start . 46)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "UAS-reaper") (:form . "UAS-reaper") (:end . 59)\n  (:start . 49) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 61) (:start . 60)\n  (:id . 57))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 63) (:start . 61)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 64) (:start . 63)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 60))\n ((:tag . "NN") (:stem . "wnt5d7") (:form . "wnt5D7") (:end . 75)\n  (:start . 69) (:id . 61))\n ((:tag . "NNS") (:stem . "stock") (:form . "stocks") (:end . 82)\n  (:start . 76) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 84) (:start . 83)\n  (:id . 63))\n ((:tag . "CD") (:stem . "56") (:form . "56") (:end . 86) (:start . 84)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 87) (:start . 86)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.287) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503400@unknown@formal@none@1@S@Dissection@(((:tag . "NN") (:stem . "dissection") (:form . "Dissection") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s10.288) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503401@unknown@formal@none@1@S@Embryos were staged and VNCs dissected out embryos as previously described [6],[61],[62].@(((:tag . "NNP") (:stem . "Embryo") (:form . "Embryos") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "stag") (:form . "staged") (:end . 19) (:start . 13)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "vnc") (:form . "VNCs") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "dissect") (:form . "dissected") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 64)\n  (:start . 54) (:id . 51))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 74)\n  (:start . 65) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "CD") (:stem . "6],[61],[62") (:form . "6],[61],[62") (:end . 87)\n  (:start . 76) (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s10.289) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503402@unknown@formal@none@1@S@For overexpression experiments embryos were grown at 29°C.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 30)\n  (:start . 19) (:id . 44))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 38)\n  (:start . 31) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 43) (:start . 39)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "grow") (:form . "grown") (:end . 49) (:start . 44)\n  (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 52) (:start . 50)\n  (:id . 48))\n ((:tag . "NN") (:stem . "29°c") (:form . "29°C") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s10.290) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503403@unknown@formal@none@1@S@VNCs were mounted with brain lobes down and VNC up to allow rapid, high-resolution, confocal imaging of transverse planes, perpendicular to the neuraxis.@(((:tag . "NNP") (:stem . "VNC") (:form . "VNCs") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "mount") (:form . "mounted") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "brain") (:form . "brain") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "lobe") (:form . "lobes") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "IN") (:stem . "down") (:form . "down") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 59) (:start . 54)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "high-resolution") (:form . "high-resolution")\n  (:end . 82) (:start . 67) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 92)\n  (:start . 84) (:id . 58))\n ((:tag . "NN") (:stem . "imaging") (:form . "imaging") (:end . 100)\n  (:start . 93) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "transverse") (:form . "transverse") (:end . 114)\n  (:start . 104) (:id . 61))\n ((:tag . "NNS") (:stem . "plane") (:form . "planes") (:end . 121)\n  (:start . 115) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "perpendicular") (:form . "perpendicular")\n  (:end . 136) (:start . 123) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 66))\n ((:tag . "NN") (:stem . "neuraxis") (:form . "neuraxis") (:end . 152)\n  (:start . 144) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s10.291) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503404@unknown@formal@none@1@S@Immunocytochemistry@(((:tag . "NNP") (:stem . "Immunocytochemistry")\n  (:form . "Immunocytochemistry") (:end . 19) (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s10.292) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503405@unknown@formal@none@1@S@We used the following primary antibodies: anti-Sema 2a (MAb 19C2, developed by C. Goodman), anti-Slit (MAb C555.6D, developed by S. Artavanis-Tsakonas), anti-Fas II (MAb 1D4, developed by C. Goodman), and anti-Repo (MAb 8D12, developed by C. Goodman) supplied by the Developmental Studies Hybridoma bank (110 dilution); anti-Sema 1a (11,000 dilution, kindly provided by A. Kolodkin [26]; anti-Plex A (1500 dilution, kindly provided by L. Luo) [23], and Cy5-conjugated goat anti-horseradish peroxidase (1100 dilution; Jackson ImmunoResearch).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "following") (:form . "following") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "JJ") (:stem . "primary") (:form . 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")") (:form . ")") (:end . 540) (:start . 539)\n  (:id . 149))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 541) (:start . 540)\n  (:id . 150)))@@@1@109@((:identifiers (:sid . :s10.293) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503406@unknown@formal@none@1@S@Secondary antibodies were used at 1500 dilution: Alexa488-conjugated donkey anti-goat, Alexa488-conjugated goat anti-rabbit, Alexa633-conjugated goat anti-mouse, Alexa633-conjugated rabbit anti-mouse (Molecular Probes).@(((:tag . "JJ") (:stem . "secondary") (:form . "Secondary") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "antibody") (:form . "antibodies") (:end . 20)\n  (:start . 10) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 25) (:start . 21)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "CD") (:stem . "1500") (:form . "1500") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dilution") (:form . "dilution") (:end . 47)\n  (:start . 39) (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "alexa488-conjugated")\n  (:form . "Alexa488-conjugated") (:end . 68) (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "donkey") (:form . "donkey") (:end . 75)\n  (:start . 69) (:id . 51))\n ((:tag . "JJ") (:stem . "anti-goat") (:form . "anti-goat") (:end . 85)\n  (:start . 76) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "alexa488-conjugated")\n  (:form . "Alexa488-conjugated") (:end . 106) (:start . 87) (:id . 54))\n ((:tag . "NN") (:stem . "goat") (:form . "goat") (:end . 111) (:start . 107)\n  (:id . 55))\n ((:tag . "NN") (:stem . "anti-rabbit") (:form . "anti-rabbit") (:end . 123)\n  (:start . 112) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "alexa633-conjugated")\n  (:form . "Alexa633-conjugated") (:end . 144) (:start . 125) (:id . 58))\n ((:tag . "NN") (:stem . "goat") (:form . "goat") (:end . 149) (:start . 145)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "anti-mouse") (:form . "anti-mouse") (:end . 160)\n  (:start . 150) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "alexa633-conjugated")\n  (:form . "Alexa633-conjugated") (:end . 181) (:start . 162) (:id . 62))\n ((:tag . "NN") (:stem . "rabbit") (:form . "rabbit") (:end . 188)\n  (:start . 182) (:id . 63))\n ((:tag . "JJ") (:stem . "anti-mouse") (:form . "anti-mouse") (:end . 199)\n  (:start . 189) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 201) (:start . 200)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "molecular") (:form . "Molecular") (:end . 210)\n  (:start . 201) (:id . 66))\n ((:tag . "NNP") (:stem . "Probe") (:form . "Probes") (:end . 217)\n  (:start . 211) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 218) (:start . 217)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.294) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503407@unknown@formal@none@1@S@Standard immunocytochemical procedures were followed [63], and immunofluorescence was visualised with Leica SP1 and Zeiss LSM confocal microscopes.@(((:tag . "JJ") (:stem . "standard") (:form . "Standard") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "immunocytochemical") (:form . "immunocytochemical")\n  (:end . 27) (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 38)\n  (:start . 28) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 43) (:start . 39)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 52)\n  (:start . 44) (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 54) (:start . 53)\n  (:id . 47))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 56) (:start . 54)\n  (:id . 48))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 57) (:start . 56)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "immunofluorescence") (:form . "immunofluorescence")\n  (:end . 81) (:start . 63) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 85) (:start . 82)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "visualise") (:form . "visualised") (:end . 96)\n  (:start . 86) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 101) (:start . 97)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Leica") (:form . "Leica") (:end . 107)\n  (:start . 102) (:id . 56))\n ((:tag . "NNP") (:stem . "SP1") (:form . "SP1") (:end . 111) (:start . 108)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Zeiss") (:form . "Zeiss") (:end . 121)\n  (:start . 116) (:id . 59))\n ((:tag . "NNP") (:stem . "LSM") (:form . "LSM") (:end . 125) (:start . 122)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 134)\n  (:start . 126) (:id . 61))\n ((:tag . "NNS") (:stem . "microscope") (:form . "microscopes") (:end . 146)\n  (:start . 135) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.295) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503408@unknown@formal@none@1@S@Images are maximum projections of confocal z series processed with Adobe Photoshop software.@(((:tag . "NNS") (:stem . "image") (:form . "Images") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "maximum") (:form . "maximum") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 30)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "VBN") (:stem . "process") (:form . "processed") (:end . 61)\n  (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Adobe") (:form . "Adobe") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Photoshop") (:form . "Photoshop") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 91)\n  (:start . 83) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.296) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503409@unknown@formal@none@1@S@Quantification Procedures@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "procedure") (:form . "Procedures") (:end . 25)\n  (:start . 15) (:id . 43)))@@@1@2@((:identifiers (:sid . :s10.297) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503410@unknown@formal@none@1@S@For quantification of Sema 2a gradients at 13-h AEL nine VNCs stained for Sema 2a were randomly chosen and A7 imaged using a Leica SP1.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "quantification") (:form . "quantification")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "gradient") (:form . "gradients") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "13-h") (:form . "13-h") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "ael") (:form . "AEL") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "CD") (:stem . "nine") (:form . "nine") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "vnc") (:form . "VNCs") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 69)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 78) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 95)\n  (:start . 87) (:id . 58))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 102)\n  (:start . 96) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "A7") (:form . "A7") (:end . 109) (:start . 107)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "image") (:form . "imaged") (:end . 116)\n  (:start . 110) (:id . 62))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 122) (:start . 117)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 124) (:start . 123)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Leica") (:form . "Leica") (:end . 130)\n  (:start . 125) (:id . 65))\n ((:tag . "NNP") (:stem . "SP1") (:form . "SP1") (:end . 134) (:start . 131)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s10.298) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503411@unknown@formal@none@1@S@A confocal section was randomly chosen from each stack, the dorso-ventral axis manually drawn, and the neuropile was divided into nine equal dorso-ventral stripes, perpendicular to the midline and the average fluorescence intensity in each stripe was calculated.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "stack") (:form . "stack") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 73) (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "RB") (:stem . "manually") (:form . "manually") (:end . 87)\n  (:start . 79) (:id . 55))\n ((:tag . "VBN") (:stem . "draw") (:form . "drawn") (:end . 93) (:start . 88)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 59))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 112)\n  (:start . 103) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "divide") (:form . "divided") (:end . 124)\n  (:start . 117) (:id . 62))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 129) (:start . 125)\n  (:id . 63))\n ((:tag . "CD") (:stem . "nine") (:form . "nine") (:end . 134) (:start . 130)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 140)\n  (:start . 135) (:id . 65))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 154) (:start . 141) (:id . 66))\n ((:tag . "NNS") (:stem . "stripe") (:form . "stripes") (:end . 162)\n  (:start . 155) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "perpendicular") (:form . "perpendicular")\n  (:end . 177) (:start . 164) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 180) (:start . 178)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 184) (:start . 181)\n  (:id . 71))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 192)\n  (:start . 185) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 196) (:start . 193)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 200) (:start . 197)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 208)\n  (:start . 201) (:id . 75))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 221)\n  (:start . 209) (:id . 76))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 231)\n  (:start . 222) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 234) (:start . 232)\n  (:id . 78))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 239) (:start . 235)\n  (:id . 79))\n ((:tag . "NN") (:stem . "stripe") (:form . "stripe") (:end . 246)\n  (:start . 240) (:id . 80))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 250) (:start . 247)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 261)\n  (:start . 251) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 262) (:start . 261)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s10.299) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503412@unknown@formal@none@1@S@Values from different nerve cords were normalized such that the average intensity from each nerve cord was 1.@(((:tag . "NNS") (:stem . "value") (:form . "Values") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "cord") (:form . "cords") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "normalize") (:form . "normalized") (:end . 49)\n  (:start . 39) (:id . 48))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 81)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 91) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 97) (:start . 92)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cord") (:form . "cord") (:end . 102) (:start . 98)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 106) (:start . 103)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 108) (:start . 107)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.300) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503413@unknown@formal@none@1@S@For quantification of the Slit gradient at 13 h, 12 VNCs stained for Slit were randomly chosen, and A7 was imaged using a Leica SP1.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "quantification") (:form . "quantification")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "vnc") (:form . "VNCs") (:end . 56) (:start . 52)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 64)\n  (:start . 57) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Slit") (:form . "Slit") (:end . 73) (:start . 69)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 78) (:start . 74)\n  (:id . 57))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 87)\n  (:start . 79) (:id . 58))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 94)\n  (:start . 88) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "A7") (:form . "A7") (:end . 102) (:start . 100)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 106) (:start . 103)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "image") (:form . "imaged") (:end . 113)\n  (:start . 107) (:id . 64))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 119) (:start . 114)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 121) (:start . 120)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Leica") (:form . "Leica") (:end . 127)\n  (:start . 122) (:id . 67))\n ((:tag . "NNP") (:stem . "SP1") (:form . "SP1") (:end . 131) (:start . 128)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.301) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503414@unknown@formal@none@1@S@A confocal section was randomly chosen from each stack, a line on either side of the midline was manually drawn, and the neuropile on either side of the midline was divided into four mediolateral stripes.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "stack") (:form . "stack") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 72)\n  (:start . 66) (:id . 55))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 77) (:start . 73)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 92)\n  (:start . 85) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 96) (:start . 93)\n  (:id . 60))\n ((:tag . "RB") (:stem . "manually") (:form . "manually") (:end . 105)\n  (:start . 97) (:id . 61))\n ((:tag . "VBN") (:stem . "draw") (:form . "drawn") (:end . 111)\n  (:start . 106) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 65))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 130)\n  (:start . 121) (:id . 66))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 133) (:start . 131)\n  (:id . 67))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 140)\n  (:start . 134) (:id . 68))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 145) (:start . 141)\n  (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 71))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 160)\n  (:start . 153) (:id . 72))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 164) (:start . 161)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "divide") (:form . "divided") (:end . 172)\n  (:start . 165) (:id . 74))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 177) (:start . 173)\n  (:id . 75))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 182) (:start . 178)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "mediolateral") (:form . "mediolateral") (:end . 195)\n  (:start . 183) (:id . 77))\n ((:tag . "NNS") (:stem . "stripe") (:form . "stripes") (:end . 203)\n  (:start . 196) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s10.302) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503415@unknown@formal@none@1@S@The average fluorescence intensity in each stripe was calculated and normalised as above.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "fluorescence") (:form . "fluorescence") (:end . 24)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "stripe") (:form . "stripe") (:end . 49)\n  (:start . 43) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 64)\n  (:start . 54) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "normalise") (:form . "normalised") (:end . 79)\n  (:start . 69) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 82) (:start . 80)\n  (:id . 53))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 88) (:start . 83)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.303) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503416@unknown@formal@none@1@S@For a statistical analysis of defects in the pattern of sensory terminals (visualized with PO163GAL4, UAS-n-syb-GFP) along the medio-lateral axis we quantified the normalised surface area occupied by sensory terminals (sensory area, SA) in the medial domain of the neuropile (SAM/T=SA[medial]/SA[medial+intermediate+lateral]) in randomly chosen transverse confocal sections from 30 different hemisegments for each genotype.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 17)\n  (:start . 6) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 63)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 73)\n  (:start . 64) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "visualize") (:form . "visualized") (:end . 85)\n  (:start . 75) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "PO163GAL4") (:form . "PO163GAL4") (:end . 100)\n  (:start . 91) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "UAS-n-syb-GFP") (:form . "UAS-n-syb-GFP")\n  (:end . 115) (:start . 102) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 60))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 122)\n  (:start . 117) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 140) (:start . 127) (:id . 63))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 145) (:start . 141)\n  (:id . 64))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 148) (:start . 146)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "quantify") (:form . "quantified") (:end . 159)\n  (:start . 149) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "normalise") (:form . "normalised") (:end . 174)\n  (:start . 164) (:id . 68))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 182)\n  (:start . 175) (:id . 69))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 187) (:start . 183)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "occupy") (:form . "occupied") (:end . 196)\n  (:start . 188) (:id . 71))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 199) (:start . 197)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 207)\n  (:start . 200) (:id . 73))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 217)\n  (:start . 208) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 219) (:start . 218)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 226)\n  (:start . 219) (:id . 76))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 231) (:start . 227)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 232) (:start . 231)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "SA") (:form . "SA") (:end . 235) (:start . 233)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 236) (:start . 235)\n  (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 239) (:start . 237)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 243) (:start . 240)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 250)\n  (:start . 244) (:id . 83))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 257)\n  (:start . 251) (:id . 84))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 260) (:start . 258)\n  (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 264) (:start . 261)\n  (:id . 86))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 274)\n  (:start . 265) (:id . 87))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 276) (:start . 275)\n  (:id . 88))\n ((:tag . "NNP") (:stem . "SAM/T=SA[medial]/SA[medial+intermediate+lateral")\n  (:form . "SAM/T=SA[medial]/SA[medial+intermediate+lateral") (:end . 323)\n  (:start . 276) (:id . 89))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 324) (:start . 323)\n  (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 325) (:start . 324)\n  (:id . 91))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 328) (:start . 326)\n  (:id . 92))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 337)\n  (:start . 329) (:id . 93))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 344)\n  (:start . 338) (:id . 94))\n ((:tag . "JJ") (:stem . "transverse") (:form . "transverse") (:end . 355)\n  (:start . 345) (:id . 95))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 364)\n  (:start . 356) (:id . 96))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 373)\n  (:start . 365) (:id . 97))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 378) (:start . 374)\n  (:id . 98))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 381) (:start . 379)\n  (:id . 99))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 391)\n  (:start . 382) (:id . 100))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 404)\n  (:start . 392) (:id . 101))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 408) (:start . 405)\n  (:id . 102))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 413) (:start . 409)\n  (:id . 103))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 422)\n  (:start . 414) (:id . 104))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 423) (:start . 422)\n  (:id . 105)))@@@1@64@((:identifiers (:sid . :s10.304) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503417@unknown@formal@none@1@S@Within a single embryo, we selected every tenth section (all confocal sections were 1-µm thick so that the analyzed sections were 10 µm apart from each other).@(((:tag . "IN") (:stem . "within") (:form . "Within") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 35)\n  (:start . 27) (:id . 48))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "tenth") (:form . "tenth") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 69)\n  (:start . 61) (:id . 54))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 78)\n  (:start . 70) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "1-µm") (:form . "1-µm") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "thick") (:form . "thick") (:end . 94) (:start . 89)\n  (:id . 58))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 102) (:start . 98)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 115)\n  (:start . 107) (:id . 62))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 124)\n  (:start . 116) (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 129) (:start . 125)\n  (:id . 64))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 135) (:start . 133)\n  (:id . 66))\n ((:tag . "RB") (:stem . "apart") (:form . "apart") (:end . 141)\n  (:start . 136) (:id . 67))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 146) (:start . 142)\n  (:id . 68))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 151) (:start . 147)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 157)\n  (:start . 152) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.305) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503418@unknown@formal@none@1@S@A Student's t-test was used to compare the mean SAM/T for the different genotypes.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "student") (:form . "Student") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "t-test") (:form . "t-test") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 38)\n  (:start . 31) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "mean") (:form . "mean") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "sam/t") (:form . "SAM/T") (:end . 53) (:start . 48)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 71)\n  (:start . 62) (:id . 55))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 81)\n  (:start . 72) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.306) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503419@unknown@formal@none@1@S@For a statistical analysis of expansion or exclusion of sensory terminals (visualized with PO163GAL4, UAS-n-syb-GFP) into different dorso-ventral layers we compared SA in layer 2 (SA2/h=SA(layer 2)/[hemisegment surface area]) or SA in layers 1, 3, and 4 (SA1+3+4/h=SA[layer 1+3+4]/[hemisegment surface area]) in randomly chosen transverse confocal sections from more than 30 different hemisegments for each genotype.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 17)\n  (:start . 6) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "exclusion") (:form . "exclusion") (:end . 52)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 63)\n  (:start . 56) (:id . 51))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 73)\n  (:start . 64) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "visualize") (:form . "visualized") (:end . 85)\n  (:start . 75) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PO163GAL4") (:form . "PO163GAL4") (:end . 100)\n  (:start . 91) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "UAS-n-syb-GFP") (:form . "UAS-n-syb-GFP")\n  (:end . 115) (:start . 102) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 59))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 121) (:start . 117)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 131)\n  (:start . 122) (:id . 61))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 145) (:start . 132) (:id . 62))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 152)\n  (:start . 146) (:id . 63))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 155) (:start . 153)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "compare") (:form . "compared") (:end . 164)\n  (:start . 156) (:id . 65))\n ((:tag . "NNP") (:stem . "SA") (:form . "SA") (:end . 167) (:start . 165)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 170) (:start . 168)\n  (:id . 67))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 176)\n  (:start . 171) (:id . 68))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 178) (:start . 177)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 180) (:start . 179)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "SA2/h=SA(layer") (:form . "SA2/h=SA(layer")\n  (:end . 194) (:start . 180) (:id . 71))\n ((:tag . "NN") (:stem . "2)/[hemisegment") (:form . "2)/[hemisegment")\n  (:end . 210) (:start . 195) (:id . 72))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 218)\n  (:start . 211) (:id . 73))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 223) (:start . 219)\n  (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 224) (:start . 223)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 225) (:start . 224)\n  (:id . 76))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 228) (:start . 226)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "SA") (:form . "SA") (:end . 231) (:start . 229)\n  (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 234) (:start . 232)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 241)\n  (:start . 235) (:id . 80))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 243) (:start . 242)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 244) (:start . 243)\n  (:id . 82))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 246) (:start . 245)\n  (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 247) (:start . 246)\n  (:id . 84))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 251) (:start . 248)\n  (:id . 85))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 253) (:start . 252)\n  (:id . 86))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 255) (:start . 254)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "SA1+3+4/h=SA[layer") (:form . "SA1+3+4/h=SA[layer")\n  (:end . 273) (:start . 255) (:id . 88))\n ((:tag . "NN") (:stem . "1+3+4]/[hemisegment")\n  (:form . "1+3+4]/[hemisegment") (:end . 293) (:start . 274) (:id . 89))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 301)\n  (:start . 294) (:id . 90))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 306) (:start . 302)\n  (:id . 91))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 307) (:start . 306)\n  (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 308) (:start . 307)\n  (:id . 93))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 311) (:start . 309)\n  (:id . 94))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 320)\n  (:start . 312) (:id . 95))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 327)\n  (:start . 321) (:id . 96))\n ((:tag . "JJ") (:stem . "transverse") (:form . "transverse") (:end . 338)\n  (:start . 328) (:id . 97))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 347)\n  (:start . 339) (:id . 98))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 356)\n  (:start . 348) (:id . 99))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 361) (:start . 357)\n  (:id . 100))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 366) (:start . 362)\n  (:id . 101))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 371) (:start . 367)\n  (:id . 102))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 374) (:start . 372)\n  (:id . 103))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 384)\n  (:start . 375) (:id . 104))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 397)\n  (:start . 385) (:id . 105))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 401) (:start . 398)\n  (:id . 106))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 406) (:start . 402)\n  (:id . 107))\n ((:tag . "NN") (:stem . "genotype") (:form . "genotype") (:end . 415)\n  (:start . 407) (:id . 108))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 416) (:start . 415)\n  (:id . 109)))@@@1@68@((:identifiers (:sid . :s10.307) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503420@unknown@formal@none@1@S@Within a single embryo, we selected every tenth section (all confocal sections were 1-µm thick so that the analyzed sections were 10 µm apart from each other).@(((:tag . "IN") (:stem . "within") (:form . "Within") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 35)\n  (:start . 27) (:id . 48))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "tenth") (:form . "tenth") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 69)\n  (:start . 61) (:id . 54))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 78)\n  (:start . 70) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "1-µm") (:form . "1-µm") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "thick") (:form . "thick") (:end . 94) (:start . 89)\n  (:id . 58))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 102) (:start . 98)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 115)\n  (:start . 107) (:id . 62))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 124)\n  (:start . 116) (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 129) (:start . 125)\n  (:id . 64))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 135) (:start . 133)\n  (:id . 66))\n ((:tag . "RB") (:stem . "apart") (:form . "apart") (:end . 141)\n  (:start . 136) (:id . 67))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 146) (:start . 142)\n  (:id . 68))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 151) (:start . 147)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 157)\n  (:start . 152) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.308) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503421@unknown@formal@none@1@S@A Student's t-test was used to compare the mean SA2/h or SA1+3+4/h for the different genotypes.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "student") (:form . "Student") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "t-test") (:form . "t-test") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 38)\n  (:start . 31) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "mean") (:form . "mean") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "SA2/h") (:form . "SA2/h") (:end . 53) (:start . 48)\n  (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "SA1+3+4/h") (:form . "SA1+3+4/h") (:end . 66)\n  (:start . 57) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 84)\n  (:start . 75) (:id . 57))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 94)\n  (:start . 85) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s10.309) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503422@unknown@formal@none@1@S@For a statistical analysis of termination defects class IV md axons in the dorso-ventral axis, we quantified the percentage of hemisegments with aberrant terminals (Hat) in layers 1, 2, and 3 per embryo (per 14 hemisegments): Hat(1, 2, or 3)=(n hemisegments with terminals in 1, 2, or 3/14)×100 and the total percentage of hemisegments with aberrant terminals per embryo [Hat(1+2+3)=Hat(1)+Hat(2)+Hat(3)].@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 17)\n  (:start . 6) (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 41)\n  (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 88) (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "quantify") (:form . "quantified") (:end . 108)\n  (:start . 98) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 60))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 123)\n  (:start . 113) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 139)\n  (:start . 127) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 144) (:start . 140)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 153)\n  (:start . 145) (:id . 65))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 163)\n  (:start . 154) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 165) (:start . 164)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Hat") (:form . "Hat") (:end . 168) (:start . 165)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 172) (:start . 170)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 179)\n  (:start . 173) (:id . 71))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 181) (:start . 180)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 182) (:start . 181)\n  (:id . 73))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 184) (:start . 183)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 189) (:start . 186)\n  (:id . 76))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 191) (:start . 190)\n  (:id . 77))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 195) (:start . 192)\n  (:id . 78))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 202)\n  (:start . 196) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 204) (:start . 203)\n  (:id . 80))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 207) (:start . 204)\n  (:id . 81))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 210) (:start . 208)\n  (:id . 82))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 223)\n  (:start . 211) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 224) (:start . 223)\n  (:id . 84))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 225) (:start . 224)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "Hat(1") (:form . "Hat(1") (:end . 231)\n  (:start . 226) (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 232) (:start . 231)\n  (:id . 87))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 234) (:start . 233)\n  (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 235) (:start . 234)\n  (:id . 89))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 238) (:start . 236)\n  (:id . 90))\n ((:tag . "NN") (:stem . "3)=(n") (:form . "3)=(n") (:end . 244)\n  (:start . 239) (:id . 91))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 257)\n  (:start . 245) (:id . 92))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 262) (:start . 258)\n  (:id . 93))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 272)\n  (:start . 263) (:id . 94))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 275) (:start . 273)\n  (:id . 95))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 277) (:start . 276)\n  (:id . 96))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 278) (:start . 277)\n  (:id . 97))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 280) (:start . 279)\n  (:id . 98))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 281) (:start . 280)\n  (:id . 99))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 284) (:start . 282)\n  (:id . 100))\n ((:tag . "NNP") (:stem . "3/14)×100") (:form . "3/14)×100") (:end . 294)\n  (:start . 285) (:id . 101))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 298) (:start . 295)\n  (:id . 102))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 302) (:start . 299)\n  (:id . 103))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 308)\n  (:start . 303) (:id . 104))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 319)\n  (:start . 309) (:id . 105))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 322) (:start . 320)\n  (:id . 106))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 335)\n  (:start . 323) (:id . 107))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 340) (:start . 336)\n  (:id . 108))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 349)\n  (:start . 341) (:id . 109))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 359)\n  (:start . 350) (:id . 110))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 363) (:start . 360)\n  (:id . 111))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 370)\n  (:start . 364) (:id . 112))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 372) (:start . 371)\n  (:id . 113))\n ((:tag . "NNP") (:stem . "Hat(1+2+3)=Hat(1)+Hat(2)+Hat(3)")\n  (:form . "Hat(1+2+3)=Hat(1)+Hat(2)+Hat(3)") (:end . 403) (:start . 372)\n  (:id . 114))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 404) (:start . 403)\n  (:id . 115))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 405) (:start . 404)\n  (:id . 116)))@@@1@75@((:identifiers (:sid . :s10.310) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503423@unknown@formal@none@1@S@A Student's t-test was used to compare the mean Hat for the different genotypes.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "student") (:form . "Student") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "t-test") (:form . "t-test") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 38)\n  (:start . 31) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "mean") (:form . "mean") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Hat") (:form . "Hat") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 55) (:start . 52)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 69)\n  (:start . 60) (:id . 55))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 79)\n  (:start . 70) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.311) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503424@unknown@formal@none@1@S@In some cases we also quantified the average (per embryo) relative proportion of hemisegments with aberrant terminal in each layer: Hat(1)/Hat(1+2+3), Hat(2)/Hat(1+2+3), and Hat(3)/Hat(1+2+3).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "quantify") (:form . "quantified") (:end . 32)\n  (:start . 22) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 56)\n  (:start . 50) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 66)\n  (:start . 58) (:id . 54))\n ((:tag . "NN") (:stem . "proportion") (:form . "proportion") (:end . 77)\n  (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 93)\n  (:start . 81) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 107)\n  (:start . 99) (:id . 59))\n ((:tag . "NN") (:stem . "terminal") (:form . "terminal") (:end . 116)\n  (:start . 108) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 124) (:start . 120)\n  (:id . 62))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 130)\n  (:start . 125) (:id . 63))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 131) (:start . 130)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Hat(1)/Hat(1+2+3)") (:form . "Hat(1)/Hat(1+2+3)")\n  (:end . 149) (:start . 132) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "CD") (:stem . "Hat(2)/Hat(1+2+3)") (:form . "Hat(2)/Hat(1+2+3)")\n  (:end . 168) (:start . 151) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 173) (:start . 170)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Hat(3)/Hat(1+2+3)") (:form . "Hat(3)/Hat(1+2+3)")\n  (:end . 191) (:start . 174) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s10.312) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503425@unknown@formal@none@1@S@We counted as “aberrant” only those hemisegments with terminals in layers 1, 2, or 3 (Figure S5A and S5B).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "count") (:form . "counted") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 23)\n  (:start . 15) (:id . 46))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 24) (:start . 23)\n  (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 29) (:start . 25)\n  (:id . 48))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 35) (:start . 30)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 48)\n  (:start . 36) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 56))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 78) (:start . 77)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 82) (:start . 80)\n  (:id . 59))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 84) (:start . 83)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 92)\n  (:start . 86) (:id . 62))\n ((:tag . "NNP") (:stem . "S5A") (:form . "S5A") (:end . 96) (:start . 93)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "S5B") (:form . "S5B") (:end . 104) (:start . 101)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s10.313) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503426@unknown@formal@none@1@S@We did not count as “aberrant” those axons that exhibit the aberrant growth, with normal termination phenotype (Figure S5C).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "VB") (:stem . "count") (:form . "count") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 29)\n  (:start . 21) (:id . 48))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 30) (:start . 29)\n  (:id . 49))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 36) (:start . 31)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 42) (:start . 37)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 47) (:start . 43)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "exhibit") (:form . "exhibit") (:end . 55)\n  (:start . 48) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 68)\n  (:start . 60) (:id . 55))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 75)\n  (:start . 69) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 81) (:start . 77)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 88)\n  (:start . 82) (:id . 59))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 100)\n  (:start . 89) (:id . 60))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 110)\n  (:start . 101) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 118)\n  (:start . 112) (:id . 63))\n ((:tag . "NNP") (:stem . "S5C") (:form . "S5C") (:end . 122) (:start . 119)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.314) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503427@unknown@formal@none@1@S@Supporting Information@(((:tag . "VBG") (:stem . "support") (:form . "Supporting") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Information") (:form . "Information") (:end . 22)\n  (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s10.315) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503428@unknown@formal@none@1@S@Figure S1 Sensory neuron termination does not correlate with nerve route and position of entry into the neuropile.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "sensory") (:form . "Sensory") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 36)\n  (:start . 25) (:id . 46))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "VB") (:stem . "correlate") (:form . "correlate") (:end . 55)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 66) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "route") (:form . "route") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 85)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 94) (:start . 89)\n  (:id . 56))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 99) (:start . 95)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 113)\n  (:start . 104) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.316) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503429@unknown@formal@none@1@S@(A) Diagram showing the pathways in the neuropile taken by sensory neurons that run in the ISN (magenta) and the SN (green) en route to their termination domains (yellow) in wild type (21 AEL), with respect to Fas II tracks (red).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Diagram") (:form . "Diagram") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 19)\n  (:start . 12) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 32)\n  (:start . 24) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . 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"ISN") (:end . 94) (:start . 91)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 61))\n ((:tag . "NN") (:stem . "magenta") (:form . "magenta") (:end . 103)\n  (:start . 96) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 115) (:start . 113)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 122)\n  (:start . 117) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n  (:id . 69))\n ((:tag . "IN") (:stem . "en") (:form . "en") (:end . 126) (:start . 124)\n  (:id . 70))\n ((:tag . "NN") (:stem . "route") (:form . "route") (:end . 132)\n  (:start . 127) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 72))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 141)\n  (:start . 136) (:id . 73))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 153)\n  (:start . 142) (:id . 74))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 161)\n  (:start . 154) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 163) (:start . 162)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 169)\n  (:start . 163) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 173) (:start . 171)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 178) (:start . 174)\n  (:id . 80))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 183) (:start . 179)\n  (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 82))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 187) (:start . 185)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "AEL") (:form . "AEL") (:end . 191) (:start . 188)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 192) (:start . 191)\n  (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 193) (:start . 192)\n  (:id . 86))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 198) (:start . 194)\n  (:id . 87))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 206)\n  (:start . 199) (:id . 88))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 209) (:start . 207)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 213) (:start . 210)\n  (:id . 90))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 216) (:start . 214)\n  (:id . 91))\n ((:tag . "NNS") (:stem . "track") (:form . "tracks") (:end . 223)\n  (:start . 217) (:id . 92))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 225) (:start . 224)\n  (:id . 93))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 228) (:start . 225)\n  (:id . 94))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 229) (:start . 228)\n  (:id . 95))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 230) (:start . 229)\n  (:id . 96)))@@@1@55@((:identifiers (:sid . :s10.317) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503430@unknown@formal@none@1@S@Diagram represents a projection of a confocal z series of transverse sections through an abdominal segment.@(((:tag . "NN") (:stem . "diagram") (:form . "Diagram") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 31)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 54)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "transverse") (:form . "transverse") (:end . 68)\n  (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 85)\n  (:start . 78) (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "abdominal") (:form . "abdominal") (:end . 98)\n  (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 106)\n  (:start . 99) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.318) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503431@unknown@formal@none@1@S@Dorsal up.@(((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 10) (:start . 9)\n  (:id . 44)))@@@1@3@((:identifiers (:sid . :s10.319) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503432@unknown@formal@none@1@S@White arrowhead shows midline.@(((:tag . "JJ") (:stem . "white") (:form . "White") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "arrowhead") (:form . "arrowhead") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 30) (:start . 29)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s10.320) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503433@unknown@formal@none@1@S@Magenta lines indicate the pathways taken by ISN neurons in the neuropile.@(((:tag . "NNP") (:stem . "Magenta") (:form . "Magenta") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "ISN") (:form . "ISN") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 73)\n  (:start . 64) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s10.321) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503434@unknown@formal@none@1@S@Green lines indicate the pathways taken by SN neurons in the neuropile.@(((:tag . "JJ") (:stem . "green") (:form . "Green") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 39) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 70)\n  (:start . 61) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s10.322) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503435@unknown@formal@none@1@S@2, 3, and 4 indicate sensory neuron termination domains in layers 2, 3, and 4, respectively.@(((:tag . "CD") (:stem . "2") (:form . "2") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 4) (:start . 3)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 46))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 11) (:start . 10)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 20)\n  (:start . 12) (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 28)\n  (:start . 21) (:id . 49))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 35)\n  (:start . 29) (:id . 50))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 47)\n  (:start . 36) (:id . 51))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 55)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 65)\n  (:start . 59) (:id . 54))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 56))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 70) (:start . 69)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 59))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 77) (:start . 76)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 61))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 91)\n  (:start . 79) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.323) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503436@unknown@formal@none@1@S@Scale bar: 10 mm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mm") (:form . "mm") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.324) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503437@unknown@formal@none@1@S@Sensory axons whose cell bodies are located ventrally in the body wall join the SN nerve, whereas axons whose cell bodies are located dorsally or laterally in the body wall join the ISN nerve.@(((:tag . "JJ") (:stem . "sensory") (:form . "Sensory") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 31) (:start . 25)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "wall") (:form . "wall") (:end . 70) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "join") (:form . "join") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 88) (:start . 83)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 58))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 97)\n  (:start . 90) (:id . 59))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 103) (:start . 98)\n  (:id . 60))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 109)\n  (:start . 104) (:id . 61))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 114) (:start . 110)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 121)\n  (:start . 115) (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 125) (:start . 122)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 133)\n  (:start . 126) (:id . 65))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 142)\n  (:start . 134) (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 145) (:start . 143)\n  (:id . 67))\n ((:tag . "RB") (:stem . "laterally") (:form . "laterally") (:end . 155)\n  (:start . 146) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 158) (:start . 156)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n  (:id . 70))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 167) (:start . 163)\n  (:id . 71))\n ((:tag . "NN") (:stem . "wall") (:form . "wall") (:end . 172) (:start . 168)\n  (:id . 72))\n ((:tag . "NN") (:stem . "join") (:form . "join") (:end . 177) (:start . 173)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 181) (:start . 178)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "ISN") (:form . "ISN") (:end . 185) (:start . 182)\n  (:id . 75))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 191)\n  (:start . 186) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s10.325) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503438@unknown@formal@none@1@S@There is no correlation between the nerve that axons travel in and the position of their termination in the neuropile.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 23)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "axon") (:form . "axons") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "travel") (:form . "travel") (:end . 59)\n  (:start . 53) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 79)\n  (:start . 71) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 88)\n  (:start . 83) (:id . 57))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 100)\n  (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 60))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 117)\n  (:start . 108) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s10.326) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503439@unknown@formal@none@1@S@Sensory axons running in the SN terminate in layers 2, 3, or 4, in correlation with their modality and dendritic morphology [9],[11].@(((:tag . "JJ") (:stem . "sensory") (:form . "Sensory") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "run") (:form . "running") (:end . 21) (:start . 14)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "terminate") (:form . "terminate") (:end . 41)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 60) (:start . 58)\n  (:id . 55))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 62) (:start . 61)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 58))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 78)\n  (:start . 67) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 83) (:start . 79)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 89)\n  (:start . 84) (:id . 61))\n ((:tag . "NN") (:stem . "modality") (:form . "modality") (:end . 98)\n  (:start . 90) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "dendritic") (:form . "dendritic") (:end . 112)\n  (:start . 103) (:id . 64))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 123)\n  (:start . 113) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 125) (:start . 124)\n  (:id . 66))\n ((:tag . "CD") (:stem . "9],[11") (:form . "9],[11") (:end . 131)\n  (:start . 125) (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 132) (:start . 131)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.327) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503440@unknown@formal@none@1@S@For example, the ventral class IV neuron (vdaB) terminates in layer 4, the ventral ch neurons terminate in layer 3, and the ventral proprioceptive class I neuron vpda terminates in layer 2 (M.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 40)\n  (:start . 34) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "vdaB") (:form . "vdaB") (:end . 46) (:start . 42)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "terminate") (:form . "terminates") (:end . 58)\n  (:start . 48) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 67) (:start . 62)\n  (:id . 55))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 69) (:start . 68)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 82)\n  (:start . 75) (:id . 59))\n ((:tag . "NN") (:stem . "ch") (:form . "ch") (:end . 85) (:start . 83)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 93)\n  (:start . 86) (:id . 61))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 103)\n  (:start . 94) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 63))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 112)\n  (:start . 107) (:id . 64))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 114) (:start . 113)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 131)\n  (:start . 124) (:id . 69))\n ((:tag . "JJ") (:stem . "proprioceptive") (:form . "proprioceptive")\n  (:end . 146) (:start . 132) (:id . 70))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 152)\n  (:start . 147) (:id . 71))\n ((:tag . "CD") (:stem . "i") (:form . "I") (:end . 154) (:start . 153)\n  (:id . 72))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 161)\n  (:start . 155) (:id . 73))\n ((:tag . "NN") (:stem . "vpda") (:form . "vpda") (:end . 166) (:start . 162)\n  (:id . 74))\n ((:tag . "VBZ") (:stem . "terminate") (:form . "terminates") (:end . 177)\n  (:start . 167) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 180) (:start . 178)\n  (:id . 76))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 186)\n  (:start . 181) (:id . 77))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 188) (:start . 187)\n  (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 190) (:start . 189)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 191) (:start . 190)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s10.328) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503441@unknown@formal@none@1@S@Zlatic, unpublished data) [9],[11].@(((:tag . "JJ") (:stem . "zlatic") (:form . "Zlatic") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "JJ") (:stem . "unpublished") (:form . "unpublished") (:end . 19)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "CD") (:stem . "9],[11") (:form . "9],[11") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 35) (:start . 34)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s10.329) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503442@unknown@formal@none@1@S@Similarly, those sensory neurons that travel in the ISN terminate in layers 2, 3, or 4, depending on their modality and dendritic morphology.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "travel") (:form . "travel") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "ISN") (:form . "ISN") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "terminate") (:form . "terminate") (:end . 65)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 75)\n  (:start . 69) (:id . 54))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 77) (:start . 76)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 56))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 84) (:start . 82)\n  (:id . 59))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 86) (:start . 85)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "depend") (:form . "depending") (:end . 97)\n  (:start . 88) (:id . 62))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 100) (:start . 98)\n  (:id . 63))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 106)\n  (:start . 101) (:id . 64))\n ((:tag . "NN") (:stem . "modality") (:form . "modality") (:end . 115)\n  (:start . 107) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "dendritic") (:form . "dendritic") (:end . 129)\n  (:start . 120) (:id . 67))\n ((:tag . "NN") (:stem . "morphology") (:form . "morphology") (:end . 140)\n  (:start . 130) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.330) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503443@unknown@formal@none@1@S@Dbd and the ddaE and ddaD class I md neurons, terminate in layer 2, the lateral ch neurons terminate in layer 3, and the dorsal class IV neuron ddaC terminates in layer 4 [9],[11].@(((:tag . "NNP") (:stem . "Dbd") (:form . "Dbd") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ddae") (:form . "ddaE") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "ddad") (:form . "ddaD") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 31) (:start . 26)\n  (:id . 48))\n ((:tag . "CD") (:stem . "i") (:form . "I") (:end . 33) (:start . 32)\n  (:id . 49))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 36) (:start . 34)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 44)\n  (:start . 37) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 55)\n  (:start . 46) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 54))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 64) (:start . 59)\n  (:id . 55))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 66) (:start . 65)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 79)\n  (:start . 72) (:id . 59))\n ((:tag . "NN") (:stem . "ch") (:form . "ch") (:end . 82) (:start . 80)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 90)\n  (:start . 83) (:id . 61))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 100)\n  (:start . 91) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 63))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 109)\n  (:start . 104) (:id . 64))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 111) (:start . 110)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 127)\n  (:start . 121) (:id . 69))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 133)\n  (:start . 128) (:id . 70))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 136) (:start . 134)\n  (:id . 71))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 143)\n  (:start . 137) (:id . 72))\n ((:tag . "NN") (:stem . "ddac") (:form . "ddaC") (:end . 148) (:start . 144)\n  (:id . 73))\n ((:tag . "VBZ") (:stem . "terminate") (:form . "terminates") (:end . 159)\n  (:start . 149) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 162) (:start . 160)\n  (:id . 75))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 168)\n  (:start . 163) (:id . 76))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 170) (:start . 169)\n  (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 172) (:start . 171)\n  (:id . 78))\n ((:tag . "CD") (:stem . "9],[11") (:form . "9],[11") (:end . 178)\n  (:start . 172) (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 179) (:start . 178)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s10.331) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503444@unknown@formal@none@1@S@Each of the three characteristic modality-specific sensory termination domains, therefore, contains some neurons that have travelled through the SN, and others that have travelled through the ISN.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 32) (:start . 18) (:id . 46))\n ((:tag . "JJ") (:stem . "modality-specific") (:form . "modality-specific")\n  (:end . 50) (:start . 33) (:id . 47))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 58)\n  (:start . 51) (:id . 48))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 70)\n  (:start . 59) (:id . 49))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 78)\n  (:start . 71) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 51))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 89)\n  (:start . 80) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 99)\n  (:start . 91) (:id . 54))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 104) (:start . 100)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 112)\n  (:start . 105) (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 117) (:start . 113)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 122) (:start . 118)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "travel") (:form . "travelled") (:end . 132)\n  (:start . 123) (:id . 59))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 140)\n  (:start . 133) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 147) (:start . 145)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 159)\n  (:start . 153) (:id . 65))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 164) (:start . 160)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 169) (:start . 165)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "travel") (:form . "travelled") (:end . 179)\n  (:start . 170) (:id . 68))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 187)\n  (:start . 180) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n  (:id . 70))\n ((:tag . "NN") (:stem . "isn") (:form . "ISN") (:end . 195) (:start . 192)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.332) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503445@unknown@formal@none@1@S@Thus, the position of termination in the neuropile does not seem to depend on the nerve through which the sensory neurons travel towards the neuropile nor on the position of entry into the neuropile.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 18)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 33)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 50)\n  (:start . 41) (:id . 50))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "VB") (:stem . "seem") (:form . "seem") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "VB") (:stem . "depend") (:form . "depend") (:end . 74)\n  (:start . 68) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 57))\n ((:tag . "NN") (:stem . "nerve") (:form . "nerve") (:end . 87) (:start . 82)\n  (:id . 58))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 95)\n  (:start . 88) (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 101)\n  (:start . 96) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 113)\n  (:start . 106) (:id . 62))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 121)\n  (:start . 114) (:id . 63))\n ((:tag . "VBP") (:stem . "travel") (:form . "travel") (:end . 128)\n  (:start . 122) (:id . 64))\n ((:tag . "IN") (:stem . "towards") (:form . "towards") (:end . 136)\n  (:start . 129) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 66))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 150)\n  (:start . 141) (:id . 67))\n ((:tag . "CC") (:stem . "nor") (:form . "nor") (:end . 154) (:start . 151)\n  (:id . 68))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 157) (:start . 155)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 70))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 170)\n  (:start . 162) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 72))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 179)\n  (:start . 174) (:id . 73))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 184) (:start . 180)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n  (:id . 75))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 198)\n  (:start . 189) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x10.333.1) (:span 60 64)))\n (:hscopes ((:id . :x10.333.1) (:span 6 198)))\n (:identifiers (:sid . :s10.333) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503446@unknown@formal@none@1@S@(B) Images show the patterns of growth and termination of md axons labelled with 109(280)GAL4, UAS-CD8GFPGFP (white) in 21-h embryos.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "image") (:form . "Images") (:end . 10) (:start . 4)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 15) (:start . 11)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 28)\n  (:start . 20) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 49))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 38)\n  (:start . 32) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 51))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 54)\n  (:start . 43) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 60) (:start . 58)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 66) (:start . 61)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "label") (:form . "labelled") (:end . 75)\n  (:start . 67) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 80) (:start . 76)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "109(280)GAL4") (:form . "109(280)GAL4") (:end . 93)\n  (:start . 81) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "UAS-CD8GFPGFP") (:form . "UAS-CD8GFPGFP")\n  (:end . 108) (:start . 95) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 115)\n  (:start . 110) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 124) (:start . 120)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 132)\n  (:start . 125) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s10.334) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503447@unknown@formal@none@1@S@Dorsal is up.@(((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 13) (:start . 12)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.335) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503448@unknown@formal@none@1@S@Red arrowheads show the midline.@(((:tag . "JJ") (:stem . "red") (:form . "Red") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "arrowhead") (:form . "arrowheads") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 32) (:start . 31)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.336) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503449@unknown@formal@none@1@S@Magenta arrows indicate pathways taken by ISN neurons in the neuropile.@(((:tag . "NNP") (:stem . "Magenta") (:form . "Magenta") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "arrow") (:form . "arrows") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "indicate") (:form . "indicate") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 38) (:start . 33)\n  (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "ISN") (:form . "ISN") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 70)\n  (:start . 61) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s10.337) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503450@unknown@formal@none@1@S@Green arrows indicate pathways taken by SN neurons in the neuropile.@(((:tag . "JJ") (:stem . "green") (:form . "Green") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "arrow") (:form . "arrows") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 36) (:start . 31)\n  (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 67)\n  (:start . 58) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s10.338) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503451@unknown@formal@none@1@S@2 and 4 indicate md neuron termination domains in layers 2 and 4, respectively.@(((:tag . "CD") (:stem . "2") (:form . "2") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 5) (:start . 2)\n  (:id . 43))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 16)\n  (:start . 8) (:id . 45))\n ((:tag . "JJ") (:stem . "md") (:form . "md") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 26)\n  (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 38)\n  (:start . 27) (:id . 48))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 56)\n  (:start . 50) (:id . 51))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 78)\n  (:start . 66) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.339) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503452@unknown@formal@none@1@S@Scale bar: 10 µm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.340) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503453@unknown@formal@none@1@S@Upper: a single section from a confocal z series through an abdominal segment showing the ISN pathways.@(((:tag . "NNP") (:stem . "Upper") (:form . "Upper") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 8) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 15) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 39)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 48)\n  (:start . 42) (:id . 51))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 56)\n  (:start . 49) (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "abdominal") (:form . "abdominal") (:end . 69)\n  (:start . 60) (:id . 54))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 77)\n  (:start . 70) (:id . 55))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 85)\n  (:start . 78) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "isn") (:form . "ISN") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.341) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503454@unknown@formal@none@1@S@Lower: a single section from the same series showing the SN pathways.@(((:tag . "NNP") (:stem . "Lower") (:form . "Lower") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 8) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 15) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 44)\n  (:start . 38) (:id . 50))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 52)\n  (:start . 45) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "sn") (:form . "SN") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 68)\n  (:start . 60) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.342) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503455@unknown@formal@none@1@S@Both ISN and SN md neurons terminate in layers 2 or 4, depending on their dendritic morphology. (0.93 MB TIF)@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "ISN") (:form . "ISN") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "SN") (:form . "SN") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 26)\n  (:start . 19) (:id . 47))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 36)\n  (:start . 27) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 46)\n  (:start . 40) (:id . 50))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 53) (:start . 52)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "depend") (:form . "depending") (:end . 64)\n  (:start . 55) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 67) (:start . 65)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 73)\n  (:start . 68) (:id . 57))\n ((:tag . "JJ") (:stem . "dendritic") (:form . "dendritic") (:end . 83)\n  (:start . 74) (:id . 58))\n ((:tag . "NN") (:stem . "morphology.") (:form . "morphology.") (:end . 95)\n  (:start . 84) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 60))\n ((:tag . "CD") (:stem . "0.93") (:form . "0.93") (:end . 101) (:start . 97)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 104) (:start . 102)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 108) (:start . 105)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 109) (:start . 108)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.343) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503456@unknown@formal@none@1@S@Figure S2 Distributions of Sema 2a and Sema 1a along the antero-posterior axis of the neuropile.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNPS") (:stem . "Distribution") (:form . "Distributions")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 52) (:start . 47)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 73) (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 95)\n  (:start . 86) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.344) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503457@unknown@formal@none@1@S@(A and B) Immunofluorescence visualisation of Sema 2a (A) and Sema 1a (B) (white) in ppkeGFP embryos (13-h AEL).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 6) (:start . 3)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 8) (:start . 7)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 9) (:start . 8) (:id . 46))\n ((:tag . "NNP") (:stem . "Immunofluorescence") (:form . "Immunofluorescence")\n  (:end . 28) (:start . 10) (:id . 47))\n ((:tag . "NN") (:stem . "visualisation") (:form . "visualisation")\n  (:end . 42) (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 66) (:start . 62)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "1a") (:form . "1a") (:end . 69) (:start . 67)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 72) (:start . 71)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 80) (:start . 75)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 64))\n ((:tag . "NN") (:stem . "ppkegfp") (:form . "ppkeGFP") (:end . 92)\n  (:start . 85) (:id . 65))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 100)\n  (:start . 93) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "13-h") (:form . "13-h") (:end . 106) (:start . 102)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "AEL") (:form . "AEL") (:end . 110) (:start . 107)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s10.345) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503458@unknown@formal@none@1@S@Upper images show projections of confocal z series of longitudinal sections through the VNC.@(((:tag . "NNP") (:stem . "Upper") (:form . "Upper") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 29)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "longitudinal") (:form . "longitudinal") (:end . 66)\n  (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 75)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 83)\n  (:start . 76) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s10.346) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503459@unknown@formal@none@1@S@Central and lower images show single more dorsal and more ventral sections from the stack, respectively.@(((:tag . "JJ") (:stem . "central") (:form . "Central") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 48)\n  (:start . 42) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "stack") (:form . "stack") (:end . 89) (:start . 84)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 103)\n  (:start . 91) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s10.347) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503460@unknown@formal@none@1@S@Anterior is to the left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "left") (:form . "left") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 24) (:start . 23)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.348) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503461@unknown@formal@none@1@S@Red arrowheads show midline.@(((:tag . "JJ") (:stem . "red") (:form . "Red") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "arrowhead") (:form . "arrowheads") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 28) (:start . 27)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s10.349) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503462@unknown@formal@none@1@S@a and p indicate the position of anterior (a) and posterior (p) commissures in each segment.@(((:tag . "DT") (:stem . "a") (:form . "a") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 5) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "p") (:form . "p") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 16)\n  (:start . 8) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 59)\n  (:start . 50) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 55))\n ((:tag . "NN") (:stem . "p") (:form . "p") (:end . 62) (:start . 61)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 63) (:start . 62)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "commissure") (:form . "commissures") (:end . 75)\n  (:start . 64) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 83) (:start . 79)\n  (:id . 60))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 91)\n  (:start . 84) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s10.350) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503463@unknown@formal@none@1@S@Scale bar: 35 µm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.351) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503464@unknown@formal@none@1@S@(A) Levels of Sema 2a are uniform along the antero-posterior axis, thus Sema 2a is unlikely to provide instructive information for controlling neurite termination along this axis.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Level") (:form . "Levels") (:end . 10) (:start . 4)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 18) (:start . 14)\n  (:id . 47))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 21) (:start . 19)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 25) (:start . 22)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "uniform") (:form . "uniform") (:end . 33)\n  (:start . 26) (:id . 50))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 39) (:start . 34)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 60) (:start . 44) (:id . 53))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 71) (:start . 67)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 76) (:start . 72)\n  (:id . 57))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 79) (:start . 77)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 82) (:start . 80)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 91)\n  (:start . 83) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 61))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 102)\n  (:start . 95) (:id . 62))\n ((:tag . "JJ") (:stem . "instructive") (:form . "instructive") (:end . 114)\n  (:start . 103) (:id . 63))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 126)\n  (:start . 115) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 130) (:start . 127)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "control") (:form . "controlling") (:end . 142)\n  (:start . 131) (:id . 66))\n ((:tag . "NN") (:stem . "neurite") (:form . "neurite") (:end . 150)\n  (:start . 143) (:id . 67))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 162)\n  (:start . 151) (:id . 68))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 168)\n  (:start . 163) (:id . 69))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 173) (:start . 169)\n  (:id . 70))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 178) (:start . 174)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x10.352.1) (:span 83 91)))\n (:hscopes ((:id . :x10.352.1) (:span 72 178)))\n (:identifiers (:sid . :s10.352) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503465@unknown@formal@none@1@S@Both in more dorsal (layer 2) and in more ventral (layer 3) longitudinal sections, levels of Sema 2a appear uniform along the antero-posterior axis.@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 26) (:start . 21)\n  (:id . 47))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 51))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 41) (:start . 37)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 49)\n  (:start . 42) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 54))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 56) (:start . 51)\n  (:id . 55))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 58) (:start . 57)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 59) (:start . 58)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "longitudinal") (:form . "longitudinal") (:end . 72)\n  (:start . 60) (:id . 58))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 81)\n  (:start . 73) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 89)\n  (:start . 83) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 97) (:start . 93)\n  (:id . 63))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 100) (:start . 98)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 107)\n  (:start . 101) (:id . 65))\n ((:tag . "JJ") (:stem . "uniform") (:form . "uniform") (:end . 115)\n  (:start . 108) (:id . 66))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 121)\n  (:start . 116) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 142) (:start . 126) (:id . 69))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 147) (:start . 143)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s10.353) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503466@unknown@formal@none@1@S@(B) Levels of Sema 1a are uniform along the antero-posterior axis.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Level") (:form . "Levels") (:end . 10) (:start . 4)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 18) (:start . 14)\n  (:id . 47))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 21) (:start . 19)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 25) (:start . 22)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "uniform") (:form . "uniform") (:end . 33)\n  (:start . 26) (:id . 50))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 39) (:start . 34)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 60) (:start . 44) (:id . 53))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.354) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503467@unknown@formal@none@1@S@Thus Sema 1a is unlikely to provide instructive information for controlling neurite termination along this axis.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "JJ") (:stem . "instructive") (:form . "instructive") (:end . 47)\n  (:start . 36) (:id . 49))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 59)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "control") (:form . "controlling") (:end . 75)\n  (:start . 64) (:id . 52))\n ((:tag . "NN") (:stem . "neurite") (:form . "neurite") (:end . 83)\n  (:start . 76) (:id . 53))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 95)\n  (:start . 84) (:id . 54))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 101) (:start . 96)\n  (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 106) (:start . 102)\n  (:id . 56))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 111) (:start . 107)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x10.355.1) (:span 16 24)))\n (:hscopes ((:id . :x10.355.1) (:span 5 111)))\n (:identifiers (:sid . :s10.355) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503468@unknown@formal@none@1@S@Both in more dorsal (layer 1) and in more ventral (layer 3) longitudinal sections, levels of Sema 1a appear uniform along the antero-posterior axis. (1.34 MB TIF)@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 26) (:start . 21)\n  (:id . 47))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 51))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 41) (:start . 37)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 49)\n  (:start . 42) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 54))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 56) (:start . 51)\n  (:id . 55))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 58) (:start . 57)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 59) (:start . 58)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "longitudinal") (:form . "longitudinal") (:end . 72)\n  (:start . 60) (:id . 58))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 81)\n  (:start . 73) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 89)\n  (:start . 83) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 97) (:start . 93)\n  (:id . 63))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 100) (:start . 98)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 107)\n  (:start . 101) (:id . 65))\n ((:tag . "JJ") (:stem . "uniform") (:form . "uniform") (:end . 115)\n  (:start . 108) (:id . 66))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 121)\n  (:start . 116) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 142) (:start . 126) (:id . 69))\n ((:tag . "NN") (:stem . "axis.") (:form . "axis.") (:end . 148)\n  (:start . 143) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 71))\n ((:tag . "CD") (:stem . "1.34") (:form . "1.34") (:end . 154) (:start . 150)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 157) (:start . 155)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 161) (:start . 158)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s10.356) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503469@unknown@formal@none@1@S@Figure S3 Cellular sources of Sema 1a in the neuropile.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "cellular") (:form . "Cellular") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "source") (:form . "sources") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 54)\n  (:start . 45) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s10.357) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503470@unknown@formal@none@1@S@(A–E) Sema 1a is brought into dorsal neuropile, in part, by motor neurons.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–E") (:form . "A–E") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 10) (:start . 6)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 13) (:start . 11)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "bring") (:form . "brought") (:end . 24)\n  (:start . 17) (:id . 48))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 29) (:start . 25)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 36)\n  (:start . 30) (:id . 50))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 46)\n  (:start . 37) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 53))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 55) (:start . 51)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 59) (:start . 57)\n  (:id . 56))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 65) (:start . 60)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 73)\n  (:start . 66) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s10.358) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503471@unknown@formal@none@1@S@(A, C) Immunofluorescence visualisation of motor neuron dendrites labelled with OK371GAL, UAS-CD8-GFP control (white), in OK371GAL4, UASCD8GFP embryos (A) and in OK371GAL4, UASCD8GFP, UAS-reaper embryos (B) at 21-h AEL.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 5) (:start . 4)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 6) (:start . 5) (:id . 46))\n ((:tag . "NNP") (:stem . "Immunofluorescence") (:form . "Immunofluorescence")\n  (:end . 25) (:start . 7) (:id . 47))\n ((:tag . "NN") (:stem . "visualisation") (:form . "visualisation")\n  (:end . 39) (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 65)\n  (:start . 56) (:id . 52))\n ((:tag . "VBN") (:stem . "label") (:form . "labelled") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "OK371GAL") (:form . "OK371GAL") (:end . 88)\n  (:start . 80) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "UAS-CD8-GFP") (:form . "UAS-CD8-GFP") (:end . 101)\n  (:start . 90) (:id . 57))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 109)\n  (:start . 102) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 116)\n  (:start . 111) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 63))\n ((:tag . "NN") (:stem . "ok371gal4") (:form . "OK371GAL4") (:end . 131)\n  (:start . 122) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "UASCD8GFP") (:form . "UASCD8GFP") (:end . 142)\n  (:start . 133) (:id . 66))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 150)\n  (:start . 143) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 152) (:start . 151)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 153) (:start . 152)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 158) (:start . 155)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 161) (:start . 159)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "OK371GAL4") (:form . "OK371GAL4") (:end . 171)\n  (:start . 162) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "UASCD8GFP") (:form . "UASCD8GFP") (:end . 182)\n  (:start . 173) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "UAS-reaper") (:form . "UAS-reaper") (:end . 194)\n  (:start . 184) (:id . 77))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 202)\n  (:start . 195) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 204) (:start . 203)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 205) (:start . 204)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 81))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 209) (:start . 207)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 214) (:start . 210)\n  (:id . 83))\n ((:tag . "NN") (:stem . "ael") (:form . "AEL") (:end . 218) (:start . 215)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s10.359) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503472@unknown@formal@none@1@S@(B, D) Immunofluorescence visualisation of Sema 1a pattern (white) in OK371GAL4, UASCD8GFP control (B) and OK371GAL4, UAS-CD8GFP, UAS-reaper (C) embryos 21-h AEL.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 5) (:start . 4)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 6) (:start . 5) (:id . 46))\n ((:tag . "NNP") (:stem . "Immunofluorescence") (:form . "Immunofluorescence")\n  (:end . 25) (:start . 7) (:id . 47))\n ((:tag . "NN") (:stem . "visualisation") (:form . "visualisation")\n  (:end . 39) (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 58)\n  (:start . 51) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "OK371GAL4") (:form . "OK371GAL4") (:end . 79)\n  (:start . 70) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "UASCD8GFP") (:form . "UASCD8GFP") (:end . 90)\n  (:start . 81) (:id . 59))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 98)\n  (:start . 91) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 101) (:start . 100)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "OK371GAL4") (:form . "OK371GAL4") (:end . 116)\n  (:start . 107) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "UAS-CD8GFP") (:form . "UAS-CD8GFP") (:end . 128)\n  (:start . 118) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "UAS-reaper") (:form . "UAS-reaper") (:end . 140)\n  (:start . 130) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 143) (:start . 142)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 72))\n ((:tag . "VBZ") (:stem . "embryo") (:form . "embryos") (:end . 152)\n  (:start . 145) (:id . 73))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 157) (:start . 153)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "AEL") (:form . "AEL") (:end . 161) (:start . 158)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s10.360) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503473@unknown@formal@none@1@S@Dorsal is up.@(((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 13) (:start . 12)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.361) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503474@unknown@formal@none@1@S@Arrowheads indicate the midline.@(((:tag . "NNS") (:stem . "arrowhead") (:form . "Arrowheads") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 31)\n  (:start . 24) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 32) (:start . 31)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s10.362) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503475@unknown@formal@none@1@S@Magenta lines, neuropile boundaries.@(((:tag . "NNP") (:stem . "Magenta") (:form . "Magenta") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "neuropile") (:form . "neuropile") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 36) (:start . 35)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.363) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503476@unknown@formal@none@1@S@Red lines, layer boundaries.@(((:tag . "JJ") (:stem . "red") (:form . "Red") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 27)\n  (:start . 17) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 28) (:start . 27)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.364) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503477@unknown@formal@none@1@S@Numbers indicate layers.@(((:tag . "NNPS") (:stem . "Number") (:form . "Numbers") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 23)\n  (:start . 17) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 24) (:start . 23)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.365) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503478@unknown@formal@none@1@S@Scale bar: 10 µm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.366) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503479@unknown@formal@none@1@S@A.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 2) (:start . 1) (:id . 43)))@@@1@2@((:identifiers (:sid . :s10.367) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503480@unknown@formal@none@1@S@In control embryos processes of motor neurons labelled with OK371GAL, UAS-CD8-GFP are readily detectable and they are located in layer 1, which normally contains high levels of Sema1a.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "VBN") (:stem . "label") (:form . "labelled") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "OK371GAL") (:form . "OK371GAL") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "UAS-CD8-GFP") (:form . "UAS-CD8-GFP") (:end . 81)\n  (:start . 70) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 104)\n  (:start . 94) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 113) (:start . 109)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 117) (:start . 114)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 125)\n  (:start . 118) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 61))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 134)\n  (:start . 129) (:id . 62))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 136) (:start . 135)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 143)\n  (:start . 138) (:id . 65))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 152)\n  (:start . 144) (:id . 66))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 161)\n  (:start . 153) (:id . 67))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 166) (:start . 162)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 173)\n  (:start . 167) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Sema1a") (:form . "Sema1a") (:end . 183)\n  (:start . 177) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.368) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503481@unknown@formal@none@1@S@(B) In control embryos Sema 1a is present at high levels in layers 1 and 3.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "In") (:end . 6) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 14)\n  (:start . 7) (:id . 46))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 22)\n  (:start . 15) (:id . 47))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 27) (:start . 23)\n  (:id . 48))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 33) (:start . 31)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 41)\n  (:start . 34) (:id . 51))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 44) (:start . 42)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 49) (:start . 45)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 56)\n  (:start . 50) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 66)\n  (:start . 60) (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 68) (:start . 67)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 58))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 74) (:start . 73)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.369) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503482@unknown@formal@none@1@S@(C) Motor neuron dendrites are not detectable in OK371GAL4, UAS-CD8GFP, UAS-reaper.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Motor") (:form . "Motor") (:end . 9) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 16)\n  (:start . 10) (:id . 46))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 26)\n  (:start . 17) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 34) (:start . 31)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 45)\n  (:start . 35) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "OK371GAL4") (:form . "OK371GAL4") (:end . 58)\n  (:start . 49) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "UAS-CD8GFP") (:form . "UAS-CD8GFP") (:end . 70)\n  (:start . 60) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "UAS-reaper") (:form . "UAS-reaper") (:end . 82)\n  (:start . 72) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.370) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503483@unknown@formal@none@1@S@(D) Sema 1a expression in the same animal, as in (C).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 11) (:start . 9)\n  (:id . 46))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 22)\n  (:start . 12) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 25) (:start . 23)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 34) (:start . 30)\n  (:id . 50))\n ((:tag . "NN") (:stem . "animal") (:form . "animal") (:end . 41)\n  (:start . 35) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 45) (:start . 43)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 51) (:start . 50)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.371) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503484@unknown@formal@none@1@S@Sema 1a levels in layer 1 are reduced relative to layer 3 in the absence of motor neuron dendrites.@(((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 37)\n  (:start . 30) (:id . 49))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 55) (:start . 50)\n  (:id . 52))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 55))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 72)\n  (:start . 65) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 57))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 81) (:start . 76)\n  (:id . 58))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 88)\n  (:start . 82) (:id . 59))\n ((:tag . "NNS") (:stem . "dendrite") (:form . "dendrites") (:end . 98)\n  (:start . 89) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.372) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503485@unknown@formal@none@1@S@(E) Quantification of Sema 1a levels in layer 1 relative to layer 3 in the same hemisegment, for OK371-GAL4, UASCD8GFP control and OK371GAL4, UAS-CD8GFP, UAS-reaper, 21-h old embryos.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Quantification") (:form . "Quantification")\n  (:end . 18) (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 36)\n  (:start . 30) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 45) (:start . 40)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 47) (:start . 46)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 56)\n  (:start . 48) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 65) (:start . 60)\n  (:id . 55))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 67) (:start . 66)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 79) (:start . 75)\n  (:id . 59))\n ((:tag . "NN") (:stem . "hemisegment") (:form . "hemisegment") (:end . 91)\n  (:start . 80) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 96) (:start . 93)\n  (:id . 62))\n ((:tag . "NN") (:stem . "ok371-gal4") (:form . "OK371-GAL4") (:end . 107)\n  (:start . 97) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "UASCD8GFP") (:form . "UASCD8GFP") (:end . 118)\n  (:start . 109) (:id . 65))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 126)\n  (:start . 119) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 67))\n ((:tag . "NN") (:stem . "ok371gal4") (:form . "OK371GAL4") (:end . 140)\n  (:start . 131) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "UAS-CD8GFP") (:form . "UAS-CD8GFP") (:end . 152)\n  (:start . 142) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "UAS-reaper") (:form . "UAS-reaper") (:end . 164)\n  (:start . 154) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 170) (:start . 166)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "old") (:form . "old") (:end . 174) (:start . 171)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 182)\n  (:start . 175) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s10.373) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503486@unknown@formal@none@1@S@For this purpose, embryos of the two genotypes were stained with antibody against GFP (to distinguish between embryos with and without motor neurons).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "purpose") (:form . "purpose") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 46)\n  (:start . 37) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "stain") (:form . "stained") (:end . 59)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 73)\n  (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 81)\n  (:start . 74) (:id . 55))\n ((:tag . "NNP") (:stem . "GFP") (:form . "GFP") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "VB") (:stem . "distinguish") (:form . "distinguish") (:end . 101)\n  (:start . 90) (:id . 59))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 109)\n  (:start . 102) (:id . 60))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 117)\n  (:start . 110) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 122) (:start . 118)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 63))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 134)\n  (:start . 127) (:id . 64))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 140)\n  (:start . 135) (:id . 65))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 148)\n  (:start . 141) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s10.374) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503487@unknown@formal@none@1@S@In each embryo seven sections from seven different hemisegments where chosen at random, and for each section the ratio of the pixel intensity (PI) for the channel showing Sema 1a staining in layer 1 relative to layer 3 (PI1/3=PI[Sema 1a in layer 1]/PI[Sema 1a in layer 3]) was calculated.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "CD") (:stem . "seven") (:form . "seven") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "CD") (:stem . "seven") (:form . "seven") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 63)\n  (:start . 51) (:id . 50))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 69) (:start . 64)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 76)\n  (:start . 70) (:id . 52))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 86)\n  (:start . 80) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 100) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "section") (:form . 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"DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 70))\n ((:tag . "NN") (:stem . "channel") (:form . "channel") (:end . 162)\n  (:start . 155) (:id . 71))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 170)\n  (:start . 163) (:id . 72))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 175) (:start . 171)\n  (:id . 73))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 178) (:start . 176)\n  (:id . 74))\n ((:tag . "NN") (:stem . "staining") (:form . "staining") (:end . 187)\n  (:start . 179) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 190) (:start . 188)\n  (:id . 76))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 196)\n  (:start . 191) (:id . 77))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 198) (:start . 197)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 207)\n  (:start . 199) (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 210) (:start . 208)\n  (:id . 80))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 216)\n  (:start . 211) (:id . 81))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 218) (:start . 217)\n  (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 220) (:start . 219)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "PI1/3=PI[Sema") (:form . "PI1/3=PI[Sema")\n  (:end . 233) (:start . 220) (:id . 84))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 236) (:start . 234)\n  (:id . 85))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 239) (:start . 237)\n  (:id . 86))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 245)\n  (:start . 240) (:id . 87))\n ((:tag . "NNP") (:stem . "1]/PI[Sema") (:form . "1]/PI[Sema") (:end . 256)\n  (:start . 246) (:id . 88))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 259) (:start . 257)\n  (:id . 89))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 262) (:start . 260)\n  (:id . 90))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 268)\n  (:start . 263) (:id . 91))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 270) (:start . 269)\n  (:id . 92))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 271) (:start . 270)\n  (:id . 93))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 272) (:start . 271)\n  (:id . 94))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 276) (:start . 273)\n  (:id . 95))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 287)\n  (:start . 277) (:id . 96))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 288) (:start . 287)\n  (:id . 97)))@@@1@56@((:identifiers (:sid . :s10.375) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503488@unknown@formal@none@1@S@A significant decrease (p=2×10-6; Student's t-test) in pixel intensity in layer 1 relative to layer 3 was observed in OK371GAL4, UAS-CD8GFP, UAS-reaper embryos (average PI1/3=0.73; standard deviation [SD]=0.09, n=65 hemisegments) compared to OK371GAL4, UAS-CD8GFP controls (average PI1/3=0.81; SD=0.08, n=48 hemisegments).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 13)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "p=2×10-6") (:form . "p=2×10-6") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Student") (:form . 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(:end . 322) (:start . 321)\n  (:id . 98)))@@@1@57@((:identifiers (:sid . :s10.376) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503489@unknown@formal@none@1@S@(F and G) Sema 1a is brought into dorsal and ventral neuropile, in part, by GABAergic interneurons.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 6) (:start . 3)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 8) (:start . 7)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 9) (:start . 8) (:id . 46))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 14) (:start . 10)\n  (:id . 47))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 17) (:start . 15)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "bring") (:form . "brought") (:end . 28)\n  (:start . 21) (:id . 50))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 33) (:start . 29)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 40)\n  (:start . 34) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 52)\n  (:start . 45) (:id . 54))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 62)\n  (:start . 53) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 57))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 71) (:start . 67)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "gabaergic") (:form . "GABAergic") (:end . 85)\n  (:start . 76) (:id . 61))\n ((:tag . "NNS") (:stem . "interneuron") (:form . "interneurons") (:end . 98)\n  (:start . 86) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.377) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503490@unknown@formal@none@1@S@(F and G) Immunofluorescence visualisation of motor neurons and GABAergic processes labelled with GADGAL, UAS-CD8-GFP (white) (F) and of Sema 1a pattern (white) in GADGAL4, UAS-CD8GFP, UAS-reaper (G), 21-h old embryos.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 6) (:start . 3)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 8) (:start . 7)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 9) (:start . 8) (:id . 46))\n ((:tag . "NNP") (:stem . "Immunofluorescence") (:form . "Immunofluorescence")\n  (:end . 28) (:start . 10) (:id . 47))\n ((:tag . "NN") (:stem . "visualisation") (:form . "visualisation")\n  (:end . 42) (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 51) (:start . 46)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 59)\n  (:start . 52) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "gabaergic") (:form . "GABAergic") (:end . 73)\n  (:start . 64) (:id . 53))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 83)\n  (:start . 74) (:id . 54))\n ((:tag . "VBN") (:stem . "label") (:form . "labelled") (:end . 92)\n  (:start . 84) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "GADGAL") (:form . "GADGAL") (:end . 104)\n  (:start . 98) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "UAS-CD8-GFP") (:form . "UAS-CD8-GFP") (:end . 117)\n  (:start . 106) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 124)\n  (:start . 119) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 127) (:start . 126)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 141) (:start . 137)\n  (:id . 68))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 144) (:start . 142)\n  (:id . 69))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 152)\n  (:start . 145) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 159)\n  (:start . 154) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 163) (:start . 161)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "GADGAL4") (:form . "GADGAL4") (:end . 171)\n  (:start . 164) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "UAS-CD8GFP") (:form . "UAS-CD8GFP") (:end . 183)\n  (:start . 173) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "UAS-reaper") (:form . "UAS-reaper") (:end . 195)\n  (:start . 185) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 197) (:start . 196)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 198) (:start . 197)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n  (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 205) (:start . 201)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "old") (:form . "old") (:end . 209) (:start . 206)\n  (:id . 85))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 217)\n  (:start . 210) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s10.378) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503491@unknown@formal@none@1@S@Dorsal is up.@(((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 13) (:start . 12)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.379) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503492@unknown@formal@none@1@S@Arrowheads indicate the midline.@(((:tag . "NNS") (:stem . "arrowhead") (:form . "Arrowheads") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 31)\n  (:start . 24) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 32) (:start . 31)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s10.380) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503493@unknown@formal@none@1@S@Magenta lines, neuropile boundaries.@(((:tag . "NNP") (:stem . "Magenta") (:form . "Magenta") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "neuropile") (:form . "neuropile") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 36) (:start . 35)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.381) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503494@unknown@formal@none@1@S@Red lines, layer boundaries.@(((:tag . "JJ") (:stem . "red") (:form . "Red") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 27)\n  (:start . 17) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 28) (:start . 27)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.382) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503495@unknown@formal@none@1@S@Numbers indicate layers.@(((:tag . "NNPS") (:stem . "Number") (:form . "Numbers") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 23)\n  (:start . 17) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 24) (:start . 23)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.383) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503496@unknown@formal@none@1@S@M, medial; I, intermediate; L, lateral domains.@(((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 9) (:start . 3)\n  (:id . 44))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 10) (:start . 9)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "i") (:form . "I") (:end . 12) (:start . 11)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 26)\n  (:start . 14) (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 27) (:start . 26)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "L") (:form . "L") (:end . 29) (:start . 28)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 38)\n  (:start . 31) (:id . 52))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 46)\n  (:start . 39) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s10.384) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503497@unknown@formal@none@1@S@Scale bar: 10 µm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.385) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503498@unknown@formal@none@1@S@(F) Processes of GABAergic interneurons and motor neurons together (white) cover the dorsal and central regions of the neuropile, which normally contain high levels of Sema 1a.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "process") (:form . "Processes") (:end . 13)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "gabaergic") (:form . "GABAergic") (:end . 26)\n  (:start . 17) (:id . 47))\n ((:tag . "NNS") (:stem . "interneuron") (:form . "interneurons") (:end . 39)\n  (:start . 27) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 57)\n  (:start . 50) (:id . 51))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 66)\n  (:start . 58) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "cover") (:form . "cover") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 91)\n  (:start . 85) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 103)\n  (:start . 96) (:id . 60))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 111)\n  (:start . 104) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 63))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 128)\n  (:start . 119) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 135)\n  (:start . 130) (:id . 66))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 144)\n  (:start . 136) (:id . 67))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 152)\n  (:start . 145) (:id . 68))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 157) (:start . 153)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 164)\n  (:start . 158) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 167) (:start . 165)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 172) (:start . 168)\n  (:id . 72))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 175) (:start . 173)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s10.386) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503499@unknown@formal@none@1@S@(G) Sema 1a (white) levels appear highly reduced in embryos that lack both GABAergic interneurons and motor neurons.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 11) (:start . 9)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 18) (:start . 13)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 19) (:start . 18)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 26)\n  (:start . 20) (:id . 50))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 33)\n  (:start . 27) (:id . 51))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 40)\n  (:start . 34) (:id . 52))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 48)\n  (:start . 41) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 59)\n  (:start . 52) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 64) (:start . 60)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "lack") (:form . "lack") (:end . 69) (:start . 65)\n  (:id . 57))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 74) (:start . 70)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "gabaergic") (:form . "GABAergic") (:end . 84)\n  (:start . 75) (:id . 59))\n ((:tag . "NNS") (:stem . "interneuron") (:form . "interneurons") (:end . 97)\n  (:start . 85) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 61))\n ((:tag . "NN") (:stem . "motor") (:form . "motor") (:end . 107)\n  (:start . 102) (:id . 62))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 115)\n  (:start . 108) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.387) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503500@unknown@formal@none@1@S@The characteristic Sema 1a distribution pattern is no longer detectable. (1.73 MB TIF)@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 39)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 47)\n  (:start . 40) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "RB") (:stem . "no") (:form . "no") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "JJR") (:stem . "long") (:form . "longer") (:end . 60) (:start . 54)\n  (:id . 50))\n ((:tag . "FW") (:stem . "detectable.") (:form . "detectable.") (:end . 72)\n  (:start . 61) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n  (:id . 52))\n ((:tag . "CD") (:stem . "1.73") (:form . "1.73") (:end . 78) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s10.388) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503501@unknown@formal@none@1@S@Figure S4 Restoration of sema 2a in midline cells partially rescues the aberrant central projection of Class IV axons.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Restoration") (:form . "Restoration") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 59)\n  (:start . 50) (:id . 51))\n ((:tag . "VBZ") (:stem . "rescue") (:form . "rescues") (:end . 67)\n  (:start . 60) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 80)\n  (:start . 72) (:id . 54))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 88)\n  (:start . 81) (:id . 55))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 99)\n  (:start . 89) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 108)\n  (:start . 103) (:id . 58))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 117)\n  (:start . 112) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.389) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503502@unknown@formal@none@1@S@(A–C) Immunofluorescence visualisation of Sema 2a (white), in sema 2a mutant (A) and in sema 2a, UAS-sema 2a; single-mindedGAL4, ppkeGFP (B and C) embryos (21-h old).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–C") (:form . "A–C") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "NNP") (:stem . "Immunofluorescence") (:form . "Immunofluorescence")\n  (:end . 24) (:start . 6) (:id . 45))\n ((:tag . "NN") (:stem . "visualisation") (:form . "visualisation")\n  (:end . 38) (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 66) (:start . 62)\n  (:id . 55))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 69) (:start . 67)\n  (:id . 56))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 76)\n  (:start . 70) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 79) (:start . 78)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 62))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 92) (:start . 88)\n  (:id . 63))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 95) (:start . 93)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "UAS-sema") (:form . "UAS-sema") (:end . 105)\n  (:start . 97) (:id . 66))\n ((:tag . "CD") (:stem . "2a") (:form . "2a") (:end . 108) (:start . 106)\n  (:id . 67))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 109) (:start . 108)\n  (:id . 68))\n ((:tag . "NN") (:stem . "single-mindedgal4") (:form . "single-mindedGAL4")\n  (:end . 127) (:start . 110) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "ppkeGFP") (:form . "ppkeGFP") (:end . 136)\n  (:start . 129) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 139) (:start . 138)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 145) (:start . 144)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 154)\n  (:start . 147) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 160) (:start . 156)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "old") (:form . "old") (:end . 164) (:start . 161)\n  (:id . 80))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s10.390) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503503@unknown@formal@none@1@S@(D) Projections of class IV axons (green) and Fas II tracts (red) in sema 2a,UAS-sema 2a;single-mindedGAL4,ppkeGFP embryos (21-h old).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "projection") (:form . "Projections") (:end . 15)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 24) (:start . 19)\n  (:id . 47))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 33) (:start . 28)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 35) (:start . 34)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 40) (:start . 35)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 41) (:start . 40)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 49) (:start . 46)\n  (:id . 54))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 52) (:start . 50)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 59)\n  (:start . 53) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 64) (:start . 61)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 65) (:start . 64)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 60))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 73) (:start . 69)\n  (:id . 61))\n ((:tag . "FW") (:stem . "2a,UAS-sema") (:form . "2a,UAS-sema") (:end . 85)\n  (:start . 74) (:id . 62))\n ((:tag . "FW") (:stem . "2a;single-mindedGAL4,ppkeGFP")\n  (:form . "2a;single-mindedGAL4,ppkeGFP") (:end . 114) (:start . 86)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 122)\n  (:start . 115) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 128) (:start . 124)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "old") (:form . "old") (:end . 132) (:start . 129)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.391) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503504@unknown@formal@none@1@S@(A and B) Image shows projections of a confocal z series of longitudinal sections through the VNC.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 6) (:start . 3)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 8) (:start . 7)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 9) (:start . 8) (:id . 46))\n ((:tag . "NN") (:stem . "image") (:form . "Image") (:end . 15) (:start . 10)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 21) (:start . 16)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 33)\n  (:start . 22) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 47)\n  (:start . 39) (:id . 52))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 49) (:start . 48)\n  (:id . 53))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 56)\n  (:start . 50) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "longitudinal") (:form . "longitudinal") (:end . 72)\n  (:start . 60) (:id . 56))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 81)\n  (:start . 73) (:id . 57))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 89)\n  (:start . 82) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 97) (:start . 94)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.392) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503505@unknown@formal@none@1@S@Anterior is to the left.@(((:tag . "NNP") (:stem . "Anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "left") (:form . "left") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 24) (:start . 23)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.393) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503506@unknown@formal@none@1@S@Red arrowheads show midline.@(((:tag . "JJ") (:stem . "red") (:form . "Red") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "arrowhead") (:form . "arrowheads") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 28) (:start . 27)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s10.394) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503507@unknown@formal@none@1@S@Magenta line: neuropile boundary.@(((:tag . "NNP") (:stem . "Magenta") (:form . "Magenta") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "neuropile") (:form . "neuropile") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "boundary") (:form . "boundary") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 33) (:start . 32)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.395) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503508@unknown@formal@none@1@S@Scale bar: 14 µm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.396) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503509@unknown@formal@none@1@S@(C and D) Images show projections of a confocal z series of transverse sections through A7.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 6) (:start . 3)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 8) (:start . 7)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 9) (:start . 8) (:id . 46))\n ((:tag . "NNP") (:stem . "Image") (:form . "Images") (:end . 16)\n  (:start . 10) (:id . 47))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 21) (:start . 17)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 33)\n  (:start . 22) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 47)\n  (:start . 39) (:id . 52))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 49) (:start . 48)\n  (:id . 53))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 56)\n  (:start . 50) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "transverse") (:form . "transverse") (:end . 70)\n  (:start . 60) (:id . 56))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 79)\n  (:start . 71) (:id . 57))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 87)\n  (:start . 80) (:id . 58))\n ((:tag . "NNP") (:stem . "A7") (:form . "A7") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.397) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503510@unknown@formal@none@1@S@Dorsal is up.@(((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 13) (:start . 12)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.398) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503511@unknown@formal@none@1@S@Arrowheads show midline.@(((:tag . "NNS") (:stem . "arrowhead") (:form . "Arrowheads") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 24) (:start . 23)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.399) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503512@unknown@formal@none@1@S@Magenta line (C): neuropile boundary.@(((:tag . "NNP") (:stem . "Magenta") (:form . "Magenta") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "neuropile") (:form . "neuropile") (:end . 27)\n  (:start . 18) (:id . 48))\n ((:tag . "NN") (:stem . "boundary") (:form . "boundary") (:end . 36)\n  (:start . 28) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 37) (:start . 36)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s10.400) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503513@unknown@formal@none@1@S@Red (C) and white (D) lines, layer boundaries.@(((:tag . "VBN") (:stem . "red") (:form . "Red") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 6) (:start . 5)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 7) (:start . 6) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 17) (:start . 12)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 19) (:start . 18)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 20) (:start . 19)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 21) (:start . 20)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 27) (:start . 22)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 52))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 34) (:start . 29)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 45)\n  (:start . 35) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.401) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503514@unknown@formal@none@1@S@Numbers indicate layers: M, medial; I, intermediate; L, lateral domains.@(((:tag . "NNPS") (:stem . "Number") (:form . "Numbers") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 23)\n  (:start . 17) (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 34)\n  (:start . 28) (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "i") (:form . "I") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 51)\n  (:start . 39) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "L") (:form . "L") (:end . 54) (:start . 53)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 63)\n  (:start . 56) (:id . 56))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 71)\n  (:start . 64) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.402) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503515@unknown@formal@none@1@S@Scale bar: 9 µm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 16) (:start . 15)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.403) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503516@unknown@formal@none@1@S@(A) Sema 2a expression is not detectable above background levels in the neuropile of 21-h-old sema 2a mutant embryos.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 11) (:start . 9)\n  (:id . 46))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 22)\n  (:start . 12) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 29) (:start . 26)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 40)\n  (:start . 30) (:id . 50))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 46) (:start . 41)\n  (:id . 51))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 57)\n  (:start . 47) (:id . 52))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 64)\n  (:start . 58) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 81)\n  (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "21-h-old") (:form . "21-h-old") (:end . 93)\n  (:start . 85) (:id . 58))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 101) (:start . 99)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 108)\n  (:start . 102) (:id . 61))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 116)\n  (:start . 109) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.404) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503517@unknown@formal@none@1@S@(B) High levels of Sema 2a expression are detectable in sema 2a, UAS-sema 2a; single-mindedGAL4, ppkeGFP embryos.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "high") (:form . "High") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 15) (:start . 9)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 23) (:start . 19)\n  (:id . 48))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 26) (:start . 24)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 37)\n  (:start . 27) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 41) (:start . 38)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 52)\n  (:start . 42) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 60) (:start . 56)\n  (:id . 54))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 63) (:start . 61)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "UAS-sema") (:form . "UAS-sema") (:end . 73)\n  (:start . 65) (:id . 57))\n ((:tag . "CD") (:stem . "2a") (:form . "2a") (:end . 76) (:start . 74)\n  (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 77) (:start . 76)\n  (:id . 59))\n ((:tag . "NN") (:stem . "single-mindedgal4") (:form . "single-mindedGAL4")\n  (:end . 95) (:start . 78) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 61))\n ((:tag . "NN") (:stem . "ppkegfp") (:form . "ppkeGFP") (:end . 104)\n  (:start . 97) (:id . 62))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 112)\n  (:start . 105) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.405) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503518@unknown@formal@none@1@S@(C) Transverse view of Sema 2a expression in sema 2a, UAS-sema 2a; single-mindedGAL4, ppkeGFP embryos.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "transverse") (:form . "Transverse") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "view") (:form . "view") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 27) (:start . 23)\n  (:id . 48))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 41)\n  (:start . 31) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 49) (:start . 45)\n  (:id . 52))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 52) (:start . 50)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "UAS-sema") (:form . "UAS-sema") (:end . 62)\n  (:start . 54) (:id . 55))\n ((:tag . "CD") (:stem . "2a") (:form . "2a") (:end . 65) (:start . 63)\n  (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 66) (:start . 65)\n  (:id . 57))\n ((:tag . "NN") (:stem . "single-mindedgal4") (:form . "single-mindedGAL4")\n  (:end . 84) (:start . 67) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 59))\n ((:tag . "NN") (:stem . "ppkegfp") (:form . "ppkeGFP") (:end . 93)\n  (:start . 86) (:id . 60))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 101)\n  (:start . 94) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s10.406) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503519@unknown@formal@none@1@S@Sema 2a expression in midline cells, in an otherwise mutant background, results in its distribution throughout the neuropile, with lower levels detectable on the lateral edges of the neuropile and in the ventral-most neuropile.@(((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 52)\n  (:start . 43) (:id . 51))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 70)\n  (:start . 60) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 79)\n  (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 86) (:start . 83)\n  (:id . 57))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 99)\n  (:start . 87) (:id . 58))\n ((:tag . "IN") (:stem . "throughout") (:form . "throughout") (:end . 110)\n  (:start . 100) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 60))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 124)\n  (:start . 115) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 130) (:start . 126)\n  (:id . 63))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 136) (:start . 131)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 143)\n  (:start . 137) (:id . 65))\n ((:tag . "JJ") (:stem . "detectable") (:form . "detectable") (:end . 154)\n  (:start . 144) (:id . 66))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 157) (:start . 155)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 169)\n  (:start . 162) (:id . 69))\n ((:tag . "NNS") (:stem . "edge") (:form . "edges") (:end . 175)\n  (:start . 170) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 178) (:start . 176)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 182) (:start . 179)\n  (:id . 72))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 192)\n  (:start . 183) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 196) (:start . 193)\n  (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 199) (:start . 197)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "ventral-most") (:form . "ventral-most") (:end . 216)\n  (:start . 204) (:id . 77))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 226)\n  (:start . 217) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s10.407) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503520@unknown@formal@none@1@S@(D) Restoration of Sema 2a expression in midline cells alone reduces the aberrant central projection of class IV neurons (compare to Figure 5C).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Restoration") (:form . "Restoration") (:end . 15)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 23) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 26) (:start . 24)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 37)\n  (:start . 27) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 48)\n  (:start . 41) (:id . 51))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 54) (:start . 49)\n  (:id . 52))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 60) (:start . 55)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "reduce") (:form . "reduces") (:end . 68)\n  (:start . 61) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 81)\n  (:start . 73) (:id . 56))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 89)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 100)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 109)\n  (:start . 104) (:id . 60))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 120)\n  (:start . 113) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . "NN") (:stem . "compare") (:form . "compare") (:end . 129)\n  (:start . 122) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 139)\n  (:start . 133) (:id . 66))\n ((:tag . "NN") (:stem . "5c") (:form . "5C") (:end . 142) (:start . 140)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.408) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503521@unknown@formal@none@1@S@However, this rescue was accompanied by additional defects in the medio-lateral axis, with increased lateral termination of class IV axons.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "rescue") (:form . "rescue") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "accompany") (:form . "accompanied") (:end . 36)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 50)\n  (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 58)\n  (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 79) (:start . 66) (:id . 53))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 84) (:start . 80)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 90) (:start . 86)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 100)\n  (:start . 91) (:id . 57))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 108)\n  (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 120)\n  (:start . 109) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 60))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 129)\n  (:start . 124) (:id . 61))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 132) (:start . 130)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 138)\n  (:start . 133) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.409) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503522@unknown@formal@none@1@S@Thus the source of the Sema 2a gradients could potentially be a subset of the midline cells, although we cannot exclude the possibility that some other cells are the endogenous source of this cue in the CNS.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "gradient") (:form . "gradients") (:end . 40)\n  (:start . 31) (:id . 49))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "RB") (:stem . "potentially") (:form . "potentially") (:end . 58)\n  (:start . 47) (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 70)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 85)\n  (:start . 78) (:id . 57))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 91) (:start . 86)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 101)\n  (:start . 93) (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 104) (:start . 102)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "cannot") (:form . "cannot") (:end . 111)\n  (:start . 105) (:id . 62))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 119)\n  (:start . 112) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 64))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 135)\n  (:start . 124) (:id . 65))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 140) (:start . 136)\n  (:id . 66))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 145) (:start . 141)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 151)\n  (:start . 146) (:id . 68))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 157)\n  (:start . 152) (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 161) (:start . 158)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 176)\n  (:start . 166) (:id . 72))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 183)\n  (:start . 177) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 186) (:start . 184)\n  (:id . 74))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 191) (:start . 187)\n  (:id . 75))\n ((:tag . "NN") (:stem . "cue") (:form . "cue") (:end . 195) (:start . 192)\n  (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 198) (:start . 196)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 202) (:start . 199)\n  (:id . 78))\n ((:tag . "NN") (:stem . "cns") (:form . "CNS") (:end . 206) (:start . 203)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x10.410.1) (:span 105 135))\n  ((:id . :x10.410.2) (:span 47 58)) ((:id . :x10.410.3) (:span 41 46)))\n (:hscopes ((:id . :x10.410.1) (:span 105 206))\n  ((:id . :x10.410.2) (:span 47 91)) ((:id . :x10.410.3) (:span 41 91)))\n (:identifiers (:sid . :s10.410) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503523@unknown@formal@none@1@S@(E) Chart shows average percentage of hemisegments per embryo (per 14 abdominal hemisegments) with aberrant class IV terminals in layer 2 (Hat(2)), in sema 2a/+, sema 2a mutant and sema 2a,UAS-sema 2a;single-mindedGAL4,ppkeGFP embryos.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Chart") (:form . "Chart") (:end . 9) (:start . 4)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 15) (:start . 10)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 23)\n  (:start . 16) (:id . 47))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 34)\n  (:start . 24) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 50)\n  (:start . 38) (:id . 50))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 69) (:start . 67)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "abdominal") (:form . "abdominal") (:end . 79)\n  (:start . 70) (:id . 56))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 92)\n  (:start . 80) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 107)\n  (:start . 99) (:id . 60))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 113)\n  (:start . 108) (:id . 61))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 116) (:start . 114)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 126)\n  (:start . 117) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 64))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 135)\n  (:start . 130) (:id . 65))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 137) (:start . 136)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Hat(2))") (:form . "Hat(2))") (:end . 146)\n  (:start . 139) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n  (:id . 70))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 155) (:start . 151)\n  (:id . 71))\n ((:tag . "NN") (:stem . "2a/+") (:form . "2a/+") (:end . 160) (:start . 156)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 73))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 166) (:start . 162)\n  (:id . 74))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 169) (:start . 167)\n  (:id . 75))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 176)\n  (:start . 170) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 180) (:start . 177)\n  (:id . 77))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 185) (:start . 181)\n  (:id . 78))\n ((:tag . "FW") (:stem . "2a,UAS-sema") (:form . "2a,UAS-sema") (:end . 197)\n  (:start . 186) (:id . 79))\n ((:tag . "FW") (:stem . "2a;single-mindedGAL4,ppkeGFP")\n  (:form . "2a;single-mindedGAL4,ppkeGFP") (:end . 226) (:start . 198)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 234)\n  (:start . 227) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 235) (:start . 234)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s10.411) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503524@unknown@formal@none@1@S@Hat(2) is significantly higher in sema 2a (p=4×10-4; Student's t-test; average Hat(2)=3.3%; n=24 embryos, 336 hemisegments), than in sema 2a/+ controls (average Hat(2)=0%, n=30 embryos, 420 hemisegments). sema 2a, UAS-sema 2a; sim-GAL4,ppkeGFP show a significant reduction in Hat(2) (red **, p=0.006; Student's t-test; average Hat(2)=0.7%, n=29 embryos, 406 hemisegments), compared to sema 2a mutant embryos (average Hat(2)=3.3%). (1.28 MB TIF)@(((:tag . "NNP") (:stem . "Hat(2)") (:form . "Hat(2)") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 30) (:start . 24)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sema") (:form . 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5503525@unknown@formal@none@1@S@Figure S5 Examples of growth and termination errors of class IV axons in mutant embryos.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "example") (:form . "Examples") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 44)\n  (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 60) (:start . 55)\n  (:id . 51))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 79)\n  (:start . 73) (:id . 55))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 87)\n  (:start . 80) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.413) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503526@unknown@formal@none@1@S@Projections of class IV axons (white) in mutant embryos (21-h AEL).@(((:tag . "NNS") (:stem . "projection") (:form . "Projections") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 47)\n  (:start . 41) (:id . 51))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 55)\n  (:start . 48) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "AEL") (:form . "AEL") (:end . 65) (:start . 62)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.414) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503527@unknown@formal@none@1@S@Images show projections of a confocal z series of transverse sections through A7.@(((:tag . "NNS") (:stem . "image") (:form . "Images") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "transverse") (:form . "transverse") (:end . 60)\n  (:start . 50) (:id . 51))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 69)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . "NNP") (:stem . "A7") (:form . "A7") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.415) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503528@unknown@formal@none@1@S@Dorsal is up.@(((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 13) (:start . 12)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.416) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503529@unknown@formal@none@1@S@Arrowheads show midline.@(((:tag . "NNS") (:stem . "arrowhead") (:form . "Arrowheads") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 24) (:start . 23)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.417) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503530@unknown@formal@none@1@S@Magenta arrows point to aberrant (dorsal or central) terminals of class IV axons.@(((:tag . "NNP") (:stem . "Magenta") (:form . "Magenta") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "arrow") (:form . "arrows") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 51)\n  (:start . 44) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.418) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503531@unknown@formal@none@1@S@Green arrows point to class IV axons that initially grow normally (ventrally) in the neuropile, but afterwards turn dorsally, and terminate in aberrant layers (1, 2, or 3).@(((:tag . "NNP") (:stem . "Green") (:form . "Green") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "arrow") (:form . "arrows") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "RB") (:stem . "initially") (:form . "initially") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 65)\n  (:start . 57) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 76)\n  (:start . 67) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 94)\n  (:start . 85) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 99) (:start . 96)\n  (:id . 60))\n ((:tag . "RB") (:stem . "afterwards") (:form . "afterwards") (:end . 110)\n  (:start . 100) (:id . 61))\n ((:tag . "VBP") (:stem . "turn") (:form . "turn") (:end . 115) (:start . 111)\n  (:id . 62))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 124)\n  (:start . 116) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 65))\n ((:tag . "VB") (:stem . "terminate") (:form . "terminate") (:end . 139)\n  (:start . 130) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 142) (:start . 140)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 151)\n  (:start . 143) (:id . 68))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 158)\n  (:start . 152) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n  (:id . 70))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 161) (:start . 160)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 72))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 164) (:start . 163)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 168) (:start . 166)\n  (:id . 75))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 170) (:start . 169)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 171) (:start . 170)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s10.419) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503532@unknown@formal@none@1@S@Red arrows point to class IV axons that grow aberrantly in dorsal or central neuropile.@(((:tag . "VBN") (:stem . "red") (:form . "Red") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "arrow") (:form . "arrows") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 34) (:start . 29)\n  (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "RB") (:stem . "aberrantly") (:form . "aberrantly") (:end . 55)\n  (:start . 45) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 65)\n  (:start . 59) (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 76)\n  (:start . 69) (:id . 55))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 86)\n  (:start . 77) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.420) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503533@unknown@formal@none@1@S@We define terminals as large structures that form at the tips of axons (although sometimes they form along the axon path, on either side of the main axon trunk, which continues growing).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "define") (:form . "define") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 39)\n  (:start . 29) (:id . 47))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "tip") (:form . "tips") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 70) (:start . 65)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 80)\n  (:start . 72) (:id . 56))\n ((:tag . "RB") (:stem . "sometimes") (:form . "sometimes") (:end . 90)\n  (:start . 81) (:id . 57))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 115) (:start . 111)\n  (:id . 62))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 120) (:start . 116)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 124) (:start . 122)\n  (:id . 65))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 131)\n  (:start . 125) (:id . 66))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 136) (:start . 132)\n  (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 139) (:start . 137)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "main") (:form . "main") (:end . 148) (:start . 144)\n  (:id . 70))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 153) (:start . 149)\n  (:id . 71))\n ((:tag . "NN") (:stem . "trunk") (:form . "trunk") (:end . 159)\n  (:start . 154) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 73))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 166)\n  (:start . 161) (:id . 74))\n ((:tag . "VBZ") (:stem . "continue") (:form . "continues") (:end . 176)\n  (:start . 167) (:id . 75))\n ((:tag . "VBG") (:stem . "grow") (:form . "growing") (:end . 184)\n  (:start . 177) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 185) (:start . 184)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s10.421) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503534@unknown@formal@none@1@S@These structures are thicker than the axon itself and we assume they contain presynaptic specialisations.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "JJR") (:stem . "thick") (:form . "thicker") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "assume") (:form . "assume") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 76)\n  (:start . 69) (:id . 54))\n ((:tag . "JJ") (:stem . "presynaptic") (:form . "presynaptic") (:end . 88)\n  (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "specialisation") (:form . "specialisations")\n  (:end . 104) (:start . 89) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x10.422.1) (:span 57 63)))\n (:hscopes ((:id . :x10.422.1) (:span 57 104)))\n (:identifiers (:sid . :s10.422) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503535@unknown@formal@none@1@S@Class IV axons exhibit several kinds of phenotypes in sema and plex mutant embryos.@(((:tag . "NNP") (:stem . "Class") (:form . "Class") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "exhibit") (:form . "exhibit") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "kind") (:form . "kinds") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 50)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 74)\n  (:start . 68) (:id . 54))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 82)\n  (:start . 75) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s10.423) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503536@unknown@formal@none@1@S@The most striking is normal initial growth with aberrant termination, where the axon initially grows appropriately towards its target area in the ventral medial neuropile, but then makes a sharp dorsal turn, and terminates in layers 1, 2, or 3 (for examples see Figures 5D, left axons, 7E, right axon, and S5A).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "striking") (:form . "striking") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 68)\n  (:start . 57) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 75) (:start . 70)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "RB") (:stem . "initially") (:form . "initially") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "VBZ") (:stem . "grow") (:form . "grows") (:end . 100) (:start . 95)\n  (:id . 57))\n ((:tag . "RB") (:stem . "appropriately") (:form . "appropriately")\n  (:end . 114) (:start . 101) (:id . 58))\n ((:tag . "IN") (:stem . "towards") (:form . "towards") (:end . 122)\n  (:start . 115) (:id . 59))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 126) (:start . 123)\n  (:id . 60))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 133)\n  (:start . 127) (:id . 61))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 138) (:start . 134)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 141) (:start . 139)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 153)\n  (:start . 146) (:id . 65))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 160)\n  (:start . 154) (:id . 66))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 170)\n  (:start . 161) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . 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"terminates") (:end . 222)\n  (:start . 212) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 225) (:start . 223)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 232)\n  (:start . 226) (:id . 80))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 234) (:start . 233)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 235) (:start . 234)\n  (:id . 82))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 237) (:start . 236)\n  (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 238) (:start . 237)\n  (:id . 84))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 241) (:start . 239)\n  (:id . 85))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 243) (:start . 242)\n  (:id . 86))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 245) (:start . 244)\n  (:id . 87))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 248) (:start . 245)\n  (:id . 88))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 257)\n  (:start . 249) (:id . 89))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 261) (:start . 258)\n  (:id . 90))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 269)\n  (:start . 262) (:id . 91))\n ((:tag . "NN") (:stem . "5d") (:form . "5D") (:end . 272) (:start . 270)\n  (:id . 92))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 273) (:start . 272)\n  (:id . 93))\n ((:tag . "JJ") (:stem . "left") (:form . "left") (:end . 278) (:start . 274)\n  (:id . 94))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 284)\n  (:start . 279) (:id . 95))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 285) (:start . 284)\n  (:id . 96))\n ((:tag . "NN") (:stem . "7e") (:form . "7E") (:end . 288) (:start . 286)\n  (:id . 97))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 289) (:start . 288)\n  (:id . 98))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 295)\n  (:start . 290) (:id . 99))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 300) (:start . 296)\n  (:id . 100))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 301) (:start . 300)\n  (:id . 101))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 305) (:start . 302)\n  (:id . 102))\n ((:tag . "NNP") (:stem . "S5A") (:form . "S5A") (:end . 309) (:start . 306)\n  (:id . 103))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 310) (:start . 309)\n  (:id . 104))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 311) (:start . 310)\n  (:id . 105)))@@@1@64@((:identifiers (:sid . :s10.424) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503537@unknown@formal@none@1@S@In the case of aberrant growth, with aberrant termination, the misrouted axon grows through and forms terminals in layers 1, 2, or 3 (for examples see Figures 5B, 6F, 7B, 7D, right axon, and S5B).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 23)\n  (:start . 15) (:id . 46))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 45)\n  (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 57)\n  (:start . 46) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "misrouted") (:form . "misrouted") (:end . 72)\n  (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "grow") (:form . "grows") (:end . 83) (:start . 78)\n  (:id . 56))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 91)\n  (:start . 84) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "form") (:form . "forms") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 111)\n  (:start . 102) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 121)\n  (:start . 115) (:id . 62))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 123) (:start . 122)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 64))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 126) (:start . 125)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 130) (:start . 128)\n  (:id . 67))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 132) (:start . 131)\n  (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 137) (:start . 134)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 146)\n  (:start . 138) (:id . 71))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 150) (:start . 147)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 158)\n  (:start . 151) (:id . 73))\n ((:tag . "NN") (:stem . "5b") (:form . "5B") (:end . 161) (:start . 159)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 162) (:start . 161)\n  (:id . 75))\n ((:tag . "NN") (:stem . "6f") (:form . "6F") (:end . 165) (:start . 163)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 77))\n ((:tag . "NN") (:stem . "7b") (:form . "7B") (:end . 169) (:start . 167)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 170) (:start . 169)\n  (:id . 79))\n ((:tag . "NN") (:stem . "7d") (:form . "7D") (:end . 173) (:start . 171)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 180)\n  (:start . 175) (:id . 82))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 185) (:start . 181)\n  (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 186) (:start . 185)\n  (:id . 84))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 190) (:start . 187)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "S5B") (:form . "S5B") (:end . 194) (:start . 191)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s10.425) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503538@unknown@formal@none@1@S@Some of these axons never reach their wild-type layer 4 (Figures 5B, 6F, 7B, and S5B) while others send a branch ventrally, after they have formed a terminal dorsally or centrally (right axon in Figure 7D).@(((:tag . "DT") (:stem . "some") (:form . "Some") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "RB") (:stem . "never") (:form . "never") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "reach") (:form . "reach") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 37)\n  (:start . 32) (:id . 48))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 64)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "5b") (:form . "5B") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "NN") (:stem . "6f") (:form . "6F") (:end . 71) (:start . 69)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 57))\n ((:tag . "NN") (:stem . "7b") (:form . "7B") (:end . 75) (:start . 73)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "S5B") (:form . "S5B") (:end . 84) (:start . 81)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 62))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 91) (:start . 86)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 98)\n  (:start . 92) (:id . 64))\n ((:tag . "VBP") (:stem . "send") (:form . "send") (:end . 103) (:start . 99)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 105) (:start . 104)\n  (:id . 66))\n ((:tag . "NN") (:stem . "branch") (:form . "branch") (:end . 112)\n  (:start . 106) (:id . 67))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 122)\n  (:start . 113) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 69))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 129)\n  (:start . 124) (:id . 70))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 134) (:start . 130)\n  (:id . 71))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 139) (:start . 135)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "form") (:form . "formed") (:end . 146)\n  (:start . 140) (:id . 73))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 148) (:start . 147)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 157)\n  (:start . 149) (:id . 75))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 166)\n  (:start . 158) (:id . 76))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 169) (:start . 167)\n  (:id . 77))\n ((:tag . "RB") (:stem . "centrally") (:form . "centrally") (:end . 179)\n  (:start . 170) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 181) (:start . 180)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 186)\n  (:start . 181) (:id . 80))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 191) (:start . 187)\n  (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 194) (:start . 192)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 201)\n  (:start . 195) (:id . 83))\n ((:tag . "NN") (:stem . "7d") (:form . "7D") (:end . 204) (:start . 202)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 205) (:start . 204)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s10.426) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503539@unknown@formal@none@1@S@In the case of aberrant growth, with normal termination, the misrouted axon turns ventrally after growing through dorsal or central layers and terminates in its wild-type layer 4 (for example see Figures 7D, left axon, and S5C).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 23)\n  (:start . 15) (:id . 46))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 43)\n  (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 55)\n  (:start . 44) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "misrouted") (:form . "misrouted") (:end . 70)\n  (:start . 61) (:id . 54))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 75) (:start . 71)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "turn") (:form . "turns") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 91)\n  (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 97) (:start . 92)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "grow") (:form . "growing") (:end . 105)\n  (:start . 98) (:id . 59))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 113)\n  (:start . 106) (:id . 60))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 120)\n  (:start . 114) (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 131)\n  (:start . 124) (:id . 63))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 138)\n  (:start . 132) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "terminate") (:form . "terminates") (:end . 153)\n  (:start . 143) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 156) (:start . 154)\n  (:id . 67))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 160) (:start . 157)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 170)\n  (:start . 161) (:id . 69))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 176)\n  (:start . 171) (:id . 70))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 178) (:start . 177)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 180) (:start . 179)\n  (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 183) (:start . 180)\n  (:id . 73))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 191)\n  (:start . 184) (:id . 74))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 195) (:start . 192)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 203)\n  (:start . 196) (:id . 76))\n ((:tag . "NN") (:stem . "7d") (:form . "7D") (:end . 206) (:start . 204)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 207) (:start . 206)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "left") (:form . "left") (:end . 212) (:start . 208)\n  (:id . 79))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 217) (:start . 213)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 218) (:start . 217)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 222) (:start . 219)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "S5C") (:form . "S5C") (:end . 226) (:start . 223)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 227) (:start . 226)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s10.427) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503540@unknown@formal@none@1@S@For all our statistical analysis of termination defects (see below) we counted as “aberrant” only those hemisegments that exhibit the aberrant termination phenotypes (Figure S5A and S5B), but we counted as “normal” those hemisegments that exhibit the aberrant growth, with normal termination phenotype (Figure S5C).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 23)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 47)\n  (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 50))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "count") (:form . "counted") (:end . 78)\n  (:start . 71) (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 91)\n  (:start . 83) (:id . 58))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 97) (:start . 93)\n  (:id . 60))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 103) (:start . 98)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 116)\n  (:start . 104) (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 121) (:start . 117)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "exhibit") (:form . "exhibit") (:end . 129)\n  (:start . 122) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 142)\n  (:start . 134) (:id . 66))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 154)\n  (:start . 143) (:id . 67))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 165)\n  (:start . 155) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 173)\n  (:start . 167) (:id . 70))\n ((:tag . "NNP") (:stem . "S5A") (:form . "S5A") (:end . 177) (:start . 174)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 181) (:start . 178)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "S5B") (:form . "S5B") (:end . 185) (:start . 182)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 186) (:start . 185)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 187) (:start . 186)\n  (:id . 75))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 191) (:start . 188)\n  (:id . 76))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 194) (:start . 192)\n  (:id . 77))\n ((:tag . "VBD") (:stem . "count") (:form . "counted") (:end . 202)\n  (:start . 195) (:id . 78))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 205) (:start . 203)\n  (:id . 79))\n ((:tag . "``") (:stem . "“") (:form . "“") (:end . 207) (:start . 206)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 213)\n  (:start . 207) (:id . 81))\n ((:tag . "''") (:stem . "”") (:form . "”") (:end . 214) (:start . 213)\n  (:id . 82))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 220)\n  (:start . 215) (:id . 83))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 233)\n  (:start . 221) (:id . 84))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 238) (:start . 234)\n  (:id . 85))\n ((:tag . "VBP") (:stem . "exhibit") (:form . "exhibit") (:end . 246)\n  (:start . 239) (:id . 86))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 250) (:start . 247)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 259)\n  (:start . 251) (:id . 88))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 266)\n  (:start . 260) (:id . 89))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 267) (:start . 266)\n  (:id . 90))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 272) (:start . 268)\n  (:id . 91))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 279)\n  (:start . 273) (:id . 92))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 291)\n  (:start . 280) (:id . 93))\n ((:tag . "NN") (:stem . "phenotype") (:form . "phenotype") (:end . 301)\n  (:start . 292) (:id . 94))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 303) (:start . 302)\n  (:id . 95))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 309)\n  (:start . 303) (:id . 96))\n ((:tag . "NNP") (:stem . "S5C") (:form . "S5C") (:end . 313) (:start . 310)\n  (:id . 97))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 314) (:start . 313)\n  (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 315) (:start . 314)\n  (:id . 99)))@@@1@58@((:identifiers (:sid . :s10.428) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503541@unknown@formal@none@1@S@(A) Examples of normal initial growth with aberrant termination, where class IV axons grew in normally, and afterwards aberrantly turned dorsally or centrally and terminated there, in sema1a, sema 2a double mutant embryos (21 AEL).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNS") (:stem . "example") (:form . "Examples") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 22)\n  (:start . 16) (:id . 47))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 30)\n  (:start . 23) (:id . 48))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 37)\n  (:start . 31) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 51)\n  (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 63)\n  (:start . 52) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 70) (:start . 65)\n  (:id . 54))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 85) (:start . 80)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "grow") (:form . "grew") (:end . 90) (:start . 86)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 102)\n  (:start . 94) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 62))\n ((:tag . "RB") (:stem . "afterwards") (:form . "afterwards") (:end . 118)\n  (:start . 108) (:id . 63))\n ((:tag . "RB") (:stem . "aberrantly") (:form . "aberrantly") (:end . 129)\n  (:start . 119) (:id . 64))\n ((:tag . "VBN") (:stem . "turn") (:form . "turned") (:end . 136)\n  (:start . 130) (:id . 65))\n ((:tag . "RB") (:stem . "dorsally") (:form . "dorsally") (:end . 145)\n  (:start . 137) (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 148) (:start . 146)\n  (:id . 67))\n ((:tag . "RB") (:stem . "centrally") (:form . "centrally") (:end . 158)\n  (:start . 149) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "terminate") (:form . "terminated") (:end . 173)\n  (:start . 163) (:id . 70))\n ((:tag . "RB") (:stem . "there") (:form . "there") (:end . 179)\n  (:start . 174) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n  (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 183) (:start . 181)\n  (:id . 73))\n ((:tag . "NN") (:stem . "sema1a") (:form . "sema1a") (:end . 190)\n  (:start . 184) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n  (:id . 75))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 196) (:start . 192)\n  (:id . 76))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 199) (:start . 197)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 206)\n  (:start . 200) (:id . 78))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 213)\n  (:start . 207) (:id . 79))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 221)\n  (:start . 214) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 223) (:start . 222)\n  (:id . 81))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 225) (:start . 223)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "AEL") (:form . "AEL") (:end . 229) (:start . 226)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 230) (:start . 229)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s10.429) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503542@unknown@formal@none@1@S@These examples show that the position of entry does not determine the position of termination.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 65)\n  (:start . 56) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 93)\n  (:start . 82) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.430) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503543@unknown@formal@none@1@S@Despite the fact that these axons initially grow appropriately in the ventral neuropile, they afterwards alter direction of growth and invade aberrant neuropile layers, where they terminate.@(((:tag . "IN") (:stem . "despite") (:form . "Despite") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "RB") (:stem . "initially") (:form . "initially") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "RB") (:stem . "appropriately") (:form . "appropriately")\n  (:end . 62) (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 87)\n  (:start . 78) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "RB") (:stem . "afterwards") (:form . "afterwards") (:end . 104)\n  (:start . 94) (:id . 57))\n ((:tag . "VBP") (:stem . "alter") (:form . "alter") (:end . 110)\n  (:start . 105) (:id . 58))\n ((:tag . "NN") (:stem . "direction") (:form . "direction") (:end . 120)\n  (:start . 111) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 60))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 130)\n  (:start . 124) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "invade") (:form . "invade") (:end . 141)\n  (:start . 135) (:id . 63))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 150)\n  (:start . 142) (:id . 64))\n ((:tag . "JJ") (:stem . "neuropile") (:form . "neuropile") (:end . 160)\n  (:start . 151) (:id . 65))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 167)\n  (:start . 161) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 67))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 174)\n  (:start . 169) (:id . 68))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 179) (:start . 175)\n  (:id . 69))\n ((:tag . "VBP") (:stem . "terminate") (:form . "terminate") (:end . 189)\n  (:start . 180) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s10.431) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503544@unknown@formal@none@1@S@(B) Example of class IV axons showing both aberrant growth and aberrant termination in a sema 1a mutant embryo.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "example") (:form . "Example") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 46))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 20) (:start . 15)\n  (:id . 47))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 23) (:start . 21)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 29) (:start . 24)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 37)\n  (:start . 30) (:id . 50))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 42) (:start . 38)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 51)\n  (:start . 43) (:id . 52))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 58)\n  (:start . 52) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 71)\n  (:start . 63) (:id . 55))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 83)\n  (:start . 72) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 88) (:start . 87)\n  (:id . 58))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 93) (:start . 89)\n  (:id . 59))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 96) (:start . 94)\n  (:id . 60))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 103)\n  (:start . 97) (:id . 61))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 110)\n  (:start . 104) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.432) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503545@unknown@formal@none@1@S@The axons initially grow in dorsal neuropile, where they also forms a terminal at the midline.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "initially") (:form . "initially") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 51) (:start . 46)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "form") (:form . "forms") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "terminal") (:form . "terminal") (:end . 78)\n  (:start . 70) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 57))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 93)\n  (:start . 86) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s10.433) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503546@unknown@formal@none@1@S@(C) Example of class IV axons showing aberrant growth, but normal termination in a plex B mutant embryo.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "example") (:form . "Example") (:end . 11)\n  (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 46))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 20) (:start . 15)\n  (:id . 47))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 23) (:start . 21)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 29) (:start . 24)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 37)\n  (:start . 30) (:id . 50))\n ((:tag . "JJ") (:stem . "aberrant") (:form . "aberrant") (:end . 46)\n  (:start . 38) (:id . 51))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 53)\n  (:start . 47) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 53))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 58) (:start . 55)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 65)\n  (:start . 59) (:id . 55))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 77)\n  (:start . 66) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 82) (:start . 81)\n  (:id . 58))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 87) (:start . 83)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 89) (:start . 88)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 96)\n  (:start . 90) (:id . 61))\n ((:tag . "NN") (:stem . "embryo") (:form . "embryo") (:end . 103)\n  (:start . 97) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.434) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503547@unknown@formal@none@1@S@The axon grows through dorsal neuropile, but turns ventrally at the midline, without forming a terminal.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "grow") (:form . "grows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "JJ") (:stem . "dorsal") (:form . "dorsal") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "turn") (:form . "turns") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "RB") (:stem . "ventrally") (:form . "ventrally") (:end . 60)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 75)\n  (:start . 68) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 84)\n  (:start . 77) (:id . 56))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 103)\n  (:start . 95) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.435) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503548@unknown@formal@none@1@S@It forms a terminal once it reaches the ventral neuropile, in its appropriate location. (1.35 MB TIF)@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "form") (:form . "forms") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "terminal") (:form . "terminal") (:end . 19)\n  (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "once") (:form . "once") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "reach") (:form . "reaches") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 57)\n  (:start . 48) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 77)\n  (:start . 66) (:id . 55))\n ((:tag . "NN") (:stem . "location.") (:form . "location.") (:end . 87)\n  (:start . 78) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1.35") (:form . "1.35") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.436) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503549@unknown@formal@none@1@S@Figure S6 Defective positioning of Fas II tracts in different mutant backgrounds.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S6") (:form . "S6") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "defective") (:form . "Defective") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "positioning") (:form . "positioning") (:end . 31)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 48)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "NNS") (:stem . "background") (:form . "backgrounds") (:end . 80)\n  (:start . 69) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s10.437) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503550@unknown@formal@none@1@S@Graphs show percentages of segments (n=175) in which L1 (blue), I2 (green), I3 (yellow), M1 (black), and M2 (white) tracts project aberrantly in sema 1aP1/+ (A), sema 1aP1 (B), sema 2a (C), and sema 1aP1, sema 2a double mutant (D) 21-h embryos.@(((:tag . "NNS") (:stem . "graph") (:form . "Graphs") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "percentage") (:form . "percentages") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "n=175") (:form . "n=175") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . 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5503551@unknown@formal@none@1@S@(A) In sema 1aP1/+ control embryos Fas II tracts grow normally in the dorso-ventral axis.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "In") (:end . 6) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 11) (:start . 7)\n  (:id . 46))\n ((:tag . "NN") (:stem . "1ap1/+") (:form . "1aP1/+") (:end . 18)\n  (:start . 12) (:id . 47))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 26)\n  (:start . 19) (:id . 48))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 34)\n  (:start . 27) (:id . 49))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 38) (:start . 35)\n  (:id . 50))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 41) (:start . 39)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 48)\n  (:start . 42) (:id . 52))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 53) (:start . 49)\n  (:id . 53))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 62)\n  (:start . 54) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 83) (:start . 70) (:id . 57))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 88) (:start . 84)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s10.439) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503552@unknown@formal@none@1@S@In both sema 1aP1 and sema 2a embryos Fas II tracts are affected (B and C) and the disruption is more severe in double mutants (D). (0.29 MB TIF)@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "1ap1") (:form . "1aP1") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 37)\n  (:start . 30) (:id . 49))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 51)\n  (:start . 45) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 55) (:start . 52)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "affect") (:form . "affected") (:end . 64)\n  (:start . 56) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 67) (:start . 66)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 73) (:start . 72)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 61))\n ((:tag . "NN") (:stem . "disruption") (:form . "disruption") (:end . 93)\n  (:start . 83) (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 96) (:start . 94)\n  (:id . 63))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 101) (:start . 97)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "severe") (:form . "severe") (:end . 108)\n  (:start . 102) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 118)\n  (:start . 112) (:id . 67))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 126)\n  (:start . 119) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "D).") (:form . "D).") (:end . 131) (:start . 128)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 71))\n ((:tag . "CD") (:stem . "0.29") (:form . "0.29") (:end . 137) (:start . 133)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 140) (:start . 138)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 144) (:start . 141)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s10.440) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503553@unknown@formal@none@1@S@Figure S7 Role of Semas in patterning the antero-posterior axis of the neuropile.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Role") (:form . "Role") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Semas") (:form . "Semas") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "pattern") (:form . "patterning") (:end . 37)\n  (:start . 27) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 58) (:start . 42) (:id . 50))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 63) (:start . 59)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 80)\n  (:start . 71) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.441) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503554@unknown@formal@none@1@S@We assessed the potential role of Sema 1a and Sema 2a in controlling termination of class IV axons in the antero-posterior axis by analysing their projections in a top-down view of the neuropile in wild type and in sema 1a, sema 2a double mutants (see Figure S5A and S5B).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "assess") (:form . "assessed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "1a") (:form . 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"CC") (:stem . "and") (:form . "and") (:end . 266) (:start . 263)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "S5B") (:form . "S5B") (:end . 270) (:start . 267)\n  (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 271) (:start . 270)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 272) (:start . 271)\n  (:id . 94)))@@@1@53@((:hcues ((:id . :x10.442.1) (:span 16 25)))\n (:hscopes ((:id . :x10.442.1) (:span 16 127)))\n (:identifiers (:sid . :s10.442) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503555@unknown@formal@none@1@S@We chose the sema 1a, sema 2a double mutant for this analysis, because it exhibited the strongest phenotypes in the dorso-ventral axis.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 26) (:start . 22)\n  (:id . 48))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 29) (:start . 27)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 36)\n  (:start . 30) (:id . 50))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 43)\n  (:start . 37) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 52) (:start . 48)\n  (:id . 53))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 61)\n  (:start . 53) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 70)\n  (:start . 63) (:id . 56))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 73) (:start . 71)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "exhibit") (:form . "exhibited") (:end . 83)\n  (:start . 74) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 59))\n ((:tag . "JJS") (:stem . "strong") (:form . "strongest") (:end . 97)\n  (:start . 88) (:id . 60))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 108)\n  (:start . 98) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 129) (:start . 116) (:id . 64))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 134) (:start . 130)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.443) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503556@unknown@formal@none@1@S@(A and B) Projections of class IV axons labelled with ppkEGFP (white) in sema 1a/+; ppkEGFP control (A) and sema 1a, sema 2a; ppkEGFP (B), 21-h embryos.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 6) (:start . 3)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 8) (:start . 7)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 9) (:start . 8) (:id . 46))\n ((:tag . "NNS") (:stem . "projection") (:form . "Projections") (:end . 21)\n  (:start . 10) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 48))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 30) (:start . 25)\n  (:id . 49))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 33) (:start . 31)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 39) (:start . 34)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "label") (:form . "labelled") (:end . 48)\n  (:start . 40) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "ppkEGFP") (:form . "ppkEGFP") (:end . 61)\n  (:start . 54) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 68) (:start . 63)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 58))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 77) (:start . 73)\n  (:id . 59))\n ((:tag . "NN") (:stem . "1a/+") (:form . "1a/+") (:end . 82) (:start . 78)\n  (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 83) (:start . 82)\n  (:id . 61))\n ((:tag . "NN") (:stem . "ppkegfp") (:form . "ppkEGFP") (:end . 91)\n  (:start . 84) (:id . 62))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 99)\n  (:start . 92) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 102) (:start . 101)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 103) (:start . 102)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 67))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 112) (:start . 108)\n  (:id . 68))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 115) (:start . 113)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 70))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 121) (:start . 117)\n  (:id . 71))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 124) (:start . 122)\n  (:id . 72))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 125) (:start . 124)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "ppkEGFP") (:form . "ppkEGFP") (:end . 133)\n  (:start . 126) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 136) (:start . 135)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 143) (:start . 139)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 151)\n  (:start . 144) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s10.444) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503557@unknown@formal@none@1@S@Images show projections of confocal z series of longitudinal sections of the VNC (from T1 to A4).@(((:tag . "NNS") (:stem . "image") (:form . "Images") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "longitudinal") (:form . "longitudinal") (:end . 60)\n  (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 69)\n  (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "VNC") (:form . "VNC") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . "NN") (:stem . "t1") (:form . "T1") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "a4") (:form . "A4") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.445) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503558@unknown@formal@none@1@S@Anterior left.@(((:tag . "JJ") (:stem . "anterior") (:form . "Anterior") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "left") (:form . "left") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 14) (:start . 13)\n  (:id . 44)))@@@1@3@((:identifiers (:sid . :s10.446) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503559@unknown@formal@none@1@S@Arrowheads show midline.@(((:tag . "NNS") (:stem . "arrowhead") (:form . "Arrowheads") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 24) (:start . 23)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.447) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503560@unknown@formal@none@1@S@a, anterior half of the segment; p, posterior half of the segment.@(((:tag . "DT") (:stem . "a") (:form . "a") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 11)\n  (:start . 3) (:id . 44))\n ((:tag . "NN") (:stem . "half") (:form . "half") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 31)\n  (:start . 24) (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 32) (:start . 31)\n  (:id . 49))\n ((:tag . "NN") (:stem . "p") (:form . "p") (:end . 34) (:start . 33)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 45)\n  (:start . 36) (:id . 52))\n ((:tag . "NN") (:stem . "half") (:form . "half") (:end . 50) (:start . 46)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 55))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 65)\n  (:start . 58) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s10.448) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503561@unknown@formal@none@1@S@Scale bar: 16 µm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.449) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503562@unknown@formal@none@1@S@(A) Top-down view of wild-type class IV projections in T1–A4.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "top-down") (:form . "Top-down") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "view") (:form . "view") (:end . 17) (:start . 13)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 30)\n  (:start . 21) (:id . 48))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 36) (:start . 31)\n  (:id . 49))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 51)\n  (:start . 40) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "t1–a4") (:form . "T1–A4") (:end . 60) (:start . 55)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s10.450) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503563@unknown@formal@none@1@S@Wild-type class IV axons grow asymmetrically, within their normal ventral and medial termination domain, forming a thick anterior branch and very thin processes that extend posteriorly.@(((:tag . "JJ") (:stem . "wild-type") (:form . "Wild-type") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "grow") (:form . "grow") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "RB") (:stem . "asymmetrically") (:form . "asymmetrically")\n  (:end . 44) (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 52)\n  (:start . 46) (:id . 49))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 58)\n  (:start . 53) (:id . 50))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 65)\n  (:start . 59) (:id . 51))\n ((:tag . "JJ") (:stem . "ventral") (:form . "ventral") (:end . 73)\n  (:start . 66) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 84)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 96)\n  (:start . 85) (:id . 55))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 103)\n  (:start . 97) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "form") (:form . "forming") (:end . 112)\n  (:start . 105) (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 114) (:start . 113)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "thick") (:form . "thick") (:end . 120)\n  (:start . 115) (:id . 60))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 129)\n  (:start . 121) (:id . 61))\n ((:tag . "NN") (:stem . "branch") (:form . "branch") (:end . 136)\n  (:start . 130) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 63))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 145) (:start . 141)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "thin") (:form . "thin") (:end . 150) (:start . 146)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 160)\n  (:start . 151) (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 165) (:start . 161)\n  (:id . 67))\n ((:tag . "VBP") (:stem . "extend") (:form . "extend") (:end . 172)\n  (:start . 166) (:id . 68))\n ((:tag . "RB") (:stem . "posteriorly") (:form . "posteriorly") (:end . 184)\n  (:start . 173) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s10.451) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503564@unknown@formal@none@1@S@(B) Top-down view of class IV projections in T1–A4 in sema 2a, sema 1a double mutants.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "JJ") (:stem . "top-down") (:form . "Top-down") (:end . 12)\n  (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "view") (:form . "view") (:end . 17) (:start . 13)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 47))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 26) (:start . 21)\n  (:id . 48))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 29) (:start . 27)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 41)\n  (:start . 30) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "t1–a4") (:form . "T1–A4") (:end . 50) (:start . 45)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 58) (:start . 54)\n  (:id . 54))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 61) (:start . 59)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 56))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 67) (:start . 63)\n  (:id . 57))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 70) (:start . 68)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 77)\n  (:start . 71) (:id . 59))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 85)\n  (:start . 78) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.452) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503565@unknown@formal@none@1@S@Note that while the class IV terminals appear disorganised compared to wild type, they still appear asymmetric and largely confined to the anterior portion of the segment.@(((:tag . "VB") (:stem . "note") (:form . "Note") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 38)\n  (:start . 29) (:id . 48))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "VBN") (:stem . "disorganise") (:form . "disorganised") (:end . 58)\n  (:start . 46) (:id . 50))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 67)\n  (:start . 59) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 70) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 99)\n  (:start . 93) (:id . 58))\n ((:tag . "JJ") (:stem . "asymmetric") (:form . "asymmetric") (:end . 110)\n  (:start . 100) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 60))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 122)\n  (:start . 115) (:id . 61))\n ((:tag . "VBN") (:stem . "confine") (:form . "confined") (:end . 131)\n  (:start . 123) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 134) (:start . 132)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 147)\n  (:start . 139) (:id . 65))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 155)\n  (:start . 148) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n  (:id . 68))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 170)\n  (:start . 163) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s10.453) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503566@unknown@formal@none@1@S@We assume the observed disorganization is a consequence of the major defects in growth and termination in the dorsoventral axis.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "assume") (:form . "assume") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "disorganization") (:form . "disorganization")\n  (:end . 38) (:start . 23) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "consequence") (:form . "consequence") (:end . 55)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 68) (:start . 63)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 86)\n  (:start . 80) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "termination") (:form . "termination") (:end . 102)\n  (:start . 91) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "dorsoventral") (:form . "dorsoventral") (:end . 122)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 127) (:start . 123)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x10.454.1) (:span 3 9)))\n (:hscopes ((:id . :x10.454.1) (:span 3 127)))\n (:identifiers (:sid . :s10.454) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503567@unknown@formal@none@1@S@(C) Quantification of the average surface area occupied by class IV terminals in the posterior half of the hemisegment, relative to the total surface area covered by class IV terminals in a hemisegment [SAp/(p+a)=SA(posterior)/SA(posterior+anterior].@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Quantification") (:form . "Quantification")\n  (:end . 18) (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "occupy") (:form . "occupied") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 64) (:start . 59)\n  (:id . 53))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 77)\n  (:start . 68) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 94)\n  (:start . 85) (:id . 58))\n ((:tag . "NN") (:stem . "half") (:form . "half") (:end . 99) (:start . 95)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "NN") (:stem . "hemisegment") (:form . "hemisegment") (:end . 118)\n  (:start . 107) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 128)\n  (:start . 120) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 131) (:start . 129)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 135) (:start . 132)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 141)\n  (:start . 136) (:id . 67))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 149)\n  (:start . 142) (:id . 68))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 154) (:start . 150)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 162)\n  (:start . 155) (:id . 70))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 165) (:start . 163)\n  (:id . 71))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 171)\n  (:start . 166) (:id . 72))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 174) (:start . 172)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 184)\n  (:start . 175) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 187) (:start . 185)\n  (:id . 75))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 189) (:start . 188)\n  (:id . 76))\n ((:tag . "NN") (:stem . "hemisegment") (:form . "hemisegment") (:end . 201)\n  (:start . 190) (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 203) (:start . 202)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "SAp/(p+a)=SA(posterior)/SA(posterior+anterior")\n  (:form . "SAp/(p+a)=SA(posterior)/SA(posterior+anterior") (:end . 248)\n  (:start . 203) (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 249) (:start . 248)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 250) (:start . 249)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s10.455) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503568@unknown@formal@none@1@S@Quantification of SAp/(p+a) does not reveal a significant increase (p=0.09; Student's t-test average SAp/(p+a)=0.22; SD=0.16; n=50 hemisegments) for the double mutants with respect to wild-type embryos (average SAp/(p+a)=0.19; SD=0.1; n=55 hemisegments).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "SAp/(p+a)") (:form . "SAp/(p+a)") (:end . 27)\n  (:start . 18) (:id . 44))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 32) (:start . 28)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "VB") (:stem . "reveal") (:form . "reveal") (:end . 43)\n  (:start . 37) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 57)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 66)\n  (:start . 58) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 51))\n ((:tag . "NN") (:stem . "p=0.09") (:form . "p=0.09") (:end . 74)\n  (:start . 68) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 83)\n  (:start . 76) (:id . 54))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "JJS") (:stem . "t-t") (:form . "t-test") (:end . 92) (:start . 86)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 100)\n  (:start . 93) (:id . 57))\n ((:tag . "NN") (:stem . "SAp/(p+a)=0.22") (:form . "SAp/(p+a)=0.22")\n  (:end . 115) (:start . 101) (:id . 58))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 116) (:start . 115)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "SD=0.16") (:form . "SD=0.16") (:end . 124)\n  (:start . 117) (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "CD") (:stem . "n=50") (:form . "n=50") (:end . 130) (:start . 126)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 143)\n  (:start . 131) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 148) (:start . 145)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 159)\n  (:start . 153) (:id . 67))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 167)\n  (:start . 160) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 172) (:start . 168)\n  (:id . 69))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 180)\n  (:start . 173) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 183) (:start . 181)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 193)\n  (:start . 184) (:id . 72))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 201)\n  (:start . 194) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 203) (:start . 202)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 210)\n  (:start . 203) (:id . 75))\n ((:tag . "NN") (:stem . "SAp/(p+a)=0.19") (:form . "SAp/(p+a)=0.19")\n  (:end . 225) (:start . 211) (:id . 76))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 226) (:start . 225)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "SD=0.1") (:form . "SD=0.1") (:end . 233)\n  (:start . 227) (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 234) (:start . 233)\n  (:id . 79))\n ((:tag . "CD") (:stem . "n=55") (:form . "n=55") (:end . 239) (:start . 235)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 252)\n  (:start . 240) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 253) (:start . 252)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 254) (:start . 253)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s10.456) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503569@unknown@formal@none@1@S@For comparison we analyzed the antero-posterior distribution of class IV projections in embryos mutant for the gene wnt 5, that has previously been implicated in controlling axon projections in the antero-posterior axis [56].@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "analyze") (:form . "analyzed") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 47) (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 60)\n  (:start . 48) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 49))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 69) (:start . 64)\n  (:id . 50))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 84)\n  (:start . 73) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 95)\n  (:start . 88) (:id . 54))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 102)\n  (:start . 96) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 106) (:start . 103)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 57))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 115) (:start . 111)\n  (:id . 58))\n ((:tag . "NN") (:stem . "wnt") (:form . "wnt") (:end . 119) (:start . 116)\n  (:id . 59))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 121) (:start . 120)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 127) (:start . 123)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 131) (:start . 128)\n  (:id . 63))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 142)\n  (:start . 132) (:id . 64))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 147) (:start . 143)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "implicate") (:form . "implicated") (:end . 158)\n  (:start . 148) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 161) (:start . 159)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "control") (:form . "controlling") (:end . 173)\n  (:start . 162) (:id . 68))\n ((:tag . "NN") (:stem . "axon") (:form . "axon") (:end . 178) (:start . 174)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 190)\n  (:start . 179) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 193) (:start . 191)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 214) (:start . 198) (:id . 73))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 219) (:start . 215)\n  (:id . 74))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 221) (:start . 220)\n  (:id . 75))\n ((:tag . "CD") (:stem . "56") (:form . "56") (:end . 223) (:start . 221)\n  (:id . 76))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 224) (:start . 223)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s10.457) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503570@unknown@formal@none@1@S@Wnt 5 is secreted by neurites in the posterior commissure of each segment.@(((:tag . "NNP") (:stem . "Wnt") (:form . "Wnt") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "secrete") (:form . "secreted") (:end . 17)\n  (:start . 9) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "neurite") (:form . "neurites") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 46)\n  (:start . 37) (:id . 50))\n ((:tag . "NN") (:stem . "commissure") (:form . "commissure") (:end . 57)\n  (:start . 47) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 65) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 73)\n  (:start . 66) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.458) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503571@unknown@formal@none@1@S@We also analyzed class IV projections in embryos in which the dominant negative form of Derailed (Drl) has been selectively targeted to sensory neurons (PO163GAL4,UAS-DN-drl).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "analyze") (:form . "analyzed") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 70)\n  (:start . 62) (:id . 53))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 79)\n  (:start . 71) (:id . 54))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 84) (:start . 80)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "derailed") (:form . "Derailed") (:end . 96)\n  (:start . 88) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Drl") (:form . "Drl") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 111) (:start . 107)\n  (:id . 62))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 123)\n  (:start . 112) (:id . 63))\n ((:tag . "VBN") (:stem . "target") (:form . "targeted") (:end . 132)\n  (:start . 124) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 143)\n  (:start . 136) (:id . 66))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 151)\n  (:start . 144) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "PO163GAL4,UAS-DN-drl")\n  (:form . "PO163GAL4,UAS-DN-drl") (:end . 173) (:start . 153) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 174) (:start . 173)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s10.459) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503572@unknown@formal@none@1@S@The Wnt 5 receptor Drl is present on the growth cones and axons of neurons crossing in the anterior commissure and is required to prevent these cells from crossing aberrantly in the posterior commissure [56].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Wnt") (:form . "Wnt") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 9) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 18)\n  (:start . 10) (:id . 45))\n ((:tag . "NNP") (:stem . "Drl") (:form . "Drl") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 47)\n  (:start . 41) (:id . 51))\n ((:tag . "NNS") (:stem . "cone") (:form . "cones") (:end . 53) (:start . 48)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 63) (:start . 58)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 74)\n  (:start . 67) (:id . 56))\n ((:tag . "VBG") (:stem . "cross") (:form . "crossing") (:end . 83)\n  (:start . 75) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 99)\n  (:start . 91) (:id . 60))\n ((:tag . "NN") (:stem . "commissure") (:form . "commissure") (:end . 110)\n  (:start . 100) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 117) (:start . 115)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 126)\n  (:start . 118) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 129) (:start . 127)\n  (:id . 65))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 137)\n  (:start . 130) (:id . 66))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 143)\n  (:start . 138) (:id . 67))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 149)\n  (:start . 144) (:id . 68))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 154) (:start . 150)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "cross") (:form . "crossing") (:end . 163)\n  (:start . 155) (:id . 70))\n ((:tag . "RB") (:stem . "aberrantly") (:form . "aberrantly") (:end . 174)\n  (:start . 164) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 177) (:start . 175)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 181) (:start . 178)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "posterior") (:form . "posterior") (:end . 191)\n  (:start . 182) (:id . 74))\n ((:tag . "NN") (:stem . "commissure") (:form . "commissure") (:end . 202)\n  (:start . 192) (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 204) (:start . 203)\n  (:id . 76))\n ((:tag . "CD") (:stem . "56") (:form . "56") (:end . 206) (:start . 204)\n  (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 207) (:start . 206)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s10.460) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503573@unknown@formal@none@1@S@In contrast, to the sema1a, sema 2a double mutants, when we analysed class IV projections in wnt 5D7 mutants and in PO163GAL4,UAS-DN-drl embryos, we did find a significant increase in SAp/(p+a) compared to wild type (for wnt 5, p=1.8×10-7; Student's t-test; average SAp/(p+a)=0.34; SD=0.12; n=16 hemisegments; for PO163-DN-drl, p=2.2×10-7; Student's t-test; average SAp/(p+a)=0.33; SD=0.12; n=30 hemisegments).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sema1a") (:form . "sema1a") (:end . 26)\n  (:start . 20) (:id . 47))\n ((:tag . 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"average") (:end . 365)\n  (:start . 358) (:id . 109))\n ((:tag . "NN") (:stem . "SAp/(p+a)=0.33") (:form . "SAp/(p+a)=0.33")\n  (:end . 380) (:start . 366) (:id . 110))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 381) (:start . 380)\n  (:id . 111))\n ((:tag . "NN") (:stem . "sd=0.12") (:form . "SD=0.12") (:end . 389)\n  (:start . 382) (:id . 112))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 390) (:start . 389)\n  (:id . 113))\n ((:tag . "CD") (:stem . "n=30") (:form . "n=30") (:end . 395) (:start . 391)\n  (:id . 114))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 408)\n  (:start . 396) (:id . 115))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 409) (:start . 408)\n  (:id . 116))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 410) (:start . 409)\n  (:id . 117)))@@@1@76@((:identifiers (:sid . :s10.461) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503574@unknown@formal@none@1@S@Thus Sema 1a and Sema 2a do not appear to play a major role in confining class IV terminals to the anterior portion of the segment. (1.15 MB TIF)@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 27) (:start . 25)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 31) (:start . 28)\n  (:id . 49))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 38)\n  (:start . 32) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 51))\n ((:tag . "VB") (:stem . "play") (:form . "play") (:end . 46) (:start . 42)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 54) (:start . 49)\n  (:id . 54))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 59) (:start . 55)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "confine") (:form . "confining") (:end . 72)\n  (:start . 63) (:id . 57))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 78) (:start . 73)\n  (:id . 58))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 81) (:start . 79)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 91)\n  (:start . 82) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "anterior") (:form . "anterior") (:end . 107)\n  (:start . 99) (:id . 63))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 115)\n  (:start . 108) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 66))\n ((:tag . "NN") (:stem . "segment.") (:form . "segment.") (:end . 131)\n  (:start . 123) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 68))\n ((:tag . "CD") (:stem . "1.15") (:form . "1.15") (:end . 137) (:start . 133)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 140) (:start . 138)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 144) (:start . 141)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 145) (:start . 144)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x10.462.1) (:span 32 38)))\n (:hscopes ((:id . :x10.462.1) (:span 5 130)))\n (:identifiers (:sid . :s10.462) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503575@unknown@formal@none@1@S@Figure S8 Plexin expression in sensory neurons (A, B, and D) and in the CNS (C).@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S8") (:form . "S8") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Plexin") (:form . "Plexin") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 52) (:start . 51)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 59) (:start . 58)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "CNS") (:form . "CNS") (:end . 75) (:start . 72)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 78) (:start . 77)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 79) (:start . 78)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.463) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503576@unknown@formal@none@1@S@(A and B) Immunofluorescence visualisation of sensory neuron cell bodies labelled with antibody against horseradish peroxidase (HRP) (A) or PPK-EGFP (red) (in B) and Plex A (A and B) at 13-h AEL.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 6) (:start . 3)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 8) (:start . 7)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 9) (:start . 8) (:id . 46))\n ((:tag . "NNP") (:stem . "Immunofluorescence") (:form . "Immunofluorescence")\n  (:end . 28) (:start . 10) (:id . 47))\n ((:tag . "NN") (:stem . "visualisation") (:form . "visualisation")\n  (:end . 42) (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 72) (:start . 66)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "label") (:form . "labelled") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 86) (:start . 82)\n  (:id . 55))\n ((:tag . "NN") (:stem . "antibody") (:form . "antibody") (:end . 95)\n  (:start . 87) (:id . 56))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 103)\n  (:start . 96) (:id . 57))\n ((:tag . "NN") (:stem . "horseradish") (:form . "horseradish") (:end . 115)\n  (:start . 104) (:id . 58))\n ((:tag . "NN") (:stem . "peroxidase") (:form . "peroxidase") (:end . 126)\n  (:start . 116) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 128) (:start . 127)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 131) (:start . 128)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 135) (:start . 134)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 65))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 139) (:start . 137)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "PPK-EGFP") (:form . "PPK-EGFP") (:end . 148)\n  (:start . 140) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 68))\n ((:tag . "NN") (:stem . "red") (:form . "red") (:end . 153) (:start . 150)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 158) (:start . 156)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 160) (:start . 159)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 161) (:start . 160)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 170) (:start . 166)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 172) (:start . 171)\n  (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 175) (:start . 174)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 181) (:start . 180)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 182) (:start . 181)\n  (:id . 82))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 185) (:start . 183)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "13-h") (:form . "13-h") (:end . 190) (:start . 186)\n  (:id . 84))\n ((:tag . "NN") (:stem . "ael") (:form . "AEL") (:end . 194) (:start . 191)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s10.464) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503577@unknown@formal@none@1@S@Dorsal is up.@(((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 13) (:start . 12)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.465) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503578@unknown@formal@none@1@S@(A) Plex A expression (white in ii and green in iii) in dorsal (d) and lateral (l) clusters of sensory neurons (white in i and red in iii).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 10) (:start . 9)\n  (:id . 46))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 21)\n  (:start . 11) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 28) (:start . 23)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "ii") (:form . "ii") (:end . 34) (:start . 32)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 44) (:start . 39)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 54))\n ((:tag . "LS") (:stem . "iii") (:form . "iii") (:end . 51) (:start . 48)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dorsal") (:form . "dorsal") (:end . 62)\n  (:start . 56) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n  (:id . 59))\n ((:tag . "NN") (:stem . "d") (:form . "d") (:end . 65) (:start . 64)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 78)\n  (:start . 71) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n  (:id . 64))\n ((:tag . "NN") (:stem . "l") (:form . "l") (:end . 81) (:start . 80)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 91)\n  (:start . 83) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 102)\n  (:start . 95) (:id . 69))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 110)\n  (:start . 103) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 117)\n  (:start . 112) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 120) (:start . 118)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 122) (:start . 121)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 75))\n ((:tag . "VBD") (:stem . "red") (:form . "red") (:end . 130) (:start . 127)\n  (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 133) (:start . 131)\n  (:id . 77))\n ((:tag . "LS") (:stem . "iii") (:form . "iii") (:end . 137) (:start . 134)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s10.466) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503579@unknown@formal@none@1@S@Strong Plex A expression is visible in sensory neuron cell bodies in both clusters.@(((:tag . "NNP") (:stem . "Strong") (:form . "Strong") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "visible") (:form . "visible") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 53)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 65) (:start . 59)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 82)\n  (:start . 74) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s10.467) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503580@unknown@formal@none@1@S@Scale bar: 15 µm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.468) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503581@unknown@formal@none@1@S@(B) Plex A protein (white in ii and green in iii) is strongly expressed in class IV md neuron cell bodies (white in i and red in iii).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 10) (:start . 9)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 18)\n  (:start . 11) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 20) (:start . 19)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 25) (:start . 20)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "ii") (:form . "ii") (:end . 31) (:start . 29)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 41) (:start . 36)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 54))\n ((:tag . "LS") (:stem . "iii") (:form . "iii") (:end . 48) (:start . 45)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n  (:id . 57))\n ((:tag . "RB") (:stem . "strongly") (:form . "strongly") (:end . 61)\n  (:start . 53) (:id . 58))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 71)\n  (:start . 62) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 60))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 80) (:start . 75)\n  (:id . 61))\n ((:tag . "CD") (:stem . "iv") (:form . "IV") (:end . 83) (:start . 81)\n  (:id . 62))\n ((:tag . "NN") (:stem . "md") (:form . "md") (:end . 86) (:start . 84)\n  (:id . 63))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 93)\n  (:start . 87) (:id . 64))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 98) (:start . 94)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "body") (:form . "bodies") (:end . 105)\n  (:start . 99) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 112)\n  (:start . 107) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 117) (:start . 116)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "red") (:form . "red") (:end . 125) (:start . 122)\n  (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 73))\n ((:tag . "LS") (:stem . "iii") (:form . "iii") (:end . 132) (:start . 129)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s10.469) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503582@unknown@formal@none@1@S@Scale bar: 10 µm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.470) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503583@unknown@formal@none@1@S@(C) Immunofluorescence visualisation of Plex A protein (white in ii and green in iii) in a transverse section of the neuropile labelled with HRP (white in i and red in iii) at 13-h AEL.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Immunofluorescence") (:form . "Immunofluorescence")\n  (:end . 22) (:start . 4) (:id . 45))\n ((:tag . "NN") (:stem . "visualisation") (:form . "visualisation")\n  (:end . 36) (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 61) (:start . 56)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "ii") (:form . "ii") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 77) (:start . 72)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "LS") (:stem . "iii") (:form . "iii") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 90) (:start . 89)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "transverse") (:form . "transverse") (:end . 101)\n  (:start . 91) (:id . 62))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 109)\n  (:start . 102) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 65))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 126)\n  (:start . 117) (:id . 66))\n ((:tag . "VBN") (:stem . "label") (:form . "labelled") (:end . 135)\n  (:start . 127) (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 140) (:start . 136)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "HRP") (:form . "HRP") (:end . 144) (:start . 141)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 151)\n  (:start . 146) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 156) (:start . 155)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 74))\n ((:tag . "VBD") (:stem . "red") (:form . "red") (:end . 164) (:start . 161)\n  (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 167) (:start . 165)\n  (:id . 76))\n ((:tag . "LS") (:stem . "iii") (:form . "iii") (:end . 171) (:start . 168)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 78))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 175) (:start . 173)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "13-h") (:form . "13-h") (:end . 180) (:start . 176)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "AEL") (:form . "AEL") (:end . 184) (:start . 181)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s10.471) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503584@unknown@formal@none@1@S@Image shows a projection of a confocal z series of 1-mm thick transverse sections through abdominal segment A7.@(((:tag . "NN") (:stem . "image") (:form . "Image") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "projection") (:form . "projection") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 38)\n  (:start . 30) (:id . 48))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 47)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "1-mm") (:form . "1-mm") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "thick") (:form . "thick") (:end . 61) (:start . 56)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "transverse") (:form . "transverse") (:end . 72)\n  (:start . 62) (:id . 54))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "JJ") (:stem . "abdominal") (:form . "abdominal") (:end . 99)\n  (:start . 90) (:id . 57))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 107)\n  (:start . 100) (:id . 58))\n ((:tag . "NN") (:stem . "a7") (:form . "A7") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.472) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503585@unknown@formal@none@1@S@Dorsal is up.@(((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 13) (:start . 12)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.473) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503586@unknown@formal@none@1@S@Arrowheads show the midline.@(((:tag . "NNS") (:stem . "arrowhead") (:form . "Arrowheads") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 28) (:start . 27)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s10.474) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503587@unknown@formal@none@1@S@Outlines indicate neuropile boundaries.@(((:tag . "NNS") (:stem . "outline") (:form . "Outlines") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "JJ") (:stem . "neuropile") (:form . "neuropile") (:end . 27)\n  (:start . 18) (:id . 44))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 38)\n  (:start . 28) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 39) (:start . 38)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s10.475) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503588@unknown@formal@none@1@S@Scale bar: 5 mm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mm") (:form . "mm") (:end . 15) (:start . 13)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 16) (:start . 15)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.476) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503589@unknown@formal@none@1@S@(D) In situ hybridisation showing plex B mRNA expression in dorsal (d) and lateral (l) clusters of sensory neurons in the embryonic body wall.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "FW") (:stem . "in") (:form . "In") (:end . 6) (:start . 4)\n  (:id . 45))\n ((:tag . "FW") (:stem . "situ") (:form . "situ") (:end . 11) (:start . 7)\n  (:id . 46))\n ((:tag . "NN") (:stem . "hybridisation") (:form . "hybridisation")\n  (:end . 25) (:start . 12) (:id . 47))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 45) (:start . 41)\n  (:id . 51))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 56)\n  (:start . 46) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "dorsal") (:form . "dorsal") (:end . 66)\n  (:start . 60) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "NN") (:stem . "d") (:form . "d") (:end . 69) (:start . 68)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 82)\n  (:start . 75) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 60))\n ((:tag . "NN") (:stem . "l") (:form . "l") (:end . 85) (:start . 84)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 95)\n  (:start . 87) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 106)\n  (:start . 99) (:id . 65))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 114)\n  (:start . 107) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 131)\n  (:start . 122) (:id . 69))\n ((:tag . "NN") (:stem . "body") (:form . "body") (:end . 136) (:start . 132)\n  (:id . 70))\n ((:tag . "NN") (:stem . "wall") (:form . "wall") (:end . 141) (:start . 137)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.477) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503590@unknown@formal@none@1@S@Dorsal is up.@(((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 13) (:start . 12)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.478) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503591@unknown@formal@none@1@S@Scale bar: 20 µm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.479) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503592@unknown@formal@none@1@S@In situ hybridization protocol: DIG-labelled RNA antisense and sense probes were generated with the Ambion Megascript kit and DIG-UTP (purchased from Roche), following the manufacturer's instructions.@(((:tag . "FW") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "situ") (:form . "situ") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "hybridization") (:form . "hybridization")\n  (:end . 21) (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "dig-labelled") (:form . "DIG-labelled") (:end . 44)\n  (:start . 32) (:id . 47))\n ((:tag . "NNP") (:stem . "RNA") (:form . "RNA") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "antisense") (:form . "antisense") (:end . 58)\n  (:start . 49) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "sense") (:form . "sense") (:end . 68) (:start . 63)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "probe") (:form . "probes") (:end . 75)\n  (:start . 69) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 80) (:start . 76)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 90)\n  (:start . 81) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 95) (:start . 91)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Ambion") (:form . "Ambion") (:end . 106)\n  (:start . 100) (:id . 57))\n ((:tag . "NNP") (:stem . "Megascript") (:form . "Megascript") (:end . 117)\n  (:start . 107) (:id . 58))\n ((:tag . "NN") (:stem . "kit") (:form . "kit") (:end . 121) (:start . 118)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "DIG-UTP") (:form . "DIG-UTP") (:end . 133)\n  (:start . 126) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "purchase") (:form . "purchased") (:end . 144)\n  (:start . 135) (:id . 63))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 149) (:start . 145)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Roche") (:form . "Roche") (:end . 155)\n  (:start . 150) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 167)\n  (:start . 158) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 171) (:start . 168)\n  (:id . 69))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 184)\n  (:start . 172) (:id . 70))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 186) (:start . 184)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "instruction") (:form . "instructions") (:end . 199)\n  (:start . 187) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s10.480) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503593@unknown@formal@none@1@S@In situ hybridization was performed according to a protocol kindly provided by Nipam Patel (University of California, Berkeley).@(((:tag . "FW") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "situ") (:form . "situ") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "hybridization") (:form . "hybridization")\n  (:end . 21) (:start . 8) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 45)\n  (:start . 36) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . "RB") (:stem . "kindly") (:form . "kindly") (:end . 66)\n  (:start . 60) (:id . 51))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 75)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Nipam") (:form . "Nipam") (:end . 84) (:start . 79)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Patel") (:form . "Patel") (:end . 90) (:start . 85)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "University") (:form . "University") (:end . 102)\n  (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "California") (:form . "California") (:end . 116)\n  (:start . 106) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Berkeley") (:form . "Berkeley") (:end . 126)\n  (:start . 118) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 127) (:start . 126)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s10.481) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503594@unknown@formal@none@1@S@DNA templates for in vitro transcription: DNA fragments were amplified by PCR with Primer1 (GCGCGCGTAATACGACTCACTATAGGG) and Primer2 (GCGCGCAATTAACCCTCACTAAAGGG) from pBluescript(SK)-PlexinB-CK00213 (AA142091) (EST, ~1.7-kb insert) using the following key PCR parameters: annealing at 66°C, 5 min extension at 72°C, 30 cycles; Primer1 and Primer2 include the T7 and T3 promoter sequences.@(((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "template") (:form . "templates") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "transcription") (:form . 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5503595@unknown@formal@none@1@S@In vitro transcription: plex B: T3 (antisense), T7 (sense). (3.90 MB TIF)@(((:tag . "FW") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "vitro") (:form . "vitro") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 22) (:start . 9) (:id . 44))\n ((:tag . "SYM") (:stem . ":") (:form . ":") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "T3") (:form . "T3") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "antisense") (:form . "antisense") (:end . 45)\n  (:start . 36) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "T7") (:form . "T7") (:end . 50) (:start . 48)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 55))\n ((:tag . "FW") (:stem . "sense).") (:form . "sense).") (:end . 59)\n  (:start . 52) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 61) (:start . 60)\n  (:id . 57))\n ((:tag . "CD") (:stem . "3.90") (:form . "3.90") (:end . 65) (:start . 61)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 68) (:start . 66)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 72) (:start . 69)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.483) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503596@unknown@formal@none@1@S@Figure S9 Plex B and Plex A prevent expansion of sensory terminals into regions with high Sema 1a levels.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S9") (:form . "S9") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "prevent") (:form . "prevent") (:end . 35)\n  (:start . 28) (:id . 49))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 45)\n  (:start . 36) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 56)\n  (:start . 49) (:id . 52))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 79)\n  (:start . 72) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 89) (:start . 85)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 94) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 104)\n  (:start . 98) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.484) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503597@unknown@formal@none@1@S@(A–D) Representative images of sensory terminals labelled with PO163GAL4, UAS-n-syb-GFP (white) in 21-h embryos (left) and diagrams showing patterns of sensory terminals superimposed for different genotypes (right).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A–D") (:form . "A–D") (:end . 4) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 5) (:start . 4) (:id . 44))\n ((:tag . "JJ") (:stem . "representative") (:form . "Representative")\n  (:end . 20) (:start . 6) (:id . 45))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 48)\n  (:start . 39) (:id . 49))\n ((:tag . "VBN") (:stem . "label") (:form . "labelled") (:end . 57)\n  (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "PO163GAL4") (:form . "PO163GAL4") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "UAS-n-syb-GFP") (:form . "UAS-n-syb-GFP")\n  (:end . 87) (:start . 74) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 94) (:start . 89)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "21-h") (:form . "21-h") (:end . 103) (:start . 99)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 111)\n  (:start . 104) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "leave") (:form . "left") (:end . 117)\n  (:start . 113) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "diagram") (:form . "diagrams") (:end . 131)\n  (:start . 123) (:id . 65))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 139)\n  (:start . 132) (:id . 66))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 148)\n  (:start . 140) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 159)\n  (:start . 152) (:id . 69))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 169)\n  (:start . 160) (:id . 70))\n ((:tag . "VBN") (:stem . "superimpose") (:form . "superimposed") (:end . 182)\n  (:start . 170) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 186) (:start . 183)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 196)\n  (:start . 187) (:id . 73))\n ((:tag . "NNS") (:stem . "genotype") (:form . "genotypes") (:end . 206)\n  (:start . 197) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 208) (:start . 207)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "right") (:form . "right") (:end . 213)\n  (:start . 208) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s10.485) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503598@unknown@formal@none@1@S@In all cases images show projections of a confocal z series of transverse sections through A7.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "projection") (:form . "projections") (:end . 36)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "confocal") (:form . "confocal") (:end . 50)\n  (:start . 42) (:id . 50))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "transverse") (:form . "transverse") (:end . 73)\n  (:start . 63) (:id . 54))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 82)\n  (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 90)\n  (:start . 83) (:id . 56))\n ((:tag . "NNP") (:stem . "A7") (:form . "A7") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.486) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503599@unknown@formal@none@1@S@Dorsal is up.@(((:tag . "NNP") (:stem . "Dorsal") (:form . "Dorsal") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 13) (:start . 12)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.487) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503600@unknown@formal@none@1@S@Arrowheads show midline.@(((:tag . "NNS") (:stem . "arrowhead") (:form . "Arrowheads") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "midline") (:form . "midline") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 24) (:start . 23)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s10.488) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503601@unknown@formal@none@1@S@White lines, layer boundaries.@(((:tag . "JJ") (:stem . "white") (:form . "White") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 30) (:start . 29)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.489) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503602@unknown@formal@none@1@S@Numbers indicate layers: M, medial; I, intermediate; L, lateral domains.@(((:tag . "NNPS") (:stem . "Number") (:form . "Numbers") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 23)\n  (:start . 17) (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "medial") (:form . "medial") (:end . 34)\n  (:start . 28) (:id . 48))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "i") (:form . "I") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 51)\n  (:start . 39) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "L") (:form . "L") (:end . 54) (:start . 53)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 63)\n  (:start . 56) (:id . 56))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 71)\n  (:start . 64) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.490) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503603@unknown@formal@none@1@S@Scale bar: 10 µm.@(((:tag . "JJ") (:stem . "scale") (:form . "Scale") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bar") (:form . "bar") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "µm") (:form . "µm") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 17) (:start . 16)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s10.491) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503604@unknown@formal@none@1@S@(A) Expressing Plex B in sensory neurons in a wild-type background results in exclusion of sensory neuron terminals from neuropile layer 2 (see also Figure 2C).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "VBG") (:stem . "express") (:form . "Expressing") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 32)\n  (:start . 25) (:id . 49))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 40)\n  (:start . 33) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 55)\n  (:start . 46) (:id . 53))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 66)\n  (:start . 56) (:id . 54))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 74)\n  (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "exclusion") (:form . "exclusion") (:end . 87)\n  (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 98)\n  (:start . 91) (:id . 59))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 105)\n  (:start . 99) (:id . 60))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 115)\n  (:start . 106) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 120) (:start . 116)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "neuropile") (:form . "neuropile") (:end . 130)\n  (:start . 121) (:id . 63))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 136)\n  (:start . 131) (:id . 64))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 66))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 143) (:start . 140)\n  (:id . 67))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 148) (:start . 144)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 155)\n  (:start . 149) (:id . 69))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 158) (:start . 156)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.492) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503605@unknown@formal@none@1@S@Quantification of SA2/h (SA2/h=SA(layer 2)/[hemisegment surface area]) reveals a significant decrease (***, p=4×10-17; Student's t-test; average SA2/h=0.003; SD=0.006; n=30 hemisegments) with respect to wild-type embryos (average SA2/h=0.06; SD=0.02; n=30 hemisegments).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "SA2/h") (:form . "SA2/h") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "SA2/h=SA(layer") (:form . "SA2/h=SA(layer")\n  (:end . 39) (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "2)/[hemisegment") (:form . "2)/[hemisegment")\n  (:end . 55) (:start . 40) (:id . 47))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 63)\n  (:start . 56) (:id . 48))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 68) (:start . 64)\n  (:id . 49))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 69) (:start . 68)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 78)\n  (:start . 71) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 80) (:start . 79)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 92)\n  (:start . 81) (:id . 54))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 101)\n  (:start . 93) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 56))\n ((:tag . "SYM") (:stem . "***") (:form . "***") (:end . 106) (:start . 103)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . "NN") (:stem . "p=4×10-17") (:form . "p=4×10-17") (:end . 117)\n  (:start . 108) (:id . 59))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 118) (:start . 117)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 126)\n  (:start . 119) (:id . 61))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . "NN") (:stem . "t-test") (:form . "t-test") (:end . 135)\n  (:start . 129) (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 144)\n  (:start . 137) (:id . 65))\n ((:tag . "NN") (:stem . "sa2/h=0.003") (:form . "SA2/h=0.003") (:end . 156)\n  (:start . 145) (:id . 66))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "SD=0.006") (:form . "SD=0.006") (:end . 166)\n  (:start . 158) (:id . 68))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 167) (:start . 166)\n  (:id . 69))\n ((:tag . "CD") (:stem . "n=30") (:form . "n=30") (:end . 172) (:start . 168)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 185)\n  (:start . 173) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 186) (:start . 185)\n  (:id . 72))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 191) (:start . 187)\n  (:id . 73))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 199)\n  (:start . 192) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 202) (:start . 200)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 212)\n  (:start . 203) (:id . 76))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 220)\n  (:start . 213) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 222) (:start . 221)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 229)\n  (:start . 222) (:id . 79))\n ((:tag . "NN") (:stem . "sa2/h=0.06") (:form . "SA2/h=0.06") (:end . 240)\n  (:start . 230) (:id . 80))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 241) (:start . 240)\n  (:id . 81))\n ((:tag . "NN") (:stem . "sd=0.02") (:form . "SD=0.02") (:end . 249)\n  (:start . 242) (:id . 82))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 250) (:start . 249)\n  (:id . 83))\n ((:tag . "CD") (:stem . "n=30") (:form . "n=30") (:end . 255) (:start . 251)\n  (:id . 84))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 268)\n  (:start . 256) (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 269) (:start . 268)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s10.493) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503606@unknown@formal@none@1@S@However, in these embryos, ectopic sensory terminals in layer 1 still remain largely excluded from intermediate and lateral portions of layer 1, which contain highest Sema 1a levels.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 34)\n  (:start . 27) (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 61) (:start . 56)\n  (:id . 52))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "remain") (:form . "remain") (:end . 76)\n  (:start . 70) (:id . 55))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 84)\n  (:start . 77) (:id . 56))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 93)\n  (:start . 85) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 111)\n  (:start . 99) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 123)\n  (:start . 116) (:id . 61))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 132)\n  (:start . 124) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 63))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 141)\n  (:start . 136) (:id . 64))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 143) (:start . 142)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 66))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 150)\n  (:start . 145) (:id . 67))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 158)\n  (:start . 151) (:id . 68))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 166)\n  (:start . 159) (:id . 69))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 171) (:start . 167)\n  (:id . 70))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 174) (:start . 172)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 181)\n  (:start . 175) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s10.494) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503607@unknown@formal@none@1@S@Right: Diagram showing the pattern of Plex B expressing sensory terminals (green) superimposed on the wild-type pattern (yellow).@(((:tag . "RB") (:stem . "right") (:form . "Right") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "diagram") (:form . "Diagram") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 55)\n  (:start . 45) (:id . 51))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 63)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 73)\n  (:start . 64) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 80) (:start . 75)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "superimpose") (:form . "superimposed") (:end . 94)\n  (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 111)\n  (:start . 102) (:id . 60))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 119)\n  (:start . 112) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 62))\n ((:tag . "NN") (:stem . "yellow") (:form . "yellow") (:end . 127)\n  (:start . 121) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.495) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503608@unknown@formal@none@1@S@(B) Expressing Plex B in sensory neurons in a sema 1a mutant background still excludes sensory terminals from neuropile layer 2.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "VBG") (:stem . "express") (:form . "Expressing") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 32)\n  (:start . 25) (:id . 49))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 40)\n  (:start . 33) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 50) (:start . 46)\n  (:id . 53))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 53) (:start . 51)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 60)\n  (:start . 54) (:id . 55))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 71)\n  (:start . 61) (:id . 56))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 77) (:start . 72)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "exclude") (:form . "excludes") (:end . 86)\n  (:start . 78) (:id . 58))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 94)\n  (:start . 87) (:id . 59))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 104)\n  (:start . 95) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 109) (:start . 105)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "neuropile") (:form . "neuropile") (:end . 119)\n  (:start . 110) (:id . 62))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 125)\n  (:start . 120) (:id . 63))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 127) (:start . 126)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s10.496) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503609@unknown@formal@none@1@S@However, in these embryos ectopic sensory terminals invade the entire layer 1 and are no longer excluded from its lateral portions, which normally contain highest Sema 1a levels.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "VBP") (:stem . "invade") (:form . "invade") (:end . 58)\n  (:start . 52) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 69)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 75) (:start . 70)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "RB") (:stem . "no") (:form . "no") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "RBR") (:stem . "longer") (:form . "longer") (:end . 95)\n  (:start . 89) (:id . 58))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 104)\n  (:start . 96) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 113) (:start . 110)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 121)\n  (:start . 114) (:id . 62))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 130)\n  (:start . 122) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 137)\n  (:start . 132) (:id . 65))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 146)\n  (:start . 138) (:id . 66))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 154)\n  (:start . 147) (:id . 67))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 162)\n  (:start . 155) (:id . 68))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 167) (:start . 163)\n  (:id . 69))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 170) (:start . 168)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 177)\n  (:start . 171) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.497) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503610@unknown@formal@none@1@S@This results in an overall increase in the surface area occupied by sensory neuron terminals in layers 1 and 3.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 50)\n  (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "occupy") (:form . "occupied") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 75)\n  (:start . 68) (:id . 54))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 82)\n  (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 92)\n  (:start . 83) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 102)\n  (:start . 96) (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 60))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s10.498) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503611@unknown@formal@none@1@S@Right: Diagram showing the patterns of Plex B expressing sensory terminals in sema 1a mutant (green) and wild-type (yellow) backgrounds, superimposed.@(((:tag . "RB") (:stem . "right") (:form . "Right") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "diagram") (:form . "Diagram") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 56)\n  (:start . 46) (:id . 51))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 74)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 92)\n  (:start . 86) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 99) (:start . 94)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 114)\n  (:start . 105) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 122)\n  (:start . 116) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "background") (:form . "backgrounds") (:end . 135)\n  (:start . 124) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "superimpose") (:form . "superimposed") (:end . 149)\n  (:start . 137) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s10.499) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503612@unknown@formal@none@1@S@Quantification reveals a significant increase in SA1+3+4/h (SA1+3+4/h=SA[layer 1+3+4]/[hemisegment surface area]) (***, p=4×10-5; Student's t-test) when Plex B is overexpressed in sensory neurons in a sema 1a mutant background (average SA1+3+4/h=0.6 and SD=0.08, n=22 hemisegments), compared to embryos in which Plex B is overexpressed in wild-type background (average SA1+3+4/h=0.5; SD=0.06; n=32 hemisegments).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 22)\n  (:start . 15) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 36)\n  (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 45)\n  (:start . 37) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . 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5503613@unknown@formal@none@1@S@(C) In plex A mutant embryos, sensory terminals aberrantly invade neuropile layers 1, 3, and to a lesser extent layer 2.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "In") (:end . 6) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 11) (:start . 7)\n  (:id . 46))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 13) (:start . 12)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 20)\n  (:start . 14) (:id . 48))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 28)\n  (:start . 21) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 37)\n  (:start . 30) (:id . 51))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 47)\n  (:start . 38) (:id . 52))\n ((:tag . "RB") (:stem . "aberrantly") (:form . "aberrantly") (:end . 58)\n  (:start . 48) (:id . 53))\n ((:tag . "VBP") (:stem . "invade") (:form . "invade") (:end . 65)\n  (:start . 59) (:id . 54))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 75)\n  (:start . 66) (:id . 55))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 82)\n  (:start . 76) (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 87) (:start . 86)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n  (:id . 63))\n ((:tag . "JJR") (:stem . "less") (:form . "lesser") (:end . 104)\n  (:start . 98) (:id . 64))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 111)\n  (:start . 105) (:id . 65))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 117)\n  (:start . 112) (:id . 66))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 119) (:start . 118)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s10.501) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503614@unknown@formal@none@1@S@As in the case of sema 1a mutant embryos, this results in an overall increase in the surface area occupied by sensory neuron terminals in layers 1 and 3.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 14) (:start . 10)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sema") (:form . "sema") (:end . 22) (:start . 18)\n  (:id . 47))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 25) (:start . 23)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 32)\n  (:start . 26) (:id . 49))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 40)\n  (:start . 33) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 51))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 46) (:start . 42)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 54)\n  (:start . 47) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 60) (:start . 58)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 68)\n  (:start . 61) (:id . 56))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 77)\n  (:start . 69) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 59))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 92)\n  (:start . 85) (:id . 60))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 97) (:start . 93)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "occupy") (:form . "occupied") (:end . 106)\n  (:start . 98) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 109) (:start . 107)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 117)\n  (:start . 110) (:id . 64))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 124)\n  (:start . 118) (:id . 65))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 134)\n  (:start . 125) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 137) (:start . 135)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 144)\n  (:start . 138) (:id . 68))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 146) (:start . 145)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 70))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 152) (:start . 151)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.502) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503615@unknown@formal@none@1@S@Right: Diagram showing the patterns of sensory terminals in plex A mutant (green) and wild-type (yellow) backgrounds, superimposed.@(((:tag . "RB") (:stem . "right") (:form . "Right") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "diagram") (:form . "Diagram") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 56)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 95)\n  (:start . 86) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 103)\n  (:start . 97) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "background") (:form . "backgrounds") (:end . 116)\n  (:start . 105) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "superimpose") (:form . "superimposed") (:end . 130)\n  (:start . 118) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.503) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503616@unknown@formal@none@1@S@Quantification reveals a significant increase of SA1+3+4/h (***, p=6×10-34; Student's t-test) in plex A mutants (average SA1+3+4/h=0.7 and SD=0.08, n=62 hemisegments), with respect to wild type (average SA1+3+4/h=0.3; SD=0.05; n=32 hemisegments).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 22)\n  (:start . 15) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 36)\n  (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 45)\n  (:start . 37) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "SA1+3+4/h") (:form . "SA1+3+4/h") (:end . 58)\n  (:start . 49) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 49))\n ((:tag . "SYM") (:stem . "***") (:form . "***") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "p=6×10-34") (:form . "p=6×10-34") (:end . 74)\n  (:start . 65) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 83)\n  (:start . 76) (:id . 54))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "t-test") (:form . "t-test") (:end . 92)\n  (:start . 86) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 101) (:start . 97)\n  (:id . 59))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 111)\n  (:start . 104) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 120)\n  (:start . 113) (:id . 63))\n ((:tag . "NN") (:stem . "sa1+3+4/h=0.7") (:form . "SA1+3+4/h=0.7")\n  (:end . 134) (:start . 121) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n  (:id . 65))\n ((:tag . "NN") (:stem . "sd=0.08") (:form . "SD=0.08") (:end . 146)\n  (:start . 139) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 67))\n ((:tag . "NN") (:stem . "n=62") (:form . "n=62") (:end . 152) (:start . 148)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 165)\n  (:start . 153) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 172) (:start . 168)\n  (:id . 72))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 180)\n  (:start . 173) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 183) (:start . 181)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "wild") (:form . "wild") (:end . 188) (:start . 184)\n  (:id . 75))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 193) (:start . 189)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 195) (:start . 194)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 202)\n  (:start . 195) (:id . 78))\n ((:tag . "NN") (:stem . "sa1+3+4/h=0.3") (:form . "SA1+3+4/h=0.3")\n  (:end . 216) (:start . 203) (:id . 79))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 217) (:start . 216)\n  (:id . 80))\n ((:tag . "NN") (:stem . "sd=0.05") (:form . "SD=0.05") (:end . 225)\n  (:start . 218) (:id . 81))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 226) (:start . 225)\n  (:id . 82))\n ((:tag . "NN") (:stem . "n=32") (:form . "n=32") (:end . 231) (:start . 227)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "hemisegment") (:form . "hemisegments") (:end . 244)\n  (:start . 232) (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 245) (:start . 244)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s10.504) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503617@unknown@formal@none@1@S@(D) Expressing Plex B in sensory neurons in a plex A mutant background is sufficient to exclude sensory terminals from lateral and intermediate portions of neuropile layer 1.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "VBG") (:stem . "express") (:form . "Expressing") (:end . 14)\n  (:start . 4) (:id . 45))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 24) (:start . 22)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 32)\n  (:start . 25) (:id . 49))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 40)\n  (:start . 33) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 50) (:start . 46)\n  (:id . 53))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 52) (:start . 51)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 59)\n  (:start . 53) (:id . 55))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 70)\n  (:start . 60) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 73) (:start . 71)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 84)\n  (:start . 74) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 95)\n  (:start . 88) (:id . 60))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 103)\n  (:start . 96) (:id . 61))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 113)\n  (:start . 104) (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 118) (:start . 114)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "lateral") (:form . "lateral") (:end . 126)\n  (:start . 119) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "intermediate") (:form . "intermediate") (:end . 143)\n  (:start . 131) (:id . 66))\n ((:tag . "NNS") (:stem . "portion") (:form . "portions") (:end . 152)\n  (:start . 144) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 155) (:start . 153)\n  (:id . 68))\n ((:tag . "NN") (:stem . "neuropile") (:form . "neuropile") (:end . 165)\n  (:start . 156) (:id . 69))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 171)\n  (:start . 166) (:id . 70))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 173) (:start . 172)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s10.505) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503618@unknown@formal@none@1@S@In these embryos ectopic sensory terminals do not invade regions of layer 1, which contain highest Sema 1a levels.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "JJ") (:stem . "ectopic") (:form . "ectopic") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "VB") (:stem . "invade") (:form . "invade") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 64)\n  (:start . 57) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 73) (:start . 68)\n  (:id . 53))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 82) (:start . 77)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 90)\n  (:start . 83) (:id . 57))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 98)\n  (:start . 91) (:id . 58))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 103) (:start . 99)\n  (:id . 59))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 106) (:start . 104)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 113)\n  (:start . 107) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s10.506) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503619@unknown@formal@none@1@S@As a result, sensory neuron terminals in layers 1 and 3 occupy a smaller surface area than in plex A mutants.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 20)\n  (:start . 13) (:id . 46))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 27)\n  (:start . 21) (:id . 47))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 47)\n  (:start . 41) (:id . 50))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "occupy") (:form . "occupy") (:end . 62)\n  (:start . 56) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 55))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 72)\n  (:start . 65) (:id . 56))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 80)\n  (:start . 73) (:id . 57))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 85) (:start . 81)\n  (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 90) (:start . 86)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 98) (:start . 94)\n  (:id . 61))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 100) (:start . 99)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 108)\n  (:start . 101) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s10.507) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503620@unknown@formal@none@1@S@Thus, in the absence of Plex A, Plex B is sufficient to exclude sensory terminals from regions of highest Sema 1a expression.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 20)\n  (:start . 13) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 30) (:start . 29)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 36) (:start . 32)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 38) (:start . 37)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 52)\n  (:start . 42) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n  (:id . 55))\n ((:tag . "VB") (:stem . "exclude") (:form . "exclude") (:end . 63)\n  (:start . 56) (:id . 56))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 71)\n  (:start . 64) (:id . 57))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 81)\n  (:start . 72) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 86) (:start . 82)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 94)\n  (:start . 87) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 61))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 105)\n  (:start . 98) (:id . 62))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 110) (:start . 106)\n  (:id . 63))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 113) (:start . 111)\n  (:id . 64))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 124)\n  (:start . 114) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.508) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503621@unknown@formal@none@1@S@Plex B may therefore function as a receptor for Sema 1a.@(((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 6) (:start . 5)\n  (:id . 43))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 20)\n  (:start . 11) (:id . 45))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 43)\n  (:start . 35) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Sema") (:form . "Sema") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "1a") (:form . "1a") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 53)))@@@1@12@((:hcues ((:id . :x10.509.1) (:span 7 10)))\n (:hscopes ((:id . :x10.509.1) (:span 7 55)))\n (:identifiers (:sid . :s10.509) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503622@unknown@formal@none@1@S@Right: Diagram showing superimposed patterns of sensory terminals with and without Plex B expression in plex A mutants.@(((:tag . "RB") (:stem . "right") (:form . "Right") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "diagram") (:form . "Diagram") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "superimpose") (:form . "superimposed") (:end . 35)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 65)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 70) (:start . 66)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 52))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 82)\n  (:start . 75) (:id . 53))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 87) (:start . 83)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 100)\n  (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "NN") (:stem . "plex") (:form . "plex") (:end . 108) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 110) (:start . 109)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 118)\n  (:start . 111) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s10.510) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503623@unknown@formal@none@1@S@Terminals with Plex B expression: green.@(((:tag . "NNS") (:stem . "terminal") (:form . "Terminals") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 40) (:start . 39)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s10.511) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503624@unknown@formal@none@1@S@Terminals without Plex B expression: yellow.@(((:tag . "NNS") (:stem . "terminal") (:form . "Terminals") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 17)\n  (:start . 10) (:id . 43))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "VB") (:stem . "yellow") (:form . "yellow") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 44) (:start . 43)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s10.512) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503625@unknown@formal@none@1@S@Quantification reveals a significant decrease of SA1+3+4/h (***, p=4×10-9; Student's t-test) when Plex B is expressed in sensory terminals in a plex A mutant background (SA1+3+4/h=0.5 and SD=0.1, n=55 hemisegments), compared to plex A mutants (SA1+3+4/h=0.7 and SD=0.08, n=62 hemisegments).@(((:tag . "NN") (:stem . "quantification") (:form . "Quantification")\n  (:end . 14) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 22)\n  (:start . 15) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 36)\n  (:start . 25) (:id . 45))\n ((:tag . "NN") (:stem . "decrease") (:form . "decrease") (:end . 45)\n  (:start . 37) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "SA1+3+4/h") (:form . 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5503626@unknown@formal@none@1@S@(E and F) Bar charts show the average SA1+3+4/h under different conditions as indicated.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 6) (:start . 3)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "F") (:form . "F") (:end . 8) (:start . 7)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 9) (:start . 8) (:id . 46))\n ((:tag . "NNP") (:stem . "Bar") (:form . "Bar") (:end . 13) (:start . 10)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "chart") (:form . "charts") (:end . 20)\n  (:start . 14) (:id . 48))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 25) (:start . 21)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 37)\n  (:start . 30) (:id . 51))\n ((:tag . "NN") (:stem . "sa1+3+4/h") (:form . "SA1+3+4/h") (:end . 47)\n  (:start . 38) (:id . 52))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 53) (:start . 48)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 63)\n  (:start . 54) (:id . 54))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 74)\n  (:start . 64) (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 87)\n  (:start . 78) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s10.514) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503627@unknown@formal@none@1@S@(E) The average SA1+3+4/h (average SA1+3+4/h=0.6, SD=0.08, n=22 hemisegments) is significantly higher (***, p=4×10-5; Student's t-test), when Plex B is expressed in a sema 1a mutant background, compared to its expression in wild-type background (average SA1+3+4/h=0.5; SD=0.06; n=32 hemisegments).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 15)\n  (:start . 8) (:id . 46))\n ((:tag . "NNP") (:stem . "SA1+3+4/h") (:form . "SA1+3+4/h") (:end . 25)\n  (:start . 16) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "average") (:form . 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5503628@unknown@formal@none@1@S@(F) The average SA1+3+4/h (average SA1+3/h=0.5 and SD=0.1, n=55 hemisegments) is significantly lower (***, p=4×10-9; Student's t-test) for sensory terminals that express Plex B in a plex A mutant background, compared to plex A mutants (average SA1+3+4/h=0.7 and SD=0.08, n=62 hemisegments).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "f") (:form . "F") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 15)\n  (:start . 8) (:id . 46))\n ((:tag . "NNP") (:stem . "SA1+3+4/h") (:form . "SA1+3+4/h") (:end . 25)\n  (:start . 16) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "average") (:form . 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5503629@unknown@formal@none@1@S@In contrast, we did not observe a significant difference (p=0.6; Student's t-test) between the SA1+3+4/h of sensory terminals that express Plex B in a plex A mutant background (average SA1+3+4/h=0.5 and SD=0.1, n=55 hemisegments) and those that express Plex B in wild-type background (SA1+3+4/h=0.5; SD=0.06; n=32 hemisegments). (1.24 MB TIF)@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "VB") (:stem . "observe") (:form . 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5503630@unknown@formal@none@1@S@Figure S10 Fas II defects are not rescued by selective restoration of Plex B expression in sensory neurons.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S10") (:form . "S10") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "defect") (:form . "defects") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "rescue") (:form . "rescued") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "selective") (:form . "selective") (:end . 54)\n  (:start . 45) (:id . 51))\n ((:tag . "NN") (:stem . "restoration") (:form . "restoration") (:end . 66)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Plex") (:form . "Plex") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 87)\n  (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 98)\n  (:start . 91) (:id . 58))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 106)\n  (:start . 99) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s10.518) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503631@unknown@formal@none@1@S@Graphs show percentage of segments (n=175) in which L1 (blue), I2 (green), I3 (yellow), M1 (black), M2 (white) tracts project aberrantly.@(((:tag . "NNS") (:stem . "graph") (:form . "Graphs") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "n=175") (:form . "n=175") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "l1") (:form . "L1") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 60) (:start . 56)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "I2") (:form . "I2") (:end . 65) (:start . 63)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 72) (:start . 67)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "I3") (:form . "I3") (:end . 77) (:start . 75)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 63))\n ((:tag . "NN") (:stem . "yellow") (:form . "yellow") (:end . 85)\n  (:start . 79) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "M1") (:form . "M1") (:end . 90) (:start . 88)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 97) (:start . 92)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 71))\n ((:tag . "NN") (:stem . "m2") (:form . "M2") (:end . 102) (:start . 100)\n  (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "white") (:form . "white") (:end . 109)\n  (:start . 104) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 117)\n  (:start . 111) (:id . 76))\n ((:tag . "NN") (:stem . "project") (:form . "project") (:end . 125)\n  (:start . 118) (:id . 77))\n ((:tag . "RB") (:stem . "aberrantly") (:form . "aberrantly") (:end . 136)\n  (:start . 126) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s10.519) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503632@unknown@formal@none@1@S@(A) In ppkEGFP; plexB embryos Fas II tracts are severely affected.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "In") (:end . 6) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "ppkegfp") (:form . "ppkEGFP") (:end . 14)\n  (:start . 7) (:id . 46))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 15) (:start . 14)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "plexB") (:form . "plexB") (:end . 21) (:start . 16)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 29)\n  (:start . 22) (:id . 49))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 33) (:start . 30)\n  (:id . 50))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 36) (:start . 34)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 43)\n  (:start . 37) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 47) (:start . 44)\n  (:id . 53))\n ((:tag . "RB") (:stem . "severely") (:form . "severely") (:end . 56)\n  (:start . 48) (:id . 54))\n ((:tag . "VBN") (:stem . "affect") (:form . "affected") (:end . 65)\n  (:start . 57) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s10.520) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503633@unknown@formal@none@1@S@(B) When Plex B expression is selectively restored in sensory neurons alone, in UAS-plexB;PO163GAL4,ppkEGFP;plexB embryos, Fas II tracts continue to exhibit the mutant phenotype. (0.19 MB TIF)@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 8) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "plex") (:form . "Plex") (:end . 13) (:start . 9)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 15) (:start . 14)\n  (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 26)\n  (:start . 16) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 49))\n ((:tag . "RB") (:stem . "selectively") (:form . "selectively") (:end . 41)\n  (:start . 30) (:id . 50))\n ((:tag . "VBN") (:stem . "restore") (:form . "restored") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 61)\n  (:start . 54) (:id . 53))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 69)\n  (:start . 62) (:id . 54))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 75) (:start . 70)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "UAS-plexB;PO163GAL4,ppkEGFP;plexB")\n  (:form . "UAS-plexB;PO163GAL4,ppkEGFP;plexB") (:end . 113) (:start . 80)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "embryo") (:form . "embryos") (:end . 121)\n  (:start . 114) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 129) (:start . 127)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 136)\n  (:start . 130) (:id . 63))\n ((:tag . "VBP") (:stem . "continue") (:form . "continue") (:end . 145)\n  (:start . 137) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 65))\n ((:tag . "VB") (:stem . "exhibit") (:form . "exhibit") (:end . 156)\n  (:start . 149) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 160) (:start . 157)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 167)\n  (:start . 161) (:id . 68))\n ((:tag . "NN") (:stem . "phenotype.") (:form . "phenotype.") (:end . 178)\n  (:start . 168) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 180) (:start . 179)\n  (:id . 70))\n ((:tag . "CD") (:stem . "0.19") (:form . "0.19") (:end . 184) (:start . 180)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 187) (:start . 185)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "TIF") (:form . "TIF") (:end . 191) (:start . 188)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 192) (:start . 191)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s10.521) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503634@unknown@formal@none@1@S@Table S1 Results of the misexpression screen.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "misexpression") (:form . "misexpression")\n  (:end . 37) (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "screen") (:form . "screen") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 45) (:start . 44)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s10.522) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503635@unknown@formal@none@1@S@We identified 11 genes (2.6%) that change the pattern of sensory terminals, without producing pronounced changes in neuron number or preventing sensory axons from reaching the CNS.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "CD") (:stem . "2.6") (:form . "2.6") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 29) (:start . 28)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "change") (:form . "change") (:end . 41)\n  (:start . 35) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 52))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 53)\n  (:start . 46) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 64)\n  (:start . 57) (:id . 55))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 74)\n  (:start . 65) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 83)\n  (:start . 76) (:id . 58))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 93)\n  (:start . 84) (:id . 59))\n ((:tag . "JJ") (:stem . "pronounced") (:form . "pronounced") (:end . 104)\n  (:start . 94) (:id . 60))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 112)\n  (:start . 105) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "NN") (:stem . "neuron") (:form . "neuron") (:end . 122)\n  (:start . 116) (:id . 63))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 129)\n  (:start . 123) (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "prevent") (:form . "preventing") (:end . 143)\n  (:start . 133) (:id . 66))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 151)\n  (:start . 144) (:id . 67))\n ((:tag . "NNS") (:stem . "axon") (:form . "axons") (:end . 157)\n  (:start . 152) (:id . 68))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 162) (:start . 158)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "reach") (:form . "reaching") (:end . 171)\n  (:start . 163) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 175) (:start . 172)\n  (:id . 71))\n ((:tag . "NN") (:stem . "cns") (:form . "CNS") (:end . 179) (:start . 176)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s10.523) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503636@unknown@formal@none@1@S@In these experiments, sensory terminals shift independently of Fas II tracts, which remain in their wild-type position and relation to each other.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "terminal") (:form . "terminals") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "VB") (:stem . "shift") (:form . "shift") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n  (:end . 59) (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Fas") (:form . "Fas") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "tract") (:form . "tracts") (:end . 76)\n  (:start . 70) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "remain") (:form . "remain") (:end . 90)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 99)\n  (:start . 94) (:id . 58))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 109)\n  (:start . 100) (:id . 59))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 118)\n  (:start . 110) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 61))\n ((:tag . "NN") (:stem . "relation") (:form . "relation") (:end . 131)\n  (:start . 123) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 134) (:start . 132)\n  (:id . 63))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 139) (:start . 135)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 145)\n  (:start . 140) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s10.524) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503637@unknown@formal@none@1@S@Of the 11 genes, two produced specific shifts along the dorso-ventral axis.@(((:tag . "IN") (:stem . "of") (:form . "Of") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 15) (:start . 10)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 20) (:start . 17)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 29)\n  (:start . 21) (:id . 48))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 38)\n  (:start . 30) (:id . 49))\n ((:tag . "NNS") (:stem . "shift") (:form . "shifts") (:end . 45)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 69) (:start . 56) (:id . 53))\n ((:tag . "NN") (:stem . "axis") (:form . "axis") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s10.525) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503638@unknown@formal@none@1@S@The table gives the list of 11 genes, which, when misexpressed in sensory neurons alone, produce specific shifts in the dorso-ventral, medio-lateral or antero-posterior axes. (0.04 MB DOC)@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "table") (:form . "table") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "give") (:form . "gives") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 36) (:start . 31)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 43) (:start . 38)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 52))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 49) (:start . 45)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "misexpresse") (:form . "misexpressed") (:end . 62)\n  (:start . 50) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "sensory") (:form . "sensory") (:end . 73)\n  (:start . 66) (:id . 56))\n ((:tag . "NNS") (:stem . "neuron") (:form . "neurons") (:end . 81)\n  (:start . 74) (:id . 57))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 87) (:start . 82)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "produce") (:form . "produce") (:end . 96)\n  (:start . 89) (:id . 60))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 105)\n  (:start . 97) (:id . 61))\n ((:tag . "NNS") (:stem . "shift") (:form . "shifts") (:end . 112)\n  (:start . 106) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "dorso-ventral") (:form . "dorso-ventral")\n  (:end . 133) (:start . 120) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "medio-lateral") (:form . "medio-lateral")\n  (:end . 148) (:start . 135) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 151) (:start . 149)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "antero-posterior") (:form . "antero-posterior")\n  (:end . 168) (:start . 152) (:id . 69))\n ((:tag . "NN") (:stem . "axes.") (:form . "axes.") (:end . 174)\n  (:start . 169) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n  (:id . 71))\n ((:tag . "CD") (:stem . "0.04") (:form . "0.04") (:end . 180) (:start . 176)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "MB") (:form . "MB") (:end . 183) (:start . 181)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "DOC") (:form . "DOC") (:end . 187) (:start . 184)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s10.526) (:did . :pmc2690435) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503639@unknown@formal@none@1@S@Time warping of evolutionary distant temporal gene expression data based on noise suppression@(((:tag . "NNP") (:stem . "Time") (:form . "Time") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "warping") (:form . "warping") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 28)\n  (:start . 16) (:id . 45))\n ((:tag . "JJ") (:stem . "distant") (:form . "distant") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 50) (:start . 46)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 61)\n  (:start . 51) (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 66) (:start . 62)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 72) (:start . 67)\n  (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 75) (:start . 73)\n  (:id . 52))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 81) (:start . 76)\n  (:id . 53))\n ((:tag . "NN") (:stem . "suppression") (:form . "suppression") (:end . 93)\n  (:start . 82) (:id . 54)))@@@1@13@((:identifiers (:sid . :s11.1) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5503640@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s11.2) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503641@unknown@formal@none@1@S@Comparative analysis of genome wide temporal gene expression data has a broad potential area of application, including evolutionary biology, developmental biology, and medicine.@(((:tag . "JJ") (:stem . "comparative") (:form . "Comparative") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 30)\n  (:start . 24) (:id . 45))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 60)\n  (:start . 50) (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 65) (:start . 61)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 69) (:start . 66)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "broad") (:form . "broad") (:end . 77) (:start . 72)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 87)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 92) (:start . 88)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "application") (:form . "application") (:end . 107)\n  (:start . 96) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 118)\n  (:start . 109) (:id . 59))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 131)\n  (:start . 119) (:id . 60))\n ((:tag . "NN") (:stem . "biology") (:form . "biology") (:end . 139)\n  (:start . 132) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 154) (:start . 141) (:id . 63))\n ((:tag . "NN") (:stem . "biology") (:form . "biology") (:end . 162)\n  (:start . 155) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 66))\n ((:tag . "NN") (:stem . "medicine") (:form . "medicine") (:end . 176)\n  (:start . 168) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s11.3) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503642@unknown@formal@none@1@S@However, at large evolutionary distances, the construction of global alignments and the consequent comparison of the time- series data are difficult.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 30)\n  (:start . 18) (:id . 46))\n ((:tag . "NNS") (:stem . "distance") (:form . "distances") (:end . 40)\n  (:start . 31) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "construction") (:form . "construction") (:end . 58)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 79)\n  (:start . 69) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "consequent") (:form . "consequent") (:end . 98)\n  (:start . 88) (:id . 56))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 109)\n  (:start . 99) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 59))\n ((:tag . "NN") (:stem . "time-") (:form . "time-") (:end . 122)\n  (:start . 117) (:id . 60))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 129)\n  (:start . 123) (:id . 61))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 134)\n  (:start . 130) (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 138) (:start . 135)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 148)\n  (:start . 139) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s11.4) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503643@unknown@formal@none@1@S@The main reason is the accumulation of variability in expression profiles of orthologous genes, in the course of evolution.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "main") (:form . "main") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "reason") (:form . "reason") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "accumulation") (:form . "accumulation") (:end . 35)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "variability") (:form . "variability") (:end . 50)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 64)\n  (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 73)\n  (:start . 65) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 88)\n  (:start . 77) (:id . 54))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 94) (:start . 89)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "NN") (:stem . "course") (:form . "course") (:end . 109)\n  (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 122)\n  (:start . 113) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s11.5) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503644@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s11.6) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503645@unknown@formal@none@1@S@We applied Pearson distance matrices, in combination with other noise-suppression techniques and data filtering to improve alignments.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "apply") (:form . "applied") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 36)\n  (:start . 28) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 52)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "noise-suppression") (:form . "noise-suppression")\n  (:end . 81) (:start . 64) (:id . 52))\n ((:tag . "NNS") (:stem . "technique") (:form . "techniques") (:end . 92)\n  (:start . 82) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 101) (:start . 97)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "filter") (:form . "filtering") (:end . 111)\n  (:start . 102) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 114) (:start . 112)\n  (:id . 57))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 122)\n  (:start . 115) (:id . 58))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 133)\n  (:start . 123) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s11.7) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503646@unknown@formal@none@1@S@This novel framework enhanced the capacity to capture the similarities between the temporal gene expression datasets separated by large evolutionary distances.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "enhance") (:form . "enhanced") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "capacity") (:form . "capacity") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "VB") (:stem . "capture") (:form . "capture") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "similarity") (:form . "similarities") (:end . 70)\n  (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 78)\n  (:start . 71) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 91)\n  (:start . 83) (:id . 54))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 96) (:start . 92)\n  (:id . 55))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 107)\n  (:start . 97) (:id . 56))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 116)\n  (:start . 108) (:id . 57))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 126)\n  (:start . 117) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 129) (:start . 127)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 135)\n  (:start . 130) (:id . 60))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 148)\n  (:start . 136) (:id . 61))\n ((:tag . "NNS") (:stem . "distance") (:form . "distances") (:end . 158)\n  (:start . 149) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s11.8) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503647@unknown@formal@none@1@S@We aligned and compared the temporal gene expression data in budding (Saccharomyces cerevisiae) and fission (Schizosaccharomyces pombe) yeast, which are separated by more then ~400 myr of evolution.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "align") (:form . "aligned") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "compare") (:form . "compared") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "bud") (:form . "budding") (:end . 68) (:start . 61)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Saccharomyces") (:form . "Saccharomyces")\n  (:end . 83) (:start . 70) (:id . 54))\n ((:tag . "NNP") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 94)\n  (:start . 84) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "fission") (:form . "fission") (:end . 107)\n  (:start . 100) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "FW") (:stem . "schizosaccharomyces")\n  (:form . "Schizosaccharomyces") (:end . 128) (:start . 109) (:id . 60))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 134)\n  (:start . 129) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 141)\n  (:start . 136) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 148)\n  (:start . 143) (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 152) (:start . 149)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 162)\n  (:start . 153) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 165) (:start . 163)\n  (:id . 68))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 170) (:start . 166)\n  (:id . 69))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 175) (:start . 171)\n  (:id . 70))\n ((:tag . "CD") (:stem . "~400") (:form . "~400") (:end . 180) (:start . 176)\n  (:id . 71))\n ((:tag . "NN") (:stem . "myr") (:form . "myr") (:end . 184) (:start . 181)\n  (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n  (:id . 73))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 197)\n  (:start . 188) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s11.9) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503648@unknown@formal@none@1@S@We found that the global alignment (time warping) properly matched the duration of cell cycle phases in these distant organisms, which was measured in prior studies.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "warping") (:form . "warping") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "RB") (:stem . "properly") (:form . "properly") (:end . 58)\n  (:start . 50) (:id . 52))\n ((:tag . "VBD") (:stem . "match") (:form . "matched") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "duration") (:form . "duration") (:end . 79)\n  (:start . 71) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 87) (:start . 83)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 93) (:start . 88)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "phase") (:form . "phases") (:end . 100)\n  (:start . 94) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 60))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 109)\n  (:start . 104) (:id . 61))\n ((:tag . "JJ") (:stem . "distant") (:form . "distant") (:end . 117)\n  (:start . 110) (:id . 62))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 127)\n  (:start . 118) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 134)\n  (:start . 129) (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 138) (:start . 135)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 147)\n  (:start . 139) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 156)\n  (:start . 151) (:id . 69))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 164)\n  (:start . 157) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s11.10) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503649@unknown@formal@none@1@S@At the same time, when applied to individual ortholog pairs, this alignment procedure revealed groups of genes with distinct alignments, different from the global alignment.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 22) (:start . 18)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 30)\n  (:start . 23) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 44)\n  (:start . 34) (:id . 50))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 53)\n  (:start . 45) (:id . 51))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 75)\n  (:start . 66) (:id . 55))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 85)\n  (:start . 76) (:id . 56))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 94)\n  (:start . 86) (:id . 57))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 101)\n  (:start . 95) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 110)\n  (:start . 105) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 115) (:start . 111)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 135)\n  (:start . 125) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 146)\n  (:start . 137) (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 151) (:start . 147)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 162)\n  (:start . 156) (:id . 68))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 172)\n  (:start . 163) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s11.11) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503650@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s11.12) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503651@unknown@formal@none@1@S@Our alignment-based predictions of differences in the cell cycle phases between the two yeast species were in a good agreement with the existing data, thus supporting the computational strategy adopted in this study.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "alignment-based") (:form . "alignment-based")\n  (:end . 19) (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 31)\n  (:start . 20) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 46)\n  (:start . 35) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 58) (:start . 54)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 64) (:start . 59)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "phase") (:form . "phases") (:end . 71)\n  (:start . 65) (:id . 51))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 79)\n  (:start . 72) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 53))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 87) (:start . 84)\n  (:id . 54))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 93) (:start . 88)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 101)\n  (:start . 94) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 106) (:start . 102)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 109) (:start . 107)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 111) (:start . 110)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "good") (:form . "good") (:end . 116) (:start . 112)\n  (:id . 60))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 126)\n  (:start . 117) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 131) (:start . 127)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 135) (:start . 132)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 144)\n  (:start . 136) (:id . 64))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 149)\n  (:start . 145) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 155) (:start . 151)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "support") (:form . "supporting") (:end . 166)\n  (:start . 156) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n  (:end . 184) (:start . 171) (:id . 70))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 193)\n  (:start . 185) (:id . 71))\n ((:tag . "VBN") (:stem . "adopt") (:form . "adopted") (:end . 201)\n  (:start . 194) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 204) (:start . 202)\n  (:id . 73))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 209) (:start . 205)\n  (:id . 74))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 215)\n  (:start . 210) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s11.13) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503652@unknown@formal@none@1@S@We propose that the existence of the alternative alignments, specific to distinct groups of genes, suggests presence of different synchronization modes between the two organisms and possible functional decoupling of particular physiological gene networks in the course of evolution.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "propose") (:form . "propose") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "existence") (:form . "existence") (:end . 29)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 48)\n  (:start . 37) (:id . 49))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 59)\n  (:start . 49) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 69)\n  (:start . 61) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "distinct") (:form . "distinct") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 88)\n  (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 97) (:start . 92)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 107)\n  (:start . 99) (:id . 59))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 116)\n  (:start . 108) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 129)\n  (:start . 120) (:id . 62))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 145) (:start . 130) (:id . 63))\n ((:tag . "NNS") (:stem . "mode") (:form . "modes") (:end . 151)\n  (:start . 146) (:id . 64))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 159)\n  (:start . 152) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 66))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 167) (:start . 164)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 177)\n  (:start . 168) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 181) (:start . 178)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 190)\n  (:start . 182) (:id . 70))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 201)\n  (:start . 191) (:id . 71))\n ((:tag . "NN") (:stem . "decoupling") (:form . "decoupling") (:end . 212)\n  (:start . 202) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 215) (:start . 213)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 226)\n  (:start . 216) (:id . 74))\n ((:tag . "JJ") (:stem . "physiological") (:form . "physiological")\n  (:end . 240) (:start . 227) (:id . 75))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 245) (:start . 241)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "network") (:form . "networks") (:end . 254)\n  (:start . 246) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 257) (:start . 255)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 261) (:start . 258)\n  (:id . 79))\n ((:tag . "NN") (:stem . "course") (:form . "course") (:end . 268)\n  (:start . 262) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 271) (:start . 269)\n  (:id . 81))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 281)\n  (:start . 272) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 282) (:start . 281)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x11.14.1) (:span 182 190)) ((:id . :x11.14.2) (:span 99 107))\n  ((:id . :x11.14.3) (:span 3 10)))\n (:hscopes ((:id . :x11.14.1) (:span 182 254))\n  ((:id . :x11.14.2) (:span 99 281)) ((:id . :x11.14.3) (:span 3 281)))\n (:identifiers (:sid . :s11.14) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503653@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s11.15) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503654@unknown@formal@none@1@S@Comparative analysis of evolutionary changes in distant organisms at the level of gene expression requires cross-matching (alignment) of temporal microarray data covering developmental time courses or cell cycles.@(((:tag . "JJ") (:stem . "comparative") (:form . "Comparative") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 36)\n  (:start . 24) (:id . 45))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 44)\n  (:start . 37) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "distant") (:form . "distant") (:end . 55)\n  (:start . 48) (:id . 48))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 65)\n  (:start . 56) (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 68) (:start . 66)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 78) (:start . 73)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 97)\n  (:start . 87) (:id . 55))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 106)\n  (:start . 98) (:id . 56))\n ((:tag . "JJ") (:stem . "cross-matching") (:form . "cross-matching")\n  (:end . 121) (:start . 107) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 58))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 132)\n  (:start . 123) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 145)\n  (:start . 137) (:id . 62))\n ((:tag . "NN") (:stem . "microarray") (:form . "microarray") (:end . 156)\n  (:start . 146) (:id . 63))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 161)\n  (:start . 157) (:id . 64))\n ((:tag . "VBG") (:stem . "cover") (:form . "covering") (:end . 170)\n  (:start . 162) (:id . 65))\n ((:tag . "JJ") (:stem . "developmental") (:form . "developmental")\n  (:end . 184) (:start . 171) (:id . 66))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 189) (:start . 185)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "course") (:form . "courses") (:end . 197)\n  (:start . 190) (:id . 68))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 200) (:start . 198)\n  (:id . 69))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 205) (:start . 201)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "cycle") (:form . "cycles") (:end . 212)\n  (:start . 206) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x11.16.1) (:span 198 200)))\n (:hscopes ((:id . :x11.16.1) (:span 185 212)))\n (:identifiers (:sid . :s11.16) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503655@unknown@formal@none@1@S@Alignment of time series data or time warping allows side by side comparison of orthologous gene expression on a relative time scale [1-5].@(((:tag . "NNP") (:stem . "Alignment") (:form . "Alignment") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "warping") (:form . "warping") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 65) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 76)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 91)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 107)\n  (:start . 97) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 112) (:start . 111)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 121)\n  (:start . 113) (:id . 61))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 126) (:start . 122)\n  (:id . 62))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 132)\n  (:start . 127) (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 134) (:start . 133)\n  (:id . 64))\n ((:tag . "CD") (:stem . "1-5") (:form . "1-5") (:end . 137) (:start . 134)\n  (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 138) (:start . 137)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s11.17) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503656@unknown@formal@none@1@S@The time warping produces non-linear alignment paths, which help estimate the relative duration of similar steps in the life cycle of diverged species.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "warping") (:form . "warping") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "VBZ") (:stem . "produce") (:form . "produces") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "non-linear") (:form . "non-linear") (:end . 36)\n  (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 46)\n  (:start . 37) (:id . 47))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 52) (:start . 47)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "help") (:form . "help") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "VB") (:stem . "estimate") (:form . "estimate") (:end . 73)\n  (:start . 65) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 86)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "duration") (:form . "duration") (:end . 95)\n  (:start . 87) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 106)\n  (:start . 99) (:id . 57))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 112)\n  (:start . 107) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 124) (:start . 120)\n  (:id . 61))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 130)\n  (:start . 125) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "diverged") (:form . "diverged") (:end . 142)\n  (:start . 134) (:id . 64))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 150)\n  (:start . 143) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s11.18) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503657@unknown@formal@none@1@S@In addition, aligned temporal datasets can reveal concordantly and discordantly expressed pairs of orthologous genes or groups of genes.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "VB") (:stem . "reveal") (:form . "reveal") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "RB") (:stem . "concordantly") (:form . "concordantly") (:end . 62)\n  (:start . 50) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "RB") (:stem . "discordantly") (:form . "discordantly") (:end . 79)\n  (:start . 67) (:id . 52))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 89)\n  (:start . 80) (:id . 53))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 95) (:start . 90)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 110)\n  (:start . 99) (:id . 56))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 116)\n  (:start . 111) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 119) (:start . 117)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 126)\n  (:start . 120) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 135)\n  (:start . 130) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x11.19.1) (:span 39 42)))\n (:hscopes ((:id . :x11.19.1) (:span 39 135)))\n (:identifiers (:sid . :s11.19) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503658@unknown@formal@none@1@S@Currently available time-warping algorithms [6] stem out from early methods of speech recognition [7].@(((:tag . "RB") (:stem . "currently") (:form . "Currently") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 19)\n  (:start . 10) (:id . 43))\n ((:tag . "JJ") (:stem . "time-warping") (:form . "time-warping") (:end . 32)\n  (:start . 20) (:id . 44))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 43)\n  (:start . 33) (:id . 45))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 45) (:start . 44)\n  (:id . 46))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 46) (:start . 45)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 47) (:start . 46)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "stem") (:form . "stem") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "early") (:form . "early") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 75)\n  (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "NN") (:stem . "speech") (:form . "speech") (:end . 85)\n  (:start . 79) (:id . 55))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 97)\n  (:start . 86) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s11.20) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503659@unknown@formal@none@1@S@Benchmarking tests show that the existing methods under perform on noisy datasets and require accommodation to temporal expression data from organisms separated by large evolutionary distances [see Additional file 1 - Figures S1-S3] (and at UC Berkeley online resource: http://flydev.berkeley.edu/cgi- bin/GTEM/yeast_analysis/similarity_matrices.html).@(((:tag . "VBG") (:stem . "benchmarke") (:form . "Benchmarking") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 18) (:start . 13)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "perform") (:form . "perform") (:end . 63)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "noisy") (:form . "noisy") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 81)\n  (:start . 73) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "VB") (:stem . "require") (:form . "require") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "NN") (:stem . "accommodation") (:form . "accommodation")\n  (:end . 107) (:start . 94) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 119)\n  (:start . 111) (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 130)\n  (:start . 120) (:id . 59))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 135)\n  (:start . 131) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 140) (:start . 136)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 150)\n  (:start . 141) (:id . 62))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 160)\n  (:start . 151) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 163) (:start . 161)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 169)\n  (:start . 164) (:id . 65))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 182)\n  (:start . 170) (:id . 66))\n ((:tag . "NNS") (:stem . "distance") (:form . "distances") (:end . 192)\n  (:start . 183) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 194) (:start . 193)\n  (:id . 68))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 197) (:start . 194)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 208)\n  (:start . 198) (:id . 70))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 213) (:start . 209)\n  (:id . 71))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 215) (:start . 214)\n  (:id . 72))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 217) (:start . 216)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 225)\n  (:start . 218) (:id . 74))\n ((:tag . "NN") (:stem . "s1-s3") (:form . "S1-S3") (:end . 231)\n  (:start . 226) (:id . 75))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 232) (:start . 231)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 234) (:start . 233)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 237) (:start . 234)\n  (:id . 78))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 240) (:start . 238)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "UC") (:form . "UC") (:end . 243) (:start . 241)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Berkeley") (:form . "Berkeley") (:end . 252)\n  (:start . 244) (:id . 81))\n ((:tag . "NN") (:stem . "online") (:form . "online") (:end . 259)\n  (:start . 253) (:id . 82))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 268)\n  (:start . 260) (:id . 83))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 269) (:start . 268)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "http://flydev.berkeley.edu/cgi-")\n  (:form . "http://flydev.berkeley.edu/cgi-") (:end . 301) (:start . 270)\n  (:id . 85))\n ((:tag . "NN") (:stem . "bin/gtem/yeast_analysis/similarity_matrices.html")\n  (:form . "bin/GTEM/yeast_analysis/similarity_matrices.html") (:end . 350)\n  (:start . 302) (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 351) (:start . 350)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 352) (:start . 351)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s11.21) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503660@unknown@formal@none@1@S@Here, we tested several noise suppression techniques, in order to optimize global alignment between the time series data from two species, separated by ~400 million years of evolution, budding (Saccharomyces cerevisiae) and fission (Schizosaccharomyces pombe) yeasts.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 15) (:start . 9)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "suppression") (:form . "suppression") (:end . 41)\n  (:start . 30) (:id . 48))\n ((:tag . "NNS") (:stem . "technique") (:form . "techniques") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "VB") (:stem . "optimize") (:form . "optimize") (:end . 74)\n  (:start . 66) (:id . 54))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 81)\n  (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 91)\n  (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 99)\n  (:start . 92) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 115)\n  (:start . 109) (:id . 60))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 120)\n  (:start . 116) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 125) (:start . 121)\n  (:id . 62))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 129) (:start . 126)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 137)\n  (:start . 130) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 148)\n  (:start . 139) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 151) (:start . 149)\n  (:id . 67))\n ((:tag . "CD") (:stem . "~400") (:form . "~400") (:end . 156) (:start . 152)\n  (:id . 68))\n ((:tag . "CD") (:stem . "million") (:form . "million") (:end . 164)\n  (:start . 157) (:id . 69))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 170)\n  (:start . 165) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 71))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 183)\n  (:start . 174) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "bud") (:form . "budding") (:end . 192)\n  (:start . 185) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 194) (:start . 193)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Saccharomyces") (:form . "Saccharomyces")\n  (:end . 207) (:start . 194) (:id . 76))\n ((:tag . "NNP") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 218)\n  (:start . 208) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 219) (:start . 218)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 223) (:start . 220)\n  (:id . 79))\n ((:tag . "NN") (:stem . "fission") (:form . "fission") (:end . 231)\n  (:start . 224) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 233) (:start . 232)\n  (:id . 81))\n ((:tag . "FW") (:stem . "schizosaccharomyces")\n  (:form . "Schizosaccharomyces") (:end . 252) (:start . 233) (:id . 82))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 258)\n  (:start . 253) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 259) (:start . 258)\n  (:id . 84))\n ((:tag . "NNS") (:stem . "yeast") (:form . "yeasts") (:end . 266)\n  (:start . 260) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 267) (:start . 266)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s11.22) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503661@unknown@formal@none@1@S@Traditionally, yeast cell cycle served as a model system to study regulation of the periodic gene expression, replication, and cell division [8,9].@(((:tag . "RB") (:stem . "traditionally") (:form . "Traditionally")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "serve") (:form . "served") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 56)\n  (:start . 50) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "VB") (:stem . "study") (:form . "study") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 76)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "periodic") (:form . "periodic") (:end . 92)\n  (:start . 84) (:id . 57))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 97) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 108)\n  (:start . 98) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 60))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 121)\n  (:start . 110) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 63))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 131) (:start . 127)\n  (:id . 64))\n ((:tag . "NN") (:stem . "division") (:form . "division") (:end . 140)\n  (:start . 132) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 142) (:start . 141)\n  (:id . 66))\n ((:tag . "CD") (:stem . "8,9") (:form . "8,9") (:end . 145) (:start . 142)\n  (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 146) (:start . 145)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s11.23) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503662@unknown@formal@none@1@S@Evolution of the periodic gene expression in yeast has been explored based on classification approaches using temporal gene expression data [10-12], where an individual periodicity score was assigned to each ortholog and these periodicities and phases were then compared.@(((:tag . "NN") (:stem . "evolution") (:form . "Evolution") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "periodic") (:form . "periodic") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "explore") (:form . "explored") (:end . 68)\n  (:start . 60) (:id . 52))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 74) (:start . 69)\n  (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "classification") (:form . "classification")\n  (:end . 92) (:start . 78) (:id . 55))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 103)\n  (:start . 93) (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 109) (:start . 104)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 118)\n  (:start . 110) (:id . 58))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 123) (:start . 119)\n  (:id . 59))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 134)\n  (:start . 124) (:id . 60))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 139)\n  (:start . 135) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 141) (:start . 140)\n  (:id . 62))\n ((:tag . "CD") (:stem . "10-12") (:form . "10-12") (:end . 146)\n  (:start . 141) (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 147) (:start . 146)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 65))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 154)\n  (:start . 149) (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 157) (:start . 155)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 168)\n  (:start . 158) (:id . 68))\n ((:tag . "NN") (:stem . "periodicity") (:form . "periodicity") (:end . 180)\n  (:start . 169) (:id . 69))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 186)\n  (:start . 181) (:id . 70))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 190) (:start . 187)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 199)\n  (:start . 191) (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 202) (:start . 200)\n  (:id . 73))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 207) (:start . 203)\n  (:id . 74))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 216)\n  (:start . 208) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 220) (:start . 217)\n  (:id . 76))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 226)\n  (:start . 221) (:id . 77))\n ((:tag . "NNS") (:stem . "periodicity") (:form . "periodicities")\n  (:end . 240) (:start . 227) (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 244) (:start . 241)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "phase") (:form . "phases") (:end . 251)\n  (:start . 245) (:id . 80))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 256) (:start . 252)\n  (:id . 81))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 261) (:start . 257)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 270)\n  (:start . 262) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 271) (:start . 270)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s11.24) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503663@unknown@formal@none@1@S@In contrast to the classification approach, time warping captures information from all orthologous profiles in a single test.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "classification") (:form . "classification")\n  (:end . 33) (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "warp") (:form . "warping") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "NNS") (:stem . "capture") (:form . "captures") (:end . 65)\n  (:start . 57) (:id . 51))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 77)\n  (:start . 66) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 82) (:start . 78)\n  (:id . 53))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 86) (:start . 83)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 98)\n  (:start . 87) (:id . 55))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 107)\n  (:start . 99) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 112) (:start . 111)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 119)\n  (:start . 113) (:id . 59))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 124) (:start . 120)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s11.25) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503664@unknown@formal@none@1@S@Exploration of alignments, constructed for S. cerevisiae and S. pombe using available methods and programs [1,6] [see Additional file 1 - Figures S1-S3] (and the UC Berkeley online resource) revealed presence of long gaps and noisy alignment paths.@(((:tag . "NNP") (:stem . "Exploration") (:form . "Exploration") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 38)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 75) (:start . 70)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 85)\n  (:start . 76) (:id . 54))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 106)\n  (:start . 98) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1,6") (:form . "1,6") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 112) (:start . 111)\n  (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 128)\n  (:start . 118) (:id . 63))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 133) (:start . 129)\n  (:id . 64))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 135) (:start . 134)\n  (:id . 65))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 137) (:start . 136)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 145)\n  (:start . 138) (:id . 67))\n ((:tag . "NN") (:stem . "s1-s3") (:form . "S1-S3") (:end . 151)\n  (:start . 146) (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 152) (:start . 151)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "UC") (:form . "UC") (:end . 164) (:start . 162)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Berkeley") (:form . "Berkeley") (:end . 173)\n  (:start . 165) (:id . 74))\n ((:tag . "NN") (:stem . "online") (:form . "online") (:end . 180)\n  (:start . 174) (:id . 75))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 189)\n  (:start . 181) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n  (:id . 77))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 199)\n  (:start . 191) (:id . 78))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 208)\n  (:start . 200) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 211) (:start . 209)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 216) (:start . 212)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "gap") (:form . "gaps") (:end . 221) (:start . 217)\n  (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 225) (:start . 222)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "noisy") (:form . "noisy") (:end . 231)\n  (:start . 226) (:id . 84))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 241)\n  (:start . 232) (:id . 85))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 247)\n  (:start . 242) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 248) (:start . 247)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s11.26) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503665@unknown@formal@none@1@S@In this study, we introduced and thoroughly tested a novel data treatment and alignment framework, based on noise-suppression methods and elements of Kruscal-Liberman alignment algorithm [6].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "introduce") (:form . "introduced") (:end . 28)\n  (:start . 18) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "RB") (:stem . "thoroughly") (:form . "thoroughly") (:end . 43)\n  (:start . 33) (:id . 49))\n ((:tag . "VBN") (:stem . "test") (:form . "tested") (:end . 50) (:start . 44)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 63) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 73)\n  (:start . 64) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 87)\n  (:start . 78) (:id . 56))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 97)\n  (:start . 88) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 104) (:start . 99)\n  (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 107) (:start . 105)\n  (:id . 60))\n ((:tag . "NN") (:stem . "noise-suppression") (:form . "noise-suppression")\n  (:end . 125) (:start . 108) (:id . 61))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 133)\n  (:start . 126) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 146)\n  (:start . 138) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Kruscal-Liberman") (:form . "Kruscal-Liberman")\n  (:end . 166) (:start . 150) (:id . 66))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 176)\n  (:start . 167) (:id . 67))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 186)\n  (:start . 177) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 188) (:start . 187)\n  (:id . 69))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 189) (:start . 188)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 190) (:start . 189)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s11.27) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503666@unknown@formal@none@1@S@The framework allowed us to override interspecific noise and to construct a global alignment for the two yeast species.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "allow") (:form . "allowed") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VB") (:stem . "override") (:form . "override") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "JJ") (:stem . "interspecific") (:form . "interspecific")\n  (:end . 50) (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 56) (:start . 51)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "VB") (:stem . "construct") (:form . "construct") (:end . 73)\n  (:start . 64) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 82)\n  (:start . 76) (:id . 54))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 92)\n  (:start . 83) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 110)\n  (:start . 105) (:id . 59))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 118)\n  (:start . 111) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s11.28) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503667@unknown@formal@none@1@S@This global alignment supported previously observed differences in duration of G1 and G2 cell cycle phases [13].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 42)\n  (:start . 32) (:id . 46))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 51)\n  (:start . 43) (:id . 47))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 63)\n  (:start . 52) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 49))\n ((:tag . "NN") (:stem . "duration") (:form . "duration") (:end . 75)\n  (:start . 67) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 51))\n ((:tag . "NN") (:stem . "g1") (:form . "G1") (:end . 81) (:start . 79)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 53))\n ((:tag . "NN") (:stem . "g2") (:form . "G2") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 93) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 99) (:start . 94)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "phase") (:form . "phases") (:end . 106)\n  (:start . 100) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s11.29) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503668@unknown@formal@none@1@S@In order to explore alternative alignments, the pairs of the orthologous expression profiles have been aligned individually and the resulting individual alignment paths were clustered using common clustering algorithms [14].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "explore") (:form . "explore") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 42)\n  (:start . 32) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 72)\n  (:start . 61) (:id . 53))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 83)\n  (:start . 73) (:id . 54))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 92)\n  (:start . 84) (:id . 55))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 102) (:start . 98)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 110)\n  (:start . 103) (:id . 58))\n ((:tag . "RB") (:stem . "individually") (:form . "individually") (:end . 123)\n  (:start . 111) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 141)\n  (:start . 132) (:id . 62))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 152)\n  (:start . 142) (:id . 63))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 162)\n  (:start . 153) (:id . 64))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 168)\n  (:start . 163) (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 173) (:start . 169)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "cluster") (:form . "clustered") (:end . 183)\n  (:start . 174) (:id . 67))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 189) (:start . 184)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 196)\n  (:start . 190) (:id . 69))\n ((:tag . "NN") (:stem . "clustering") (:form . "clustering") (:end . 207)\n  (:start . 197) (:id . 70))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 218)\n  (:start . 208) (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 220) (:start . 219)\n  (:id . 72))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 222) (:start . 220)\n  (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 223) (:start . 222)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s11.30) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503669@unknown@formal@none@1@S@Using this approach, we found gene groups or "time clusters," in which the relative synchronization modes (alignment paths, characteristic to each time cluster) were different from the global alignment path.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 41)\n  (:start . 35) (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 50) (:start . 46)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 59)\n  (:start . 51) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 61) (:start . 60)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 70) (:start . 65)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 83)\n  (:start . 75) (:id . 59))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 99) (:start . 84) (:id . 60))\n ((:tag . "NNS") (:stem . "mode") (:form . "modes") (:end . 105)\n  (:start . 100) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 62))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 116)\n  (:start . 107) (:id . 63))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 122)\n  (:start . 117) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 138) (:start . 124) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 141) (:start . 139)\n  (:id . 67))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 146) (:start . 142)\n  (:id . 68))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 151) (:start . 147)\n  (:id . 69))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 159)\n  (:start . 152) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 165) (:start . 161)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 175)\n  (:start . 166) (:id . 73))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 180) (:start . 176)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 184) (:start . 181)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 191)\n  (:start . 185) (:id . 76))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 201)\n  (:start . 192) (:id . 77))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 206) (:start . 202)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s11.31) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503670@unknown@formal@none@1@S@Our analysis suggested that evolutionary shifts in durations of G1/G2 cell cycle phases are manifested in the expression timing of replication machinery and ribosomal genes.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "suggest") (:form . "suggested") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 40)\n  (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "shift") (:form . "shifts") (:end . 47)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "duration") (:form . "durations") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "NN") (:stem . "g1/g2") (:form . "G1/G2") (:end . 69) (:start . 64)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 80) (:start . 75)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "phase") (:form . "phases") (:end . 87)\n  (:start . 81) (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "manifest") (:form . "manifested") (:end . 102)\n  (:start . 92) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 105) (:start . 103)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 120)\n  (:start . 110) (:id . 59))\n ((:tag . "NN") (:stem . "timing") (:form . "timing") (:end . 127)\n  (:start . 121) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 61))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 142)\n  (:start . 131) (:id . 62))\n ((:tag . "NN") (:stem . "machinery") (:form . "machinery") (:end . 152)\n  (:start . 143) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "ribosomal") (:form . "ribosomal") (:end . 166)\n  (:start . 157) (:id . 65))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 172)\n  (:start . 167) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x11.32.1) (:span 13 22)))\n (:hscopes ((:id . :x11.32.1) (:span 13 172)))\n (:identifiers (:sid . :s11.32) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503671@unknown@formal@none@1@S@Instead, gene expression in mitochondria was desynchronized or evolutionary "disconnected" from the replication and housekeeping genes due to high autonomy of that organelle.@(((:tag . "RB") (:stem . "instead") (:form . "Instead") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "mitochondrion") (:form . "mitochondria")\n  (:end . 40) (:start . 28) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "desynchronize") (:form . "desynchronized")\n  (:end . 59) (:start . 45) (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 75)\n  (:start . 63) (:id . 51))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 77) (:start . 76)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "disconnect") (:form . "disconnected") (:end . 89)\n  (:start . 77) (:id . 53))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 90) (:start . 89)\n  (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 95) (:start . 91)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 56))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 111)\n  (:start . 100) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 58))\n ((:tag . "NN") (:stem . "housekeeping") (:form . "housekeeping") (:end . 128)\n  (:start . 116) (:id . 59))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 134)\n  (:start . 129) (:id . 60))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 138) (:start . 135)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 141) (:start . 139)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 146) (:start . 142)\n  (:id . 63))\n ((:tag . "NN") (:stem . "autonomy") (:form . "autonomy") (:end . 155)\n  (:start . 147) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n  (:id . 65))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 163) (:start . 159)\n  (:id . 66))\n ((:tag . "NN") (:stem . "organelle") (:form . "organelle") (:end . 173)\n  (:start . 164) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s11.33) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503672@unknown@formal@none@1@S@Results and discussion@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "discussion") (:form . "discussion") (:end . 22)\n  (:start . 12) (:id . 44)))@@@1@3@((:identifiers (:sid . :s11.34) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503673@unknown@formal@none@1@S@Data selection and noise removal@(((:tag . "NNP") (:stem . "Data") (:form . "Data") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "removal") (:form . "removal") (:end . 32)\n  (:start . 25) (:id . 46)))@@@1@5@((:identifiers (:sid . :s11.35) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503674@unknown@formal@none@1@S@Success of the cross-specific time warping critically depends on the level of noise in time series expression data, "internal noise" and on the evolutionary variability in the gene expression between the two species or "external noise".@(((:tag . "NNP") (:stem . "Success") (:form . "Success") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "cross-specific") (:form . "cross-specific")\n  (:end . 29) (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "warp") (:form . "warping") (:end . 42)\n  (:start . 35) (:id . 47))\n ((:tag . "RB") (:stem . "critically") (:form . "critically") (:end . 53)\n  (:start . 43) (:id . 48))\n ((:tag . "VBZ") (:stem . "depend") (:form . "depends") (:end . 61)\n  (:start . 54) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 51))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 83) (:start . 78)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 98)\n  (:start . 92) (:id . 57))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 109)\n  (:start . 99) (:id . 58))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 114)\n  (:start . 110) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 60))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 125)\n  (:start . 117) (:id . 62))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 131)\n  (:start . 126) (:id . 63))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 132) (:start . 131)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n  (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 139) (:start . 137)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 156)\n  (:start . 144) (:id . 68))\n ((:tag . "NN") (:stem . "variability") (:form . "variability") (:end . 168)\n  (:start . 157) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 171) (:start . 169)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 175) (:start . 172)\n  (:id . 71))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 180) (:start . 176)\n  (:id . 72))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 191)\n  (:start . 181) (:id . 73))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 199)\n  (:start . 192) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n  (:id . 75))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 207) (:start . 204)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 215)\n  (:start . 208) (:id . 77))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 218) (:start . 216)\n  (:id . 78))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 220) (:start . 219)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "external") (:form . "external") (:end . 228)\n  (:start . 220) (:id . 80))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 234)\n  (:start . 229) (:id . 81))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 235) (:start . 234)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 236) (:start . 235)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s11.36) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503675@unknown@formal@none@1@S@The internal noise appears, for instance, due to the measurement errors between different microarrays (time points) and due to desynchronization of cell culture over time; the external noise is the result of accumulated in evolution differences in the orthologous expression or differences in expression caused by experimental conditions, such as selection of cell culture synchronization method.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . 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5503676@unknown@formal@none@1@S@In this perspective, problems connected with the alignment construction are largely problems related to noise reduction and noise overriding.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "perspective") (:form . "perspective") (:end . 19)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "problem") (:form . "problems") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "VBN") (:stem . "connect") (:form . "connected") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 58)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "construction") (:form . "construction") (:end . 71)\n  (:start . 59) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 83)\n  (:start . 76) (:id . 53))\n ((:tag . "NNS") (:stem . "problem") (:form . "problems") (:end . 92)\n  (:start . 84) (:id . 54))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 100)\n  (:start . 93) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 103) (:start . 101)\n  (:id . 56))\n ((:tag . "VB") (:stem . "noise") (:form . "noise") (:end . 109)\n  (:start . 104) (:id . 57))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 119)\n  (:start . 110) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 59))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 129)\n  (:start . 124) (:id . 60))\n ((:tag . "NN") (:stem . "overriding") (:form . "overriding") (:end . 140)\n  (:start . 130) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s11.38) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503677@unknown@formal@none@1@S@Ability to judge quality of alignments critically depends on the input data; data selection helps to find the least noisy/most reliable datasets.@(((:tag . "NN") (:stem . "ability") (:form . "Ability") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "VB") (:stem . "judge") (:form . "judge") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "RB") (:stem . "critically") (:form . "critically") (:end . 49)\n  (:start . 39) (:id . 48))\n ((:tag . "VBZ") (:stem . "depend") (:form . "depends") (:end . 57)\n  (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 70) (:start . 65)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 91)\n  (:start . 82) (:id . 56))\n ((:tag . "VBZ") (:stem . "help") (:form . "helps") (:end . 97) (:start . 92)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "VB") (:stem . "find") (:form . "find") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 115)\n  (:start . 110) (:id . 61))\n ((:tag . "RB") (:stem . "noisy/most") (:form . "noisy/most") (:end . 126)\n  (:start . 116) (:id . 62))\n ((:tag . "JJ") (:stem . "reliable") (:form . "reliable") (:end . 135)\n  (:start . 127) (:id . 63))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 144)\n  (:start . 136) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s11.39) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503678@unknown@formal@none@1@S@Therefore all 70 pairwise combinations of publicly available S. cerevisiae and S. pombe datasets [10-13,15-17] were explored using Kruscal-Liberman algorithm [6] based on either Euclidean or Pearson distance matrices (see Methods and UC Berkeley online resource).@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "pairwise") (:form . "pairwise") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "combination") (:form . "combinations") (:end . 38)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "RB") (:stem . "publicly") (:form . "publicly") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 74)\n  (:start . 64) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 52))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 87) (:start . 82)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 96)\n  (:start . 88) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 98) (:start . 97)\n  (:id . 56))\n ((:tag . "CD") (:stem . "10-13,15-17") (:form . "10-13,15-17") (:end . 109)\n  (:start . 98) (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 110) (:start . 109)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "explore") (:form . "explored") (:end . 124)\n  (:start . 116) (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 130) (:start . 125)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Kruscal-Liberman") (:form . "Kruscal-Liberman")\n  (:end . 147) (:start . 131) (:id . 62))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 157)\n  (:start . 148) (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 159) (:start . 158)\n  (:id . 64))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 160) (:start . 159)\n  (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 161) (:start . 160)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 167)\n  (:start . 162) (:id . 67))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 170) (:start . 168)\n  (:id . 68))\n ((:tag . "DT") (:stem . "either") (:form . "either") (:end . 177)\n  (:start . 171) (:id . 69))\n ((:tag . "NNP") (:stem . "Euclidean") (:form . "Euclidean") (:end . 187)\n  (:start . 178) (:id . 70))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 190) (:start . 188)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 198)\n  (:start . 191) (:id . 72))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 207)\n  (:start . 199) (:id . 73))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 216)\n  (:start . 208) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 218) (:start . 217)\n  (:id . 75))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 221) (:start . 218)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Methods") (:form . "Methods") (:end . 229)\n  (:start . 222) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 233) (:start . 230)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "UC") (:form . "UC") (:end . 236) (:start . 234)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Berkeley") (:form . "Berkeley") (:end . 245)\n  (:start . 237) (:id . 80))\n ((:tag . "NN") (:stem . "online") (:form . "online") (:end . 252)\n  (:start . 246) (:id . 81))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 261)\n  (:start . 253) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 262) (:start . 261)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 263) (:start . 262)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s11.40) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503679@unknown@formal@none@1@S@We adopted Pearson distance matrices to produce highly informative comparisons between time series and to cope with the external (evolutionary) noise (see Methods).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "adopt") (:form . "adopted") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 36)\n  (:start . 28) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 47)\n  (:start . 40) (:id . 48))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 54)\n  (:start . 48) (:id . 49))\n ((:tag . "JJ") (:stem . "informative") (:form . "informative") (:end . 66)\n  (:start . 55) (:id . 50))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 78)\n  (:start . 67) (:id . 51))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 86)\n  (:start . 79) (:id . 52))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 91) (:start . 87)\n  (:id . 53))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 98)\n  (:start . 92) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n  (:id . 56))\n ((:tag . "VB") (:stem . "cope") (:form . "cope") (:end . 110) (:start . 106)\n  (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 115) (:start . 111)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "external") (:form . "external") (:end . 128)\n  (:start . 120) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 142)\n  (:start . 130) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 63))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 149)\n  (:start . 144) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n  (:id . 65))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 154) (:start . 151)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 162)\n  (:start . 155) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 163) (:start . 162)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s11.41) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503680@unknown@formal@none@1@S@The distance matrices revealed discernible periodic patterns similar to that observed in simulated periodic datasets [see Additional file 1 - Figure S1].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "JJ") (:stem . "discernible") (:form . "discernible") (:end . 42)\n  (:start . 31) (:id . 46))\n ((:tag . "JJ") (:stem . "periodic") (:form . "periodic") (:end . 51)\n  (:start . 43) (:id . 47))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 60)\n  (:start . 52) (:id . 48))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 68)\n  (:start . 61) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 50))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 76) (:start . 72)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 85)\n  (:start . 77) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "simulated") (:form . "simulated") (:end . 98)\n  (:start . 89) (:id . 54))\n ((:tag . "JJ") (:stem . "periodic") (:form . "periodic") (:end . 107)\n  (:start . 99) (:id . 55))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 116)\n  (:start . 108) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 118) (:start . 117)\n  (:id . 57))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 121) (:start . 118)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 132)\n  (:start . 122) (:id . 59))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 137) (:start . 133)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 139) (:start . 138)\n  (:id . 61))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 141) (:start . 140)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 148)\n  (:start . 142) (:id . 63))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 151) (:start . 149)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s11.42) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503681@unknown@formal@none@1@S@Notably, alignments based on the Pearson distance matrices sustained much higher external noise and were capable of capturing even subtle similarities between orthologous datasets [see Additional file 1 - Figures S1-S3] (and the matrices for all 72 pairwise comparisons, available from UC Berkeley web resource).@(((:tag . "RB") (:stem . "notably") (:form . "Notably") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 25) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 58)\n  (:start . 50) (:id . 50))\n ((:tag . "VBD") (:stem . "sustain") (:form . "sustained") (:end . 68)\n  (:start . 59) (:id . 51))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 80) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "external") (:form . "external") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 95) (:start . 90)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 104) (:start . 100)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "capable") (:form . "capable") (:end . 112)\n  (:start . 105) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "capture") (:form . "capturing") (:end . 125)\n  (:start . 116) (:id . 60))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 130) (:start . 126)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "subtle") (:form . "subtle") (:end . 137)\n  (:start . 131) (:id . 62))\n ((:tag . "NNS") (:stem . "similarity") (:form . "similarities") (:end . 150)\n  (:start . 138) (:id . 63))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 158)\n  (:start . 151) (:id . 64))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 170)\n  (:start . 159) (:id . 65))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 179)\n  (:start . 171) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 181) (:start . 180)\n  (:id . 67))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 184) (:start . 181)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 195)\n  (:start . 185) (:id . 69))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 200) (:start . 196)\n  (:id . 70))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 202) (:start . 201)\n  (:id . 71))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 204) (:start . 203)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 212)\n  (:start . 205) (:id . 73))\n ((:tag . "NN") (:stem . "s1-s3") (:form . "S1-S3") (:end . 218)\n  (:start . 213) (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 219) (:start . 218)\n  (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 221) (:start . 220)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 224) (:start . 221)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 228) (:start . 225)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 237)\n  (:start . 229) (:id . 79))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 241) (:start . 238)\n  (:id . 80))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 245) (:start . 242)\n  (:id . 81))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 248) (:start . 246)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "pairwise") (:form . "pairwise") (:end . 257)\n  (:start . 249) (:id . 83))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 269)\n  (:start . 258) (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 270) (:start . 269)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 280)\n  (:start . 271) (:id . 86))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 285) (:start . 281)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "UC") (:form . "UC") (:end . 288) (:start . 286)\n  (:id . 88))\n ((:tag . "NNP") (:stem . "Berkeley") (:form . "Berkeley") (:end . 297)\n  (:start . 289) (:id . 89))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 301) (:start . 298)\n  (:id . 90))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 310)\n  (:start . 302) (:id . 91))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 311) (:start . 310)\n  (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 312) (:start . 311)\n  (:id . 93)))@@@1@52@((:identifiers (:sid . :s11.43) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503682@unknown@formal@none@1@S@Judged by the quality of the observed periodic patterns, we have selected for detailed analysis two pairs of datasets: S. cerevisiae synchronized by α-factor [12], and S. pombe synchronized either using cdc25 temperature sensitive mutant or elutriation [17].@(((:tag . "VBN") (:stem . "judge") (:form . "Judged") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "JJ") (:stem . "periodic") (:form . "periodic") (:end . 46)\n  (:start . 38) (:id . 49))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 73)\n  (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 95)\n  (:start . 87) (:id . 57))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 105)\n  (:start . 100) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 117)\n  (:start . 109) (:id . 61))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 121) (:start . 119)\n  (:id . 63))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 132)\n  (:start . 122) (:id . 64))\n ((:tag . "VBN") (:stem . "synchronize") (:form . "synchronized") (:end . 145)\n  (:start . 133) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 148) (:start . 146)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "α-factor") (:form . "α-factor") (:end . 157)\n  (:start . 149) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 159) (:start . 158)\n  (:id . 68))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 161) (:start . 159)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 162) (:start . 161)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "S.") (:form . "S.") (:end . 170) (:start . 168)\n  (:id . 73))\n ((:tag . "NN") (:stem . "pombe") (:form . "pombe") (:end . 176)\n  (:start . 171) (:id . 74))\n ((:tag . "VBD") (:stem . "synchronize") (:form . "synchronized") (:end . 189)\n  (:start . 177) (:id . 75))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 196)\n  (:start . 190) (:id . 76))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 202) (:start . 197)\n  (:id . 77))\n ((:tag . "NN") (:stem . "cdc25") (:form . "cdc25") (:end . 208)\n  (:start . 203) (:id . 78))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 220)\n  (:start . 209) (:id . 79))\n ((:tag . "JJ") (:stem . "sensitive") (:form . "sensitive") (:end . 230)\n  (:start . 221) (:id . 80))\n ((:tag . "NN") (:stem . "mutant") (:form . "mutant") (:end . 237)\n  (:start . 231) (:id . 81))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 240) (:start . 238)\n  (:id . 82))\n ((:tag . "NN") (:stem . "elutriation") (:form . "elutriation") (:end . 252)\n  (:start . 241) (:id . 83))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 254) (:start . 253)\n  (:id . 84))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 256) (:start . 254)\n  (:id . 85))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 257) (:start . 256)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 258) (:start . 257)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s11.44) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503683@unknown@formal@none@1@S@Based on the amplitude of gene expression in the course of the life cycle, all genes in the yeast genome can be conditionally separated into (i) cell-cycle dependent (oscillating) (ii) constitutively expressed and (iii) inducible (not expressed or expressed constitutively in our datasets).@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "amplitude") (:form . "amplitude") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 41)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "course") (:form . "course") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "life") (:form . "life") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 73) (:start . 68)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 78) (:start . 75)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 84) (:start . 79)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 60))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 97) (:start . 92)\n  (:id . 61))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 104)\n  (:start . 98) (:id . 62))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 108) (:start . 105)\n  (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 111) (:start . 109)\n  (:id . 64))\n ((:tag . "RB") (:stem . "conditionally") (:form . "conditionally")\n  (:end . 125) (:start . 112) (:id . 65))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 135)\n  (:start . 126) (:id . 66))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 140) (:start . 136)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 68))\n ((:tag . "LS") (:stem . "i") (:form . "i") (:end . 143) (:start . 142)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 70))\n ((:tag . "NN") (:stem . "cell-cycle") (:form . "cell-cycle") (:end . 155)\n  (:start . 145) (:id . 71))\n ((:tag . "JJ") (:stem . "dependent") (:form . "dependent") (:end . 165)\n  (:start . 156) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "oscillating") (:form . "oscillating") (:end . 178)\n  (:start . 167) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 181) (:start . 180)\n  (:id . 76))\n ((:tag . "LS") (:stem . "ii") (:form . "ii") (:end . 183) (:start . 181)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n  (:id . 78))\n ((:tag . "RB") (:stem . "constitutively") (:form . "constitutively")\n  (:end . 199) (:start . 185) (:id . 79))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 209)\n  (:start . 200) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 213) (:start . 210)\n  (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 215) (:start . 214)\n  (:id . 82))\n ((:tag . "LS") (:stem . "iii") (:form . "iii") (:end . 218) (:start . 215)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 219) (:start . 218)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "inducible") (:form . "inducible") (:end . 229)\n  (:start . 220) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 231) (:start . 230)\n  (:id . 86))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 234) (:start . 231)\n  (:id . 87))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 244)\n  (:start . 235) (:id . 88))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 247) (:start . 245)\n  (:id . 89))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 257)\n  (:start . 248) (:id . 90))\n ((:tag . "RB") (:stem . "constitutively") (:form . "constitutively")\n  (:end . 272) (:start . 258) (:id . 91))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 275) (:start . 273)\n  (:id . 92))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 279) (:start . 276)\n  (:id . 93))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 288)\n  (:start . 280) (:id . 94))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 289) (:start . 288)\n  (:id . 95))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 290) (:start . 289)\n  (:id . 96)))@@@1@55@((:hcues ((:id . :x11.45.1) (:span 245 247)))\n (:hscopes ((:id . :x11.45.1) (:span 231 272)))\n (:identifiers (:sid . :s11.45) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503684@unknown@formal@none@1@S@Low oscillating and constitutive genes contribute less or no information to the global alignment, moreover, their actual expression dynamics can be masked by the internal noise.@(((:tag . "JJ") (:stem . "low") (:form . "Low") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "oscillating") (:form . "oscillating") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "constitutive") (:form . "constitutive") (:end . 32)\n  (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 38) (:start . 33)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "contribute") (:form . "contribute") (:end . 49)\n  (:start . 39) (:id . 47))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 54) (:start . 50)\n  (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 72)\n  (:start . 61) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 75) (:start . 73)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 86)\n  (:start . 80) (:id . 54))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 96)\n  (:start . 87) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 56))\n ((:tag . "RB") (:stem . "moreover") (:form . "moreover") (:end . 106)\n  (:start . 98) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 113)\n  (:start . 108) (:id . 59))\n ((:tag . "JJ") (:stem . "actual") (:form . "actual") (:end . 120)\n  (:start . 114) (:id . 60))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 131)\n  (:start . 121) (:id . 61))\n ((:tag . "NNS") (:stem . "dynamic") (:form . "dynamics") (:end . 140)\n  (:start . 132) (:id . 62))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 144) (:start . 141)\n  (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 147) (:start . 145)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "mask") (:form . "masked") (:end . 154)\n  (:start . 148) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 157) (:start . 155)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 170)\n  (:start . 162) (:id . 68))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 176)\n  (:start . 171) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x11.46.1) (:span 141 144)))\n (:hscopes ((:id . :x11.46.1) (:span 108 176)))\n (:identifiers (:sid . :s11.46) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503685@unknown@formal@none@1@S@Therefore, we removed the low-variant genes from the selected datasets to improve sensitivity of the method.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "remove") (:form . "removed") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "low-variant") (:form . "low-variant") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 61)\n  (:start . 53) (:id . 51))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 81)\n  (:start . 74) (:id . 54))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 93)\n  (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 107)\n  (:start . 101) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s11.47) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503686@unknown@formal@none@1@S@In the prior studies [10,17], Fourier analysis was used to eliminate the low-cycling genes.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "CD") (:stem . "10,17") (:form . "10,17") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 49))\n ((:tag . "JJR") (:stem . "fouri") (:form . "Fourier") (:end . 37)\n  (:start . 30) (:id . 50))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 46)\n  (:start . 38) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 50) (:start . 47)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 54))\n ((:tag . "VB") (:stem . "eliminate") (:form . "eliminate") (:end . 68)\n  (:start . 59) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "low-cycling") (:form . "low-cycling") (:end . 84)\n  (:start . 73) (:id . 57))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 90) (:start . 85)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s11.48) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503687@unknown@formal@none@1@S@However, several factors, such as biased contribution of synchronization approaches, short duration of the datasets (two cell cycles) and high internal noise can make Fourier analysis fail for many genes, which, in fact, do cycle significantly.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "biased") (:form . "biased") (:end . 40)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "contribution") (:form . "contribution") (:end . 53)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 72) (:start . 57) (:id . 52))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 83)\n  (:start . 73) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 90) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "duration") (:form . "duration") (:end . 99)\n  (:start . 91) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 115)\n  (:start . 107) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 60))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 125) (:start . 121)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "cycle") (:form . "cycles") (:end . 132)\n  (:start . 126) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 142) (:start . 138)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 151)\n  (:start . 143) (:id . 67))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 157)\n  (:start . 152) (:id . 68))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 161) (:start . 158)\n  (:id . 69))\n ((:tag . "VB") (:stem . "make") (:form . "make") (:end . 166) (:start . 162)\n  (:id . 70))\n ((:tag . "JJR") (:stem . "fouri") (:form . "Fourier") (:end . 174)\n  (:start . 167) (:id . 71))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 183)\n  (:start . 175) (:id . 72))\n ((:tag . "NN") (:stem . "fail") (:form . "fail") (:end . 188) (:start . 184)\n  (:id . 73))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 192) (:start . 189)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 197) (:start . 193)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 203)\n  (:start . 198) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 204) (:start . 203)\n  (:id . 77))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 210)\n  (:start . 205) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 211) (:start . 210)\n  (:id . 79))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 214) (:start . 212)\n  (:id . 80))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 219) (:start . 215)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 220) (:start . 219)\n  (:id . 82))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 223) (:start . 221)\n  (:id . 83))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 229)\n  (:start . 224) (:id . 84))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 243) (:start . 230) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 86)))@@@1@45@((:hcues ((:id . :x11.49.1) (:span 158 161)))\n (:hscopes ((:id . :x11.49.1) (:span 158 203)))\n (:identifiers (:sid . :s11.49) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503688@unknown@formal@none@1@S@In the case of the yeast cell cycle, biological replicates were not available, and standard ANOVA-based filtering could not be applied.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 24) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 29) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 35) (:start . 30)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 47)\n  (:start . 37) (:id . 51))\n ((:tag . "NNS") (:stem . "replicate") (:form . "replicates") (:end . 58)\n  (:start . 48) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 63) (:start . 59)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 77)\n  (:start . 68) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 91)\n  (:start . 83) (:id . 58))\n ((:tag . "JJ") (:stem . "anova-based") (:form . "ANOVA-based") (:end . 103)\n  (:start . 92) (:id . 59))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 113)\n  (:start . 104) (:id . 60))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 119)\n  (:start . 114) (:id . 61))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 123) (:start . 120)\n  (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 126) (:start . 124)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 134)\n  (:start . 127) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s11.50) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503689@unknown@formal@none@1@S@Therefore, we designed SNR (Signal-to-Noise Ratio) filter to eliminate noisy and low-cycling profiles.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "design") (:form . "designed") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "NNP") (:stem . "SNR") (:form . "SNR") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Signal-to-Noise") (:form . "Signal-to-Noise")\n  (:end . 43) (:start . 28) (:id . 48))\n ((:tag . "NNP") (:stem . "Ratio") (:form . "Ratio") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 57)\n  (:start . 51) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "VB") (:stem . "eliminate") (:form . "eliminate") (:end . 70)\n  (:start . 61) (:id . 53))\n ((:tag . "JJ") (:stem . "noisy") (:form . "noisy") (:end . 76) (:start . 71)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "low-cycling") (:form . "low-cycling") (:end . 92)\n  (:start . 81) (:id . 56))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 101)\n  (:start . 93) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s11.51) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503690@unknown@formal@none@1@S@The SNR filter is analogous to ANOVA, but requires no replicates [see Additional file 1 - Figures S4, S5] (and Methods section).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "SNR") (:form . "SNR") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "analogous") (:form . "analogous") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "ANOVA") (:form . "ANOVA") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "replicate") (:form . "replicates") (:end . 64)\n  (:start . 54) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 80)\n  (:start . 70) (:id . 56))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 89) (:start . 88)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 97)\n  (:start . 90) (:id . 60))\n ((:tag . "NN") (:stem . "s4") (:form . "S4") (:end . 100) (:start . 98)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 104) (:start . 102)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 105) (:start . 104)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 118)\n  (:start . 111) (:id . 67))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 126)\n  (:start . 119) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 127) (:start . 126)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s11.52) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503691@unknown@formal@none@1@S@Statistical model for SNR takes into account assumption that periodically expressed genes would gradually increase or decrease expression level from one time point to another.@(((:tag . "JJ") (:stem . "statistical") (:form . "Statistical") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 17) (:start . 12)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "SNR") (:form . "SNR") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "take") (:form . "takes") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "account") (:form . "account") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "assumption") (:form . "assumption") (:end . 55)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "RB") (:stem . "periodically") (:form . "periodically") (:end . 73)\n  (:start . 61) (:id . 51))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 83)\n  (:start . 74) (:id . 52))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 89) (:start . 84)\n  (:id . 53))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 95) (:start . 90)\n  (:id . 54))\n ((:tag . "RB") (:stem . "gradually") (:form . "gradually") (:end . 105)\n  (:start . 96) (:id . 55))\n ((:tag . "VB") (:stem . "increase") (:form . "increase") (:end . 114)\n  (:start . 106) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 117) (:start . 115)\n  (:id . 57))\n ((:tag . "VB") (:stem . "decrease") (:form . "decrease") (:end . 126)\n  (:start . 118) (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 137)\n  (:start . 127) (:id . 59))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 143)\n  (:start . 138) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 148) (:start . 144)\n  (:id . 61))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 152) (:start . 149)\n  (:id . 62))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 157) (:start . 153)\n  (:id . 63))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 163)\n  (:start . 158) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 166) (:start . 164)\n  (:id . 65))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 174)\n  (:start . 167) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x11.53.1) (:span 115 117)) ((:id . :x11.53.2) (:span 90 95))\n  ((:id . :x11.53.3) (:span 45 55)))\n (:hscopes ((:id . :x11.53.1) (:span 106 126))\n  ((:id . :x11.53.2) (:span 90 174)) ((:id . :x11.53.3) (:span 45 174)))\n (:identifiers (:sid . :s11.53) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503692@unknown@formal@none@1@S@In mathematical terms, the variance of point-to-point changes in a gene expression profile should be less than the variance of the data itself.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "mathematical") (:form . "mathematical") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "variance") (:form . "variance") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "point-to-point") (:form . "point-to-point")\n  (:end . 53) (:start . 39) (:id . 49))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 82)\n  (:start . 72) (:id . 54))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 90)\n  (:start . 83) (:id . 55))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 97)\n  (:start . 91) (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 105) (:start . 101)\n  (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 110) (:start . 106)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 60))\n ((:tag . "NN") (:stem . "variance") (:form . "variance") (:end . 123)\n  (:start . 115) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 135)\n  (:start . 131) (:id . 64))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 142)\n  (:start . 136) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s11.54) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503693@unknown@formal@none@1@S@The two selected datasets were filtered using the SNR method to remove the low-variance profiles and smoothed using Gaussian method to minimize the internal noise (see Methods section).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "filter") (:form . "filtered") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "snr") (:form . "SNR") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 70)\n  (:start . 64) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "low-variance") (:form . "low-variance") (:end . 87)\n  (:start . 75) (:id . 55))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 96)\n  (:start . 88) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "smooth") (:form . "smoothed") (:end . 109)\n  (:start . 101) (:id . 58))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 115) (:start . 110)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "gaussian") (:form . "Gaussian") (:end . 124)\n  (:start . 116) (:id . 60))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 131)\n  (:start . 125) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 134) (:start . 132)\n  (:id . 62))\n ((:tag . "VB") (:stem . "minimize") (:form . "minimize") (:end . 143)\n  (:start . 135) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 156)\n  (:start . 148) (:id . 65))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 162)\n  (:start . 157) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 164) (:start . 163)\n  (:id . 67))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 167) (:start . 164)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 175)\n  (:start . 168) (:id . 69))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 183)\n  (:start . 176) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 184) (:start . 183)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s11.55) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503694@unknown@formal@none@1@S@The SNR filtering reduced the initial number of the orthologous profile pairs in the selected datasets (α-factor - S. cerevisiae vs. cdc25 - S. pombe) to 3193 or otherwise to 2518 genes in S. pombe and 2169 genes in S. cerevisiae (see ortholog matching in Methods).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "snr") (:form . "SNR") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "VBD") (:stem . "reduce") (:form . "reduced") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . 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5503695@unknown@formal@none@1@S@An apparent contradiction between the previously reported number of cycling genes (500) [18] and the number of genes investigated in this study (>2000) is explained by the fact that all significantly changing profiles (high variance) were scored in our study, even if they displayed moderate Fourier power at the desired period [see Additional file 1 - Figure S5].@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "apparent") (:form . "apparent") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "contradiction") (:form . "contradiction")\n  (:end . 25) (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 33)\n  (:start . 26) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 48)\n  (:start . 38) (:id . 47))\n ((:tag . 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"the") (:end . 312) (:start . 309)\n  (:id . 99))\n ((:tag . "VBN") (:stem . "desire") (:form . "desired") (:end . 320)\n  (:start . 313) (:id . 100))\n ((:tag . "NN") (:stem . "period") (:form . "period") (:end . 327)\n  (:start . 321) (:id . 101))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 329) (:start . 328)\n  (:id . 102))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 332) (:start . 329)\n  (:id . 103))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 343)\n  (:start . 333) (:id . 104))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 348) (:start . 344)\n  (:id . 105))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 350) (:start . 349)\n  (:id . 106))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 352) (:start . 351)\n  (:id . 107))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 359)\n  (:start . 353) (:id . 108))\n ((:tag . "NNP") (:stem . "S5") (:form . "S5") (:end . 362) (:start . 360)\n  (:id . 109))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 363) (:start . 362)\n  (:id . 110))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 364) (:start . 363)\n  (:id . 111)))@@@1@70@((:hcues ((:id . :x11.57.1) (:span 3 11)))\n (:hscopes ((:id . :x11.57.1) (:span 3 25)))\n (:identifiers (:sid . :s11.57) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503696@unknown@formal@none@1@S@We believe that in most instances low Fourier scores reflected biased expression at the start of the cell culture synchronization, desynchronization of cells after several cycles and/or measurement errors.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "believe") (:form . "believe") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Fourier") (:form . "Fourier") (:end . 45)\n  (:start . 38) (:id . 49))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . "VBD") (:stem . "reflect") (:form . "reflected") (:end . 62)\n  (:start . 53) (:id . 51))\n ((:tag . "VBN") (:stem . "bias") (:form . "biased") (:end . 69) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 80)\n  (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 83) (:start . 81)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "start") (:form . "start") (:end . 93) (:start . 88)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 113)\n  (:start . 106) (:id . 60))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 129) (:start . 114) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "NN") (:stem . "desynchronization") (:form . "desynchronization")\n  (:end . 148) (:start . 131) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 157)\n  (:start . 152) (:id . 65))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 163)\n  (:start . 158) (:id . 66))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 171)\n  (:start . 164) (:id . 67))\n ((:tag . "NNS") (:stem . "cycle") (:form . "cycles") (:end . 178)\n  (:start . 172) (:id . 68))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 185)\n  (:start . 179) (:id . 69))\n ((:tag . "NN") (:stem . "measurement") (:form . "measurement") (:end . 197)\n  (:start . 186) (:id . 70))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 204)\n  (:start . 198) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x11.58.1) (:span 3 10)))\n (:hscopes ((:id . :x11.58.1) (:span 3 204)))\n (:identifiers (:sid . :s11.58) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503697@unknown@formal@none@1@S@After removal of the previously reported best cycling 500 profiles from our dataset, the distance matrix and the alignment did not change significantly [see Additional file 1 - Figure S6].@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "removal") (:form . "removal") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cycling") (:form . "cycling") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "CD") (:stem . "500") (:form . "500") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 66)\n  (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 75) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 83)\n  (:start . 76) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 97)\n  (:start . 89) (:id . 57))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 104)\n  (:start . 98) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 60))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 122)\n  (:start . 113) (:id . 61))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 126) (:start . 123)\n  (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "VB") (:stem . "change") (:form . "change") (:end . 137)\n  (:start . 131) (:id . 64))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 151) (:start . 138) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 153) (:start . 152)\n  (:id . 66))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 156) (:start . 153)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 167)\n  (:start . 157) (:id . 68))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 172) (:start . 168)\n  (:id . 69))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 174) (:start . 173)\n  (:id . 70))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 176) (:start . 175)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 183)\n  (:start . 177) (:id . 72))\n ((:tag . "NNP") (:stem . "S6") (:form . "S6") (:end . 186) (:start . 184)\n  (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 187) (:start . 186)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s11.59) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503698@unknown@formal@none@1@S@This test provided evidence that periodicity is present in the additional genes, as compared to prior studies, although it might be masked by the noise or conditions of the culture synchronization.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "provide") (:form . "provided") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "periodicity") (:form . "periodicity") (:end . 44)\n  (:start . 33) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 73)\n  (:start . 63) (:id . 52))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 79) (:start . 74)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 83) (:start . 81)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 101) (:start . 96)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 109)\n  (:start . 102) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 60))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 119)\n  (:start . 111) (:id . 61))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 128)\n  (:start . 123) (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 131) (:start . 129)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "mask") (:form . "masked") (:end . 138)\n  (:start . 132) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 141) (:start . 139)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 67))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 151)\n  (:start . 146) (:id . 68))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 154) (:start . 152)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 165)\n  (:start . 155) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 172) (:start . 169)\n  (:id . 72))\n ((:tag . "NN") (:stem . "culture") (:form . "culture") (:end . 180)\n  (:start . 173) (:id . 73))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 196) (:start . 181) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x11.60.1) (:span 123 128)))\n (:hscopes ((:id . :x11.60.1) (:span 120 196)))\n (:identifiers (:sid . :s11.60) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503699@unknown@formal@none@1@S@We also found that Gaussian smoothing significantly improved detection of periodicity in the expression profiles (data not shown).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "gaussian") (:form . "Gaussian") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "smoothing") (:form . "smoothing") (:end . 37)\n  (:start . 28) (:id . 47))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 51) (:start . 38) (:id . 48))\n ((:tag . "VBD") (:stem . "improve") (:form . "improved") (:end . 60)\n  (:start . 52) (:id . 49))\n ((:tag . "NN") (:stem . "detection") (:form . "detection") (:end . 70)\n  (:start . 61) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 51))\n ((:tag . "NN") (:stem . "periodicity") (:form . "periodicity") (:end . 85)\n  (:start . 74) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 54))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 103)\n  (:start . 93) (:id . 55))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 112)\n  (:start . 104) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 118)\n  (:start . 114) (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 122) (:start . 119)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 128)\n  (:start . 123) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s11.61) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503700@unknown@formal@none@1@S@Time warping results@(((:tag . "NNP") (:stem . "Time") (:form . "Time") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "warp") (:form . "warping") (:end . 12) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 20)\n  (:start . 13) (:id . 44)))@@@1@3@((:identifiers (:sid . :s11.62) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503701@unknown@formal@none@1@S@Distance matrices for the full datasets, each spanning approximately 2 cell cycles, were inspected to identify data ranges, corresponding to a single cell cycle in each species (see Figure 1B).@(((:tag . "NNP") (:stem . "Distance") (:form . "Distance") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "span") (:form . "spanning") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 68) (:start . 55) (:id . 51))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 70) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cycle") (:form . "cycles") (:end . 82)\n  (:start . 76) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "inspect") (:form . "inspected") (:end . 98)\n  (:start . 89) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 58))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 110)\n  (:start . 102) (:id . 59))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 115)\n  (:start . 111) (:id . 60))\n ((:tag . "NNS") (:stem . "range") (:form . "ranges") (:end . 122)\n  (:start . 116) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 137)\n  (:start . 124) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 140) (:start . 138)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 142) (:start . 141)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 149)\n  (:start . 143) (:id . 66))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 154) (:start . 150)\n  (:id . 67))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 160)\n  (:start . 155) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 163) (:start . 161)\n  (:id . 69))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 168) (:start . 164)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 176)\n  (:start . 169) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 178) (:start . 177)\n  (:id . 72))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 181) (:start . 178)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 188)\n  (:start . 182) (:id . 74))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 191) (:start . 189)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 192) (:start . 191)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s11.63) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503702@unknown@formal@none@1@S@A global alignment path has been constructed using time warping based on Kruscal-Liberman algorithm [6] using Pearson distance matrices (Figure 1A, B).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 44)\n  (:start . 33) (:id . 48))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "warp") (:form . "warping") (:end . 63)\n  (:start . 56) (:id . 51))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Kruscal-Liberman") (:form . "Kruscal-Liberman")\n  (:end . 89) (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 99)\n  (:start . 90) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 101) (:start . 100)\n  (:id . 56))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 102) (:start . 101)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 109) (:start . 104)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 117)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 126)\n  (:start . 118) (:id . 61))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 135)\n  (:start . 127) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 137) (:start . 136)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 143)\n  (:start . 137) (:id . 64))\n ((:tag . "NN") (:stem . "1a") (:form . "1A") (:end . 146) (:start . 144)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 149) (:start . 148)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 150) (:start . 149)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s11.64) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503703@unknown@formal@none@1@S@Variations in the data treatment and the Pearson matrix construction parameters produced several possible paths; nevertheless, all successful alignments (gapless or with minimal gaps) followed nearly identical paths [see Additional file 1 - Figure S7].@(((:tag . "NNS") (:stem . "variation") (:form . "Variations") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "treatment") (:form . "treatment") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "construction") (:form . "construction") (:end . 68)\n  (:start . 56) (:id . 51))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 79)\n  (:start . 69) (:id . 52))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 88)\n  (:start . 80) (:id . 53))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 96)\n  (:start . 89) (:id . 54))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 105)\n  (:start . 97) (:id . 55))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 111)\n  (:start . 106) (:id . 56))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 112) (:start . 111)\n  (:id . 57))\n ((:tag . "RB") (:stem . "nevertheless") (:form . "nevertheless") (:end . 125)\n  (:start . 113) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 59))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 130) (:start . 127)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "successful") (:form . "successful") (:end . 141)\n  (:start . 131) (:id . 61))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 152)\n  (:start . 142) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "gapless") (:form . "gapless") (:end . 161)\n  (:start . 154) (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 164) (:start . 162)\n  (:id . 65))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 169) (:start . 165)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "minimal") (:form . "minimal") (:end . 177)\n  (:start . 170) (:id . 67))\n ((:tag . "NNS") (:stem . "gap") (:form . "gaps") (:end . 182) (:start . 178)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n  (:id . 69))\n ((:tag . "VBD") (:stem . "follow") (:form . "followed") (:end . 192)\n  (:start . 184) (:id . 70))\n ((:tag . "RB") (:stem . "nearly") (:form . "nearly") (:end . 199)\n  (:start . 193) (:id . 71))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 209)\n  (:start . 200) (:id . 72))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 215)\n  (:start . 210) (:id . 73))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 217) (:start . 216)\n  (:id . 74))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 220) (:start . 217)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 231)\n  (:start . 221) (:id . 76))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 236) (:start . 232)\n  (:id . 77))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 238) (:start . 237)\n  (:id . 78))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 240) (:start . 239)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 247)\n  (:start . 241) (:id . 80))\n ((:tag . "NNP") (:stem . "S7") (:form . "S7") (:end . 250) (:start . 248)\n  (:id . 81))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 251) (:start . 250)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s11.65) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503704@unknown@formal@none@1@S@Data ranges, corresponding to a single cell cycle were selected based on the periodic patterns observed on the distance matrix and standard cell cycle markers, characteristic to specific phases of the cell cycle [10,17].@(((:tag . "NNP") (:stem . "Data") (:form . "Data") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "range") (:form . "ranges") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 26)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "periodic") (:form . "periodic") (:end . 85)\n  (:start . 77) (:id . 56))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 94)\n  (:start . 86) (:id . 57))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 103)\n  (:start . 95) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 119)\n  (:start . 111) (:id . 61))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 126)\n  (:start . 120) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 139)\n  (:start . 131) (:id . 64))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 144) (:start . 140)\n  (:id . 65))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . "NNS") (:stem . "marker") (:form . "markers") (:end . 158)\n  (:start . 151) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 159) (:start . 158)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 174) (:start . 160) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 177) (:start . 175)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 186)\n  (:start . 178) (:id . 71))\n ((:tag . "NNS") (:stem . "phase") (:form . "phases") (:end . 193)\n  (:start . 187) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 196) (:start . 194)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 200) (:start . 197)\n  (:id . 74))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 205) (:start . 201)\n  (:id . 75))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 211)\n  (:start . 206) (:id . 76))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 213) (:start . 212)\n  (:id . 77))\n ((:tag . "CD") (:stem . "10,17") (:form . "10,17") (:end . 218)\n  (:start . 213) (:id . 78))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 219) (:start . 218)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s11.66) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503705@unknown@formal@none@1@S@The selected data ranges were aligned according to the global alignment path shown in the Figure 1C.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "range") (:form . "ranges") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 61)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 71)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 82) (:start . 77)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 96)\n  (:start . 90) (:id . 57))\n ((:tag . "NN") (:stem . "1c") (:form . "1C") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s11.67) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503706@unknown@formal@none@1@S@Time warping for a single cell cycle has clearly shown that the comparative duration of cell cycle phases in the two species is different (see Figure 2E) and it is in a good agreement with the existing data [13].@(((:tag . "NNP") (:stem . "Time") (:form . "Time") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "warp") (:form . "warping") (:end . 12) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "comparative") (:form . "comparative") (:end . 75)\n  (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "duration") (:form . "duration") (:end . 84)\n  (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 92) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 98) (:start . 93)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "phase") (:form . "phases") (:end . 105)\n  (:start . 99) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 61))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 116) (:start . 113)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 124)\n  (:start . 117) (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 127) (:start . 125)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 137)\n  (:start . 128) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 66))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 142) (:start . 139)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 149)\n  (:start . 143) (:id . 68))\n ((:tag . "NN") (:stem . "2e") (:form . "2E") (:end . 152) (:start . 150)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 71))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 160) (:start . 158)\n  (:id . 72))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 163) (:start . 161)\n  (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 166) (:start . 164)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 168) (:start . 167)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "good") (:form . "good") (:end . 173) (:start . 169)\n  (:id . 76))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 183)\n  (:start . 174) (:id . 77))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 188) (:start . 184)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 192) (:start . 189)\n  (:id . 79))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 201)\n  (:start . 193) (:id . 80))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 206)\n  (:start . 202) (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 208) (:start . 207)\n  (:id . 82))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 210) (:start . 208)\n  (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 211) (:start . 210)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s11.68) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503707@unknown@formal@none@1@S@According to the global alignment path, S. pombe has longer G2 phase and shorter G1 phase.@(((:tag . "VBG") (:stem . "accord") (:form . "According") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "JJR") (:stem . "long") (:form . "longer") (:end . 59) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "g2") (:form . "G2") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "phase") (:form . "phase") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . "JJR") (:stem . "short") (:form . "shorter") (:end . 80)\n  (:start . 73) (:id . 56))\n ((:tag . "NN") (:stem . "g1") (:form . "G1") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "phase") (:form . "phase") (:end . 89) (:start . 84)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s11.69) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503708@unknown@formal@none@1@S@This result supported our computational strategy, selected with respect to the high divergence between the analyzed species.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "support") (:form . "supported") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "computational") (:form . "computational")\n  (:end . 39) (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 48)\n  (:start . 40) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 58)\n  (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 63) (:start . 59)\n  (:id . 50))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 71)\n  (:start . 64) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "divergence") (:form . "divergence") (:end . 94)\n  (:start . 84) (:id . 55))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 102)\n  (:start . 95) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 115)\n  (:start . 107) (:id . 58))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 123)\n  (:start . 116) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s11.70) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503709@unknown@formal@none@1@S@Time warping and concordantly expressed genes.@(((:tag . "NNP") (:stem . "Time") (:form . "Time") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "warp") (:form . "warping") (:end . 12) (:start . 5)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "concordantly") (:form . "concordantly") (:end . 29)\n  (:start . 17) (:id . 45))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 39)\n  (:start . 30) (:id . 46))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 45) (:start . 40)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s11.71) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503710@unknown@formal@none@1@S@(A, B) Orthologous expression profiles for genes from the two yeast species are superimposed on the absolute timescale, before alignment.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 5) (:start . 4)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 6) (:start . 5) (:id . 46))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "Orthologous") (:end . 18)\n  (:start . 7) (:id . 47))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 29)\n  (:start . 19) (:id . 48))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 38)\n  (:start . 30) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 48) (:start . 43)\n  (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 61) (:start . 58)\n  (:id . 54))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 67) (:start . 62)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 75)\n  (:start . 68) (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 79) (:start . 76)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "superimpose") (:form . "superimposed") (:end . 92)\n  (:start . 80) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "absolute") (:form . "absolute") (:end . 108)\n  (:start . 100) (:id . 61))\n ((:tag . "NN") (:stem . "timescale") (:form . "timescale") (:end . 118)\n  (:start . 109) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 63))\n ((:tag . "IN") (:stem . "before") (:form . "before") (:end . 126)\n  (:start . 120) (:id . 64))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 136)\n  (:start . 127) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s11.72) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503711@unknown@formal@none@1@S@The selected data ranges correspond to ranges marked in Figure 1B.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "range") (:form . "ranges") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "VBP") (:stem . "correspond") (:form . "correspond") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "range") (:form . "ranges") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 52) (:start . 46)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "1b") (:form . "1B") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s11.73) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503712@unknown@formal@none@1@S@(C, D) Profiles for the same genes, adjusted according to the global alignment path, (relative time scale).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 5) (:start . 4)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 6) (:start . 5) (:id . 46))\n ((:tag . "NNP") (:stem . "Profile") (:form . "Profiles") (:end . 15)\n  (:start . 7) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 19) (:start . 16)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 28) (:start . 24)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 34) (:start . 29)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "adjust") (:form . "adjusted") (:end . 44)\n  (:start . 36) (:id . 53))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 54)\n  (:start . 45) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 68)\n  (:start . 62) (:id . 57))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 78)\n  (:start . 69) (:id . 58))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 83) (:start . 79)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 94)\n  (:start . 86) (:id . 62))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 99) (:start . 95)\n  (:id . 63))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 105)\n  (:start . 100) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s11.74) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503713@unknown@formal@none@1@S@(E) Correspondence between the cell cycle phases in S. cerevisiae and S. pombe, established based on the global alignment.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "correspondence") (:form . "Correspondence")\n  (:end . 18) (:start . 4) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "phase") (:form . "phases") (:end . 48)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 65)\n  (:start . 55) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 78) (:start . 73)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "establish") (:form . "established") (:end . 91)\n  (:start . 80) (:id . 58))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 97) (:start . 92)\n  (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 100) (:start . 98)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 111)\n  (:start . 105) (:id . 62))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 121)\n  (:start . 112) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s11.75) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503714@unknown@formal@none@1@S@Notice collapse of M-G1 phase and expansion of S-G2 phase region in S. pombe.@(((:tag . "NNP") (:stem . "Notice") (:form . "Notice") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "collapse") (:form . "collapse") (:end . 15)\n  (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "m-g1") (:form . "M-G1") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "phase") (:form . "phase") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "expansion") (:form . "expansion") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "s-g2") (:form . "S-G2") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "phase") (:form . "phase") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 64)\n  (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s11.76) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5503715@unknown@formal@none@1@S@Inspection of orthologous profile pairs in the aligned datasets revealed instances of both concordantly and discordantly expressed genes.@(((:tag . "NNP") (:stem . "Inspection") (:form . "Inspection") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 33)\n  (:start . 26) (:id . 45))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 39) (:start . 34)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 63)\n  (:start . 55) (:id . 50))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 72)\n  (:start . 64) (:id . 51))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 82)\n  (:start . 73) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 53))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 90) (:start . 86)\n  (:id . 54))\n ((:tag . "RB") (:stem . "concordantly") (:form . "concordantly") (:end . 103)\n  (:start . 91) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 56))\n ((:tag . "RB") (:stem . "discordantly") (:form . "discordantly") (:end . 120)\n  (:start . 108) (:id . 57))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 130)\n  (:start . 121) (:id . 58))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 136)\n  (:start . 131) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s11.77) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503716@unknown@formal@none@1@S@518 expression profiles, corresponding to approximately ~400 genes had very similar or nearly identical expression phasing in both organisms.@(((:tag . "CD") (:stem . "518") (:form . "518") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 38)\n  (:start . 25) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 55) (:start . 42) (:id . 48))\n ((:tag . "CD") (:stem . "~400") (:form . "~400") (:end . 60) (:start . 56)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 66) (:start . 61)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 70) (:start . 67)\n  (:id . 51))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 75) (:start . 71)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 83)\n  (:start . 76) (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 86) (:start . 84)\n  (:id . 54))\n ((:tag . "RB") (:stem . "nearly") (:form . "nearly") (:end . 93)\n  (:start . 87) (:id . 55))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 103)\n  (:start . 94) (:id . 56))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 114)\n  (:start . 104) (:id . 57))\n ((:tag . "NN") (:stem . "phasing") (:form . "phasing") (:end . 122)\n  (:start . 115) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 125) (:start . 123)\n  (:id . 59))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 130) (:start . 126)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 140)\n  (:start . 131) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s11.78) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503717@unknown@formal@none@1@S@Figure 2 shows the expression profiles of two orthologous pairs, which appear discordant on the absolute timescale (unaligned) and are nearly identical on the relative timescale, after time warping.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 57)\n  (:start . 46) (:id . 50))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "JJ") (:stem . "discordant") (:form . "discordant") (:end . 88)\n  (:start . 78) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "absolute") (:form . "absolute") (:end . 104)\n  (:start . 96) (:id . 58))\n ((:tag . "NN") (:stem . "timescale") (:form . "timescale") (:end . 114)\n  (:start . 105) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "unaligned") (:form . "unaligned") (:end . 125)\n  (:start . 116) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 134) (:start . 131)\n  (:id . 64))\n ((:tag . "RB") (:stem . "nearly") (:form . "nearly") (:end . 141)\n  (:start . 135) (:id . 65))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 151)\n  (:start . 142) (:id . 66))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 167)\n  (:start . 159) (:id . 69))\n ((:tag . "NN") (:stem . "timescale") (:form . "timescale") (:end . 177)\n  (:start . 168) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 178) (:start . 177)\n  (:id . 71))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 184)\n  (:start . 179) (:id . 72))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 189) (:start . 185)\n  (:id . 73))\n ((:tag . "NN") (:stem . "warping") (:form . "warping") (:end . 197)\n  (:start . 190) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s11.79) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503718@unknown@formal@none@1@S@DIA2 (Figure 2A, C) is the origin-binding F-box protein that plays a critical role in DNA replication and maintaining genome integrity.@(((:tag . "NNP") (:stem . "DIA2") (:form . "DIA2") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 12)\n  (:start . 6) (:id . 44))\n ((:tag . "NN") (:stem . "2a") (:form . "2A") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 18) (:start . 17)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 19) (:start . 18)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 22) (:start . 20)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "origin-binding") (:form . "origin-binding")\n  (:end . 41) (:start . 27) (:id . 51))\n ((:tag . "NN") (:stem . "f-box") (:form . "F-box") (:end . 47) (:start . 42)\n  (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 55)\n  (:start . 48) (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 60) (:start . 56)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "play") (:form . "plays") (:end . 66) (:start . 61)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 77)\n  (:start . 69) (:id . 57))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 82) (:start . 78)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "DNA") (:form . "DNA") (:end . 89) (:start . 86)\n  (:id . 60))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 101)\n  (:start . 90) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "maintain") (:form . "maintaining") (:end . 117)\n  (:start . 106) (:id . 63))\n ((:tag . "NN") (:stem . "genome") (:form . "genome") (:end . 124)\n  (:start . 118) (:id . 64))\n ((:tag . "NN") (:stem . "integrity") (:form . "integrity") (:end . 134)\n  (:start . 125) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s11.80) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503719@unknown@formal@none@1@S@S. cerevisiae strains with DIA2 deletions have a high rate of endogenous DNA damage and are defective in S-phase progression [19,20].@(((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NNS") (:stem . "strain") (:form . "strains") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "NN") (:stem . "dia2") (:form . "DIA2") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "deletion") (:form . "deletions") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "endogenous") (:form . "endogenous") (:end . 72)\n  (:start . 62) (:id . 53))\n ((:tag . "NN") (:stem . "dna") (:form . "DNA") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "damage") (:form . "damage") (:end . 83)\n  (:start . 77) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 91) (:start . 88)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "defective") (:form . "defective") (:end . 101)\n  (:start . 92) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "S-phase") (:form . "S-phase") (:end . 112)\n  (:start . 105) (:id . 60))\n ((:tag . "NN") (:stem . "progression") (:form . "progression") (:end . 124)\n  (:start . 113) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 126) (:start . 125)\n  (:id . 62))\n ((:tag . "CD") (:stem . "19,20") (:form . "19,20") (:end . 131)\n  (:start . 126) (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 132) (:start . 131)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s11.81) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503720@unknown@formal@none@1@S@Gene pof3, the ortholog of DIA2 in S. pombe has a similar function.@(((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "pof3") (:form . "pof3") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 23)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "dia2") (:form . "DIA2") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 37) (:start . 35)\n  (:id . 50))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 43) (:start . 38)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 57)\n  (:start . 50) (:id . 54))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 66)\n  (:start . 58) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s11.82) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503721@unknown@formal@none@1@S@In pof3 mutants the telomeres are substantially shortened and the normal telomere transcription/silencing is disrupted [21].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "pof3") (:form . "pof3") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "mutant") (:form . "mutants") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "telomere") (:form . "telomeres") (:end . 29)\n  (:start . 20) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "RB") (:stem . "substantially") (:form . "substantially")\n  (:end . 47) (:start . 34) (:id . 48))\n ((:tag . "VBN") (:stem . "shorten") (:form . "shortened") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 72)\n  (:start . 66) (:id . 52))\n ((:tag . "NN") (:stem . "telomere") (:form . "telomere") (:end . 81)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "transcription/silencing")\n  (:form . "transcription/silencing") (:end . 105) (:start . 82) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 108) (:start . 106)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "disrupt") (:form . "disrupted") (:end . 118)\n  (:start . 109) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 120) (:start . 119)\n  (:id . 57))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 122) (:start . 120)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 123) (:start . 122)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s11.83) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503722@unknown@formal@none@1@S@Another example, gene RPS17B (Figure 2B, D) encodes the ribosomal protein 51 (rp51) of the small (40S) subunit and displays concordant expression in the unaligned data sets as well.@(((:tag . "DT") (:stem . "another") (:form . "Another") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "RPS17B") (:form . "RPS17B") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "NN") (:stem . "2b") (:form . "2B") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 42) (:start . 41)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 51)\n  (:start . 44) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "ribosomal") (:form . "ribosomal") (:end . 65)\n  (:start . 56) (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 73)\n  (:start . 66) (:id . 56))\n ((:tag . "CD") (:stem . "51") (:form . "51") (:end . 76) (:start . 74)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 58))\n ((:tag . "NN") (:stem . "rp51") (:form . "rp51") (:end . 82) (:start . 78)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 96) (:start . 91)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 64))\n ((:tag . "NN") (:stem . "40s") (:form . "40S") (:end . 101) (:start . 98)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 66))\n ((:tag . "NN") (:stem . "subunit") (:form . "subunit") (:end . 110)\n  (:start . 103) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "display") (:form . "displays") (:end . 123)\n  (:start . 115) (:id . 69))\n ((:tag . "JJ") (:stem . "concordant") (:form . "concordant") (:end . 134)\n  (:start . 124) (:id . 70))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 145)\n  (:start . 135) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "unaligned") (:form . "unaligned") (:end . 162)\n  (:start . 153) (:id . 74))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 167)\n  (:start . 163) (:id . 75))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 172) (:start . 168)\n  (:id . 76))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 175) (:start . 173)\n  (:id . 77))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 180) (:start . 176)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s11.84) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503723@unknown@formal@none@1@S@However, after time warping, the ribosomal protein has identical expression phasing in both yeast species.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "warping") (:form . "warping") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "ribosomal") (:form . "ribosomal") (:end . 42)\n  (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 50)\n  (:start . 43) (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 64)\n  (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 75)\n  (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "phasing") (:form . "phasing") (:end . 83)\n  (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 97) (:start . 92)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 105)\n  (:start . 98) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s11.85) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503724@unknown@formal@none@1@S@The majority of other ribosomal genes and genes involved into the ribosome biogenesis also displayed identical phasing of expression in the aligned datasets [see Additional file 1 - Figure S8] (and Figure 3).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "ribosomal") (:form . "ribosomal") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "ribosome") (:form . "ribosome") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "NN") (:stem . "biogenesis") (:form . "biogenesis") (:end . 85)\n  (:start . 75) (:id . 54))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 90) (:start . 86)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "display") (:form . "displayed") (:end . 100)\n  (:start . 91) (:id . 56))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 110)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "phasing") (:form . "phasing") (:end . 118)\n  (:start . 111) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 59))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 132)\n  (:start . 122) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 147)\n  (:start . 140) (:id . 63))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 156)\n  (:start . 148) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 158) (:start . 157)\n  (:id . 65))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 161) (:start . 158)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 172)\n  (:start . 162) (:id . 67))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 177) (:start . 173)\n  (:id . 68))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 179) (:start . 178)\n  (:id . 69))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 181) (:start . 180)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 188)\n  (:start . 182) (:id . 71))\n ((:tag . "NNP") (:stem . "S8") (:form . "S8") (:end . 191) (:start . 189)\n  (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 192) (:start . 191)\n  (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 194) (:start . 193)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 197) (:start . 194)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 204)\n  (:start . 198) (:id . 76))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 206) (:start . 205)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 207) (:start . 206)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s11.86) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503725@unknown@formal@none@1@S@Alternative alignment paths and heterochrony@(((:tag . "JJ") (:stem . "alternative") (:form . "Alternative") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 21)\n  (:start . 12) (:id . 43))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 27) (:start . 22)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 31) (:start . 28)\n  (:id . 45))\n ((:tag . "NN") (:stem . "heterochrony") (:form . "heterochrony") (:end . 44)\n  (:start . 32) (:id . 46)))@@@1@5@((:identifiers (:sid . :s11.87) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503726@unknown@formal@none@1@S@Along with the global alignment, alignments for each individual pair of orthologs from the selected datasets were constructed and explored as well.@(((:tag . "IN") (:stem . "along") (:form . "Along") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 63)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 81)\n  (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 86) (:start . 82)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 99)\n  (:start . 91) (:id . 57))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 108)\n  (:start . 100) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 113) (:start . 109)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 125)\n  (:start . 114) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "explore") (:form . "explored") (:end . 138)\n  (:start . 130) (:id . 62))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 141) (:start . 139)\n  (:id . 63))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 146) (:start . 142)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s11.88) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503727@unknown@formal@none@1@S@This analysis has shown that the majority of concordantly expressed orthologous genes produced pairwise alignment paths similar to the global one (see examples in Figure 2 and Figure 3C).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "RB") (:stem . "concordantly") (:form . "concordantly") (:end . 57)\n  (:start . 45) (:id . 50))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 67)\n  (:start . 58) (:id . 51))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 79)\n  (:start . 68) (:id . 52))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 85) (:start . 80)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 94)\n  (:start . 86) (:id . 54))\n ((:tag . "JJ") (:stem . "pairwise") (:form . "pairwise") (:end . 103)\n  (:start . 95) (:id . 55))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 113)\n  (:start . 104) (:id . 56))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 119)\n  (:start . 114) (:id . 57))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 127)\n  (:start . 120) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 141)\n  (:start . 135) (:id . 61))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 145) (:start . 142)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 63))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 150) (:start . 147)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 159)\n  (:start . 151) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 162) (:start . 160)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 169)\n  (:start . 163) (:id . 67))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 171) (:start . 170)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 182)\n  (:start . 176) (:id . 70))\n ((:tag . "NN") (:stem . "3c") (:form . "3C") (:end . 185) (:start . 183)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 186) (:start . 185)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s11.89) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503728@unknown@formal@none@1@S@At the same time, individual alignments of discordantly expressed ortholog pairs often produced alignment paths different from the global (Figure 3A, B).@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 28)\n  (:start . 18) (:id . 47))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 39)\n  (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "RB") (:stem . "discordantly") (:form . "discordantly") (:end . 55)\n  (:start . 43) (:id . 50))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 65)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 74)\n  (:start . 66) (:id . 52))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 80) (:start . 75)\n  (:id . 53))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 86) (:start . 81)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 95)\n  (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 105)\n  (:start . 96) (:id . 56))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 111)\n  (:start . 106) (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 121)\n  (:start . 112) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 126) (:start . 122)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 137)\n  (:start . 131) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 145)\n  (:start . 139) (:id . 63))\n ((:tag . "NN") (:stem . "3a") (:form . "3A") (:end . 148) (:start . 146)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 151) (:start . 150)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s11.90) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503729@unknown@formal@none@1@S@We explored the pairwise alignments to see whether there are alternative alignment paths, common to certain groups of genes expressed discordantly with respect to the global alignment (idea first proposed by J. Aach and G. Church [1]).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "explore") (:form . "explored") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "pairwise") (:form . "pairwise") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 35)\n  (:start . 25) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 56) (:start . 51)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 72)\n  (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 88) (:start . 83)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 96)\n  (:start . 90) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 107)\n  (:start . 100) (:id . 58))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 114)\n  (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 123)\n  (:start . 118) (:id . 61))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 133)\n  (:start . 124) (:id . 62))\n ((:tag . "RB") (:stem . "discordantly") (:form . "discordantly") (:end . 146)\n  (:start . 134) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 151) (:start . 147)\n  (:id . 64))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 159)\n  (:start . 152) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 162) (:start . 160)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 173)\n  (:start . 167) (:id . 68))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 183)\n  (:start . 174) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 70))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 189) (:start . 185)\n  (:id . 71))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 195)\n  (:start . 190) (:id . 72))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 204)\n  (:start . 196) (:id . 73))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 207) (:start . 205)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "J.") (:form . "J.") (:end . 210) (:start . 208)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Aach") (:form . "Aach") (:end . 215) (:start . 211)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 219) (:start . 216)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "G.") (:form . "G.") (:end . 222) (:start . 220)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Church") (:form . "Church") (:end . 229)\n  (:start . 223) (:id . 79))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 231) (:start . 230)\n  (:id . 80))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 232) (:start . 231)\n  (:id . 81))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 233) (:start . 232)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 234) (:start . 233)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 235) (:start . 234)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x11.91.1) (:span 43 50)))\n (:hscopes ((:id . :x11.91.1) (:span 43 183)))\n (:identifiers (:sid . :s11.91) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503730@unknown@formal@none@1@S@In order to reveal the alternative paths of time warping, all ortholog pairs were aligned one by one, using the Gene-warp program and the resulting individual alignment paths were clustered using k-means clustering with arbitrarily selected number of clusters k = 10 [14] (see Methods section).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "reveal") (:form . "reveal") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 34)\n  (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "warping") (:form . "warping") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "ortholog") (:form . "ortholog") (:end . 70)\n  (:start . 62) (:id . 54))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 89)\n  (:start . 82) (:id . 57))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 107) (:start . 102)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "gene-warp") (:form . "Gene-warp") (:end . 121)\n  (:start . 112) (:id . 64))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 129)\n  (:start . 122) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 147)\n  (:start . 138) (:id . 68))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 158)\n  (:start . 148) (:id . 69))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 168)\n  (:start . 159) (:id . 70))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 174)\n  (:start . 169) (:id . 71))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 179) (:start . 175)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "cluster") (:form . "clustered") (:end . 189)\n  (:start . 180) (:id . 73))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 195) (:start . 190)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "k-mean") (:form . "k-means") (:end . 203)\n  (:start . 196) (:id . 75))\n ((:tag . "VBG") (:stem . "cluster") (:form . "clustering") (:end . 214)\n  (:start . 204) (:id . 76))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 219) (:start . 215)\n  (:id . 77))\n ((:tag . "RB") (:stem . "arbitrarily") (:form . "arbitrarily") (:end . 231)\n  (:start . 220) (:id . 78))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 240)\n  (:start . 232) (:id . 79))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 247)\n  (:start . 241) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 250) (:start . 248)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 259)\n  (:start . 251) (:id . 82))\n ((:tag . "NN") (:stem . "k") (:form . "k") (:end . 261) (:start . 260)\n  (:id . 83))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 263) (:start . 262)\n  (:id . 84))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 266) (:start . 264)\n  (:id . 85))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 268) (:start . 267)\n  (:id . 86))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 270) (:start . 268)\n  (:id . 87))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 271) (:start . 270)\n  (:id . 88))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 273) (:start . 272)\n  (:id . 89))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 276) (:start . 273)\n  (:id . 90))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 284)\n  (:start . 277) (:id . 91))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 292)\n  (:start . 285) (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 293) (:start . 292)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 294) (:start . 293)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s11.92) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503731@unknown@formal@none@1@S@Figure 3 shows "time clusters" produced by the clustering of individual alignment paths.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 39)\n  (:start . 31) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "clustering") (:form . "clustering") (:end . 57)\n  (:start . 47) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 71)\n  (:start . 61) (:id . 54))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 81)\n  (:start . 72) (:id . 55))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 87) (:start . 82)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s11.93) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503732@unknown@formal@none@1@S@Technically, each time cluster corresponds to a group of individual profile pairs with similar pairwise time warping.@(((:tag . "RB") (:stem . "technically") (:form . "Technically") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 42)\n  (:start . 31) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 75)\n  (:start . 68) (:id . 53))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 86) (:start . 82)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 94)\n  (:start . 87) (:id . 56))\n ((:tag . "JJ") (:stem . "pairwise") (:form . "pairwise") (:end . 103)\n  (:start . 95) (:id . 57))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 108) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "warping") (:form . "warping") (:end . 116)\n  (:start . 109) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s11.94) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503733@unknown@formal@none@1@S@From the biological standpoint, the time clusters correspond to synchronization groups; within each group, the expression synchrony among all genes is maintained during evolution, while synchrony between the groups (time clusters) is apparently lost (see Figure 3A- C).@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "standpoint") (:form . "standpoint") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "cluster") (:form . 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",") (:end . 179) (:start . 178)\n  (:id . 69))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 185)\n  (:start . 180) (:id . 70))\n ((:tag . "NN") (:stem . "synchrony") (:form . "synchrony") (:end . 195)\n  (:start . 186) (:id . 71))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 203)\n  (:start . 196) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 207) (:start . 204)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 214)\n  (:start . 208) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 216) (:start . 215)\n  (:id . 75))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 220) (:start . 216)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 229)\n  (:start . 221) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 230) (:start . 229)\n  (:id . 78))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 233) (:start . 231)\n  (:id . 79))\n ((:tag . "RB") (:stem . "apparently") (:form . "apparently") (:end . 244)\n  (:start . 234) (:id . 80))\n ((:tag . "VBN") (:stem . "lose") (:form . "lost") (:end . 249) (:start . 245)\n  (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 251) (:start . 250)\n  (:id . 82))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 254) (:start . 251)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 261)\n  (:start . 255) (:id . 84))\n ((:tag . "NNP") (:stem . "3A-") (:form . "3A-") (:end . 265) (:start . 262)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 267) (:start . 266)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 268) (:start . 267)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 269) (:start . 268)\n  (:id . 88)))@@@1@47@((:hcues ((:id . :x11.95.1) (:span 234 244)))\n (:hscopes ((:id . :x11.95.1) (:span 186 249)))\n (:identifiers (:sid . :s11.95) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503734@unknown@formal@none@1@S@The concordantly expressed genes (regardless of the phasing of their expression) formed the largest time cluster or the largest synchronization group (Figure 3C, D), containing 518 expression profiles.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "concordantly") (:form . "concordantly") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 26)\n  (:start . 17) (:id . 44))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 32) (:start . 27)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 34) (:start . 33)\n  (:id . 46))\n ((:tag . "RB") (:stem . "regardless") (:form . "regardless") (:end . 44)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "phasing") (:form . "phasing") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 68)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 79)\n  (:start . 69) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "form") (:form . "formed") (:end . 87) (:start . 81)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "JJS") (:stem . "large") (:form . "largest") (:end . 99)\n  (:start . 92) (:id . 57))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 104) (:start . 100)\n  (:id . 58))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 112)\n  (:start . 105) (:id . 59))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 61))\n ((:tag . "JJS") (:stem . "large") (:form . "largest") (:end . 127)\n  (:start . 120) (:id . 62))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 143) (:start . 128) (:id . 63))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 149)\n  (:start . 144) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 157)\n  (:start . 151) (:id . 66))\n ((:tag . "NN") (:stem . "3c") (:form . "3C") (:end . 160) (:start . 158)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 163) (:start . 162)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 164) (:start . 163)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 176)\n  (:start . 166) (:id . 72))\n ((:tag . "CD") (:stem . "518") (:form . "518") (:end . 180) (:start . 177)\n  (:id . 73))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 191)\n  (:start . 181) (:id . 74))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 200)\n  (:start . 192) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s11.96) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503735@unknown@formal@none@1@S@As expected, the average alignment path of this largest synchronization cluster was close to the global alignment path.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "JJS") (:stem . "large") (:form . "largest") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 71) (:start . 56) (:id . 52))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 79)\n  (:start . 72) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "RB") (:stem . "close") (:form . "close") (:end . 89) (:start . 84)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 113)\n  (:start . 104) (:id . 59))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 118) (:start . 114)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s11.97) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503736@unknown@formal@none@1@S@Other time clusters revealed different levels of desynchronization with the global path, varying from moderate (see cluster 8 in Figure 3D) to extreme (clusters 3 and 4 in Figure 3D).@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 28)\n  (:start . 20) (:id . 45))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 45)\n  (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "NN") (:stem . "desynchronization") (:form . "desynchronization")\n  (:end . 66) (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 71) (:start . 67)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 82)\n  (:start . 76) (:id . 52))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 87) (:start . 83)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "vary") (:form . "varying") (:end . 96)\n  (:start . 89) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 101) (:start . 97)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "moderate") (:form . "moderate") (:end . 110)\n  (:start . 102) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 58))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 115) (:start . 112)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 123)\n  (:start . 116) (:id . 60))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 135)\n  (:start . 129) (:id . 63))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 138) (:start . 136)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "extreme") (:form . "extreme") (:end . 150)\n  (:start . 143) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 152) (:start . 151)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 160)\n  (:start . 152) (:id . 69))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 162) (:start . 161)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n  (:id . 71))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 168) (:start . 167)\n  (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 171) (:start . 169)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 178)\n  (:start . 172) (:id . 74))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 181) (:start . 179)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 182) (:start . 181)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s11.98) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503737@unknown@formal@none@1@S@To explore why certain gene groups maintained synchronization in evolution, expression data, composing individual time clusters, have been explored further in S. cerevisiae dataset by consequent clustering of the expression profiles and GO-terms enrichment analysis.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "explore") (:form . "explore") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "WRB") (:stem . "why") (:form . "why") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "VBD") (:stem . "maintain") (:form . "maintained") (:end . 45)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 61) (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 50))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 74)\n  (:start . 65) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 86)\n  (:start . 76) (:id . 53))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 91) (:start . 87)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "compose") (:form . "composing") (:end . 102)\n  (:start . 93) (:id . 56))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 113)\n  (:start . 103) (:id . 57))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 118) (:start . 114)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 127)\n  (:start . 119) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 133) (:start . 129)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 138) (:start . 134)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "explore") (:form . "explored") (:end . 147)\n  (:start . 139) (:id . 63))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 155)\n  (:start . 148) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 158) (:start . 156)\n  (:id . 65))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 161) (:start . 159)\n  (:id . 66))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 172)\n  (:start . 162) (:id . 67))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 180)\n  (:start . 173) (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 183) (:start . 181)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "consequent") (:form . "consequent") (:end . 194)\n  (:start . 184) (:id . 70))\n ((:tag . "NN") (:stem . "clustering") (:form . "clustering") (:end . 205)\n  (:start . 195) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 208) (:start . 206)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 212) (:start . 209)\n  (:id . 73))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 223)\n  (:start . 213) (:id . 74))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 232)\n  (:start . 224) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 236) (:start . 233)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "go-term") (:form . "GO-terms") (:end . 245)\n  (:start . 237) (:id . 77))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 256)\n  (:start . 246) (:id . 78))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 265)\n  (:start . 257) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 266) (:start . 265)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s11.99) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503738@unknown@formal@none@1@S@It has been found that the largest S. cerevisiae time cluster (Figure 3C) matched the global alignment path and contained expression profiles for many ribosomal and replication-related genes (Figure 3I, J) [see also Additional file 1 - Table S1].@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "JJS") (:stem . "large") (:form . "largest") (:end . 34)\n  (:start . 27) (:id . 48))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 48)\n  (:start . 38) (:id . 50))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 69)\n  (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "3c") (:form . "3C") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "match") (:form . "matched") (:end . 81)\n  (:start . 74) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 92)\n  (:start . 86) (:id . 59))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 102)\n  (:start . 93) (:id . 60))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 107) (:start . 103)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 121)\n  (:start . 112) (:id . 63))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 132)\n  (:start . 122) (:id . 64))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 141)\n  (:start . 133) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 145) (:start . 142)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 150) (:start . 146)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "ribosomal") (:form . "ribosomal") (:end . 160)\n  (:start . 151) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "replication-related")\n  (:form . "replication-related") (:end . 184) (:start . 165) (:id . 70))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 190)\n  (:start . 185) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 192) (:start . 191)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 198)\n  (:start . 192) (:id . 73))\n ((:tag . "NNP") (:stem . "3I") (:form . "3I") (:end . 201) (:start . 199)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 202) (:start . 201)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 204) (:start . 203)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 205) (:start . 204)\n  (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 207) (:start . 206)\n  (:id . 78))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 210) (:start . 207)\n  (:id . 79))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 215) (:start . 211)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 226)\n  (:start . 216) (:id . 81))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 231) (:start . 227)\n  (:id . 82))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 233) (:start . 232)\n  (:id . 83))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 235) (:start . 234)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 241)\n  (:start . 236) (:id . 85))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 244) (:start . 242)\n  (:id . 86))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 245) (:start . 244)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s11.100) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503739@unknown@formal@none@1@S@Synchronization between the replication machinery, ribosomal and housekeeping genes suggests coordination between the cell division and the cell growth [22] in both yeast species.@(((:tag . "NN") (:stem . "synchronization") (:form . "Synchronization")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 23)\n  (:start . 16) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 44))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 39)\n  (:start . 28) (:id . 45))\n ((:tag . "NN") (:stem . "machinery") (:form . "machinery") (:end . 49)\n  (:start . 40) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "ribosomal") (:form . "ribosomal") (:end . 60)\n  (:start . 51) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "housekeeping") (:form . "housekeeping") (:end . 77)\n  (:start . 65) (:id . 50))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 83) (:start . 78)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 92)\n  (:start . 84) (:id . 52))\n ((:tag . "NN") (:stem . "coordination") (:form . "coordination") (:end . 105)\n  (:start . 93) (:id . 53))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 113)\n  (:start . 106) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 122) (:start . 118)\n  (:id . 56))\n ((:tag . "NN") (:stem . "division") (:form . "division") (:end . 131)\n  (:start . 123) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 59))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 144) (:start . 140)\n  (:id . 60))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 151)\n  (:start . 145) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 153) (:start . 152)\n  (:id . 62))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 155) (:start . 153)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 156) (:start . 155)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 159) (:start . 157)\n  (:id . 65))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 164) (:start . 160)\n  (:id . 66))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 170)\n  (:start . 165) (:id . 67))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 178)\n  (:start . 171) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x11.101.1) (:span 84 92)))\n (:hscopes ((:id . :x11.101.1) (:span 84 178)))\n (:identifiers (:sid . :s11.101) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503740@unknown@formal@none@1@S@We also inspected the composition of the time clusters deviating from the global alignment path (Figure 3D, clusters 0 and 5).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "inspect") (:form . "inspected") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "composition") (:form . "composition") (:end . 33)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "VBG") (:stem . "deviate") (:form . "deviating") (:end . 64)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 69) (:start . 65)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 80)\n  (:start . 74) (:id . 54))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 90)\n  (:start . 81) (:id . 55))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 95) (:start . 91)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 116)\n  (:start . 108) (:id . 61))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 63))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 124) (:start . 123)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s11.102) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503741@unknown@formal@none@1@S@According to the results of the GO-term enrichment assays, some of these time clusters contained genes involved in respiration and protein synthesis in mitochondria (see Figure 3E-H).@(((:tag . "VBG") (:stem . "accord") (:form . "According") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "go-term") (:form . "GO-term") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 50)\n  (:start . 40) (:id . 49))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 57)\n  (:start . 51) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 96)\n  (:start . 87) (:id . 57))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 102) (:start . 97)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 111)\n  (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . "NN") (:stem . "respiration") (:form . "respiration") (:end . 126)\n  (:start . 115) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 138)\n  (:start . 131) (:id . 63))\n ((:tag . "NN") (:stem . "synthesis") (:form . "synthesis") (:end . 148)\n  (:start . 139) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 151) (:start . 149)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "mitochondrion") (:form . "mitochondria")\n  (:end . 164) (:start . 152) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 166) (:start . 165)\n  (:id . 67))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 169) (:start . 166)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 176)\n  (:start . 170) (:id . 69))\n ((:tag . "NN") (:stem . "3e-h") (:form . "3E-H") (:end . 181) (:start . 177)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 182) (:start . 181)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s11.103) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503742@unknown@formal@none@1@S@Such desynchronization or heterochrony observed between the mitochondrial and the ribosomal/replication genes can be attributed to the semi-autonomy of mitochondria and the mitochondrial gene expression [23].@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "desynchronization") (:form . "desynchronization")\n  (:end . 22) (:start . 5) (:id . 43))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 25) (:start . 23)\n  (:id . 44))\n ((:tag . "NN") (:stem . "heterochrony") (:form . "heterochrony") (:end . 38)\n  (:start . 26) (:id . 45))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 47)\n  (:start . 39) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 55)\n  (:start . 48) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "mitochondrial") (:form . "mitochondrial")\n  (:end . 73) (:start . 60) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 51))\n ((:tag . "NN") (:stem . "ribosomal/replication")\n  (:form . "ribosomal/replication") (:end . 103) (:start . 82) (:id . 52))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 109)\n  (:start . 104) (:id . 53))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 113) (:start . 110)\n  (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 116) (:start . 114)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "attribute") (:form . "attributed") (:end . 127)\n  (:start . 117) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n  (:id . 58))\n ((:tag . "NN") (:stem . "semi-autonomy") (:form . "semi-autonomy")\n  (:end . 148) (:start . 135) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "mitochondrion") (:form . "mitochondria")\n  (:end . 164) (:start . 152) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 172) (:start . 169)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "mitochondrial") (:form . "mitochondrial")\n  (:end . 186) (:start . 173) (:id . 64))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 191) (:start . 187)\n  (:id . 65))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 202)\n  (:start . 192) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 204) (:start . 203)\n  (:id . 67))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 206) (:start . 204)\n  (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 207) (:start . 206)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x11.104.1) (:span 110 113)))\n (:hscopes ((:id . :x11.104.1) (:span 0 202)))\n (:identifiers (:sid . :s11.104) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503743@unknown@formal@none@1@S@Mitochondrial biogenesis in S. pombe is more similar to higher eukaryotes [24], so it is quite possible that the independent synchronization of some mitochondrial genes is maintained in higher eukaryotes as well.@(((:tag . "JJ") (:stem . "mitochondrial") (:form . "Mitochondrial")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "biogenesis") (:form . "biogenesis") (:end . 24)\n  (:start . 14) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 44))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 36) (:start . 31)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 62) (:start . 56)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "eukaryote") (:form . "eukaryotes") (:end . 73)\n  (:start . 63) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 85) (:start . 83)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 88) (:start . 86)\n  (:id . 59))\n ((:tag . "RB") (:stem . "quite") (:form . "quite") (:end . 94) (:start . 89)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 103)\n  (:start . 95) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 124)\n  (:start . 113) (:id . 64))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 140) (:start . 125) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 66))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 148) (:start . 144)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "mitochondrial") (:form . "mitochondrial")\n  (:end . 162) (:start . 149) (:id . 68))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 168)\n  (:start . 163) (:id . 69))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 171) (:start . 169)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "maintain") (:form . "maintained") (:end . 182)\n  (:start . 172) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 185) (:start . 183)\n  (:id . 72))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 192)\n  (:start . 186) (:id . 73))\n ((:tag . "NNS") (:stem . "eukaryote") (:form . "eukaryotes") (:end . 203)\n  (:start . 193) (:id . 74))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 206) (:start . 204)\n  (:id . 75))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 211) (:start . 207)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x11.105.1) (:span 95 103)))\n (:hscopes ((:id . :x11.105.1) (:span 95 211)))\n (:identifiers (:sid . :s11.105) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503744@unknown@formal@none@1@S@According to endosymbiotic theory [25], mitochondria entered eukaryotic cells nearly a billion years ago.@(((:tag . "VBG") (:stem . "accord") (:form . "According") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "endosymbiotic") (:form . "endosymbiotic")\n  (:end . 26) (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "theory") (:form . "theory") (:end . 33)\n  (:start . 27) (:id . 45))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 35) (:start . 34)\n  (:id . 46))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "mitochondrion") (:form . "mitochondria")\n  (:end . 52) (:start . 40) (:id . 50))\n ((:tag . "VBD") (:stem . "enter") (:form . "entered") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "JJ") (:stem . "eukaryotic") (:form . "eukaryotic") (:end . 71)\n  (:start . 61) (:id . 52))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 77) (:start . 72)\n  (:id . 53))\n ((:tag . "RB") (:stem . "nearly") (:form . "nearly") (:end . 84)\n  (:start . 78) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 86) (:start . 85)\n  (:id . 55))\n ((:tag . "CD") (:stem . "billion") (:form . "billion") (:end . 94)\n  (:start . 87) (:id . 56))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 100) (:start . 95)\n  (:id . 57))\n ((:tag . "RB") (:stem . "ago") (:form . "ago") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s11.106) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503745@unknown@formal@none@1@S@Apparently, since then, some of the mitochondrial pathways (respiration, ribosome biogenesis) maintained their own, internal, synchronization of gene expression.@(((:tag . "RB") (:stem . "apparently") (:form . "Apparently") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "mitochondrial") (:form . "mitochondrial")\n  (:end . 49) (:start . 36) (:id . 50))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 58)\n  (:start . 50) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "respiration") (:form . "respiration") (:end . 71)\n  (:start . 60) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "ribosome") (:form . "ribosome") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "biogenesis") (:form . "biogenesis") (:end . 92)\n  (:start . 82) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "maintain") (:form . "maintained") (:end . 104)\n  (:start . 94) (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 110)\n  (:start . 105) (:id . 59))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 114) (:start . 111)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "internal") (:form . "internal") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 63))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 141) (:start . 126) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 149) (:start . 145)\n  (:id . 66))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 160)\n  (:start . 150) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x11.107.1) (:span 0 10)))\n (:hscopes ((:id . :x11.107.1) (:span 0 160)))\n (:identifiers (:sid . :s11.107) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503746@unknown@formal@none@1@S@Phase shift in expression of ribosomal and mitochondrial ribosomal genes detected in this study (see Figure 3G-J) appears to support hypothesis of decoupling of oxidative and reductive biochemical pathways in the yeast cell cycle [26,27], and possibly represents an example of heterochrony [28] at the level of gene expression.@(((:tag . "NN") (:stem . "phase") (:form . "Phase") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "ribosomal") (:form . "ribosomal") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . 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5503747@unknown@formal@none@1@S@Time clustering, combined with the consequent profile clustering, helps in the superimposing and interpretation the evolutionary changes in gene expression.@(((:tag . "NNP") (:stem . "Time") (:form . "Time") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "clustering") (:form . "clustering") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "consequent") (:form . "consequent") (:end . 45)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "clustering") (:form . "clustering") (:end . 64)\n  (:start . 54) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 65) (:start . 64)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "help") (:form . "helps") (:end . 71) (:start . 66)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "superimposing") (:form . "superimposing")\n  (:end . 92) (:start . 79) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "interpretation") (:form . "interpretation")\n  (:end . 111) (:start . 97) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 128)\n  (:start . 116) (:id . 59))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 136)\n  (:start . 129) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 139) (:start . 137)\n  (:id . 61))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 144) (:start . 140)\n  (:id . 62))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 155)\n  (:start . 145) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s11.109) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503748@unknown@formal@none@1@S@Without time clustering [see Additional file 1 - Figure S9], superposition of the orthologous profiles is much less informative (compare Figure 3E- J with Figure S9 D, E).@(((:tag . "IN") (:stem . "without") (:form . "Without") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "clustering") (:form . "clustering") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 25) (:start . 24)\n  (:id . 45))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 39)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "NNP") (:stem . "S9") (:form . "S9") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "superposition") (:form . "superposition")\n  (:end . 74) (:start . 61) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 93)\n  (:start . 82) (:id . 58))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 105) (:start . 103)\n  (:id . 60))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 110) (:start . 106)\n  (:id . 61))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 115) (:start . 111)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "informative") (:form . "informative") (:end . 127)\n  (:start . 116) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 64))\n ((:tag . "NN") (:stem . "compare") (:form . "compare") (:end . 136)\n  (:start . 129) (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 143)\n  (:start . 137) (:id . 66))\n ((:tag . "NNP") (:stem . "3E-") (:form . "3E-") (:end . 147) (:start . 144)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "J") (:form . "J") (:end . 149) (:start . 148)\n  (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 154) (:start . 150)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 161)\n  (:start . 155) (:id . 70))\n ((:tag . "NNP") (:stem . "S9") (:form . "S9") (:end . 164) (:start . 162)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 166) (:start . 165)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 169) (:start . 168)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 170) (:start . 169)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s11.110) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503749@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s11.111) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503750@unknown@formal@none@1@S@Desynchronization of gene expression in evolution@(((:tag . "NN") (:stem . "desynchronization") (:form . "Desynchronization")\n  (:end . 17) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 43))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 25) (:start . 21)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 36)\n  (:start . 26) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 46))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 49)\n  (:start . 40) (:id . 47)))@@@1@6@((:identifiers (:sid . :s11.112) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503751@unknown@formal@none@1@S@Data selection/filtering and noise suppression strategy made it possible to build a global alignment between very diverse temporal expression data for yeast species, separated by ~400 million years of evolution.@(((:tag . "NNP") (:stem . "Data") (:form . "Data") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "selection/filtering")\n  (:form . "selection/filtering") (:end . 24) (:start . 5) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 44))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 34) (:start . 29)\n  (:id . 45))\n ((:tag . "NN") (:stem . "suppression") (:form . "suppression") (:end . 46)\n  (:start . 35) (:id . 46))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 55)\n  (:start . 47) (:id . 47))\n ((:tag . "VBD") (:stem . "make") (:form . "made") (:end . 60) (:start . 56)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 63) (:start . 61)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 72)\n  (:start . 64) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 75) (:start . 73)\n  (:id . 51))\n ((:tag . "VB") (:stem . "build") (:form . "build") (:end . 81) (:start . 76)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 83) (:start . 82)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 90)\n  (:start . 84) (:id . 54))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 100)\n  (:start . 91) (:id . 55))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 108)\n  (:start . 101) (:id . 56))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 113) (:start . 109)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 121)\n  (:start . 114) (:id . 58))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 130)\n  (:start . 122) (:id . 59))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 141)\n  (:start . 131) (:id . 60))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 146)\n  (:start . 142) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 150) (:start . 147)\n  (:id . 62))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 156)\n  (:start . 151) (:id . 63))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 164)\n  (:start . 157) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 175)\n  (:start . 166) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 178) (:start . 176)\n  (:id . 67))\n ((:tag . "CD") (:stem . "~400") (:form . "~400") (:end . 183) (:start . 179)\n  (:id . 68))\n ((:tag . "CD") (:stem . "million") (:form . "million") (:end . 191)\n  (:start . 184) (:id . 69))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 197)\n  (:start . 192) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 200) (:start . 198)\n  (:id . 71))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 210)\n  (:start . 201) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s11.113) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503752@unknown@formal@none@1@S@Specifically, it has been found that the Pearson metrics in the context of Kruscal-Liberman time warping enables aligning very diverse time series data.@(((:tag . "RB") (:stem . "specifically") (:form . "Specifically") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "metric") (:form . "metrics") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 71)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Kruscal-Liberman") (:form . "Kruscal-Liberman")\n  (:end . 91) (:start . 75) (:id . 56))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "warp") (:form . "warping") (:end . 104)\n  (:start . 97) (:id . 58))\n ((:tag . "NNS") (:stem . "enable") (:form . "enables") (:end . 112)\n  (:start . 105) (:id . 59))\n ((:tag . "VBG") (:stem . "align") (:form . "aligning") (:end . 121)\n  (:start . 113) (:id . 60))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 126) (:start . 122)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 134)\n  (:start . 127) (:id . 62))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 139) (:start . 135)\n  (:id . 63))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 146)\n  (:start . 140) (:id . 64))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 151)\n  (:start . 147) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s11.114) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503753@unknown@formal@none@1@S@Alignments, constructed for the yeast species have been validated using prior biological knowledge.@(((:tag . "NNS") (:stem . "alignment") (:form . "Alignments") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "construct") (:form . "constructed") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "validate") (:form . "validated") (:end . 65)\n  (:start . 56) (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 71) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 77) (:start . 72)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 88)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 98)\n  (:start . 89) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s11.115) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503754@unknown@formal@none@1@S@Recent studies in the evolutionary genomics field suggested presence of conservation between sub domains of large gene networks [29-31].@(((:tag . "JJ") (:stem . "recent") (:form . "Recent") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 34)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "genomic") (:form . "genomics") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 49) (:start . 44)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "suggest") (:form . "suggested") (:end . 59)\n  (:start . 50) (:id . 49))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 68)\n  (:start . 60) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 84)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 92)\n  (:start . 85) (:id . 53))\n ((:tag . "NN") (:stem . "sub") (:form . "sub") (:end . 96) (:start . 93)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 104)\n  (:start . 97) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 113)\n  (:start . 108) (:id . 57))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 118) (:start . 114)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "network") (:form . "networks") (:end . 127)\n  (:start . 119) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 129) (:start . 128)\n  (:id . 60))\n ((:tag . "CD") (:stem . "29-31") (:form . "29-31") (:end . 134)\n  (:start . 129) (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x11.116.1) (:span 50 59)))\n (:hscopes ((:id . :x11.116.1) (:span 50 127)))\n (:identifiers (:sid . :s11.116) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503755@unknown@formal@none@1@S@Preceding genome-wide studies of conserved genetic interactions in S. cerevisiae and S. pombe demonstrated conservation of genetic interactions between particular sets of genes, corresponding to protein complexes or pathways [32].@(((:tag . "VBG") (:stem . "precede") (:form . "Preceding") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "genome-wide") (:form . "genome-wide") (:end . 21)\n  (:start . 10) (:id . 43))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 29)\n  (:start . 22) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 42)\n  (:start . 33) (:id . 46))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 50)\n  (:start . 43) (:id . 47))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 63)\n  (:start . 51) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 49))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 69) (:start . 67)\n  (:id . 50))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 80)\n  (:start . 70) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 52))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 87) (:start . 85)\n  (:id . 53))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 93) (:start . 88)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "demonstrate") (:form . "demonstrated") (:end . 106)\n  (:start . 94) (:id . 55))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 119)\n  (:start . 107) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "genetic") (:form . "genetic") (:end . 130)\n  (:start . 123) (:id . 58))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 143)\n  (:start . 131) (:id . 59))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 151)\n  (:start . 144) (:id . 60))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 162)\n  (:start . 152) (:id . 61))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 167) (:start . 163)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 170) (:start . 168)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 176)\n  (:start . 171) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 191)\n  (:start . 178) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 194) (:start . 192)\n  (:id . 67))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 202)\n  (:start . 195) (:id . 68))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 212)\n  (:start . 203) (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 215) (:start . 213)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 224)\n  (:start . 216) (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 226) (:start . 225)\n  (:id . 72))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 228) (:start . 226)\n  (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 229) (:start . 228)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 230) (:start . 229)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s11.117) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503756@unknown@formal@none@1@S@In this work, comparative analysis of gene expression dynamics has shown that parts of large gene networks (presumably corresponding to time-clusters) maintained substantial temporal synchrony in the course of evolution.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "comparative") (:form . "comparative") (:end . 25)\n  (:start . 14) (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 53)\n  (:start . 43) (:id . 50))\n ((:tag . "NNS") (:stem . "dynamic") (:form . "dynamics") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 72) (:start . 67)\n  (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 97) (:start . 93)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "network") (:form . "networks") (:end . 106)\n  (:start . 98) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "RB") (:stem . "presumably") (:form . "presumably") (:end . 118)\n  (:start . 108) (:id . 61))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 132)\n  (:start . 119) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "time-cluster") (:form . "time-clusters")\n  (:end . 149) (:start . 136) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 150) (:start . 149)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "maintain") (:form . "maintained") (:end . 161)\n  (:start . 151) (:id . 66))\n ((:tag . "JJ") (:stem . "substantial") (:form . "substantial") (:end . 173)\n  (:start . 162) (:id . 67))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 182)\n  (:start . 174) (:id . 68))\n ((:tag . "NN") (:stem . "synchrony") (:form . "synchrony") (:end . 192)\n  (:start . 183) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 195) (:start . 193)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 199) (:start . 196)\n  (:id . 71))\n ((:tag . "NN") (:stem . "course") (:form . "course") (:end . 206)\n  (:start . 200) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 209) (:start . 207)\n  (:id . 73))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 219)\n  (:start . 210) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x11.118.1) (:span 108 118)))\n (:hscopes ((:id . :x11.118.1) (:span 108 149)))\n (:identifiers (:sid . :s11.118) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503757@unknown@formal@none@1@S@The time warping in combination with the path and profile clustering allowed tracing synchronization for some housekeeping, structural and replication genes.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "warp") (:form . "warping") (:end . 16) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "path") (:form . "path") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 57)\n  (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "clustering") (:form . "clustering") (:end . 68)\n  (:start . 58) (:id . 52))\n ((:tag . "VBD") (:stem . "allow") (:form . "allowed") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "VBG") (:stem . "trace") (:form . "tracing") (:end . 84)\n  (:start . 77) (:id . 54))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 100) (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 104) (:start . 101)\n  (:id . 56))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 109) (:start . 105)\n  (:id . 57))\n ((:tag . "NN") (:stem . "housekeeping") (:form . "housekeeping") (:end . 122)\n  (:start . 110) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 134)\n  (:start . 124) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n  (:id . 61))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 150)\n  (:start . 139) (:id . 62))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 156)\n  (:start . 151) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s11.119) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503758@unknown@formal@none@1@S@However, analysis of regulatory components of cell cycle, such as cyclins, revealed no such synchronization or other shared evolutionary trends (data not shown).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 42)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 56) (:start . 51)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "cyclin") (:form . "cyclins") (:end . 73)\n  (:start . 66) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "reveal") (:form . "revealed") (:end . 83)\n  (:start . 75) (:id . 56))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 91) (:start . 87)\n  (:id . 58))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 107) (:start . 92) (:id . 59))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 116)\n  (:start . 111) (:id . 61))\n ((:tag . "VBD") (:stem . "share") (:form . "shared") (:end . 123)\n  (:start . 117) (:id . 62))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 136)\n  (:start . 124) (:id . 63))\n ((:tag . "NNS") (:stem . "trend") (:form . "trends") (:end . 143)\n  (:start . 137) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 145) (:start . 144)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 149)\n  (:start . 145) (:id . 66))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 153) (:start . 150)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 159)\n  (:start . 154) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s11.120) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503759@unknown@formal@none@1@S@One possible reason for this is the dramatic rewiring of regulatory pathways during evolution.@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "reason") (:form . "reason") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dramatic") (:form . "dramatic") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "NN") (:stem . "rewiring") (:form . "rewiring") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 76)\n  (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 83)\n  (:start . 77) (:id . 54))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 93)\n  (:start . 84) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x11.121.1) (:span 4 12)))\n (:hscopes ((:id . :x11.121.1) (:span 4 28)))\n (:identifiers (:sid . :s11.121) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503760@unknown@formal@none@1@S@Mathematical strategies, described in the current work, can be applied to comparative analysis of expression data in any pair of organisms, separated by hundreds of millions years of evolution.@(((:tag . "JJ") (:stem . "mathematical") (:form . "Mathematical") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 23)\n  (:start . 13) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "comparative") (:form . "comparative") (:end . 85)\n  (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 94)\n  (:start . 86) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 108)\n  (:start . 98) (:id . 58))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 113)\n  (:start . 109) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 125) (:start . 121)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 138)\n  (:start . 129) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 149)\n  (:start . 140) (:id . 66))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 152) (:start . 150)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "hundred") (:form . "hundreds") (:end . 161)\n  (:start . 153) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 164) (:start . 162)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "million") (:form . "millions") (:end . 173)\n  (:start . 165) (:id . 70))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 179)\n  (:start . 174) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 182) (:start . 180)\n  (:id . 72))\n ((:tag . "NN") (:stem . "evolution") (:form . "evolution") (:end . 192)\n  (:start . 183) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s11.122) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503761@unknown@formal@none@1@S@The following factors may limit the area of application: (i) variability in gene expression under different experimental conditions (synchronization method, [see Additional file 1 - Figure S10 and Table S2]; (ii) strikingly different alternative alignment paths, specific to large group of genes (heterochrony, see Figure 3); (iii) distortion of gene expression profiles as the result of normalization and Gaussian smoothing.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "VB") (:stem . "limit") (:form . "limit") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . 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5503762@unknown@formal@none@1@S@Methods@(((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s11.124) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503763@unknown@formal@none@1@S@Microarray data and low- level data processing@(((:tag . "NNP") (:stem . "Microarray") (:form . "Microarray") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "low-") (:form . "low-") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 46)\n  (:start . 36) (:id . 48)))@@@1@7@((:identifiers (:sid . :s11.125) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503764@unknown@formal@none@1@S@All available microarray time-series data sets for S. cerevisiae and S. pombe [10-13,15-17] were downloaded from the author's sources [33] or NCBI GEO database [34]; ortholog tables were obtained from Valerie Wood (Sanger Institute) [35].@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "microarray") (:form . "microarray") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "time-series") (:form . "time-series") (:end . 36)\n  (:start . 25) (:id . 45))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 41) (:start . 37)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 46) (:start . 42)\n  (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 64)\n  (:start . 54) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 51))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 77) (:start . 72)\n  (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "CD") (:stem . "10-13,15-17") (:form . "10-13,15-17") (:end . 90)\n  (:start . 79) (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 91) (:start . 90)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 107)\n  (:start . 97) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 112) (:start . 108)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "NN") (:stem . "author") (:form . "author") (:end . 123)\n  (:start . 117) (:id . 61))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 125) (:start . 123)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "source") (:form . "sources") (:end . 133)\n  (:start . 126) (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 135) (:start . 134)\n  (:id . 64))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 137) (:start . 135)\n  (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 138) (:start . 137)\n  (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 141) (:start . 139)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "NCBI") (:form . "NCBI") (:end . 146) (:start . 142)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "GEO") (:form . "GEO") (:end . 150) (:start . 147)\n  (:id . 69))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 159)\n  (:start . 151) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 161) (:start . 160)\n  (:id . 71))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 163) (:start . 161)\n  (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 164) (:start . 163)\n  (:id . 73))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 165) (:start . 164)\n  (:id . 74))\n ((:tag . "NN") (:stem . "ortholog") (:form . "ortholog") (:end . 174)\n  (:start . 166) (:id . 75))\n ((:tag . "NNS") (:stem . "table") (:form . "tables") (:end . 181)\n  (:start . 175) (:id . 76))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 186) (:start . 182)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 195)\n  (:start . 187) (:id . 78))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 200) (:start . 196)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Valerie") (:form . "Valerie") (:end . 208)\n  (:start . 201) (:id . 80))\n ((:tag . "NNP") (:stem . "Wood") (:form . "Wood") (:end . 213) (:start . 209)\n  (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 215) (:start . 214)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Sanger") (:form . "Sanger") (:end . 221)\n  (:start . 215) (:id . 83))\n ((:tag . "NNP") (:stem . "Institute") (:form . "Institute") (:end . 231)\n  (:start . 222) (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 232) (:start . 231)\n  (:id . 85))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 234) (:start . 233)\n  (:id . 86))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 236) (:start . 234)\n  (:id . 87))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 237) (:start . 236)\n  (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s11.126) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503765@unknown@formal@none@1@S@In cases where a single gene in one species corresponded to multiple orthologs in another species, multiple profile pairs were generated by duplicating the single expression profile and superimposing it to all matching orthologs.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 43)\n  (:start . 36) (:id . 50))\n ((:tag . "VBD") (:stem . "correspond") (:form . "corresponded") (:end . 56)\n  (:start . 44) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 78)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "NN") (:stem . "species") (:form . "species") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 107)\n  (:start . 99) (:id . 59))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 115)\n  (:start . 108) (:id . 60))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 121)\n  (:start . 116) (:id . 61))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 126) (:start . 122)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 136)\n  (:start . 127) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 139) (:start . 137)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "duplicate") (:form . "duplicating") (:end . 151)\n  (:start . 140) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 162)\n  (:start . 156) (:id . 67))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 173)\n  (:start . 163) (:id . 68))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 181)\n  (:start . 174) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "superimpose") (:form . "superimposing")\n  (:end . 199) (:start . 186) (:id . 71))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 202) (:start . 200)\n  (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 205) (:start . 203)\n  (:id . 73))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 209) (:start . 206)\n  (:id . 74))\n ((:tag . "VBG") (:stem . "match") (:form . "matching") (:end . 218)\n  (:start . 210) (:id . 75))\n ((:tag . "NNS") (:stem . "ortholog") (:form . "orthologs") (:end . 228)\n  (:start . 219) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s11.127) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503766@unknown@formal@none@1@S@Alignment of data, obtained using different methods of cell synchronization has shown that there is 50-80% of consistency between dataset pairs displaying clear periodic patterns [see Additional file 1 - Figure S10 and Table S2].@(((:tag . "NNP") (:stem . "Alignment") (:form . "Alignment") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "synchronization") (:form . "synchronization")\n  (:end . 75) (:start . 60) (:id . 52))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 79) (:start . 76)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 85) (:start . 80)\n  (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 90) (:start . 86)\n  (:id . 55))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "CD") (:stem . "50-80") (:form . "50-80") (:end . 105)\n  (:start . 100) (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "consistency") (:form . "consistency") (:end . 121)\n  (:start . 110) (:id . 61))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 129)\n  (:start . 122) (:id . 62))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 137)\n  (:start . 130) (:id . 63))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 143)\n  (:start . 138) (:id . 64))\n ((:tag . "VBG") (:stem . "display") (:form . "displaying") (:end . 154)\n  (:start . 144) (:id . 65))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 160)\n  (:start . 155) (:id . 66))\n ((:tag . "JJ") (:stem . "periodic") (:form . "periodic") (:end . 169)\n  (:start . 161) (:id . 67))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 178)\n  (:start . 170) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 180) (:start . 179)\n  (:id . 69))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 183) (:start . 180)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 194)\n  (:start . 184) (:id . 71))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 199) (:start . 195)\n  (:id . 72))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 201) (:start . 200)\n  (:id . 73))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 203) (:start . 202)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 210)\n  (:start . 204) (:id . 75))\n ((:tag . "NNP") (:stem . "S10") (:form . "S10") (:end . 214) (:start . 211)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 218) (:start . 215)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 224)\n  (:start . 219) (:id . 78))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 227) (:start . 225)\n  (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 228) (:start . 227)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s11.128) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503767@unknown@formal@none@1@S@Low-level data processing included the following steps: signal-to-noise filtering (SNR), upsampling, Gaussian smoothing and Z-score normalization.@(((:tag . "JJ") (:stem . "low-level") (:form . "Low-level") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "VBD") (:stem . "include") (:form . "included") (:end . 34)\n  (:start . 26) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "following") (:form . "following") (:end . 48)\n  (:start . 39) (:id . 47))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 54) (:start . 49)\n  (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 55) (:start . 54)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "signal-to-noise") (:form . "signal-to-noise")\n  (:end . 71) (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 81)\n  (:start . 72) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "SNR") (:form . "SNR") (:end . 86) (:start . 83)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "upsample") (:form . "upsampling") (:end . 99)\n  (:start . 89) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "gaussian") (:form . "Gaussian") (:end . 109)\n  (:start . 101) (:id . 58))\n ((:tag . "NN") (:stem . "smoothing") (:form . "smoothing") (:end . 119)\n  (:start . 110) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 60))\n ((:tag . "NN") (:stem . "z-score") (:form . "Z-score") (:end . 131)\n  (:start . 124) (:id . 61))\n ((:tag . "NN") (:stem . "normalization") (:form . "normalization")\n  (:end . 145) (:start . 132) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s11.129) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503768@unknown@formal@none@1@S@Z-score normalization was done using standard methods [36].@(((:tag . "NNP") (:stem . "Z-score") (:form . "Z-score") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "normalization") (:form . "normalization")\n  (:end . 21) (:start . 8) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "do") (:form . "done") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 36) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 53)\n  (:start . 46) (:id . 48))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 55) (:start . 54)\n  (:id . 49))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s11.130) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503769@unknown@formal@none@1@S@Upsampling and Gaussian smoothing were performed in order to reduce noise and improve quality of alignments.@(((:tag . "VBG") (:stem . "upsample") (:form . "Upsampling") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "gaussian") (:form . "Gaussian") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "smoothing") (:form . "smoothing") (:end . 33)\n  (:start . 24) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 48)\n  (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 48))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 57) (:start . 52)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "VB") (:stem . "reduce") (:form . "reduce") (:end . 67)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 73) (:start . 68)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 85)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 107)\n  (:start . 97) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s11.131) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503770@unknown@formal@none@1@S@Upsampling is a standard way of converting analog signals to digital, new sample rate should be at least 2× higher than the highest frequency in the original signal (Nyquist- Shannon sampling theorem).@(((:tag . "NNP") (:stem . "Upsampling") (:form . "Upsampling") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "convert") (:form . "converting") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "analog") (:form . "analog") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "NNS") (:stem . "signal") (:form . "signals") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "digital") (:form . "digital") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 80)\n  (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 92)\n  (:start . 86) (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 104)\n  (:start . 99) (:id . 60))\n ((:tag . "CD") (:stem . "2×") (:form . "2×") (:end . 107) (:start . 105)\n  (:id . 61))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 114)\n  (:start . 108) (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 119) (:start . 115)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 64))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 131)\n  (:start . 124) (:id . 65))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 141)\n  (:start . 132) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 157)\n  (:start . 149) (:id . 69))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 164)\n  (:start . 158) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 166) (:start . 165)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Nyquist-") (:form . "Nyquist-") (:end . 174)\n  (:start . 166) (:id . 72))\n ((:tag . "NNP") (:stem . "Shannon") (:form . "Shannon") (:end . 182)\n  (:start . 175) (:id . 73))\n ((:tag . "NN") (:stem . "sampling") (:form . "sampling") (:end . 191)\n  (:start . 183) (:id . 74))\n ((:tag . "NN") (:stem . "theorem") (:form . "theorem") (:end . 199)\n  (:start . 192) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 200) (:start . 199)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x11.132.1) (:span 86 92)))\n (:hscopes ((:id . :x11.132.1) (:span 86 200)))\n (:identifiers (:sid . :s11.132) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503771@unknown@formal@none@1@S@Accordingly, all input datasets (37 time points maximum) were upsampled in this study to 100 time points.@(((:tag . "RB") (:stem . "accordingly") (:form . "Accordingly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 47)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "maximum") (:form . "maximum") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "upsample") (:form . "upsampled") (:end . 71)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 79) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 85) (:start . 80)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 92) (:start . 89)\n  (:id . 59))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 97) (:start . 93)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 104)\n  (:start . 98) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s11.133) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503772@unknown@formal@none@1@S@Gaussian filter was used to remove high frequencies, much higher than frequencies related to the cell cycle, assuming that the high frequencies are noise.@(((:tag . "JJ") (:stem . "gaussian") (:form . "Gaussian") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "frequency") (:form . "frequencies") (:end . 51)\n  (:start . 40) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 64) (:start . 58)\n  (:id . 52))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "frequency") (:form . "frequencies") (:end . 81)\n  (:start . 70) (:id . 54))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 89)\n  (:start . 82) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 107)\n  (:start . 102) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "assume") (:form . "assuming") (:end . 117)\n  (:start . 109) (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 122) (:start . 118)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 131) (:start . 127)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "frequency") (:form . "frequencies") (:end . 143)\n  (:start . 132) (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 147) (:start . 144)\n  (:id . 66))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 153)\n  (:start . 148) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x11.134.1) (:span 109 117)))\n (:hscopes ((:id . :x11.134.1) (:span 109 153)))\n (:identifiers (:sid . :s11.134) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503773@unknown@formal@none@1@S@Together, upsampling and Gaussian filtering might have effects similar to the interpolated time warping described earlier [1].@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "upsampling") (:form . "upsampling") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "gaussian") (:form . "Gaussian") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 49) (:start . 44)\n  (:id . 48))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "effect") (:form . "effects") (:end . 62)\n  (:start . 55) (:id . 50))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 70)\n  (:start . 63) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "interpolated") (:form . "interpolated") (:end . 90)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 95) (:start . 91)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "warp") (:form . "warping") (:end . 103)\n  (:start . 96) (:id . 56))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 113)\n  (:start . 104) (:id . 57))\n ((:tag . "RBR") (:stem . "earlier") (:form . "earlier") (:end . 121)\n  (:start . 114) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 123) (:start . 122)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 124) (:start . 123)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x11.135.1) (:span 44 49)))\n (:hscopes ((:id . :x11.135.1) (:span 44 121)))\n (:identifiers (:sid . :s11.135) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503774@unknown@formal@none@1@S@Attempts to filter out non-periodic profiles using Fourier methods [10] eliminated too many profiles with high variance, which is not surprising given very small number of periods in the microarray data (~2.5).@(((:tag . "NNS") (:stem . "attempt") (:form . "Attempts") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "VB") (:stem . "filter") (:form . "filter") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "non-periodic") (:form . "non-periodic") (:end . 35)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 50) (:start . 45)\n  (:id . 48))\n ((:tag . "JJR") (:stem . "fouri") (:form . "Fourier") (:end . 58)\n  (:start . 51) (:id . 49))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 66)\n  (:start . 59) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 68) (:start . 67)\n  (:id . 51))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 70) (:start . 68)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "eliminate") (:form . "eliminated") (:end . 82)\n  (:start . 72) (:id . 54))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 100)\n  (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 105) (:start . 101)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 110) (:start . 106)\n  (:id . 59))\n ((:tag . "NN") (:stem . "variance") (:form . "variance") (:end . 119)\n  (:start . 111) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 126)\n  (:start . 121) (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 133) (:start . 130)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "surprising") (:form . "surprising") (:end . 144)\n  (:start . 134) (:id . 65))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 155) (:start . 151)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 161)\n  (:start . 156) (:id . 68))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 168)\n  (:start . 162) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "period") (:form . "periods") (:end . 179)\n  (:start . 172) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 182) (:start . 180)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 186) (:start . 183)\n  (:id . 73))\n ((:tag . "NN") (:stem . "microarray") (:form . "microarray") (:end . 197)\n  (:start . 187) (:id . 74))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 202)\n  (:start . 198) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 204) (:start . 203)\n  (:id . 76))\n ((:tag . "CD") (:stem . "~2.5") (:form . "~2.5") (:end . 208) (:start . 204)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 209) (:start . 208)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s11.136) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503775@unknown@formal@none@1@S@Therefore, Fourier filter was replaced by signal-to-noise filter (SNR) [see Additional file 1 - Figure S1].@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "JJR") (:stem . "fouri") (:form . "Fourier") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "replace") (:form . "replaced") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "signal-to-noise") (:form . "signal-to-noise")\n  (:end . 57) (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 64)\n  (:start . 58) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "SNR") (:form . "SNR") (:end . 69) (:start . 66)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 86)\n  (:start . 76) (:id . 56))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 91) (:start . 87)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 102)\n  (:start . 96) (:id . 60))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 106) (:start . 105)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s11.137) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503776@unknown@formal@none@1@S@Original SNR filter based on non-parametric statistics has been designed for the analysis of microarray time series data, which lacks biological replicates.@(((:tag . "JJ") (:stem . "original") (:form . "Original") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "SNR") (:form . "SNR") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 25) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "non-parametric") (:form . "non-parametric")\n  (:end . 43) (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 54)\n  (:start . 44) (:id . 48))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 58) (:start . 55)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 63) (:start . 59)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 72)\n  (:start . 64) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 76) (:start . 73)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 53))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "microarray") (:form . "microarray") (:end . 103)\n  (:start . 93) (:id . 56))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 108) (:start . 104)\n  (:id . 57))\n ((:tag . "NN") (:stem . "series") (:form . "series") (:end . 115)\n  (:start . 109) (:id . 58))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 120)\n  (:start . 116) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 127)\n  (:start . 122) (:id . 61))\n ((:tag . "VBZ") (:stem . "lack") (:form . "lacks") (:end . 133)\n  (:start . 128) (:id . 62))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 144)\n  (:start . 134) (:id . 63))\n ((:tag . "NNS") (:stem . "replicate") (:form . "replicates") (:end . 155)\n  (:start . 145) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s11.138) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503777@unknown@formal@none@1@S@Consider local point-to-point variation Δx between the neighboring time points i and i+1 in jth expression profile:@(((:tag . "VB") (:stem . "consider") (:form . "Consider") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "point-to-point") (:form . "point-to-point")\n  (:end . 29) (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "variation") (:form . "variation") (:end . 39)\n  (:start . 30) (:id . 45))\n ((:tag . "NNP") (:stem . "Δx") (:form . "Δx") (:end . 42) (:start . 40)\n  (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 50)\n  (:start . 43) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "neighboring") (:form . "neighboring") (:end . 66)\n  (:start . 55) (:id . 49))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 71) (:start . 67)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 78)\n  (:start . 72) (:id . 51))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 80) (:start . 79)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 53))\n ((:tag . "NN") (:stem . "i+1") (:form . "i+1") (:end . 88) (:start . 85)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "jth") (:form . "jth") (:end . 95) (:start . 92)\n  (:id . 56))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 106)\n  (:start . 96) (:id . 57))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 114)\n  (:start . 107) (:id . 58))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 115) (:start . 114)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s11.139) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503778@unknown@formal@none@1@S@If the variance , the noise is high and the profile (probe) needs to be excluded from consideration (see additional file 1).@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "variance") (:form . "variance") (:end . 15)\n  (:start . 7) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 35) (:start . 31)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 51)\n  (:start . 44) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n  (:id . 53))\n ((:tag . "NN") (:stem . "probe") (:form . "probe") (:end . 58) (:start . 53)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 59) (:start . 58)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "need") (:form . "needs") (:end . 65) (:start . 60)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 71) (:start . 69)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 80)\n  (:start . 72) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 85) (:start . 81)\n  (:id . 60))\n ((:tag . "NN") (:stem . "consideration") (:form . "consideration")\n  (:end . 99) (:start . 86) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 62))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 104) (:start . 101)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 115)\n  (:start . 105) (:id . 64))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 120) (:start . 116)\n  (:id . 65))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 122) (:start . 121)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s11.140) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503779@unknown@formal@none@1@S@Each expression profile in every data set was scored using the following log- ratio:@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "every") (:form . "every") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "score") (:form . "scored") (:end . 52)\n  (:start . 46) (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 58) (:start . 53)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 72)\n  (:start . 63) (:id . 53))\n ((:tag . "JJ") (:stem . "log-") (:form . "log-") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 84) (:start . 83)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s11.141) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503780@unknown@formal@none@1@S@In this formula, σ2(Αx) (pseudocount) is the average variance of the point-to point variation (noise) taken for all profiles of the entire data set (see eq. S1-S6 in the additional file 1).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "formula") (:form . "formula") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "FW") (:stem . "σ2(Αx)") (:form . "σ2(Αx)") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "pseudocount") (:form . "pseudocount") (:end . 36)\n  (:start . 25) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 52)\n  (:start . 45) (:id . 52))\n ((:tag . "NN") (:stem . "variance") (:form . "variance") (:end . 61)\n  (:start . 53) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "point-to") (:form . "point-to") (:end . 77)\n  (:start . 69) (:id . 56))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 83) (:start . 78)\n  (:id . 57))\n ((:tag . "NN") (:stem . "variation") (:form . "variation") (:end . 93)\n  (:start . 84) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "noise") (:form . "noise") (:end . 100) (:start . 95)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 107)\n  (:start . 102) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 111) (:start . 108)\n  (:id . 63))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 115) (:start . 112)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 124)\n  (:start . 116) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 138)\n  (:start . 132) (:id . 68))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 143)\n  (:start . 139) (:id . 69))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 147) (:start . 144)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 149) (:start . 148)\n  (:id . 71))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 152) (:start . 149)\n  (:id . 72))\n ((:tag . "NN") (:stem . "eq.") (:form . "eq.") (:end . 156) (:start . 153)\n  (:id . 73))\n ((:tag . "NN") (:stem . "s1-s6") (:form . "S1-S6") (:end . 162)\n  (:start . 157) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 165) (:start . 163)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 180)\n  (:start . 170) (:id . 77))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 185) (:start . 181)\n  (:id . 78))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 187) (:start . 186)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s11.142) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503781@unknown@formal@none@1@S@Similarity matrices and Time warping@(((:tag . "NN") (:stem . "similarity") (:form . "Similarity") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Time") (:form . "Time") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "warp") (:form . "warping") (:end . 36)\n  (:start . 29) (:id . 46)))@@@1@5@((:identifiers (:sid . :s11.143) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503782@unknown@formal@none@1@S@Euclidean similarity matrices take into account only the levels of gene expression at a given time point [1].@(((:tag . "JJ") (:stem . "euclidean") (:form . "Euclidean") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 20)\n  (:start . 10) (:id . 43))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 29)\n  (:start . 21) (:id . 44))\n ((:tag . "VBP") (:stem . "take") (:form . "take") (:end . 34) (:start . 30)\n  (:id . 45))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "NN") (:stem . "account") (:form . "account") (:end . 47)\n  (:start . 40) (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 52) (:start . 48)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 63)\n  (:start . 57) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 82)\n  (:start . 72) (:id . 53))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 85) (:start . 83)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 93) (:start . 88)\n  (:id . 56))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 98) (:start . 94)\n  (:id . 57))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 104) (:start . 99)\n  (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s11.144) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503783@unknown@formal@none@1@S@We found that this commonly used method failed in the case of alignment between S. cerevisiae and S. pombe [see Additional file 1 - Figure S2].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "VBD") (:stem . "fail") (:form . "failed") (:end . 46) (:start . 40)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 71)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 79)\n  (:start . 72) (:id . 55))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 93)\n  (:start . 83) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . "FW") (:stem . "pombe") (:form . "pombe") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 111) (:start . 108)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 122)\n  (:start . 112) (:id . 63))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 127) (:start . 123)\n  (:id . 64))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 131) (:start . 130)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 138)\n  (:start . 132) (:id . 67))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 141) (:start . 139)\n  (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 142) (:start . 141)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s11.145) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503784@unknown@formal@none@1@S@To improve sensitivity of time warping, we replaced Euclidean matrices by Pearson similarity matrices.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "warping") (:form . "warping") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "replace") (:form . "replaced") (:end . 51)\n  (:start . 43) (:id . 50))\n ((:tag . "JJ") (:stem . "euclidean") (:form . "Euclidean") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 81)\n  (:start . 74) (:id . 54))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 92)\n  (:start . 82) (:id . 55))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 101)\n  (:start . 93) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s11.146) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503785@unknown@formal@none@1@S@Given time window size parameter n, {n ∈ (2N + 1){ one can compute value of the Uncentered Pearson correlation r for a given kth pair of the orthologous profiles a and b at the time points i and j as follows:@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "window") (:form . "window") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "parameter") (:form . "parameter") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "{") (:form . "{") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "∈") (:form . "∈") (:end . 40) (:start . 39)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 52))\n ((:tag . "NN") (:stem . "2n") (:form . "2N") (:end . 44) (:start . 42)\n  (:id . 53))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 46) (:start . 45)\n  (:id . 54))\n ((:tag . "CD") (:stem . "1){") (:form . "1){") (:end . 50) (:start . 47)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "one") (:form . "one") (:end . 54) (:start . 51)\n  (:id . 56))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 58) (:start . 55)\n  (:id . 57))\n ((:tag . "VB") (:stem . "compute") (:form . "compute") (:end . 66)\n  (:start . 59) (:id . 58))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 72) (:start . 67)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Uncentered") (:form . "Uncentered") (:end . 90)\n  (:start . 80) (:id . 62))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 98)\n  (:start . 91) (:id . 63))\n ((:tag . "NN") (:stem . "correlation") (:form . "correlation") (:end . 110)\n  (:start . 99) (:id . 64))\n ((:tag . "NN") (:stem . "r") (:form . "r") (:end . 112) (:start . 111)\n  (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 116) (:start . 113)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 118) (:start . 117)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 124)\n  (:start . 119) (:id . 68))\n ((:tag . "NN") (:stem . "kth") (:form . "kth") (:end . 128) (:start . 125)\n  (:id . 69))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 133) (:start . 129)\n  (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 152)\n  (:start . 141) (:id . 73))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 161)\n  (:start . 153) (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 163) (:start . 162)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 76))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 169) (:start . 168)\n  (:id . 77))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 172) (:start . 170)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 176) (:start . 173)\n  (:id . 79))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 181) (:start . 177)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 188)\n  (:start . 182) (:id . 81))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 190) (:start . 189)\n  (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "j") (:form . "j") (:end . 196) (:start . 195)\n  (:id . 84))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 199) (:start . 197)\n  (:id . 85))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 207)\n  (:start . 200) (:id . 86))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 208) (:start . 207)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s11.147) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503786@unknown@formal@none@1@S@This procedure returns agreement between segments of the two profiles, each of length n time points, centered on time point i and j correspondingly.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "return") (:form . "returns") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 40)\n  (:start . 33) (:id . 46))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 49)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 69)\n  (:start . 61) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 52))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 85)\n  (:start . 79) (:id . 55))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 92) (:start . 88)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 99)\n  (:start . 93) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "center") (:form . "centered") (:end . 109)\n  (:start . 101) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 117) (:start . 113)\n  (:id . 62))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 123)\n  (:start . 118) (:id . 63))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 65))\n ((:tag . "NN") (:stem . "j") (:form . "j") (:end . 131) (:start . 130)\n  (:id . 66))\n ((:tag . "RB") (:stem . "correspondingly") (:form . "correspondingly")\n  (:end . 147) (:start . 132) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s11.148) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503787@unknown@formal@none@1@S@Similarity between the time point i from dataset and the time point j from dataset , for all M pairs of orthologous profiles, was computed as a standard Pearson distance:@(((:tag . "NN") (:stem . "similarity") (:form . "Similarity") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 18)\n  (:start . 11) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "j") (:form . "j") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 74) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 82)\n  (:start . 75) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 88) (:start . 85)\n  (:id . 58))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 92) (:start . 89)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "M") (:form . "M") (:end . 94) (:start . 93)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 100) (:start . 95)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 115)\n  (:start . 104) (:id . 63))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 124)\n  (:start . 116) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 65))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 129) (:start . 126)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "compute") (:form . "computed") (:end . 138)\n  (:start . 130) (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 141) (:start . 139)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 143) (:start . 142)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 152)\n  (:start . 144) (:id . 70))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 160)\n  (:start . 153) (:id . 71))\n ((:tag . "NN") (:stem . "distance") (:form . "distance") (:end . 169)\n  (:start . 161) (:id . 72))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 170) (:start . 169)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s11.149) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503788@unknown@formal@none@1@S@The Pearson similarity matrices have higher sensitivity and produce better alignments [see Additional file 1 - Figure S2] (and UC Berkeley web resource) then Euclidean as they collect more information in each point-to- point comparison (see eq. S7-S12 in the additional file 1 for more details).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 43) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 55)\n  (:start . 44) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 49))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 67)\n  (:start . 60) (:id . 50))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 74) (:start . 68)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 85)\n  (:start . 75) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 87) (:start . 86)\n  (:id . 53))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 90) (:start . 87)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 101)\n  (:start . 91) (:id . 55))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 106) (:start . 102)\n  (:id . 56))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 108) (:start . 107)\n  (:id . 57))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 110) (:start . 109)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 117)\n  (:start . 111) (:id . 59))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 120) (:start . 118)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 121) (:start . 120)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "UC") (:form . "UC") (:end . 129) (:start . 127)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Berkeley") (:form . "Berkeley") (:end . 138)\n  (:start . 130) (:id . 65))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 142) (:start . 139)\n  (:id . 66))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 151)\n  (:start . 143) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 68))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 157) (:start . 153)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "euclidean") (:form . "Euclidean") (:end . 167)\n  (:start . 158) (:id . 70))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 170) (:start . 168)\n  (:id . 71))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 175) (:start . 171)\n  (:id . 72))\n ((:tag . "VBP") (:stem . "collect") (:form . "collect") (:end . 183)\n  (:start . 176) (:id . 73))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 188) (:start . 184)\n  (:id . 74))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 200)\n  (:start . 189) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 203) (:start . 201)\n  (:id . 76))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 208) (:start . 204)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "point-to-") (:form . "point-to-") (:end . 218)\n  (:start . 209) (:id . 78))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 224)\n  (:start . 219) (:id . 79))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 235)\n  (:start . 225) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 237) (:start . 236)\n  (:id . 81))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 240) (:start . 237)\n  (:id . 82))\n ((:tag . "NN") (:stem . "eq.") (:form . "eq.") (:end . 244) (:start . 241)\n  (:id . 83))\n ((:tag . "NN") (:stem . "s7-s12") (:form . "S7-S12") (:end . 251)\n  (:start . 245) (:id . 84))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 254) (:start . 252)\n  (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 258) (:start . 255)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 269)\n  (:start . 259) (:id . 87))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 274) (:start . 270)\n  (:id . 88))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 276) (:start . 275)\n  (:id . 89))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 280) (:start . 277)\n  (:id . 90))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 285) (:start . 281)\n  (:id . 91))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 293)\n  (:start . 286) (:id . 92))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 294) (:start . 293)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 295) (:start . 294)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s11.150) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503789@unknown@formal@none@1@S@The described method has been implemented in software package GT-Warp.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 41)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 53)\n  (:start . 45) (:id . 49))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "NNP") (:stem . "GT-Warp") (:form . "GT-Warp") (:end . 69)\n  (:start . 62) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s11.151) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503790@unknown@formal@none@1@S@The package includes the following programs and utilities: "AVF-filer" and "RZ-smooth" are programs for low-level data filtering and processing.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "utility") (:form . "utilities") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 60) (:start . 59)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "AVF-filer") (:form . "AVF-filer") (:end . 69)\n  (:start . 60) (:id . 52))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "rz-smooth") (:form . "RZ-smooth") (:end . 85)\n  (:start . 76) (:id . 56))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 99)\n  (:start . 91) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "low-level") (:form . "low-level") (:end . 113)\n  (:start . 104) (:id . 61))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 118)\n  (:start . 114) (:id . 62))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 128)\n  (:start . 119) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 64))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 143)\n  (:start . 133) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s11.152) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503791@unknown@formal@none@1@S@These programs include common methods such as Fourier analysis, ANOVA, F-test, Gaussian smoothing, resampling, and normalization.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 29)\n  (:start . 23) (:id . 45))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "JJR") (:stem . "fouri") (:form . "Fourier") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "ANOVA") (:form . "ANOVA") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "F-test") (:form . "F-test") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "gaussian") (:form . "Gaussian") (:end . 87)\n  (:start . 79) (:id . 56))\n ((:tag . "NN") (:stem . "smoothing") (:form . "smoothing") (:end . 97)\n  (:start . 88) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "resampling") (:form . "resampling") (:end . 109)\n  (:start . 99) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 61))\n ((:tag . "NN") (:stem . "normalization") (:form . "normalization")\n  (:end . 128) (:start . 115) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s11.153) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503792@unknown@formal@none@1@S@AVF-filer program also includes SNR method described above and "VF-stat" utility for simulating SNR score distribution in random data.@(((:tag . "NNP") (:stem . "AVF-filer") (:form . "AVF-filer") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 17)\n  (:start . 10) (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "NNP") (:stem . "SNR") (:form . "SNR") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 42)\n  (:start . 36) (:id . 47))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 52)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 58) (:start . 53)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 64) (:start . 63)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "vf-stat") (:form . "VF-stat") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 72) (:start . 71)\n  (:id . 53))\n ((:tag . "NN") (:stem . "utility") (:form . "utility") (:end . 80)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "simulate") (:form . "simulating") (:end . 95)\n  (:start . 85) (:id . 56))\n ((:tag . "NNP") (:stem . "SNR") (:form . "SNR") (:end . 99) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 105)\n  (:start . 100) (:id . 58))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 118)\n  (:start . 106) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 128)\n  (:start . 122) (:id . 61))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 133)\n  (:start . 129) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s11.154) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503793@unknown@formal@none@1@S@The program "Time-warp" incorporates both Euclidean and Pearson methods (see above), generates global alignment matrices using Kruscal-Liberman algorithm [6], and has graphical outputs, such as shown in Figure 1.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Time-warp") (:form . "Time-warp") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "incorporate") (:form . "incorporates") (:end . 36)\n  (:start . 24) (:id . 47))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Euclidean") (:form . "Euclidean") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Pearson") (:form . "Pearson") (:end . 63)\n  (:start . 56) (:id . 51))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 82) (:start . 77)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "generate") (:form . "generates") (:end . 94)\n  (:start . 85) (:id . 58))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 101)\n  (:start . 95) (:id . 59))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 111)\n  (:start . 102) (:id . 60))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 120)\n  (:start . 112) (:id . 61))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 126) (:start . 121)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Kruscal-Liberman") (:form . "Kruscal-Liberman")\n  (:end . 143) (:start . 127) (:id . 63))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 153)\n  (:start . 144) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 155) (:start . 154)\n  (:id . 65))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 156) (:start . 155)\n  (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 69))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 166) (:start . 163)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "graphical") (:form . "graphical") (:end . 176)\n  (:start . 167) (:id . 71))\n ((:tag . "NNS") (:stem . "output") (:form . "outputs") (:end . 184)\n  (:start . 177) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 190) (:start . 186)\n  (:id . 74))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 193) (:start . 191)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 199)\n  (:start . 194) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 202) (:start . 200)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 209)\n  (:start . 203) (:id . 78))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 211) (:start . 210)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s11.155) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503794@unknown@formal@none@1@S@The program "Gene-warp" incorporates the same methods and is intended for one-to-one alignment of orthologous profiles.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Gene-warp") (:form . "Gene-warp") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "incorporate") (:form . "incorporates") (:end . 36)\n  (:start . 24) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "intend") (:form . "intended") (:end . 69)\n  (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "one-to-one") (:form . "one-to-one") (:end . 84)\n  (:start . 74) (:id . 55))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 109)\n  (:start . 98) (:id . 58))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 118)\n  (:start . 110) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s11.156) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503795@unknown@formal@none@1@S@Gene-warp produces alignment paths data, which can be clustered using standard methods, such as Cluster 3.0 [37].@(((:tag . "NNP") (:stem . "Gene-warp") (:form . "Gene-warp") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "produce") (:form . "produces") (:end . 18)\n  (:start . 10) (:id . 43))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 28)\n  (:start . 19) (:id . 44))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 34) (:start . 29)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 46) (:start . 41)\n  (:id . 48))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "cluster") (:form . "clustered") (:end . 63)\n  (:start . 54) (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 78)\n  (:start . 70) (:id . 53))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 86)\n  (:start . 79) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Cluster") (:form . "Cluster") (:end . 103)\n  (:start . 96) (:id . 58))\n ((:tag . "CD") (:stem . "3.0") (:form . "3.0") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 109) (:start . 108)\n  (:id . 60))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 111) (:start . 109)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 112) (:start . 111)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s11.157) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503796@unknown@formal@none@1@S@GT-Warp package also includes program "M-align" for aligning datasets based on matrices produced by Time-warp and a "Prf-browser" to browse and display orthologous profiles on the same plot.@(((:tag . "JJ") (:stem . "gt-warp") (:form . "GT-Warp") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 39) (:start . 38)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "M-align") (:form . "M-align") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "align") (:form . "aligning") (:end . 60)\n  (:start . 52) (:id . 51))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 69)\n  (:start . 61) (:id . 52))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 75) (:start . 70)\n  (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 87)\n  (:start . 79) (:id . 55))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 96)\n  (:start . 88) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Time-warp") (:form . "Time-warp") (:end . 109)\n  (:start . 100) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n  (:id . 60))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Prf-browser") (:form . "Prf-browser") (:end . 128)\n  (:start . 117) (:id . 62))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 129) (:start . 128)\n  (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 132) (:start . 130)\n  (:id . 64))\n ((:tag . "VB") (:stem . "browse") (:form . "browse") (:end . 139)\n  (:start . 133) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 66))\n ((:tag . "VB") (:stem . "display") (:form . "display") (:end . 151)\n  (:start . 144) (:id . 67))\n ((:tag . "JJ") (:stem . "orthologous") (:form . "orthologous") (:end . 163)\n  (:start . 152) (:id . 68))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 172)\n  (:start . 164) (:id . 69))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 175) (:start . 173)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 184) (:start . 180)\n  (:id . 72))\n ((:tag . "NN") (:stem . "plot") (:form . "plot") (:end . 189) (:start . 185)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s11.158) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503797@unknown@formal@none@1@S@GT-Warp package has been written in Perl and compiled for Win32; source code is available upon request, Win32 distribution, help, and test files are available from UC Berkeley online resource.@(((:tag . "JJ") (:stem . "gt-warp") (:form . "GT-Warp") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "write") (:form . "written") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Perl") (:form . "Perl") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "compile") (:form . "compiled") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Win32") (:form . "Win32") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 71)\n  (:start . 65) (:id . 54))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 89)\n  (:start . 80) (:id . 57))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 94) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "request") (:form . "request") (:end . 102)\n  (:start . 95) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "win32") (:form . "Win32") (:end . 109)\n  (:start . 104) (:id . 61))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 122)\n  (:start . 110) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 63))\n ((:tag . "NN") (:stem . "help") (:form . "help") (:end . 128) (:start . 124)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 138) (:start . 134)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 144)\n  (:start . 139) (:id . 68))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 148) (:start . 145)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 158)\n  (:start . 149) (:id . 70))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 163) (:start . 159)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "UC") (:form . "UC") (:end . 166) (:start . 164)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "Berkeley") (:form . "Berkeley") (:end . 175)\n  (:start . 167) (:id . 73))\n ((:tag . "JJ") (:stem . "online") (:form . "online") (:end . 182)\n  (:start . 176) (:id . 74))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 191)\n  (:start . 183) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s11.159) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503798@unknown@formal@none@1@S@Clustering alignment paths@(((:tag . "VBG") (:stem . "cluster") (:form . "Clustering") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 20)\n  (:start . 11) (:id . 43))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 26) (:start . 21)\n  (:id . 44)))@@@1@3@((:identifiers (:sid . :s11.160) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503799@unknown@formal@none@1@S@Alignment paths for individual profile pairs were generated using Euclidean method (Gene-warp program).@(((:tag . "NNP") (:stem . "Alignment") (:form . "Alignment") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 44) (:start . 39)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 59)\n  (:start . 50) (:id . 49))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 65) (:start . 60)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "euclidean") (:form . "Euclidean") (:end . 75)\n  (:start . 66) (:id . 51))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 82)\n  (:start . 76) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "gene-warp") (:form . "Gene-warp") (:end . 93)\n  (:start . 84) (:id . 54))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 101)\n  (:start . 94) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s11.161) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503800@unknown@formal@none@1@S@The paths were clustered using K-means clustering method, producing 10 temporal clusters using Cluster 3.0 program with default parameter settings [14,37].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "path") (:form . "paths") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "cluster") (:form . "clustered") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "k-mean") (:form . "K-means") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "VBG") (:stem . "cluster") (:form . "clustering") (:end . 49)\n  (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 56)\n  (:start . 50) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 67)\n  (:start . 58) (:id . 51))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 70) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 88)\n  (:start . 80) (:id . 54))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 94) (:start . 89)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Cluster") (:form . "Cluster") (:end . 102)\n  (:start . 95) (:id . 56))\n ((:tag . "CD") (:stem . "3.0") (:form . "3.0") (:end . 106) (:start . 103)\n  (:id . 57))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 114)\n  (:start . 107) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 119) (:start . 115)\n  (:id . 59))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 127)\n  (:start . 120) (:id . 60))\n ((:tag . "NN") (:stem . "parameter") (:form . "parameter") (:end . 137)\n  (:start . 128) (:id . 61))\n ((:tag . "NNS") (:stem . "setting") (:form . "settings") (:end . 146)\n  (:start . 138) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 148) (:start . 147)\n  (:id . 63))\n ((:tag . "CD") (:stem . "14,37") (:form . "14,37") (:end . 153)\n  (:start . 148) (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 154) (:start . 153)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s11.162) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503801@unknown@formal@none@1@S@S. cerevisiae expression profiles from each temporal cluster (or "time cluster") were clustered again, using K-mean clustering method, producing 10 sub-clusters within each of the 10 time clusters.@(((:tag . "FW") (:stem . "s.") (:form . "S.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "FW") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 52)\n  (:start . 44) (:id . 48))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 60)\n  (:start . 53) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 50))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 70) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 78)\n  (:start . 71) (:id . 54))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "cluster") (:form . "clustered") (:end . 95)\n  (:start . 86) (:id . 58))\n ((:tag . "RB") (:stem . "again") (:form . "again") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 108) (:start . 103)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "k-mean") (:form . "K-mean") (:end . 115)\n  (:start . 109) (:id . 62))\n ((:tag . "NN") (:stem . "clustering") (:form . "clustering") (:end . 126)\n  (:start . 116) (:id . 63))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 133)\n  (:start . 127) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 144)\n  (:start . 135) (:id . 66))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 147) (:start . 145)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "sub-cluster") (:form . "sub-clusters") (:end . 160)\n  (:start . 148) (:id . 68))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 167)\n  (:start . 161) (:id . 69))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 172) (:start . 168)\n  (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 72))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 182) (:start . 180)\n  (:id . 73))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 187) (:start . 183)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 196)\n  (:start . 188) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s11.163) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503802@unknown@formal@none@1@S@Enrichment of gene ontology terms in the time clusters and subclusters was carried out using GeneMapp 2.0 package [38] [see Additional file 1 - Table S1].@(((:tag . "NNP") (:stem . "Enrichment") (:form . "Enrichment") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ontology") (:form . "ontology") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "subcluster") (:form . "subclusters") (:end . 70)\n  (:start . 59) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 74) (:start . 71)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 82)\n  (:start . 75) (:id . 54))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 92) (:start . 87)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "GeneMapp") (:form . "GeneMapp") (:end . 101)\n  (:start . 93) (:id . 57))\n ((:tag . "CD") (:stem . "2.0") (:form . "2.0") (:end . 105) (:start . 102)\n  (:id . 58))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 113)\n  (:start . 106) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 115) (:start . 114)\n  (:id . 60))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 117) (:start . 115)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 120) (:start . 119)\n  (:id . 63))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 123) (:start . 120)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 134)\n  (:start . 124) (:id . 65))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 139) (:start . 135)\n  (:id . 66))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 141) (:start . 140)\n  (:id . 67))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 143) (:start . 142)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 149)\n  (:start . 144) (:id . 69))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 152) (:start . 150)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 153) (:start . 152)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s11.164) (:did . :pmc2771023) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503803@unknown@formal@none@1@S@Construction of an annotated corpus to support biomedical information extraction@(((:tag . "NN") (:stem . "construction") (:form . "Construction") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 35)\n  (:start . 29) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "VB") (:stem . "support") (:form . "support") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 69)\n  (:start . 58) (:id . 50))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 80)\n  (:start . 70) (:id . 51)))@@@1@10@((:identifiers (:sid . :s12.1) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5503804@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s12.2) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503805@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s12.3) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503806@unknown@formal@none@1@S@Information Extraction (IE) is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections.@(((:tag . "NNP") (:stem . "Information") (:form . "Information") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Extraction") (:form . "Extraction") (:end . 22)\n  (:start . 12) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "IE") (:form . "IE") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 42)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "mining") (:form . "mining") (:end . 57)\n  (:start . 51) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "facilitate") (:form . "facilitates") (:end . 74)\n  (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 84)\n  (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "discovery") (:form . "discovery") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "RB") (:stem . "automatically") (:form . "automatically")\n  (:end . 111) (:start . 98) (:id . 58))\n ((:tag . "VBG") (:stem . "locate") (:form . "locating") (:end . 120)\n  (:start . 112) (:id . 59))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 130)\n  (:start . 121) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "interesting") (:form . "interesting") (:end . 145)\n  (:start . 134) (:id . 62))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 156)\n  (:start . 146) (:id . 63))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 163)\n  (:start . 157) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 168) (:start . 164)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "huge") (:form . "huge") (:end . 173) (:start . 169)\n  (:id . 66))\n ((:tag . "NN") (:stem . "document") (:form . "document") (:end . 182)\n  (:start . 174) (:id . 67))\n ((:tag . "NNS") (:stem . "collection") (:form . "collections") (:end . 194)\n  (:start . 183) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.4) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503807@unknown@formal@none@1@S@As events are usually centred on verbs and nominalised verbs, understanding the syntactic and semantic behaviour of these words is highly important.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "VBN") (:stem . "centre") (:form . "centred") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 54)\n  (:start . 43) (:id . 50))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 60) (:start . 55)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "understand") (:form . "understanding") (:end . 75)\n  (:start . 62) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "syntactic") (:form . "syntactic") (:end . 89)\n  (:start . 80) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 102)\n  (:start . 94) (:id . 57))\n ((:tag . "NN") (:stem . "behaviour") (:form . "behaviour") (:end . 112)\n  (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 59))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 121)\n  (:start . 116) (:id . 60))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 127)\n  (:start . 122) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 137)\n  (:start . 131) (:id . 63))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 147)\n  (:start . 138) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.5) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503808@unknown@formal@none@1@S@Corpora annotated with information concerning this behaviour can constitute a valuable resource in the training of IE components and resources.@(((:tag . "NNP") (:stem . "Corpora") (:form . "Corpora") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "annotate") (:form . "annotated") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 34)\n  (:start . 23) (:id . 45))\n ((:tag . "VBG") (:stem . "concern") (:form . "concerning") (:end . 45)\n  (:start . 35) (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 50) (:start . 46)\n  (:id . 47))\n ((:tag . "NN") (:stem . "behaviour") (:form . "behaviour") (:end . 60)\n  (:start . 51) (:id . 48))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 64) (:start . 61)\n  (:id . 49))\n ((:tag . "VB") (:stem . "constitute") (:form . "constitute") (:end . 75)\n  (:start . 65) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "valuable") (:form . "valuable") (:end . 86)\n  (:start . 78) (:id . 52))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 95)\n  (:start . 87) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 55))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 111)\n  (:start . 103) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "ie") (:form . "IE") (:end . 117) (:start . 115)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 128)\n  (:start . 118) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 142)\n  (:start . 133) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x12.6.1) (:span 61 64)))\n (:hscopes ((:id . :x12.6.1) (:span 61 142)))\n (:identifiers (:sid . :s12.6) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503809@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s12.7) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503810@unknown@formal@none@1@S@We have defined a new scheme for annotating sentence-bound gene regulation events, centred on both verbs and nominalised verbs.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 28)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "annotate") (:form . "annotating") (:end . 43)\n  (:start . 33) (:id . 49))\n ((:tag . "JJ") (:stem . "sentence-bound") (:form . "sentence-bound")\n  (:end . 58) (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 63) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 74)\n  (:start . 64) (:id . 52))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 81)\n  (:start . 75) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "centre") (:form . "centred") (:end . 90)\n  (:start . 83) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 93) (:start . 91)\n  (:id . 56))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 98) (:start . 94)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 104) (:start . 99)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 120)\n  (:start . 109) (:id . 60))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 126)\n  (:start . 121) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.8) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503811@unknown@formal@none@1@S@For each event instance, all participants (arguments) in the same sentence are identified and assigned a semantic role from a rich set of 13 roles tailored to biomedical research articles, together with a biological concept type linked to the Gene Regulation Ontology.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "participant") (:form . "participants") (:end . 41)\n  (:start . 29) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 74)\n  (:start . 66) (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 89)\n  (:start . 79) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 113)\n  (:start . 105) (:id . 61))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 118) (:start . 114)\n  (:id . 62))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 123) (:start . 119)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "rich") (:form . "rich") (:end . 130) (:start . 126)\n  (:id . 65))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 134) (:start . 131)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 67))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 140) (:start . 138)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 146)\n  (:start . 141) (:id . 69))\n ((:tag . "VBN") (:stem . "tailor") (:form . "tailored") (:end . 155)\n  (:start . 147) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 158) (:start . 156)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 169)\n  (:start . 159) (:id . 72))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 178)\n  (:start . 170) (:id . 73))\n ((:tag . "NNS") (:stem . "article") (:form . "articles") (:end . 187)\n  (:start . 179) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 188) (:start . 187)\n  (:id . 75))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 197)\n  (:start . 189) (:id . 76))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 202) (:start . 198)\n  (:id . 77))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 204) (:start . 203)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 215)\n  (:start . 205) (:id . 79))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 223)\n  (:start . 216) (:id . 80))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 228) (:start . 224)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "link") (:form . "linked") (:end . 235)\n  (:start . 229) (:id . 82))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 238) (:start . 236)\n  (:id . 83))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 242) (:start . 239)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 247) (:start . 243)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "Regulation") (:form . "Regulation") (:end . 258)\n  (:start . 248) (:id . 86))\n ((:tag . "NNP") (:stem . "Ontology") (:form . "Ontology") (:end . 267)\n  (:start . 259) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 268) (:start . 267)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s12.9) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503812@unknown@formal@none@1@S@To our knowledge, our scheme is unique within the biomedical field in terms of the range of event arguments identified.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 28)\n  (:start . 22) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 38)\n  (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 45)\n  (:start . 39) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 60)\n  (:start . 50) (:id . 52))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 66) (:start . 61)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 75) (:start . 70)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 88) (:start . 83)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 97) (:start . 92)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 107)\n  (:start . 98) (:id . 61))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 118)\n  (:start . 108) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s12.10) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503813@unknown@formal@none@1@S@Using the scheme, we have created the Gene Regulation Event Corpus (GREC), consisting of 240 MEDLINE abstracts, in which events relating to gene regulation and expression have been annotated by biologists.@(((:tag . "VBG") (:stem . "use") (:form . "Using") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "create") (:form . "created") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Regulation") (:form . "Regulation") (:end . 53)\n  (:start . 43) (:id . 51))\n ((:tag . "NNP") (:stem . "Event") (:form . "Event") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Corpus") (:form . "Corpus") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "consist") (:form . "consisting") (:end . 85)\n  (:start . 75) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 59))\n ((:tag . "CD") (:stem . "240") (:form . "240") (:end . 92) (:start . 89)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "MEDLINE") (:form . "MEDLINE") (:end . 100)\n  (:start . 93) (:id . 61))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 110)\n  (:start . 101) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 120)\n  (:start . 115) (:id . 65))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 127)\n  (:start . 121) (:id . 66))\n ((:tag . "VBG") (:stem . "relate") (:form . "relating") (:end . 136)\n  (:start . 128) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 139) (:start . 137)\n  (:id . 68))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 144) (:start . 140)\n  (:id . 69))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 155)\n  (:start . 145) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 71))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 170)\n  (:start . 160) (:id . 72))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 175) (:start . 171)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 180) (:start . 176)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 190)\n  (:start . 181) (:id . 75))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 193) (:start . 191)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "biologist") (:form . "biologists") (:end . 204)\n  (:start . 194) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s12.11) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503814@unknown@formal@none@1@S@A novel method of evaluating various different facets of the annotation task showed that average inter-annotator agreement rates fall within the range of 66% - 90%.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "evaluate") (:form . "evaluating") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "facet") (:form . "facets") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 71)\n  (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 83) (:start . 77)\n  (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 96)\n  (:start . 89) (:id . 56))\n ((:tag . "JJ") (:stem . "inter-annotator") (:form . "inter-annotator")\n  (:end . 112) (:start . 97) (:id . 57))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 122)\n  (:start . 113) (:id . 58))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 128)\n  (:start . 123) (:id . 59))\n ((:tag . "VBP") (:stem . "fall") (:form . "fall") (:end . 133) (:start . 129)\n  (:id . 60))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 140)\n  (:start . 134) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 62))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 150)\n  (:start . 145) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 153) (:start . 151)\n  (:id . 64))\n ((:tag . "CD") (:stem . "66") (:form . "66") (:end . 156) (:start . 154)\n  (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 157) (:start . 156)\n  (:id . 66))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 159) (:start . 158)\n  (:id . 67))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 162) (:start . 160)\n  (:id . 68))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 163) (:start . 162)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s12.12) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503815@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s12.13) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503816@unknown@formal@none@1@S@The GREC is a unique resource within the biomedical field, in that it annotates not only core relationships between entities, but also a range of other important details about these relationships, e.g., location, temporal, manner and environmental conditions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 20)\n  (:start . 14) (:id . 46))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 51)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 66) (:start . 62)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 69) (:start . 67)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "annotate") (:form . "annotates") (:end . 79)\n  (:start . 70) (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 88) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 93) (:start . 89)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "relationship") (:form . "relationships")\n  (:end . 107) (:start . 94) (:id . 60))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 115)\n  (:start . 108) (:id . 61))\n ((:tag . "NNS") (:stem . "entity") (:form . "entities") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 63))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 129) (:start . 126)\n  (:id . 64))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 134) (:start . 130)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 136) (:start . 135)\n  (:id . 66))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 142)\n  (:start . 137) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 151)\n  (:start . 146) (:id . 69))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 161)\n  (:start . 152) (:id . 70))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 169)\n  (:start . 162) (:id . 71))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 175)\n  (:start . 170) (:id . 72))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 181)\n  (:start . 176) (:id . 73))\n ((:tag . "NNS") (:stem . "relationship") (:form . "relationships")\n  (:end . 195) (:start . 182) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 196) (:start . 195)\n  (:id . 75))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 201) (:start . 197)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 202) (:start . 201)\n  (:id . 77))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 211)\n  (:start . 203) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 212) (:start . 211)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "temporal") (:form . "temporal") (:end . 221)\n  (:start . 213) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 222) (:start . 221)\n  (:id . 81))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 229)\n  (:start . 223) (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 233) (:start . 230)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "environmental") (:form . "environmental")\n  (:end . 247) (:start . 234) (:id . 84))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 258)\n  (:start . 248) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 259) (:start . 258)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s12.14) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503817@unknown@formal@none@1@S@As such, it is specifically designed to support bio-specific tool and resource development.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 11) (:start . 9)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 46))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 27)\n  (:start . 15) (:id . 47))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "VB") (:stem . "support") (:form . "support") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "JJ") (:stem . "bio-specific") (:form . "bio-specific") (:end . 60)\n  (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 90)\n  (:start . 79) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.15) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503818@unknown@formal@none@1@S@It has already been used to acquire semantic frames for inclusion within the BioLexicon (a lexical, terminological resource to aid biomedical text mining).@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VB") (:stem . "acquire") (:form . "acquire") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "NNS") (:stem . "frame") (:form . "frames") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "inclusion") (:form . "inclusion") (:end . 65)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 72)\n  (:start . 66) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "BioLexicon") (:form . "BioLexicon") (:end . 87)\n  (:start . 77) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "lexical") (:form . "lexical") (:end . 98)\n  (:start . 91) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "terminological") (:form . "terminological")\n  (:end . 114) (:start . 100) (:id . 60))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 123)\n  (:start . 115) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 126) (:start . 124)\n  (:id . 62))\n ((:tag . "VB") (:stem . "aid") (:form . "aid") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 141)\n  (:start . 131) (:id . 64))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 146) (:start . 142)\n  (:id . 65))\n ((:tag . "NN") (:stem . "mining") (:form . "mining") (:end . 153)\n  (:start . 147) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 154) (:start . 153)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s12.16) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503819@unknown@formal@none@1@S@Initial experiments have also shown that the corpus may viably be used to train IE components, such as semantic role labellers.@(((:tag . "JJ") (:stem . "initial") (:form . "Initial") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 19)\n  (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 24) (:start . 20)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "RB") (:stem . "viably") (:form . "viably") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 70) (:start . 66)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "VB") (:stem . "train") (:form . "train") (:end . 79) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "ie") (:form . "IE") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 93)\n  (:start . 83) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 99) (:start . 95)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 111)\n  (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 116) (:start . 112)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "labeller") (:form . "labellers") (:end . 126)\n  (:start . 117) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x12.17.1) (:span 52 55)))\n (:hscopes ((:id . :x12.17.1) (:span 41 126)))\n (:identifiers (:sid . :s12.17) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503820@unknown@formal@none@1@S@The corpus and annotation guidelines are freely available for academic purposes.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 36)\n  (:start . 26) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "RB") (:stem . "freely") (:form . "freely") (:end . 47)\n  (:start . 41) (:id . 48))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "academic") (:form . "academic") (:end . 70)\n  (:start . 62) (:id . 51))\n ((:tag . "NNS") (:stem . "purpose") (:form . "purposes") (:end . 79)\n  (:start . 71) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s12.18) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503821@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s12.19) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503822@unknown@formal@none@1@S@Due to the rapid advances in biomedical research, scientific literature is being published at an ever-increasing rate [1].@(((:tag . "JJ") (:stem . "due") (:form . "Due") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "advance") (:form . "advances") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 39)\n  (:start . 29) (:id . 48))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "scientific") (:form . "scientific") (:end . 60)\n  (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "literature") (:form . "literature") (:end . 71)\n  (:start . 61) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 80) (:start . 75)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "publish") (:form . "published") (:end . 90)\n  (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 93) (:start . 91)\n  (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "ever-increasing") (:form . "ever-increasing")\n  (:end . 112) (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 117) (:start . 113)\n  (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 121) (:start . 120)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s12.20) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503823@unknown@formal@none@1@S@Without automated means, it is difficult for researchers to keep abreast of developments within biomedicine [2-6].@(((:tag . "IN") (:stem . "without") (:form . "Without") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBN") (:stem . "automate") (:form . "automated") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "mean") (:form . "means") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "researcher") (:form . "researchers") (:end . 56)\n  (:start . 45) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "VB") (:stem . "keep") (:form . "keep") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "abreast") (:form . "abreast") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "development") (:form . "developments") (:end . 88)\n  (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 95)\n  (:start . 89) (:id . 56))\n ((:tag . "NN") (:stem . "biomedicine") (:form . "biomedicine") (:end . 107)\n  (:start . 96) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 109) (:start . 108)\n  (:id . 58))\n ((:tag . "CD") (:stem . "2-6") (:form . "2-6") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s12.21) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503824@unknown@formal@none@1@S@Text mining, which is receiving increasing interest within the biomedical field [7,8], enriches text via the addition of semantic metadata, and thus permits tasks such as analysing molecular pathways [9] and semantic searching.@(((:tag . "JJ") (:stem . "text") (:form . "Text") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "mining") (:form . "mining") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "receive") (:form . "receiving") (:end . 31)\n  (:start . 22) (:id . 47))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 58)\n  (:start . 52) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 73)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 79) (:start . 74)\n  (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 81) (:start . 80)\n  (:id . 54))\n ((:tag . "CD") (:stem . "7,8") (:form . "7,8") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "enrich") (:form . "enriches") (:end . 95)\n  (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 117)\n  (:start . 109) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 129)\n  (:start . 121) (:id . 64))\n ((:tag . "NNS") (:stem . "metadata") (:form . "metadata") (:end . 138)\n  (:start . 130) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 67))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 148) (:start . 144)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "permit") (:form . "permits") (:end . 156)\n  (:start . 149) (:id . 69))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 162)\n  (:start . 157) (:id . 70))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 167) (:start . 163)\n  (:id . 71))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 170) (:start . 168)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "analyse") (:form . "analysing") (:end . 180)\n  (:start . 171) (:id . 73))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 190)\n  (:start . 181) (:id . 74))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 199)\n  (:start . 191) (:id . 75))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 201) (:start . 200)\n  (:id . 76))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 202) (:start . 201)\n  (:id . 77))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 203) (:start . 202)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 207) (:start . 204)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 216)\n  (:start . 208) (:id . 80))\n ((:tag . "NN") (:stem . "searching") (:form . "searching") (:end . 226)\n  (:start . 217) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s12.22) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503825@unknown@formal@none@1@S@Semantic searching above the level of concepts depends on prior processing to recognise relations or events in texts, which is carried out by information extraction (IE) systems.@(((:tag . "JJ") (:stem . "semantic") (:form . "Semantic") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "searching") (:form . "searching") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 24) (:start . 19)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "VBZ") (:stem . "depend") (:form . "depends") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 74)\n  (:start . 64) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n  (:id . 53))\n ((:tag . "VB") (:stem . "recognise") (:form . "recognise") (:end . 87)\n  (:start . 78) (:id . 54))\n ((:tag . "NNS") (:stem . "relation") (:form . "relations") (:end . 97)\n  (:start . 88) (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 107)\n  (:start . 101) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 116)\n  (:start . 111) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 123)\n  (:start . 118) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 126) (:start . 124)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 134)\n  (:start . 127) (:id . 63))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 138) (:start . 135)\n  (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 141) (:start . 139)\n  (:id . 65))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 153)\n  (:start . 142) (:id . 66))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 164)\n  (:start . 154) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 166) (:start . 165)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "IE") (:form . "IE") (:end . 168) (:start . 166)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 177)\n  (:start . 170) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s12.23) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503826@unknown@formal@none@1@S@Due to domain-specific features of texts and the types of events to be recognised, IE systems must be adapted to deal with specific domains.@(((:tag . "JJ") (:stem . "due") (:form . "Due") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "domain-specific") (:form . "domain-specific")\n  (:end . 22) (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 40) (:start . 35)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 64)\n  (:start . 58) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "recognise") (:form . "recognised") (:end . 81)\n  (:start . 71) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "ie") (:form . "IE") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 93)\n  (:start . 86) (:id . 58))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 101) (:start . 99)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "adapt") (:form . "adapted") (:end . 109)\n  (:start . 102) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . "VB") (:stem . "deal") (:form . "deal") (:end . 117) (:start . 113)\n  (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 122) (:start . 118)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 131)\n  (:start . 123) (:id . 65))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 139)\n  (:start . 132) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s12.24) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503827@unknown@formal@none@1@S@A well-established method of carrying out this adaptation is through training using annotated corpora (e.g., [10-12]).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "well-established") (:form . "well-established")\n  (:end . 18) (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 25)\n  (:start . 19) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "adaptation") (:form . "adaptation") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 68)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 77)\n  (:start . 69) (:id . 52))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 83) (:start . 78)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 93)\n  (:start . 84) (:id . 54))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 101)\n  (:start . 94) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 56))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 107) (:start . 103)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 110) (:start . 109)\n  (:id . 59))\n ((:tag . "CD") (:stem . "10-12") (:form . "10-12") (:end . 115)\n  (:start . 110) (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 117) (:start . 116)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s12.25) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503828@unknown@formal@none@1@S@Our work has been concerned with the development of such a corpus for the biomedical field, the Gene Regulation Event Corpus (GREC), consisting of MEDLINE abstracts semantically annotated with event information.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "concern") (:form . "concerned") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 48)\n  (:start . 37) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 65)\n  (:start . 59) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 84)\n  (:start . 74) (:id . 56))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Regulation") (:form . "Regulation") (:end . 111)\n  (:start . 101) (:id . 61))\n ((:tag . "NNP") (:stem . "Event") (:form . "Event") (:end . 117)\n  (:start . 112) (:id . 62))\n ((:tag . "NNP") (:stem . "Corpus") (:form . "Corpus") (:end . 124)\n  (:start . 118) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 130) (:start . 126)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "consist") (:form . "consisting") (:end . 143)\n  (:start . 133) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 146) (:start . 144)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "MEDLINE") (:form . "MEDLINE") (:end . 154)\n  (:start . 147) (:id . 70))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 164)\n  (:start . 155) (:id . 71))\n ((:tag . "RB") (:stem . "semantically") (:form . "semantically") (:end . 177)\n  (:start . 165) (:id . 72))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 187)\n  (:start . 178) (:id . 73))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 192) (:start . 188)\n  (:id . 74))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 198)\n  (:start . 193) (:id . 75))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 210)\n  (:start . 199) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s12.26) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503829@unknown@formal@none@1@S@Our approach is based on the fact that many events are focussed on either verbs (e.g., transcribe, regulate) or nominalised verbs (e.g., transcription, regulation).@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 43) (:start . 39)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 50)\n  (:start . 44) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "focusse") (:form . "focussed") (:end . 63)\n  (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 73)\n  (:start . 67) (:id . 55))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 79) (:start . 74)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 85) (:start . 81)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "transcribe") (:form . "transcribe") (:end . 97)\n  (:start . 87) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "regulate") (:form . "regulate") (:end . 107)\n  (:start . 99) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 111) (:start . 109)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 123)\n  (:start . 112) (:id . 65))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 129)\n  (:start . 124) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 67))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 135) (:start . 131)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 69))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 150) (:start . 137) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n  (:id . 71))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 162)\n  (:start . 152) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 163) (:start . 162)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s12.27) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503830@unknown@formal@none@1@S@Both types of word behave in similar ways, in that they specify arguments that can convey a range of different types of information related to the event.@(((:tag . "DT") (:stem . "both") (:form . "Both") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "word") (:form . "word") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "behave") (:form . "behave") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "NNS") (:stem . "way") (:form . "ways") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 50) (:start . 46)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "specify") (:form . "specify") (:end . 63)\n  (:start . 56) (:id . 54))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 73)\n  (:start . 64) (:id . 55))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 78) (:start . 74)\n  (:id . 56))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "VB") (:stem . "convey") (:form . "convey") (:end . 89)\n  (:start . 83) (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 97) (:start . 92)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 110)\n  (:start . 101) (:id . 62))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 116)\n  (:start . 111) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 64))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 131)\n  (:start . 120) (:id . 65))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 139)\n  (:start . 132) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 68))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 152)\n  (:start . 147) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x12.28.1) (:span 79 82)))\n (:hscopes ((:id . :x12.28.1) (:span 79 152)))\n (:identifiers (:sid . :s12.28) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503831@unknown@formal@none@1@S@For each relevant event, our annotation aims to identify, as exhaustively as possible, all structurally-related arguments within the same sentence.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 39)\n  (:start . 29) (:id . 48))\n ((:tag . "VBZ") (:stem . "aim") (:form . "aims") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 56)\n  (:start . 48) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "RB") (:stem . "exhaustively") (:form . "exhaustively") (:end . 73)\n  (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 85)\n  (:start . 77) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "structurally-related")\n  (:form . "structurally-related") (:end . 111) (:start . 91) (:id . 59))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 121)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 128)\n  (:start . 122) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 137) (:start . 133)\n  (:id . 63))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 146)\n  (:start . 138) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.29) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503832@unknown@formal@none@1@S@Each argument is assigned a semantic role from a fixed set of 13 roles.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 70) (:start . 65)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.30) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503833@unknown@formal@none@1@S@Where appropriate, arguments are also assigned a biological concept type.@(((:tag . "WRB") (:stem . "where") (:form . "Where") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 17)\n  (:start . 6) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 59)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 67)\n  (:start . 60) (:id . 51))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s12.31) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503834@unknown@formal@none@1@S@The GREC may be downloaded from http://www.nactem.ac.uk/GREC/.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "downloade") (:form . "downloaded") (:end . 26)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "http://www.nactem.ac.uk/GREC/")\n  (:form . "http://www.nactem.ac.uk/GREC/") (:end . 61) (:start . 32)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 62) (:start . 61)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s12.32) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503835@unknown@formal@none@1@S@A copy of the corpus is also available in Additional file 1.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "copy") (:form . "copy") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 20)\n  (:start . 14) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 38)\n  (:start . 29) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 52)\n  (:start . 42) (:id . 51))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.33) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503836@unknown@formal@none@1@S@To our knowledge, the GREC provides the richest annotation to date within the biomedical field, in terms of the number of arguments types and their characterisation.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 35)\n  (:start . 27) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "JJS") (:stem . "rich") (:form . "richest") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 58)\n  (:start . 48) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 88)\n  (:start . 78) (:id . 56))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 94) (:start . 89)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 104) (:start . 99)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 62))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 118)\n  (:start . 112) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 131)\n  (:start . 122) (:id . 65))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 137)\n  (:start . 132) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 67))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 147)\n  (:start . 142) (:id . 68))\n ((:tag . "NN") (:stem . "characterisation") (:form . "characterisation")\n  (:end . 164) (:start . 148) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s12.34) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503837@unknown@formal@none@1@S@As such, the corpus is specifically designed to contribute to the development of bio-specific semantic frame resources and semantic role labellers (SRLs) which, although active areas of research within the general language domain, have received less attention within the bio-IE domain.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 19)\n  (:start . 13) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 22) (:start . 20)\n  (:id . 47))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 35)\n  (:start . 23) (:id . 48))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "VB") (:stem . "contribute") (:form . "contribute") (:end . 58)\n  (:start . 48) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 77)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "bio-specific") (:form . "bio-specific") (:end . 93)\n  (:start . 81) (:id . 56))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 102)\n  (:start . 94) (:id . 57))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 108)\n  (:start . 103) (:id . 58))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 118)\n  (:start . 109) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 131)\n  (:start . 123) (:id . 61))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 136) (:start . 132)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "labeller") (:form . "labellers") (:end . 146)\n  (:start . 137) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "SRL") (:form . "SRLs") (:end . 152) (:start . 148)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 66))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 159)\n  (:start . 154) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 68))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 169)\n  (:start . 161) (:id . 69))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 176)\n  (:start . 170) (:id . 70))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 182)\n  (:start . 177) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 185) (:start . 183)\n  (:id . 72))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 194)\n  (:start . 186) (:id . 73))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 201)\n  (:start . 195) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 205) (:start . 202)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 213)\n  (:start . 206) (:id . 76))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 222)\n  (:start . 214) (:id . 77))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 229)\n  (:start . 223) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 230) (:start . 229)\n  (:id . 79))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 235) (:start . 231)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "receive") (:form . "received") (:end . 244)\n  (:start . 236) (:id . 81))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 249) (:start . 245)\n  (:id . 82))\n ((:tag . "NN") (:stem . "attention") (:form . "attention") (:end . 259)\n  (:start . 250) (:id . 83))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 266)\n  (:start . 260) (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 270) (:start . 267)\n  (:id . 85))\n ((:tag . "NN") (:stem . "bio-ie") (:form . "bio-IE") (:end . 277)\n  (:start . 271) (:id . 86))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 284)\n  (:start . 278) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 285) (:start . 284)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s12.35) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503838@unknown@formal@none@1@S@Related work@(((:tag . "VBN") (:stem . "relate") (:form . "Related") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 12) (:start . 8)\n  (:id . 43)))@@@1@2@((:identifiers (:sid . :s12.36) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503839@unknown@formal@none@1@S@Within the field of bio-IE, evaluations such as the LLL05 challenge [13] and BioCreative II [14] have focussed attention on the recognition of protein-protein interaction (PPI) events from the literature.@(((:tag . "IN") (:stem . "within") (:form . "Within") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "bio-IE") (:form . "bio-IE") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "evaluation") (:form . "evaluations") (:end . 39)\n  (:start . 28) (:id . 48))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "lll05") (:form . "LLL05") (:end . 57) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "challenge") (:form . "challenge") (:end . 67)\n  (:start . 58) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "BioCreative") (:form . "BioCreative") (:end . 88)\n  (:start . 77) (:id . 58))\n ((:tag . "CD") (:stem . "ii") (:form . "II") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 95) (:start . 93)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 96) (:start . 95)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 101) (:start . 97)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "focusse") (:form . "focussed") (:end . 110)\n  (:start . 102) (:id . 64))\n ((:tag . "NN") (:stem . "attention") (:form . "attention") (:end . 120)\n  (:start . 111) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 123) (:start . 121)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 67))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 139)\n  (:start . 128) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "protein-protein") (:form . "protein-protein")\n  (:end . 158) (:start . 143) (:id . 70))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 170)\n  (:start . 159) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "PPI") (:form . "PPI") (:end . 175) (:start . 172)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 176) (:start . 175)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 183)\n  (:start . 177) (:id . 75))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 188) (:start . 184)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 192) (:start . 189)\n  (:id . 77))\n ((:tag . "NN") (:stem . "literature") (:form . "literature") (:end . 203)\n  (:start . 193) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s12.37) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503840@unknown@formal@none@1@S@There now exists a number of corpora (e.g., [13,15,16]) and systems (e.g., [17-19]) tailored to this task.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "exist") (:form . "exists") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 51))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "CD") (:stem . "13,15,16") (:form . "13,15,16") (:end . 53)\n  (:start . 45) (:id . 53))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 54) (:start . 53)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 67)\n  (:start . 60) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 58))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 73) (:start . 69)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 76) (:start . 75)\n  (:id . 61))\n ((:tag . "CD") (:stem . "17-19") (:form . "17-19") (:end . 81) (:start . 76)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 82) (:start . 81)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "tailor") (:form . "tailored") (:end . 92)\n  (:start . 84) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 66))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 100) (:start . 96)\n  (:id . 67))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 105) (:start . 101)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.38) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503841@unknown@formal@none@1@S@However, many other types of events and information are relevant within biomedicine, such as gene regulation and expression events, location of protein in the cell, protein-DNA interaction, etc. [20].@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 35)\n  (:start . 29) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 51)\n  (:start . 40) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 71)\n  (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "biomedicine") (:form . "biomedicine") (:end . 83)\n  (:start . 72) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 97) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 108)\n  (:start . 98) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 60))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 123)\n  (:start . 113) (:id . 61))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 130)\n  (:start . 124) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 140)\n  (:start . 132) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 143) (:start . 141)\n  (:id . 65))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 151)\n  (:start . 144) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n  (:id . 68))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 163) (:start . 159)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "protein-dna") (:form . "protein-DNA") (:end . 176)\n  (:start . 165) (:id . 71))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 188)\n  (:start . 177) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 73))\n ((:tag . "FW") (:stem . "etc.") (:form . "etc.") (:end . 194) (:start . 190)\n  (:id . 74))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 196) (:start . 195)\n  (:id . 75))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 198) (:start . 196)\n  (:id . 76))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 199) (:start . 198)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s12.39) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503842@unknown@formal@none@1@S@Extraction of such events often requires the recognition of more complex information than just interacting proteins.@(((:tag . "NN") (:stem . "extraction") (:form . "Extraction") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 25)\n  (:start . 19) (:id . 45))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 56)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 72)\n  (:start . 65) (:id . 52))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 84)\n  (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 89) (:start . 85)\n  (:id . 54))\n ((:tag . "RB") (:stem . "just") (:form . "just") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 106)\n  (:start . 95) (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 115)\n  (:start . 107) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.40) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503843@unknown@formal@none@1@S@Several corpora and systems concerned with the annotation of more complex events have recently been developed, e.g., [21-24].@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "VBN") (:stem . "concern") (:form . "concerned") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 57)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 73)\n  (:start . 66) (:id . 52))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 80)\n  (:start . 74) (:id . 53))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 85) (:start . 81)\n  (:id . 54))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 94)\n  (:start . 86) (:id . 55))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "develop") (:form . "developed") (:end . 109)\n  (:start . 100) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 58))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "CD") (:stem . "21-24") (:form . "21-24") (:end . 123)\n  (:start . 118) (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s12.41) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503844@unknown@formal@none@1@S@These differ in a number of ways, including:@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "differ") (:form . "differ") (:end . 12)\n  (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "way") (:form . "ways") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 43)\n  (:start . 34) (:id . 50))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 44) (:start . 43)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s12.42) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503845@unknown@formal@none@1@S@• Range of events - whether a single type of event or multiple event types are annotated.@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Range") (:form . "Range") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 17)\n  (:start . 11) (:id . 45))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 27)\n  (:start . 20) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 36)\n  (:start . 30) (:id . 49))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 50) (:start . 45)\n  (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 53) (:start . 51)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 62)\n  (:start . 54) (:id . 54))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 68) (:start . 63)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 74) (:start . 69)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 78) (:start . 75)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 88)\n  (:start . 79) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x12.43.1) (:span 51 53)) ((:id . :x12.43.2) (:span 20 27)))\n (:hscopes ((:id . :x12.43.1) (:span 28 74)) ((:id . :x12.43.2) (:span 20 88)))\n (:identifiers (:sid . :s12.43) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503846@unknown@formal@none@1@S@• Event arguments - the number and types of arguments (i.e., participants) in each event may be fixed or flexible.@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Event") (:form . "Event") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . ":") (:stem . "-") (:form . "-") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 53)\n  (:start . 44) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 59) (:start . 55)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "participant") (:form . "participants") (:end . 73)\n  (:start . 61) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 57))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 82) (:start . 78)\n  (:id . 58))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 88) (:start . 83)\n  (:id . 59))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 92) (:start . 89)\n  (:id . 60))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 95) (:start . 93)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "fix") (:form . "fixed") (:end . 101) (:start . 96)\n  (:id . 62))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 104) (:start . 102)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "flexible") (:form . "flexible") (:end . 113)\n  (:start . 105) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x12.44.1) (:span 102 104)) ((:id . :x12.44.2) (:span 89 92)))\n (:hscopes ((:id . :x12.44.1) (:span 96 113))\n  ((:id . :x12.44.2) (:span 20 113)))\n (:identifiers (:sid . :s12.44) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503847@unknown@formal@none@1@S@More detailed information types, e.g., location, time or experimental setup may or may not be identified as event arguments.@(((:tag . "RBR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 31) (:start . 26)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 46))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 47)\n  (:start . 39) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 69)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "setup") (:form . "setup") (:end . 75) (:start . 70)\n  (:id . 54))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 86) (:start . 83)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 104)\n  (:start . 94) (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 107) (:start . 105)\n  (:id . 61))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 113)\n  (:start . 108) (:id . 62))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 123)\n  (:start . 114) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x12.45.1) (:span 76 90)))\n (:hscopes ((:id . :x12.45.1) (:span 0 123)))\n (:identifiers (:sid . :s12.45) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503848@unknown@formal@none@1@S@• Scope of events - whether event arguments must occur within a single sentence or whether they may occur across multiple sentences.@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Scope") (:form . "Scope") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 17)\n  (:start . 11) (:id . 45))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 27)\n  (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 33) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "VB") (:stem . "occur") (:form . "occur") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 70)\n  (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 79)\n  (:start . 71) (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 90)\n  (:start . 83) (:id . 57))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "VB") (:stem . "occur") (:form . "occur") (:end . 105)\n  (:start . 100) (:id . 60))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 112)\n  (:start . 106) (:id . 61))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 121)\n  (:start . 113) (:id . 62))\n ((:tag . "NNS") (:stem . "sentence") (:form . "sentences") (:end . 131)\n  (:start . 122) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x12.46.1) (:span 96 99)) ((:id . :x12.46.2) (:span 83 90))\n  ((:id . :x12.46.3) (:span 80 82)) ((:id . :x12.46.4) (:span 20 27)))\n (:hscopes ((:id . :x12.46.1) (:span 96 131))\n  ((:id . :x12.46.2) (:span 83 131)) ((:id . :x12.46.4) (:span 20 79))\n  ((:id . :x12.46.3) (:span 20 131)))\n (:identifiers (:sid . :s12.46) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503849@unknown@formal@none@1@S@• Semantic information assigned to arguments - this may correspond to named entity types and/or semantic roles.@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "semantic") (:form . "Semantic") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 44)\n  (:start . 35) (:id . 47))\n ((:tag . ":") (:stem . "-") (:form . "-") (:end . 46) (:start . 45)\n  (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 51) (:start . 47)\n  (:id . 49))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "VB") (:stem . "correspond") (:form . "correspond") (:end . 66)\n  (:start . 56) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "name") (:form . "named") (:end . 75) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "entity") (:form . "entity") (:end . 82)\n  (:start . 76) (:id . 54))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 88) (:start . 83)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 95)\n  (:start . 89) (:id . 56))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 104)\n  (:start . 96) (:id . 57))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 110)\n  (:start . 105) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x12.47.1) (:span 52 55)))\n (:hscopes ((:id . :x12.47.1) (:span 52 110)))\n (:identifiers (:sid . :s12.47) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503850@unknown@formal@none@1@S@In the case of semantic roles being assigned, they may be tailored to a particular type of event, or they may apply to a large range of different events.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 23)\n  (:start . 15) (:id . 46))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "tailor") (:form . "tailored") (:end . 66)\n  (:start . 58) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 82)\n  (:start . 72) (:id . 57))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 87) (:start . 83)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 96) (:start . 91)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 100) (:start . 98)\n  (:id . 62))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 105) (:start . 101)\n  (:id . 63))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 109) (:start . 106)\n  (:id . 64))\n ((:tag . "VB") (:stem . "apply") (:form . "apply") (:end . 115)\n  (:start . 110) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 118) (:start . 116)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 120) (:start . 119)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 126)\n  (:start . 121) (:id . 68))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 132)\n  (:start . 127) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 145)\n  (:start . 136) (:id . 71))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 152)\n  (:start . 146) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x12.48.1) (:span 106 109)) ((:id . :x12.48.2) (:span 51 54)))\n (:hscopes ((:id . :x12.48.1) (:span 106 152))\n  ((:id . :x12.48.2) (:span 46 96)))\n (:identifiers (:sid . :s12.48) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503851@unknown@formal@none@1@S@Whilst events are often identified by verbs, nominalised verbs play a particularly important role within biomedical texts, and often outnumber other domain-specific verbal forms [25].@(((:tag . "JJ") (:stem . "whilst") (:form . "Whilst") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 13) (:start . 7)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 56)\n  (:start . 45) (:id . 50))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 62) (:start . 57)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "play") (:form . "play") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 82)\n  (:start . 70) (:id . 54))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 92)\n  (:start . 83) (:id . 55))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 104)\n  (:start . 98) (:id . 57))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 115)\n  (:start . 105) (:id . 58))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 121)\n  (:start . 116) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 132)\n  (:start . 127) (:id . 62))\n ((:tag . "VBP") (:stem . "outnumber") (:form . "outnumber") (:end . 142)\n  (:start . 133) (:id . 63))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 148)\n  (:start . 143) (:id . 64))\n ((:tag . "JJ") (:stem . "domain-specific") (:form . "domain-specific")\n  (:end . 164) (:start . 149) (:id . 65))\n ((:tag . "JJ") (:stem . "verbal") (:form . "verbal") (:end . 171)\n  (:start . 165) (:id . 66))\n ((:tag . "NNS") (:stem . "form") (:form . "forms") (:end . 177)\n  (:start . 172) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 179) (:start . 178)\n  (:id . 68))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 181) (:start . 179)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 182) (:start . 181)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s12.49) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503852@unknown@formal@none@1@S@However, it is acknowledged that they are more difficult to process than verbs [26] and are currently only dealt with by a small number of systems, often in a limited way (e.g., [17,27,28]).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "acknowledge") (:form . "acknowledged") (:end . 27)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 56)\n  (:start . 47) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "VB") (:stem . "process") (:form . "process") (:end . 67)\n  (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 78) (:start . 73)\n  (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 80) (:start . 79)\n  (:id . 56))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 83) (:start . 82)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 91) (:start . 88)\n  (:id . 60))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 101)\n  (:start . 92) (:id . 61))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 106) (:start . 102)\n  (:id . 62))\n ((:tag . "VB") (:stem . "dealt") (:form . "dealt") (:end . 112)\n  (:start . 107) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 117) (:start . 113)\n  (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 120) (:start . 118)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 122) (:start . 121)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 128)\n  (:start . 123) (:id . 67))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 135)\n  (:start . 129) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 146)\n  (:start . 139) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 71))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 153)\n  (:start . 148) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 156) (:start . 154)\n  (:id . 73))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 158) (:start . 157)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 166)\n  (:start . 159) (:id . 75))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 170) (:start . 167)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 77))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 176) (:start . 172)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 79))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 179) (:start . 178)\n  (:id . 80))\n ((:tag . "CD") (:stem . "17,27,28") (:form . "17,27,28") (:end . 187)\n  (:start . 179) (:id . 81))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 188) (:start . 187)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s12.50) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503853@unknown@formal@none@1@S@Due to the central nature of verbs and nominalised verbs in the description of events, accurate event extraction requires information about the way they behave in text, in terms of:@(((:tag . "JJ") (:stem . "due") (:form . "Due") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 18)\n  (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "nature") (:form . "nature") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 34) (:start . 29)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 50)\n  (:start . 39) (:id . 50))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "description") (:form . "description") (:end . 75)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 85)\n  (:start . 79) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "accurate") (:form . "accurate") (:end . 95)\n  (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 112)\n  (:start . 102) (:id . 60))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 121)\n  (:start . 113) (:id . 61))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 133)\n  (:start . 122) (:id . 62))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 139)\n  (:start . 134) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 64))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 147) (:start . 144)\n  (:id . 65))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 152) (:start . 148)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "behave") (:form . "behave") (:end . 159)\n  (:start . 153) (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 162) (:start . 160)\n  (:id . 68))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 167) (:start . 163)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 171) (:start . 169)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 177)\n  (:start . 172) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 180) (:start . 178)\n  (:id . 73))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 181) (:start . 180)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s12.51) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503854@unknown@formal@none@1@S@• Their syntactically-related arguments, e.g. causality, location, manner, etc.@(((:tag . "VB") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP$") (:stem . "their") (:form . "Their") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "syntactically-related")\n  (:form . "syntactically-related") (:end . 29) (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 39)\n  (:start . 30) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 46))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 45) (:start . 41)\n  (:id . 47))\n ((:tag . "NN") (:stem . "causality") (:form . "causality") (:end . 55)\n  (:start . 46) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 49))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 65)\n  (:start . 57) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 51))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 73)\n  (:start . 67) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 53))\n ((:tag . "FW") (:stem . "etc") (:form . "etc") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s12.52) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503855@unknown@formal@none@1@S@• Semantic information relating to each argument (e.g., semantic roles or restrictions on the types of phrase that can constitute each argument).@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "semantic") (:form . "Semantic") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 22)\n  (:start . 11) (:id . 44))\n ((:tag . "VBG") (:stem . "relate") (:form . "relating") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 48)\n  (:start . 40) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "restriction") (:form . "restrictions") (:end . 86)\n  (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 99) (:start . 94)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 59))\n ((:tag . "NN") (:stem . "phrase") (:form . "phrase") (:end . 109)\n  (:start . 103) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 114) (:start . 110)\n  (:id . 61))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 118) (:start . 115)\n  (:id . 62))\n ((:tag . "VB") (:stem . "constitute") (:form . "constitute") (:end . 129)\n  (:start . 119) (:id . 63))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 134) (:start . 130)\n  (:id . 64))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 143)\n  (:start . 135) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s12.53) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503856@unknown@formal@none@1@S@The production of corpora annotated with such information allows real usage within text to be taken into account.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 57)\n  (:start . 46) (:id . 49))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 64)\n  (:start . 58) (:id . 50))\n ((:tag . "JJ") (:stem . "real") (:form . "real") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . "NN") (:stem . "usage") (:form . "usage") (:end . 75) (:start . 70)\n  (:id . 52))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 82)\n  (:start . 76) (:id . 53))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 87) (:start . 83)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 93) (:start . 91)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 99) (:start . 94)\n  (:id . 57))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 104) (:start . 100)\n  (:id . 58))\n ((:tag . "NN") (:stem . "account") (:form . "account") (:end . 112)\n  (:start . 105) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.54) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503857@unknown@formal@none@1@S@Large-scale annotation of corpora within the general language domain at this level of detail has resulted in the production of resources containing syntactic and semantic frame information, which deal with both verbs and nominalised verbs [29-32].@(((:tag . "JJ") (:stem . "large-scale") (:form . "Large-scale") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 22)\n  (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 44))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 33)\n  (:start . 26) (:id . 45))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 40)\n  (:start . 34) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 61)\n  (:start . 53) (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 68)\n  (:start . 62) (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 71) (:start . 69)\n  (:id . 51))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 76) (:start . 72)\n  (:id . 52))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 82) (:start . 77)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 54))\n ((:tag . "NN") (:stem . "detail") (:form . "detail") (:end . 92)\n  (:start . 86) (:id . 55))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "result") (:form . "resulted") (:end . 105)\n  (:start . 97) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 123)\n  (:start . 113) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 136)\n  (:start . 127) (:id . 62))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 147)\n  (:start . 137) (:id . 63))\n ((:tag . "JJ") (:stem . "syntactic") (:form . "syntactic") (:end . 157)\n  (:start . 148) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 161) (:start . 158)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 170)\n  (:start . 162) (:id . 66))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 176)\n  (:start . 171) (:id . 67))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 188)\n  (:start . 177) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 69))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 195)\n  (:start . 190) (:id . 70))\n ((:tag . "VBP") (:stem . "deal") (:form . "deal") (:end . 200) (:start . 196)\n  (:id . 71))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 205) (:start . 201)\n  (:id . 72))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 210) (:start . 206)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 216)\n  (:start . 211) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 220) (:start . 217)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 232)\n  (:start . 221) (:id . 76))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 238)\n  (:start . 233) (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 240) (:start . 239)\n  (:id . 78))\n ((:tag . "CD") (:stem . "29-32") (:form . "29-32") (:end . 245)\n  (:start . 240) (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 246) (:start . 245)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 247) (:start . 246)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s12.55) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503858@unknown@formal@none@1@S@Such annotated corpora also facilitate the training of components of IE systems, with a large amount of research having been devoted to semantic role labelling (SRL) [33].@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "facilitate") (:form . "facilitate") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 51)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 65)\n  (:start . 55) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "ie") (:form . "IE") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 79)\n  (:start . 72) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 100)\n  (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 112)\n  (:start . 104) (:id . 60))\n ((:tag . "VBG") (:stem . "have") (:form . "having") (:end . 119)\n  (:start . 113) (:id . 61))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 124) (:start . 120)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "devote") (:form . "devoted") (:end . 132)\n  (:start . 125) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 144)\n  (:start . 136) (:id . 65))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 149) (:start . 145)\n  (:id . 66))\n ((:tag . "NN") (:stem . "labelling") (:form . "labelling") (:end . 159)\n  (:start . 150) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 161) (:start . 160)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "SRL") (:form . "SRL") (:end . 164) (:start . 161)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 169) (:start . 167)\n  (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 170) (:start . 169)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s12.56) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503859@unknown@formal@none@1@S@Some studies (e.g., [34,35]) have shown that, to a certain extent, general language resources can also be useful in the training of SRLs for biomedical texts, due to the fact that many verbs appear in texts from both the general language and biomedical domains, and often behave in similar ways.@(((:tag . "DT") (:stem . "some") (:form . "Some") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "CD") (:stem . "34,35") (:form . "34,35") (:end . 26) (:start . 21)\n  (:id . 48))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 27) (:start . 26)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 28) (:start . 27)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 33) (:start . 29)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 39) (:start . 34)\n  (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 44) (:start . 40)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 58)\n  (:start . 51) (:id . 57))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 65)\n  (:start . 59) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 74)\n  (:start . 67) (:id . 60))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 83)\n  (:start . 75) (:id . 61))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 93)\n  (:start . 84) (:id . 62))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 97) (:start . 94)\n  (:id . 63))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 102) (:start . 98)\n  (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 105) (:start . 103)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 112)\n  (:start . 106) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 68))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 128)\n  (:start . 120) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "srl") (:form . "SRLs") (:end . 136) (:start . 132)\n  (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 140) (:start . 137)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 151)\n  (:start . 141) (:id . 73))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 157)\n  (:start . 152) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 162) (:start . 159)\n  (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 165) (:start . 163)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n  (:id . 78))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 174) (:start . 170)\n  (:id . 79))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 179) (:start . 175)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 184) (:start . 180)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 190)\n  (:start . 185) (:id . 82))\n ((:tag . "VBP") (:stem . "appear") (:form . "appear") (:end . 197)\n  (:start . 191) (:id . 83))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 200) (:start . 198)\n  (:id . 84))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 206)\n  (:start . 201) (:id . 85))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 211) (:start . 207)\n  (:id . 86))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 216) (:start . 212)\n  (:id . 87))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 220) (:start . 217)\n  (:id . 88))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 228)\n  (:start . 221) (:id . 89))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 237)\n  (:start . 229) (:id . 90))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 241) (:start . 238)\n  (:id . 91))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 252)\n  (:start . 242) (:id . 92))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 260)\n  (:start . 253) (:id . 93))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 261) (:start . 260)\n  (:id . 94))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 265) (:start . 262)\n  (:id . 95))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 271)\n  (:start . 266) (:id . 96))\n ((:tag . "VBP") (:stem . "behave") (:form . "behave") (:end . 278)\n  (:start . 272) (:id . 97))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 281) (:start . 279)\n  (:id . 98))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 289)\n  (:start . 282) (:id . 99))\n ((:tag . "NNS") (:stem . "way") (:form . "ways") (:end . 294) (:start . 290)\n  (:id . 100))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 295) (:start . 294)\n  (:id . 101)))@@@1@60@((:hcues ((:id . :x12.57.1) (:span 94 97)))\n (:hscopes ((:id . :x12.57.1) (:span 94 157)))\n (:identifiers (:sid . :s12.57) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503860@unknown@formal@none@1@S@However, the cited works concede that, whilst such SRLs may produce adequate results for certain predicates, training using biomedical corpora is also needed.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "cite") (:form . "cited") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "work") (:form . "works") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "concede") (:form . "concede") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "IN") (:stem . "whilst") (:form . "whilst") (:end . 45)\n  (:start . 39) (:id . 50))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 50) (:start . 46)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "srl") (:form . "SRLs") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 67)\n  (:start . 60) (:id . 54))\n ((:tag . "JJ") (:stem . "adequate") (:form . "adequate") (:end . 76)\n  (:start . 68) (:id . 55))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 84)\n  (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 96)\n  (:start . 89) (:id . 58))\n ((:tag . "NNS") (:stem . "predicate") (:form . "predicates") (:end . 107)\n  (:start . 97) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 117)\n  (:start . 109) (:id . 61))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 123) (:start . 118)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 134)\n  (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 142)\n  (:start . 135) (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 145) (:start . 143)\n  (:id . 65))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 150) (:start . 146)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "need") (:form . "needed") (:end . 157)\n  (:start . 151) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x12.58.1) (:span 56 59)))\n (:hscopes ((:id . :x12.58.1) (:span 56 107)))\n (:identifiers (:sid . :s12.58) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503861@unknown@formal@none@1@S@This is because domains such as biomedicine employ sublanguages [36], in which the "informational content and structure form a specialized language that can be delineated in the form of a sublanguage grammar".@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "biomedicine") (:form . "biomedicine") (:end . 43)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "employ") (:form . "employ") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "sublanguage") (:form . "sublanguages") (:end . 63)\n  (:start . 51) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 65) (:start . 64)\n  (:id . 51))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 78) (:start . 73)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 84) (:start . 83)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "informational") (:form . "informational")\n  (:end . 97) (:start . 84) (:id . 59))\n ((:tag . "NN") (:stem . "content") (:form . "content") (:end . 105)\n  (:start . 98) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 61))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 119)\n  (:start . 110) (:id . 62))\n ((:tag . "VBP") (:stem . "form") (:form . "form") (:end . 124) (:start . 120)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 126) (:start . 125)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "specialize") (:form . "specialized") (:end . 138)\n  (:start . 127) (:id . 65))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 147)\n  (:start . 139) (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 152) (:start . 148)\n  (:id . 67))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 156) (:start . 153)\n  (:id . 68))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 159) (:start . 157)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "delineate") (:form . "delineated") (:end . 170)\n  (:start . 160) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 173) (:start . 171)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 72))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 182) (:start . 178)\n  (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 185) (:start . 183)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 187) (:start . 186)\n  (:id . 75))\n ((:tag . "NN") (:stem . "sublanguage") (:form . "sublanguage") (:end . 199)\n  (:start . 188) (:id . 76))\n ((:tag . "NN") (:stem . "grammar") (:form . "grammar") (:end . 207)\n  (:start . 200) (:id . 77))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 208) (:start . 207)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s12.59) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503862@unknown@formal@none@1@S@NLP systems must take such grammars into account to allow accurate processing of text within specialist domains [37].@(((:tag . "NNP") (:stem . "NLP") (:form . "NLP") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VB") (:stem . "take") (:form . "take") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "grammar") (:form . "grammars") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "account") (:form . "account") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "accurate") (:form . "accurate") (:end . 66)\n  (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 77)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 92)\n  (:start . 86) (:id . 56))\n ((:tag . "JJ") (:stem . "specialist") (:form . "specialist") (:end . 103)\n  (:start . 93) (:id . 57))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 111)\n  (:start . 104) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 116) (:start . 115)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.60) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503863@unknown@formal@none@1@S@Sublanguage grammar features that are relevant to our work include the following:@(((:tag . "NN") (:stem . "sublanguage") (:form . "Sublanguage") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "grammar") (:form . "grammar") (:end . 19)\n  (:start . 12) (:id . 43))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 28)\n  (:start . 20) (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 46)\n  (:start . 38) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "following") (:form . "following") (:end . 80)\n  (:start . 71) (:id . 53))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 81) (:start . 80)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.61) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503864@unknown@formal@none@1@S@• The types of events found in biological sciences are often described using verbs/nominalised verbs that do not feature prominently in general language [26], e.g., methylate.@(((:tag . "PDT") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 5) (:start . 2)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 21)\n  (:start . 15) (:id . 46))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 41)\n  (:start . 31) (:id . 49))\n ((:tag . "NNS") (:stem . "science") (:form . "sciences") (:end . 50)\n  (:start . 42) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 70)\n  (:start . 61) (:id . 53))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 76) (:start . 71)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "verbs/nominalised") (:form . "verbs/nominalised")\n  (:end . 94) (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 100) (:start . 95)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 105) (:start . 101)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 108) (:start . 106)\n  (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "VB") (:stem . "feature") (:form . "feature") (:end . 120)\n  (:start . 113) (:id . 60))\n ((:tag . "RB") (:stem . "prominently") (:form . "prominently") (:end . 132)\n  (:start . 121) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 143)\n  (:start . 136) (:id . 63))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 152)\n  (:start . 144) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 154) (:start . 153)\n  (:id . 65))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 156) (:start . 154)\n  (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 68))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 163) (:start . 159)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 70))\n ((:tag . "NN") (:stem . "methylate") (:form . "methylate") (:end . 174)\n  (:start . 165) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s12.62) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503865@unknown@formal@none@1@S@• Verbs/nominalised verbs that occur in both the general and specialised language domains may have different syntactic and semantic properties in each domain, e.g., differing numbers of arguments [38], as well as different meanings.@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "verbs/nominalise") (:form . "Verbs/nominalised")\n  (:end . 19) (:start . 2) (:id . 43))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 25) (:start . 20)\n  (:id . 44))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 36) (:start . 31)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "specialise") (:form . "specialised") (:end . 72)\n  (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 81)\n  (:start . 73) (:id . 53))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 89)\n  (:start . 82) (:id . 54))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 98) (:start . 94)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 108)\n  (:start . 99) (:id . 57))\n ((:tag . "JJ") (:stem . "syntactic") (:form . "syntactic") (:end . 118)\n  (:start . 109) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 131)\n  (:start . 123) (:id . 60))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 142)\n  (:start . 132) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 145) (:start . 143)\n  (:id . 62))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 150) (:start . 146)\n  (:id . 63))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 157)\n  (:start . 151) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 65))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 163) (:start . 159)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "differ") (:form . "differing") (:end . 174)\n  (:start . 165) (:id . 68))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 182)\n  (:start . 175) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 185) (:start . 183)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 195)\n  (:start . 186) (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 197) (:start . 196)\n  (:id . 72))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 199) (:start . 197)\n  (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 200) (:start . 199)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 201) (:start . 200)\n  (:id . 75))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 204) (:start . 202)\n  (:id . 76))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 209) (:start . 205)\n  (:id . 77))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 212) (:start . 210)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 222)\n  (:start . 213) (:id . 79))\n ((:tag . "NNS") (:stem . "meaning") (:form . "meanings") (:end . 231)\n  (:start . 223) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x12.63.1) (:span 90 93)))\n (:hscopes ((:id . :x12.63.1) (:span 90 231)))\n (:identifiers (:sid . :s12.63) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503866@unknown@formal@none@1@S@For example, translation generally means rendering one language into other, while in Molecular Biology it specifies the process of protein synthesis from an mRNA template.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "RB") (:stem . "generally") (:form . "generally") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 40) (:start . 35)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "render") (:form . "rendering") (:end . 50)\n  (:start . 41) (:id . 48))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 63)\n  (:start . 55) (:id . 50))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Molecular") (:form . "Molecular") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "NNP") (:stem . "Biology") (:form . "Biology") (:end . 102)\n  (:start . 95) (:id . 57))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "specify") (:form . "specifies") (:end . 115)\n  (:start . 106) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 127)\n  (:start . 120) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 138)\n  (:start . 131) (:id . 63))\n ((:tag . "NN") (:stem . "synthesis") (:form . "synthesis") (:end . 148)\n  (:start . 139) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 153) (:start . 149)\n  (:id . 65))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 156) (:start . 154)\n  (:id . 66))\n ((:tag . "NN") (:stem . "mrna") (:form . "mRNA") (:end . 161) (:start . 157)\n  (:id . 67))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 170)\n  (:start . 162) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.64) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503867@unknown@formal@none@1@S@Whilst there have been some attempts to produce bio-specific extensions to the general language resources described above, e.g., [38,39], together with semantic role labellers [20,40], they currently have limited coverage.@(((:tag . "IN") (:stem . "whilst") (:form . "Whilst") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "attempt") (:form . "attempts") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "VB") (:stem . "produce") (:form . "produce") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "JJ") (:stem . "bio-specific") (:form . "bio-specific") (:end . 60)\n  (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "extension") (:form . "extensions") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 86)\n  (:start . 79) (:id . 54))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 95)\n  (:start . 87) (:id . 55))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 105)\n  (:start . 96) (:id . 56))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 115)\n  (:start . 106) (:id . 57))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 121)\n  (:start . 116) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 59))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 127) (:start . 123)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 130) (:start . 129)\n  (:id . 62))\n ((:tag . "CD") (:stem . "38,39") (:form . "38,39") (:end . 135)\n  (:start . 130) (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 65))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 146)\n  (:start . 138) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 151) (:start . 147)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 160)\n  (:start . 152) (:id . 68))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 165) (:start . 161)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "labeller") (:form . "labellers") (:end . 175)\n  (:start . 166) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 177) (:start . 176)\n  (:id . 71))\n ((:tag . "CD") (:stem . "20,40") (:form . "20,40") (:end . 182)\n  (:start . 177) (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 183) (:start . 182)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 74))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 189) (:start . 185)\n  (:id . 75))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 199)\n  (:start . 190) (:id . 76))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 204) (:start . 200)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 212)\n  (:start . 205) (:id . 78))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 221)\n  (:start . 213) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s12.65) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503868@unknown@formal@none@1@S@The UMLS SPECIALIST lexicon [41], which includes many biomedical terms, is larger scale, but includes only syntactic, and not semantic, information about verbs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "UMLS") (:form . "UMLS") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "SPECIALIST") (:form . "SPECIALIST") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "lexicon") (:form . "lexicon") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 39) (:start . 34)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 48)\n  (:start . 40) (:id . 51))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 64)\n  (:start . 54) (:id . 53))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 70) (:start . 65)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 81)\n  (:start . 75) (:id . 57))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 87) (:start . 82)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 59))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 92) (:start . 89)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 101)\n  (:start . 93) (:id . 61))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 106) (:start . 102)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "syntactic") (:form . "syntactic") (:end . 116)\n  (:start . 107) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 65))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 125) (:start . 122)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 134)\n  (:start . 126) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 68))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 147)\n  (:start . 136) (:id . 69))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 153)\n  (:start . 148) (:id . 70))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 159)\n  (:start . 154) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s12.66) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503869@unknown@formal@none@1@S@Motivation@(((:tag . "NN") (:stem . "motivation") (:form . "Motivation") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s12.67) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503870@unknown@formal@none@1@S@Existing event corpora within the domain (e.g., [21] and [23]) are not specifically geared to support the acquisition of semantic frame information for verbs.@(((:tag . "VBG") (:stem . "exist") (:form . "Existing") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 29)\n  (:start . 23) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 58) (:start . 57)\n  (:id . 55))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 60) (:start . 58)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 61) (:start . 60)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 66) (:start . 63)\n  (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 70) (:start . 67)\n  (:id . 60))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 83)\n  (:start . 71) (:id . 61))\n ((:tag . "VBN") (:stem . "gear") (:form . "geared") (:end . 90) (:start . 84)\n  (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 63))\n ((:tag . "VB") (:stem . "support") (:form . "support") (:end . 101)\n  (:start . 94) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 65))\n ((:tag . "NN") (:stem . "acquisition") (:form . "acquisition") (:end . 117)\n  (:start . 106) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 129)\n  (:start . 121) (:id . 68))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 135)\n  (:start . 130) (:id . 69))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 147)\n  (:start . 136) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 151) (:start . 148)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 157)\n  (:start . 152) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s12.68) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503871@unknown@formal@none@1@S@The bio-NLP community has, until now, lacked a domain-specific linguistically-oriented corpus in which detailed semantic information for a wide range of both verbs and nominalised verbs has been annotated.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "bio-nlp") (:form . "bio-NLP") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "community") (:form . "community") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "until") (:form . "until") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "lack") (:form . "lacked") (:end . 44) (:start . 38)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "domain-specific") (:form . "domain-specific")\n  (:end . 62) (:start . 47) (:id . 52))\n ((:tag . "JJ") (:stem . "linguistically-oriented")\n  (:form . "linguistically-oriented") (:end . 86) (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 93)\n  (:start . 87) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 102)\n  (:start . 97) (:id . 56))\n ((:tag . "VBD") (:stem . "detail") (:form . "detailed") (:end . 111)\n  (:start . 103) (:id . 57))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 120)\n  (:start . 112) (:id . 58))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 132)\n  (:start . 121) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 136) (:start . 133)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 138) (:start . 137)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 143) (:start . 139)\n  (:id . 62))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 149)\n  (:start . 144) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n  (:id . 64))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 157) (:start . 153)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 163)\n  (:start . 158) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 179)\n  (:start . 168) (:id . 68))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 185)\n  (:start . 180) (:id . 69))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 189) (:start . 186)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 194) (:start . 190)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 204)\n  (:start . 195) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s12.69) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503872@unknown@formal@none@1@S@This has limited the amount of research undertaken on the production of domain-specific semantic frame resources and SRLs.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "VBN") (:stem . "undertake") (:form . "undertaken") (:end . 50)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 68)\n  (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "domain-specific") (:form . "domain-specific")\n  (:end . 87) (:start . 72) (:id . 54))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 96)\n  (:start . 88) (:id . 55))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 102) (:start . 97)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 112)\n  (:start . 103) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "srl") (:form . "SRLs") (:end . 121) (:start . 117)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.70) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503873@unknown@formal@none@1@S@In response to this, we have designed a new event annotation scheme which is specifically tailored to this purpose.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 37)\n  (:start . 29) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 39) (:start . 38)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 49) (:start . 44)\n  (:id . 52))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 60)\n  (:start . 50) (:id . 53))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 67)\n  (:start . 61) (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 73) (:start . 68)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 89)\n  (:start . 77) (:id . 57))\n ((:tag . "VBN") (:stem . "tailor") (:form . "tailored") (:end . 98)\n  (:start . 90) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "purpose") (:form . "purpose") (:end . 114)\n  (:start . 107) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.71) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503874@unknown@formal@none@1@S@The scheme has subsequently been applied to the annotation of event instances relating to gene regulation and expression in MEDLINE abstracts.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 27)\n  (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 58)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 77)\n  (:start . 68) (:id . 53))\n ((:tag . "VBG") (:stem . "relate") (:form . "relating") (:end . 86)\n  (:start . 78) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 105)\n  (:start . 95) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 120)\n  (:start . 110) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "MEDLINE") (:form . "MEDLINE") (:end . 131)\n  (:start . 124) (:id . 61))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 141)\n  (:start . 132) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s12.72) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503875@unknown@formal@none@1@S@Our scheme differs from those of previous event corpora in the field in a number of important ways:@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "differ") (:form . "differs") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 80)\n  (:start . 74) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 93)\n  (:start . 84) (:id . 58))\n ((:tag . "NNS") (:stem . "way") (:form . "ways") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 99) (:start . 98)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.73) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503876@unknown@formal@none@1@S@• It captures the semantic annotation of as many structurally-related arguments as possible of a large number of verbs and nominalised verbs describing gene regulation and expression events.@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "capture") (:form . "captures") (:end . 13)\n  (:start . 5) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "structurally-related")\n  (:form . "structurally-related") (:end . 69) (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 79)\n  (:start . 70) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 82) (:start . 80)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 91)\n  (:start . 83) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 102) (:start . 97)\n  (:id . 57))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 109)\n  (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 118)\n  (:start . 113) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 134)\n  (:start . 123) (:id . 62))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 140)\n  (:start . 135) (:id . 63))\n ((:tag . "VBG") (:stem . "describe") (:form . "describing") (:end . 151)\n  (:start . 141) (:id . 64))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 156) (:start . 152)\n  (:id . 65))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 167)\n  (:start . 157) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n  (:id . 67))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 182)\n  (:start . 172) (:id . 68))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 189)\n  (:start . 183) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s12.74) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503877@unknown@formal@none@1@S@This is important since, according to [20], and as confirmed by us through consultation with biologists, types of information such as location, manner, timing and condition, which can appear in various syntactic positions, are all essential for describing biomedical relations.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 34)\n  (:start . 25) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 42) (:start . 41)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 47) (:start . 44)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 50) (:start . 48)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 60)\n  (:start . 51) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 63) (:start . 61)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 66) (:start . 64)\n  (:id . 57))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 74)\n  (:start . 67) (:id . 58))\n ((:tag . "NN") (:stem . "consultation") (:form . "consultation") (:end . 87)\n  (:start . 75) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 92) (:start . 88)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "biologist") (:form . "biologists") (:end . 103)\n  (:start . 93) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 110)\n  (:start . 105) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 64))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 125)\n  (:start . 114) (:id . 65))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 130) (:start . 126)\n  (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 133) (:start . 131)\n  (:id . 67))\n ((:tag . "NN") (:stem . "location") (:form . "location") (:end . 142)\n  (:start . 134) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 69))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 150)\n  (:start . 144) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 151) (:start . 150)\n  (:id . 71))\n ((:tag . "NN") (:stem . "timing") (:form . "timing") (:end . 158)\n  (:start . 152) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 73))\n ((:tag . "NN") (:stem . "condition") (:form . "condition") (:end . 172)\n  (:start . 163) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 75))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 179)\n  (:start . 174) (:id . 76))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 183) (:start . 180)\n  (:id . 77))\n ((:tag . "VB") (:stem . "appear") (:form . "appear") (:end . 190)\n  (:start . 184) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 193) (:start . 191)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 201)\n  (:start . 194) (:id . 80))\n ((:tag . "JJ") (:stem . "syntactic") (:form . "syntactic") (:end . 211)\n  (:start . 202) (:id . 81))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 221)\n  (:start . 212) (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 222) (:start . 221)\n  (:id . 83))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 226) (:start . 223)\n  (:id . 84))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 230) (:start . 227)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 240)\n  (:start . 231) (:id . 86))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 244) (:start . 241)\n  (:id . 87))\n ((:tag . "VBG") (:stem . "describe") (:form . "describing") (:end . 255)\n  (:start . 245) (:id . 88))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 266)\n  (:start . 256) (:id . 89))\n ((:tag . "NNS") (:stem . "relation") (:form . "relations") (:end . 276)\n  (:start . 267) (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 277) (:start . 276)\n  (:id . 91)))@@@1@50@((:hcues ((:id . :x12.75.1) (:span 180 183)))\n (:hscopes ((:id . :x12.75.1) (:span 180 221)))\n (:identifiers (:sid . :s12.75) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503878@unknown@formal@none@1@S@A sentence-based approach facilitates the linking between semantic information and syntactic structure.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "sentence-based") (:form . "sentence-based")\n  (:end . 16) (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "VBZ") (:stem . "facilitate") (:form . "facilitates") (:end . 37)\n  (:start . 26) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 46))\n ((:tag . "NN") (:stem . "linking") (:form . "linking") (:end . 49)\n  (:start . 42) (:id . 47))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 57)\n  (:start . 50) (:id . 48))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 66)\n  (:start . 58) (:id . 49))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 78)\n  (:start . 67) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "syntactic") (:form . "syntactic") (:end . 92)\n  (:start . 83) (:id . 52))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 102)\n  (:start . 93) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.76) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503879@unknown@formal@none@1@S@• It bridges linguistic and biological knowledge:@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "bridge") (:form . "bridges") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "JJ") (:stem . "linguistic") (:form . "linguistic") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 49) (:start . 48)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s12.77) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503880@unknown@formal@none@1@S@From the linguistic perspective, all arguments are characterised using semantic roles.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "linguistic") (:form . "linguistic") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "perspective") (:form . "perspective") (:end . 31)\n  (:start . 20) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 46))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "characterise") (:form . "characterised")\n  (:end . 64) (:start . 51) (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 70) (:start . 65)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 79)\n  (:start . 71) (:id . 52))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 85) (:start . 80)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.78) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503881@unknown@formal@none@1@S@We have defined a new, closed set of event-independent roles which are designed for application to arguments of a range of types of biomedical events.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "closed") (:form . "closed") (:end . 29)\n  (:start . 23) (:id . 48))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 33) (:start . 30)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "event-independent") (:form . "event-independent")\n  (:end . 54) (:start . 37) (:id . 51))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 66) (:start . 61)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 79)\n  (:start . 71) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "NN") (:stem . "application") (:form . "application") (:end . 95)\n  (:start . 84) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 108)\n  (:start . 99) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 113) (:start . 112)\n  (:id . 61))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 119)\n  (:start . 114) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 128)\n  (:start . 123) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 142)\n  (:start . 132) (:id . 66))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 149)\n  (:start . 143) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s12.79) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503882@unknown@formal@none@1@S@Closed sets of semantic roles are advantageous in that they facilitate generalization over different types of events [25,42].@(((:tag . "JJ") (:stem . "closed") (:form . "Closed") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "advantageous") (:form . "advantageous") (:end . 46)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "facilitate") (:form . "facilitate") (:end . 70)\n  (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "generalization") (:form . "generalization")\n  (:end . 85) (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 90) (:start . 86)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 100)\n  (:start . 91) (:id . 55))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 106)\n  (:start . 101) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 116)\n  (:start . 110) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 118) (:start . 117)\n  (:id . 59))\n ((:tag . "CD") (:stem . "25,42") (:form . "25,42") (:end . 123)\n  (:start . 118) (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 124) (:start . 123)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.80) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503883@unknown@formal@none@1@S@Although their application to general language may be problematic [30], the use of a closed set is viable in a restricted domain, as domain-specific definitions can be provided for each semantic role type.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 14) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "application") (:form . "application") (:end . 26)\n  (:start . 15) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 46)\n  (:start . 38) (:id . 47))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "problematic") (:form . "problematic") (:end . 65)\n  (:start . 54) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 67) (:start . 66)\n  (:id . 51))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 84) (:start . 83)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "close") (:form . "closed") (:end . 91)\n  (:start . 85) (:id . 59))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 95) (:start . 92)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 98) (:start . 96)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "viable") (:form . "viable") (:end . 105)\n  (:start . 99) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 110) (:start . 109)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "restricted") (:form . "restricted") (:end . 121)\n  (:start . 111) (:id . 65))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 128)\n  (:start . 122) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 132) (:start . 130)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "domain-specific") (:form . "domain-specific")\n  (:end . 148) (:start . 133) (:id . 69))\n ((:tag . "NNS") (:stem . "definition") (:form . "definitions") (:end . 160)\n  (:start . 149) (:id . 70))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 164) (:start . 161)\n  (:id . 71))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 167) (:start . 165)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 176)\n  (:start . 168) (:id . 73))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 180) (:start . 177)\n  (:id . 74))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 185) (:start . 181)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 194)\n  (:start . 186) (:id . 76))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 199) (:start . 195)\n  (:id . 77))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 204) (:start . 200)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x12.81.1) (:span 161 164)) ((:id . :x12.81.2) (:span 47 50)))\n (:hscopes ((:id . :x12.81.1) (:span 133 204))\n  ((:id . :x12.81.2) (:span 47 65)))\n (:identifiers (:sid . :s12.81) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503884@unknown@formal@none@1@S@From the biological perspective, appropriate arguments are additionally assigned a biological concept type from a hierarchically-structured set that is tailored to the gene regulation domain.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "perspective") (:form . "perspective") (:end . 31)\n  (:start . 20) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 44)\n  (:start . 33) (:id . 47))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 54)\n  (:start . 45) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 58) (:start . 55)\n  (:id . 49))\n ((:tag . "RB") (:stem . "additionally") (:form . "additionally") (:end . 71)\n  (:start . 59) (:id . 50))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 80)\n  (:start . 72) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 82) (:start . 81)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 93)\n  (:start . 83) (:id . 53))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 101)\n  (:start . 94) (:id . 54))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 106) (:start . 102)\n  (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 111) (:start . 107)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 113) (:start . 112)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "hierarchically-structured")\n  (:form . "hierarchically-structured") (:end . 139) (:start . 114)\n  (:id . 58))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 143) (:start . 140)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 148) (:start . 144)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 151) (:start . 149)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "tailor") (:form . "tailored") (:end . 160)\n  (:start . 152) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 163) (:start . 161)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 64))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 172) (:start . 168)\n  (:id . 65))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 183)\n  (:start . 173) (:id . 66))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 190)\n  (:start . 184) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s12.82) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503885@unknown@formal@none@1@S@The concepts are mapped to classes in the Gene Regulation Ontology (GRO) [43].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "map") (:form . "mapped") (:end . 23) (:start . 17)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Regulation") (:form . "Regulation") (:end . 57)\n  (:start . 47) (:id . 51))\n ((:tag . "NNP") (:stem . "Ontology") (:form . "Ontology") (:end . 66)\n  (:start . 58) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "GRO") (:form . "GRO") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 76) (:start . 74)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 77) (:start . 76)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s12.83) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503886@unknown@formal@none@1@S@The combination of semantic role and biological concept labels provides a rich annotation, aimed at allowing users to have a large amount of flexibility over the type of query they specify and to have control over the specificity or generality of certain parts of the query, e.g.:@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 55)\n  (:start . 48) (:id . 49))\n ((:tag . "NNS") (:stem . "label") (:form . "labels") (:end . 62)\n  (:start . 56) (:id . 50))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 71)\n  (:start . 63) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "rich") (:form . "rich") (:end . 78) (:start . 74)\n  (:id . 53))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 89)\n  (:start . 79) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "aim") (:form . "aimed") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "allow") (:form . "allowing") (:end . 108)\n  (:start . 100) (:id . 58))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 114)\n  (:start . 109) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 122) (:start . 118)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 124) (:start . 123)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 130)\n  (:start . 125) (:id . 63))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 137)\n  (:start . 131) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . "NN") (:stem . "flexibility") (:form . "flexibility") (:end . 152)\n  (:start . 141) (:id . 66))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 157) (:start . 153)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 68))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 166) (:start . 162)\n  (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 169) (:start . 167)\n  (:id . 70))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 175)\n  (:start . 170) (:id . 71))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 180) (:start . 176)\n  (:id . 72))\n ((:tag . "VBP") (:stem . "specify") (:form . "specify") (:end . 188)\n  (:start . 181) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 192) (:start . 189)\n  (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 195) (:start . 193)\n  (:id . 75))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 200) (:start . 196)\n  (:id . 76))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 208)\n  (:start . 201) (:id . 77))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 213) (:start . 209)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 217) (:start . 214)\n  (:id . 79))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 229)\n  (:start . 218) (:id . 80))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 232) (:start . 230)\n  (:id . 81))\n ((:tag . "NN") (:stem . "generality") (:form . "generality") (:end . 243)\n  (:start . 233) (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 246) (:start . 244)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 254)\n  (:start . 247) (:id . 84))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 260)\n  (:start . 255) (:id . 85))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 263) (:start . 261)\n  (:id . 86))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 267) (:start . 264)\n  (:id . 87))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 273)\n  (:start . 268) (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 274) (:start . 273)\n  (:id . 89))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 279) (:start . 275)\n  (:id . 90))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 280) (:start . 279)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s12.84) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503887@unknown@formal@none@1@S@In LOCATION:E. coli, AGENT:NifA activates which THEME:GENE.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "LOCATION:E.") (:form . "LOCATION:E.") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "AGENT:NifA") (:form . "AGENT:NifA") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "VBZ") (:stem . "activate") (:form . "activates") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 47) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "THEME:GENE") (:form . "THEME:GENE") (:end . 58)\n  (:start . 48) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s12.85) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503888@unknown@formal@none@1@S@This query would search for instances of events in which a LOCATION, AGENT and THEME are specified.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VB") (:stem . "search") (:form . "search") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 37)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "location") (:form . "LOCATION") (:end . 67)\n  (:start . 59) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "AGENT") (:form . "AGENT") (:end . 74) (:start . 69)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "THEME") (:form . "THEME") (:end . 84) (:start . 79)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 88) (:start . 85)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 98)\n  (:start . 89) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.86) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503889@unknown@formal@none@1@S@The values of the semantic roles may be specified either as specific words or phrases (e.g., E. coli or NifA) or more general named entity categories (e.g., GENE).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 49)\n  (:start . 40) (:id . 50))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 56)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "phrase") (:form . "phrases") (:end . 85)\n  (:start . 78) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 91) (:start . 87)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 95) (:start . 93)\n  (:id . 60))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 100) (:start . 96)\n  (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 103) (:start . 101)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "NifA") (:form . "NifA") (:end . 108) (:start . 104)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 109) (:start . 108)\n  (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 112) (:start . 110)\n  (:id . 65))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 117) (:start . 113)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 125)\n  (:start . 118) (:id . 67))\n ((:tag . "VBN") (:stem . "name") (:form . "named") (:end . 131)\n  (:start . 126) (:id . 68))\n ((:tag . "NN") (:stem . "entity") (:form . "entity") (:end . 138)\n  (:start . 132) (:id . 69))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 149)\n  (:start . 139) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n  (:id . 71))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 155) (:start . 151)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "GENE") (:form . "GENE") (:end . 161) (:start . 157)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x12.87.1) (:span 50 56))\n  ((:id . :x12.87.2) (:span 33 36 110 112)))\n (:hscopes ((:id . :x12.87.1) (:span 50 108))\n  ((:id . :x12.87.2) (:span 0 162)))\n (:identifiers (:sid . :s12.87) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503890@unknown@formal@none@1@S@The GREC consists of 240 MEDLINE abstracts, which have been annotated with a total of 3067 events.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "CD") (:stem . "240") (:form . "240") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "MEDLINE") (:form . "MEDLINE") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 42)\n  (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 69)\n  (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 82) (:start . 77)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "CD") (:stem . "3067") (:form . "3067") (:end . 90) (:start . 86)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 97)\n  (:start . 91) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.88) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503891@unknown@formal@none@1@S@Whilst of modest size compared to some other domain-specific event-annotated corpora (e.g., [21]), this is balanced by the richness of the annotations.@(((:tag . "IN") (:stem . "whilst") (:form . "Whilst") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "modest") (:form . "modest") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "domain-specific") (:form . "domain-specific")\n  (:end . 60) (:start . 45) (:id . 50))\n ((:tag . "JJ") (:stem . "event-annotated") (:form . "event-annotated")\n  (:end . 76) (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 84)\n  (:start . 77) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 53))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 90) (:start . 86)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 93) (:start . 92)\n  (:id . 56))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 60))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 103) (:start . 99)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "balance") (:form . "balanced") (:end . 115)\n  (:start . 107) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 118) (:start . 116)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 65))\n ((:tag . "NN") (:stem . "richness") (:form . "richness") (:end . 131)\n  (:start . 123) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "annotation") (:form . "annotations") (:end . 150)\n  (:start . 139) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s12.89) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503892@unknown@formal@none@1@S@The corpus has already been used in the development of the BioLexicon [44].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 51)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "BioLexicon") (:form . "BioLexicon") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s12.90) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503893@unknown@formal@none@1@S@This unique text mining resource for biology provides and links syntactic and semantic frame information for a large number of biomedical sublanguage verbs.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "mining") (:form . "mining") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "biology") (:form . "biology") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 53)\n  (:start . 45) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "link") (:form . "links") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "syntactic") (:form . "syntactic") (:end . 73)\n  (:start . 64) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 86)\n  (:start . 78) (:id . 54))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 92) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 104)\n  (:start . 93) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 108) (:start . 105)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 110) (:start . 109)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 116)\n  (:start . 111) (:id . 59))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 123)\n  (:start . 117) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 137)\n  (:start . 127) (:id . 62))\n ((:tag . "NN") (:stem . "sublanguage") (:form . "sublanguage") (:end . 149)\n  (:start . 138) (:id . 63))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 155)\n  (:start . 150) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.91) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503894@unknown@formal@none@1@S@In addition, the lexicon contains (1) derived forms of these verbs (including nominalisations), (2) general English words frequently used within the biology domain and (3) domain terms, gathered (and interlinked) both from existing databases and through the application of text mining techniques.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "lexicon") (:form . "lexicon") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 35) (:start . 34)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 45)\n  (:start . 38) (:id . 51))\n ((:tag . "NNS") (:stem . "form") (:form . "forms") (:end . 51) (:start . 46)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 53))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 60) (:start . 55)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 66) (:start . 61)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 77)\n  (:start . 68) (:id . 57))\n ((:tag . "NNS") (:stem . "nominalisation") (:form . "nominalisations")\n  (:end . 93) (:start . 78) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 94) (:start . 93)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 98) (:start . 97)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 107)\n  (:start . 100) (:id . 64))\n ((:tag . "JJ") (:stem . "english") (:form . "English") (:end . 115)\n  (:start . 108) (:id . 65))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 121)\n  (:start . 116) (:id . 66))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 132)\n  (:start . 122) (:id . 67))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 137) (:start . 133)\n  (:id . 68))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 144)\n  (:start . 138) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 70))\n ((:tag . "NN") (:stem . "biology") (:form . "biology") (:end . 156)\n  (:start . 149) (:id . 71))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 163)\n  (:start . 157) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 169) (:start . 168)\n  (:id . 74))\n ((:tag . "LS") (:stem . "3") (:form . "3") (:end . 170) (:start . 169)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 171) (:start . 170)\n  (:id . 76))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 178)\n  (:start . 172) (:id . 77))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 184)\n  (:start . 179) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "gather") (:form . "gathered") (:end . 194)\n  (:start . 186) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 196) (:start . 195)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 199) (:start . 196)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "interlink") (:form . "interlinked") (:end . 211)\n  (:start . 200) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 212) (:start . 211)\n  (:id . 84))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 217) (:start . 213)\n  (:id . 85))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 222) (:start . 218)\n  (:id . 86))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 231)\n  (:start . 223) (:id . 87))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 241)\n  (:start . 232) (:id . 88))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 245) (:start . 242)\n  (:id . 89))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 253)\n  (:start . 246) (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 257) (:start . 254)\n  (:id . 91))\n ((:tag . "NN") (:stem . "application") (:form . "application") (:end . 269)\n  (:start . 258) (:id . 92))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 272) (:start . 270)\n  (:id . 93))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 277) (:start . 273)\n  (:id . 94))\n ((:tag . "NN") (:stem . "mining") (:form . "mining") (:end . 284)\n  (:start . 278) (:id . 95))\n ((:tag . "NNS") (:stem . "technique") (:form . "techniques") (:end . 295)\n  (:start . 285) (:id . 96))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 296) (:start . 295)\n  (:id . 97)))@@@1@56@((:identifiers (:sid . :s12.92) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503895@unknown@formal@none@1@S@Initial machine learning experiments using the GREC [45] suggest that it can be used to train IE components with reasonably good performance, with both named entity extraction and semantic role labelling having achieved F-scores of around 60%, based on 10-fold cross validation.@(((:tag . "JJ") (:stem . "initial") (:form . "Initial") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "machine") (:form . "machine") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 24)\n  (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 36)\n  (:start . 25) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 42) (:start . 37)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 53) (:start . 52)\n  (:id . 49))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 64)\n  (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "VB") (:stem . "train") (:form . "train") (:end . 93) (:start . 88)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "ie") (:form . "IE") (:end . 96) (:start . 94)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 107)\n  (:start . 97) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 112) (:start . 108)\n  (:id . 62))\n ((:tag . "RB") (:stem . "reasonably") (:form . "reasonably") (:end . 123)\n  (:start . 113) (:id . 63))\n ((:tag . "JJ") (:stem . "good") (:form . "good") (:end . 128) (:start . 124)\n  (:id . 64))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 140)\n  (:start . 129) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 146) (:start . 142)\n  (:id . 67))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 151) (:start . 147)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "name") (:form . "named") (:end . 157)\n  (:start . 152) (:id . 69))\n ((:tag . "NN") (:stem . "entity") (:form . "entity") (:end . 164)\n  (:start . 158) (:id . 70))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 175)\n  (:start . 165) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 188)\n  (:start . 180) (:id . 73))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 193) (:start . 189)\n  (:id . 74))\n ((:tag . "NN") (:stem . "labelling") (:form . "labelling") (:end . 203)\n  (:start . 194) (:id . 75))\n ((:tag . "VBG") (:stem . "have") (:form . "having") (:end . 210)\n  (:start . 204) (:id . 76))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 219)\n  (:start . 211) (:id . 77))\n ((:tag . "NNS") (:stem . "f-score") (:form . "F-scores") (:end . 228)\n  (:start . 220) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 231) (:start . 229)\n  (:id . 79))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 238)\n  (:start . 232) (:id . 80))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 241) (:start . 239)\n  (:id . 81))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 242) (:start . 241)\n  (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 243) (:start . 242)\n  (:id . 83))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 249)\n  (:start . 244) (:id . 84))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 252) (:start . 250)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "10-fold") (:form . "10-fold") (:end . 260)\n  (:start . 253) (:id . 86))\n ((:tag . "NN") (:stem . "cross") (:form . "cross") (:end . 266)\n  (:start . 261) (:id . 87))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 277)\n  (:start . 267) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 278) (:start . 277)\n  (:id . 89)))@@@1@48@((:hcues ((:id . :x12.93.1) (:span 73 76)) ((:id . :x12.93.2) (:span 57 64)))\n (:hscopes ((:id . :x12.93.1) (:span 70 277))\n  ((:id . :x12.93.2) (:span 57 277)))\n (:identifiers (:sid . :s12.93) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503896@unknown@formal@none@1@S@A further direction of research which could help to improve the performance of IE systems trained on the GREC is introduced in [46], in which it is demonstrated that, due to the differing perspectives of different annotation schemes, it is not always the case that larger corpora contain the most useful information.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "direction") (:form . "direction") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 59)\n  (:start . 52) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 75)\n  (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "ie") (:form . "IE") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "VBN") (:stem . "train") (:form . "trained") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 112) (:start . 110)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "introduce") (:form . "introduced") (:end . 123)\n  (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 126) (:start . 124)\n  (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 130) (:start . 128)\n  (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 131) (:start . 130)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 68))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 141)\n  (:start . 136) (:id . 69))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 144) (:start . 142)\n  (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 147) (:start . 145)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "demonstrate") (:form . "demonstrated") (:end . 160)\n  (:start . 148) (:id . 72))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 165) (:start . 161)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 74))\n ((:tag . "IN") (:stem . "due") (:form . "due") (:end . 170) (:start . 167)\n  (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 173) (:start . 171)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 77))\n ((:tag . "VBG") (:stem . "differ") (:form . "differing") (:end . 187)\n  (:start . 178) (:id . 78))\n ((:tag . "NNS") (:stem . "perspective") (:form . "perspectives") (:end . 200)\n  (:start . 188) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 203) (:start . 201)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 213)\n  (:start . 204) (:id . 81))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 224)\n  (:start . 214) (:id . 82))\n ((:tag . "NNS") (:stem . "scheme") (:form . "schemes") (:end . 232)\n  (:start . 225) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 233) (:start . 232)\n  (:id . 84))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 236) (:start . 234)\n  (:id . 85))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 239) (:start . 237)\n  (:id . 86))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 243) (:start . 240)\n  (:id . 87))\n ((:tag . "RB") (:stem . "always") (:form . "always") (:end . 250)\n  (:start . 244) (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 254) (:start . 251)\n  (:id . 89))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 259) (:start . 255)\n  (:id . 90))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 264) (:start . 260)\n  (:id . 91))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 271)\n  (:start . 265) (:id . 92))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 279)\n  (:start . 272) (:id . 93))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 287)\n  (:start . 280) (:id . 94))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 291) (:start . 288)\n  (:id . 95))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 296) (:start . 292)\n  (:id . 96))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 303)\n  (:start . 297) (:id . 97))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 315)\n  (:start . 304) (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 316) (:start . 315)\n  (:id . 99)))@@@1@58@((:hcues ((:id . :x12.94.1) (:span 38 43)))\n (:hscopes ((:id . :x12.94.1) (:span 38 109)))\n (:identifiers (:sid . :s12.94) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503897@unknown@formal@none@1@S@The reported study found that, whilst small corpora may not be large enough to train IE systems in their own right, augmenting such corpora with training instances derived from other corpora can help to improve the performance of the trained system.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "find") (:form . "found") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "IN") (:stem . "whilst") (:form . "whilst") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 51)\n  (:start . 44) (:id . 50))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "RB") (:stem . "enough") (:form . "enough") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "VB") (:stem . "train") (:form . "train") (:end . 84) (:start . 79)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "ie") (:form . "IE") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 95)\n  (:start . 88) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 104)\n  (:start . 99) (:id . 61))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 108) (:start . 105)\n  (:id . 62))\n ((:tag . "NN") (:stem . "right") (:form . "right") (:end . 114)\n  (:start . 109) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "augment") (:form . "augmenting") (:end . 126)\n  (:start . 116) (:id . 65))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 131) (:start . 127)\n  (:id . 66))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 139)\n  (:start . 132) (:id . 67))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 144) (:start . 140)\n  (:id . 68))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 153)\n  (:start . 145) (:id . 69))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 163)\n  (:start . 154) (:id . 70))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 171)\n  (:start . 164) (:id . 71))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 176) (:start . 172)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 182)\n  (:start . 177) (:id . 73))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 190)\n  (:start . 183) (:id . 74))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 194) (:start . 191)\n  (:id . 75))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 199) (:start . 195)\n  (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 202) (:start . 200)\n  (:id . 77))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 210)\n  (:start . 203) (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 214) (:start . 211)\n  (:id . 79))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 226)\n  (:start . 215) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 229) (:start . 227)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 233) (:start . 230)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "trained") (:form . "trained") (:end . 241)\n  (:start . 234) (:id . 83))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 248)\n  (:start . 242) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 249) (:start . 248)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x12.95.1) (:span 191 194)) ((:id . :x12.95.2) (:span 52 55)))\n (:hscopes ((:id . :x12.95.1) (:span 191 248))\n  ((:id . :x12.95.2) (:span 52 114)))\n (:identifiers (:sid . :s12.95) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503898@unknown@formal@none@1@S@This provides convincing evidence that combining smaller, richly annotated corpora, such as our own, with larger corpora which are slightly poorer in information content, could provide a future direction of research for training more accurate biomedical IE systems.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBG") (:stem . "convince") (:form . "convincing") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "combine") (:form . "combining") (:end . 48)\n  (:start . 39) (:id . 47))\n ((:tag . "JJR") (:stem . "small") (:form . "smaller") (:end . 56)\n  (:start . 49) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 49))\n ((:tag . "RB") (:stem . "richly") (:form . "richly") (:end . 64)\n  (:start . 58) (:id . 50))\n ((:tag . "VBD") (:stem . "annotate") (:form . "annotated") (:end . 74)\n  (:start . 65) (:id . 51))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 82)\n  (:start . 75) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 88) (:start . 84)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 95) (:start . 92)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 99) (:start . 96)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 112)\n  (:start . 106) (:id . 60))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 120)\n  (:start . 113) (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 126)\n  (:start . 121) (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 139)\n  (:start . 131) (:id . 64))\n ((:tag . "JJR") (:stem . "poor") (:form . "poorer") (:end . 146)\n  (:start . 140) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 66))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 161)\n  (:start . 150) (:id . 67))\n ((:tag . "NN") (:stem . "content") (:form . "content") (:end . 169)\n  (:start . 162) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 170) (:start . 169)\n  (:id . 69))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 176)\n  (:start . 171) (:id . 70))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 184)\n  (:start . 177) (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 186) (:start . 185)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "future") (:form . "future") (:end . 193)\n  (:start . 187) (:id . 73))\n ((:tag . "NN") (:stem . "direction") (:form . "direction") (:end . 203)\n  (:start . 194) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 206) (:start . 204)\n  (:id . 75))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 215)\n  (:start . 207) (:id . 76))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 219) (:start . 216)\n  (:id . 77))\n ((:tag . "VBG") (:stem . "train") (:form . "training") (:end . 228)\n  (:start . 220) (:id . 78))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 233) (:start . 229)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "accurate") (:form . "accurate") (:end . 242)\n  (:start . 234) (:id . 80))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 253)\n  (:start . 243) (:id . 81))\n ((:tag . "NN") (:stem . "ie") (:form . "IE") (:end . 256) (:start . 254)\n  (:id . 82))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 264)\n  (:start . 257) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x12.96.1) (:span 171 176)))\n (:hscopes ((:id . :x12.96.1) (:span 171 264)))\n (:identifiers (:sid . :s12.96) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503899@unknown@formal@none@1@S@This idea is especially attractive, given that the production of large, richly annotated corpora can be very time consuming.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "RB") (:stem . "especially") (:form . "especially") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "JJ") (:stem . "attractive") (:form . "attractive") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 61)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 70) (:start . 65)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "RB") (:stem . "richly") (:form . "richly") (:end . 78)\n  (:start . 72) (:id . 55))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 88)\n  (:start . 79) (:id . 56))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 96)\n  (:start . 89) (:id . 57))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 103) (:start . 101)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "very") (:form . "very") (:end . 108) (:start . 104)\n  (:id . 60))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "NN") (:stem . "consuming") (:form . "consuming") (:end . 123)\n  (:start . 114) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x12.97.1) (:span 97 100)))\n (:hscopes ((:id . :x12.97.1) (:span 97 123)))\n (:identifiers (:sid . :s12.97) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503900@unknown@formal@none@1@S@In the remainder of this paper, we firstly cover the key aspects of our annotation scheme, followed by a description of the recruitment and training of annotators.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "remainder") (:form . "remainder") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "paper") (:form . "paper") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "RB") (:stem . "firstly") (:form . "firstly") (:end . 42)\n  (:start . 35) (:id . 50))\n ((:tag . "VBP") (:stem . "cover") (:form . "cover") (:end . 48) (:start . 43)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "aspect") (:form . "aspects") (:end . 64)\n  (:start . 57) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 55))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 71) (:start . 68)\n  (:id . 56))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 82)\n  (:start . 72) (:id . 57))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 89)\n  (:start . 83) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 99)\n  (:start . 91) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 102) (:start . 100)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "NN") (:stem . "description") (:form . "description") (:end . 116)\n  (:start . 105) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 119) (:start . 117)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 65))\n ((:tag . "NN") (:stem . "recruitment") (:form . "recruitment") (:end . 135)\n  (:start . 124) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 67))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 148)\n  (:start . 140) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 162)\n  (:start . 152) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s12.98) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503901@unknown@formal@none@1@S@We follow this by providing detailed statistics, results and evaluation of the GREC, and finally present some conclusions and directions for further research.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "follow") (:form . "follow") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "provide") (:form . "providing") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 47)\n  (:start . 37) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 71)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "RB") (:stem . "finally") (:form . "finally") (:end . 96)\n  (:start . 89) (:id . 58))\n ((:tag . "VBP") (:stem . "present") (:form . "present") (:end . 104)\n  (:start . 97) (:id . 59))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "conclusion") (:form . "conclusions") (:end . 121)\n  (:start . 110) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "direction") (:form . "directions") (:end . 136)\n  (:start . 126) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 140) (:start . 137)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 148)\n  (:start . 141) (:id . 65))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 157)\n  (:start . 149) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s12.99) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503902@unknown@formal@none@1@S@Methods@(((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s12.100) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5503903@unknown@formal@none@1@S@This section is concerned with the preparatory work required prior to the annotation of the GREC.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "concern") (:form . "concerned") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "preparatory") (:form . "preparatory") (:end . 46)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 51) (:start . 47)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "require") (:form . "required") (:end . 60)\n  (:start . 52) (:id . 50))\n ((:tag . "RB") (:stem . "prior") (:form . "prior") (:end . 66) (:start . 61)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 84)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.101) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503904@unknown@formal@none@1@S@Beginning with a clarification of our notion of an event, we then provide a description of the key features of our annotation scheme.@(((:tag . "VBG") (:stem . "begin") (:form . "Beginning") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "clarification") (:form . "clarification")\n  (:end . 30) (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 73)\n  (:start . 66) (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 75) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "description") (:form . "description") (:end . 87)\n  (:start . 76) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 98) (:start . 95)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 107)\n  (:start . 99) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 114) (:start . 111)\n  (:id . 63))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 125)\n  (:start . 115) (:id . 64))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 132)\n  (:start . 126) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s12.102) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503905@unknown@formal@none@1@S@A brief overview of the annotation software used and of its customisation is followed by details regarding the annotators and their training.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "brief") (:form . "brief") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "overview") (:form . "overview") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 34)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "NN") (:stem . "customisation") (:form . "customisation")\n  (:end . 73) (:start . 60) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 85)\n  (:start . 77) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 96)\n  (:start . 89) (:id . 57))\n ((:tag . "VBG") (:stem . "regard") (:form . "regarding") (:end . 106)\n  (:start . 97) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 121)\n  (:start . 111) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 131)\n  (:start . 126) (:id . 62))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 140)\n  (:start . 132) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s12.103) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503906@unknown@formal@none@1@S@As performance during training was measured quantitively through the calculation of inter-annotator agreement (IAA) scores following each cycle of training, we provide details and motivation for our chosen evaluation metric, the F-measure.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "RB") (:stem . "quantitively") (:form . "quantitively") (:end . 56)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 64)\n  (:start . 57) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 50))\n ((:tag . "NN") (:stem . "calculation") (:form . "calculation") (:end . 80)\n  (:start . 69) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 52))\n ((:tag . "NN") (:stem . "inter-annotator") (:form . "inter-annotator")\n  (:end . 99) (:start . 84) (:id . 53))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 109)\n  (:start . 100) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "IAA") (:form . "IAA") (:end . 114) (:start . 111)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 122)\n  (:start . 116) (:id . 58))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 132)\n  (:start . 123) (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 137) (:start . 133)\n  (:id . 60))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 143)\n  (:start . 138) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 146) (:start . 144)\n  (:id . 62))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 155)\n  (:start . 147) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 64))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 159) (:start . 157)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 167)\n  (:start . 160) (:id . 66))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 175)\n  (:start . 168) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n  (:id . 68))\n ((:tag . "NN") (:stem . "motivation") (:form . "motivation") (:end . 190)\n  (:start . 180) (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 194) (:start . 191)\n  (:id . 70))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 198) (:start . 195)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 205)\n  (:start . 199) (:id . 72))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 216)\n  (:start . 206) (:id . 73))\n ((:tag . "JJ") (:stem . "metric") (:form . "metric") (:end . 223)\n  (:start . 217) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 224) (:start . 223)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 228) (:start . 225)\n  (:id . 76))\n ((:tag . "NN") (:stem . "f-measure") (:form . "F-measure") (:end . 238)\n  (:start . 229) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s12.104) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503907@unknown@formal@none@1@S@Finally, we provide an analysis of the IAA results attained during training.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "IAA") (:form . "IAA") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 50)\n  (:start . 43) (:id . 51))\n ((:tag . "VBN") (:stem . "attain") (:form . "attained") (:end . 59)\n  (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 75)\n  (:start . 67) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s12.105) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503908@unknown@formal@none@1@S@Events in biomedical texts@(((:tag . "NNS") (:stem . "event") (:form . "Events") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 26) (:start . 21)\n  (:id . 45)))@@@1@4@((:identifiers (:sid . :s12.106) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503909@unknown@formal@none@1@S@In this section, we clarify our notion of an event.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "clarify") (:form . "clarify") (:end . 27)\n  (:start . 20) (:id . 47))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 38)\n  (:start . 32) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 50) (:start . 45)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 51) (:start . 50)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s12.107) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503910@unknown@formal@none@1@S@Firstly, we provide some simple examples of event instances that relate to gene regulation and expression within biomedical texts:@(((:tag . "RB") (:stem . "firstly") (:form . "Firstly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "simple") (:form . "simple") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 59)\n  (:start . 50) (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "relate") (:form . "relate") (:end . 71)\n  (:start . 65) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 90)\n  (:start . 80) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 57))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 105)\n  (:start . 95) (:id . 58))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 112)\n  (:start . 106) (:id . 59))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 123)\n  (:start . 113) (:id . 60))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 129)\n  (:start . 124) (:id . 61))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 130) (:start . 129)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.108) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503911@unknown@formal@none@1@S@1) In Escherichia Coli, glnAP2 may be activated by NifA.@(((:tag . "LS") (:stem . "1") (:form . "1") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "In") (:end . 5) (:start . 3)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Escherichia") (:form . "Escherichia") (:end . 17)\n  (:start . 6) (:id . 45))\n ((:tag . "NNP") (:stem . "Coli") (:form . "Coli") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "glnap2") (:form . "glnAP2") (:end . 30)\n  (:start . 24) (:id . 48))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 34) (:start . 31)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 37) (:start . 35)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 47)\n  (:start . 38) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "NifA") (:form . "NifA") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 54)))@@@1@13@((:hcues ((:id . :x12.109.1) (:span 31 34)))\n (:hscopes ((:id . :x12.109.1) (:span 24 55)))\n (:identifiers (:sid . :s12.109) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503912@unknown@formal@none@1@S@2) Our results show that glnA encodes glutamine synthetase.@(((:tag . "LS") (:stem . "2") (:form . "2") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 6) (:start . 3)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 14)\n  (:start . 7) (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 47))\n ((:tag . "NN") (:stem . "glna") (:form . "glnA") (:end . 29) (:start . 25)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "encode") (:form . "encodes") (:end . 37)\n  (:start . 30) (:id . 49))\n ((:tag . "NN") (:stem . "glutamine") (:form . "glutamine") (:end . 47)\n  (:start . 38) (:id . 50))\n ((:tag . "NN") (:stem . "synthetase") (:form . "synthetase") (:end . 58)\n  (:start . 48) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s12.110) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503913@unknown@formal@none@1@S@For each event, two types of information may be specified in the text, both of which are important to its correct interpretation:@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 25) (:start . 20)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 40)\n  (:start . 29) (:id . 49))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 57)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 69) (:start . 65)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 75) (:start . 71)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 84) (:start . 79)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 88) (:start . 85)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 98)\n  (:start . 89) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 105) (:start . 102)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "correct") (:form . "correct") (:end . 113)\n  (:start . 106) (:id . 64))\n ((:tag . "NN") (:stem . "interpretation") (:form . "interpretation")\n  (:end . 128) (:start . 114) (:id . 65))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 129) (:start . 128)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x12.111.1) (:span 41 44)))\n (:hscopes ((:id . :x12.111.1) (:span 16 69)))\n (:identifiers (:sid . :s12.111) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503914@unknown@formal@none@1@S@• The participants (or arguments) of the event.@(((:tag . "PDT") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 5) (:start . 2)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "participant") (:form . "participants") (:end . 18)\n  (:start . 6) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 32)\n  (:start . 23) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 46) (:start . 41)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s12.112) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503915@unknown@formal@none@1@S@In sentence 1), there are 3 arguments specified by the verb activated, i.e., In Escherichia Coli, glnAP2 and NifA.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 21) (:start . 16)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 25) (:start . 22)\n  (:id . 48))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 27) (:start . 26)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 37)\n  (:start . 28) (:id . 50))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 47)\n  (:start . 38) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 53))\n ((:tag . "NN") (:stem . "verb") (:form . "verb") (:end . 59) (:start . 55)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "activate") (:form . "activated") (:end . 69)\n  (:start . 60) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 75) (:start . 71)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "In") (:end . 79) (:start . 77)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Escherichia") (:form . "Escherichia") (:end . 91)\n  (:start . 80) (:id . 60))\n ((:tag . "NNP") (:stem . "Coli") (:form . "Coli") (:end . 96) (:start . 92)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 62))\n ((:tag . "NN") (:stem . "glnap2") (:form . "glnAP2") (:end . 104)\n  (:start . 98) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "NifA") (:form . "NifA") (:end . 113) (:start . 109)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s12.113) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503916@unknown@formal@none@1@S@• Higher level information (called modality) about how the event should be interpreted.@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJR") (:stem . "high") (:form . "Higher") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 34) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "modality") (:form . "modality") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 64) (:start . 59)\n  (:id . 53))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 71)\n  (:start . 65) (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "interpret") (:form . "interpreted") (:end . 86)\n  (:start . 75) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x12.114.1) (:span 65 71)))\n (:hscopes ((:id . :x12.114.1) (:span 51 86)))\n (:identifiers (:sid . :s12.114) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503917@unknown@formal@none@1@S@For example, the word may in sentence 1) indicates that there is some uncertainty about the truth of the event, whilst the phrase Our results show that in 2) indicates that there is experimental evidence to back up the event described by encodes.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "word") (:form . "word") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 37)\n  (:start . 29) (:id . 49))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 39) (:start . 38)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 40) (:start . 39)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 50)\n  (:start . 41) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 61) (:start . 56)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 64) (:start . 62)\n  (:id . 55))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 69) (:start . 65)\n  (:id . 56))\n ((:tag . "NN") (:stem . "uncertainty") (:form . "uncertainty") (:end . 81)\n  (:start . 70) (:id . 57))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 87) (:start . 82)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "truth") (:form . "truth") (:end . 97) (:start . 92)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 62))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 110)\n  (:start . 105) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 64))\n ((:tag . "IN") (:stem . "whilst") (:form . "whilst") (:end . 118)\n  (:start . 112) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 66))\n ((:tag . "NN") (:stem . "phrase") (:form . "phrase") (:end . 129)\n  (:start . 123) (:id . 67))\n ((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 133) (:start . 130)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 141)\n  (:start . 134) (:id . 69))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 146) (:start . 142)\n  (:id . 70))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 151) (:start . 147)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n  (:id . 72))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 156) (:start . 155)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 74))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 167)\n  (:start . 158) (:id . 75))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 172) (:start . 168)\n  (:id . 76))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 178)\n  (:start . 173) (:id . 77))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 181) (:start . 179)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 194)\n  (:start . 182) (:id . 79))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 203)\n  (:start . 195) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 206) (:start . 204)\n  (:id . 81))\n ((:tag . "VB") (:stem . "back") (:form . "back") (:end . 211) (:start . 207)\n  (:id . 82))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 214) (:start . 212)\n  (:id . 83))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 218) (:start . 215)\n  (:id . 84))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 224)\n  (:start . 219) (:id . 85))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 234)\n  (:start . 225) (:id . 86))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 237) (:start . 235)\n  (:id . 87))\n ((:tag . "NNS") (:stem . "encode") (:form . "encodes") (:end . 245)\n  (:start . 238) (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s12.115) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503918@unknown@formal@none@1@S@Several recent articles (e.g., [47-51]) have reported on attempts to annotate information such as certainty, evidence or negation within biomedical texts.@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "article") (:form . "articles") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 45))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "CD") (:stem . "47-51") (:form . "47-51") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 39) (:start . 38)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 44) (:start . 40)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 53)\n  (:start . 45) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 56) (:start . 54)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "attempt") (:form . "attempts") (:end . 65)\n  (:start . 57) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 56))\n ((:tag . "VB") (:stem . "annotate") (:form . "annotate") (:end . 77)\n  (:start . 69) (:id . 57))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 89)\n  (:start . 78) (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 94) (:start . 90)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 97) (:start . 95)\n  (:id . 60))\n ((:tag . "NN") (:stem . "certainty") (:form . "certainty") (:end . 107)\n  (:start . 98) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 62))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 117)\n  (:start . 109) (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 120) (:start . 118)\n  (:id . 64))\n ((:tag . "NN") (:stem . "negation") (:form . "negation") (:end . 129)\n  (:start . 121) (:id . 65))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 136)\n  (:start . 130) (:id . 66))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 147)\n  (:start . 137) (:id . 67))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 153)\n  (:start . 148) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.116) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503919@unknown@formal@none@1@S@Our current work concerns the first of these information types.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "concern") (:form . "concerns") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 56)\n  (:start . 45) (:id . 50))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 62) (:start . 57)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s12.117) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503920@unknown@formal@none@1@S@Specifically, the annotation task consists of the following, in sequence:@(((:tag . "RB") (:stem . "specifically") (:form . "Specifically") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "following") (:form . "following") (:end . 59)\n  (:start . 50) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 73) (:start . 72)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.118) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503921@unknown@formal@none@1@S@a) Identifying relevant instances of events that relate to gene regulation and expression.@(((:tag . "DT") (:stem . "a") (:form . "a") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "VBG") (:stem . "identify") (:form . "Identifying") (:end . 14)\n  (:start . 3) (:id . 44))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "relate") (:form . "relate") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 74)\n  (:start . 64) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 89)\n  (:start . 79) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.119) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503922@unknown@formal@none@1@S@b) Identifying all arguments of the event that are specified within the same sentence.@(((:tag . "NN") (:stem . "b") (:form . "b") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "VBG") (:stem . "identify") (:form . "Identifying") (:end . 14)\n  (:start . 3) (:id . 44))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 60)\n  (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 67)\n  (:start . 61) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 85)\n  (:start . 77) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s12.120) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503923@unknown@formal@none@1@S@c) Finally, assigning semantic roles and biological concepts to these arguments.@(((:tag . "NN") (:stem . "c") (:form . "c") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 10)\n  (:start . 3) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "assign") (:form . "assigning") (:end . 21)\n  (:start . 12) (:id . 46))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 51)\n  (:start . 41) (:id . 50))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 60)\n  (:start . 52) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 79)\n  (:start . 70) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s12.121) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503924@unknown@formal@none@1@S@Table 1 illustrates the type of information that would be annotated for sentences 1) and 2) above.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "illustrate") (:form . "illustrates") (:end . 19)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 43)\n  (:start . 32) (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 67)\n  (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "sentence") (:form . "sentences") (:end . 81)\n  (:start . 72) (:id . 54))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 97) (:start . 92)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s12.122) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503925@unknown@formal@none@1@S@Example annotation output@(((:tag . "NN") (:stem . "example") (:form . "Example") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 25)\n  (:start . 19) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.123) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5503926@unknown@formal@none@1@S@Annotation scheme@(((:tag . "NNP") (:stem . "Annotation") (:form . "Annotation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 17)\n  (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s12.124) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503927@unknown@formal@none@1@S@In this section, we outline some key aspects of the annotation scheme.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "outline") (:form . "outline") (:end . 27)\n  (:start . 20) (:id . 47))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "aspect") (:form . "aspects") (:end . 44)\n  (:start . 37) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 62)\n  (:start . 52) (:id . 53))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 69)\n  (:start . 63) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s12.125) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503928@unknown@formal@none@1@S@Firstly, we describe the types of events on which the annotation is focussed, i.e., gene regulation and expression.@(((:tag . "RB") (:stem . "firstly") (:form . "Firstly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 40)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 43) (:start . 41)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 49) (:start . 44)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 64)\n  (:start . 54) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "focusse") (:form . "focussed") (:end . 76)\n  (:start . 68) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 82) (:start . 78)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 58))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 88) (:start . 84)\n  (:id . 59))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 99)\n  (:start . 89) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 61))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 114)\n  (:start . 104) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s12.126) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503929@unknown@formal@none@1@S@This is followed by a more detailed description of the semantic roles and biological concepts assigned to event arguments.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 35)\n  (:start . 27) (:id . 48))\n ((:tag . "NN") (:stem . "description") (:form . "description") (:end . 47)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 84)\n  (:start . 74) (:id . 55))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 93)\n  (:start . 85) (:id . 56))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 102)\n  (:start . 94) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n  (:id . 58))\n ((:tag . "VB") (:stem . "event") (:form . "event") (:end . 111)\n  (:start . 106) (:id . 59))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 121)\n  (:start . 112) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s12.127) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503930@unknown@formal@none@1@S@Finally, we provide an account of some of the steps taken to ensure the consistency of annotated text spans.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "account") (:form . "account") (:end . 30)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 51) (:start . 46)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 57) (:start . 52)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 54))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 67)\n  (:start . 61) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 56))\n ((:tag . "NN") (:stem . "consistency") (:form . "consistency") (:end . 83)\n  (:start . 72) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 96)\n  (:start . 87) (:id . 59))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 101) (:start . 97)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "span") (:form . "spans") (:end . 107)\n  (:start . 102) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.128) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503931@unknown@formal@none@1@S@To accompany the annotation scheme, we have produced a detailed set of annotation guidelines, as these are necessary to aid in the achievement of high quality annotations [52-54].@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "accompany") (:form . "accompany") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 52)\n  (:start . 44) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 81)\n  (:start . 71) (:id . 55))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 92)\n  (:start . 82) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 102) (:start . 97)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 116)\n  (:start . 107) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 119) (:start . 117)\n  (:id . 62))\n ((:tag . "VB") (:stem . "aid") (:form . "aid") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 126) (:start . 124)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 65))\n ((:tag . "NN") (:stem . "achievement") (:form . "achievement") (:end . 142)\n  (:start . 131) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 150) (:start . 146)\n  (:id . 68))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 158)\n  (:start . 151) (:id . 69))\n ((:tag . "NNS") (:stem . "annotation") (:form . "annotations") (:end . 170)\n  (:start . 159) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 172) (:start . 171)\n  (:id . 71))\n ((:tag . "CD") (:stem . "52-54") (:form . "52-54") (:end . 177)\n  (:start . 172) (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 178) (:start . 177)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s12.129) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503932@unknown@formal@none@1@S@The structure and content of these guidelines were iteratively refined in discussion with domain experts and with annotators (via group discussion sessions following annotation training phrases and full annotation cycles).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "content") (:form . "content") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 45)\n  (:start . 35) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "RB") (:stem . "iteratively") (:form . "iteratively") (:end . 62)\n  (:start . 51) (:id . 50))\n ((:tag . "VBN") (:stem . "refine") (:form . "refined") (:end . 70)\n  (:start . 63) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 52))\n ((:tag . "NN") (:stem . "discussion") (:form . "discussion") (:end . 84)\n  (:start . 74) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 89) (:start . 85)\n  (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 96)\n  (:start . 90) (:id . 55))\n ((:tag . "NNS") (:stem . "expert") (:form . "experts") (:end . 104)\n  (:start . 97) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 113) (:start . 109)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 124)\n  (:start . 114) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 60))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 129) (:start . 126)\n  (:id . 61))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 135)\n  (:start . 130) (:id . 62))\n ((:tag . "NN") (:stem . "discussion") (:form . "discussion") (:end . 146)\n  (:start . 136) (:id . 63))\n ((:tag . "NNS") (:stem . "session") (:form . "sessions") (:end . 155)\n  (:start . 147) (:id . 64))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 165)\n  (:start . 156) (:id . 65))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 176)\n  (:start . 166) (:id . 66))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 185)\n  (:start . 177) (:id . 67))\n ((:tag . "NNS") (:stem . "phrase") (:form . "phrases") (:end . 193)\n  (:start . 186) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 197) (:start . 194)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 202) (:start . 198)\n  (:id . 70))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 213)\n  (:start . 203) (:id . 71))\n ((:tag . "NNS") (:stem . "cycle") (:form . "cycles") (:end . 220)\n  (:start . 214) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s12.130) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503933@unknown@formal@none@1@S@The guidelines are available to download from http://www.nactem.ac.uk/GREC/, and are also available in Additional file 1.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "VB") (:stem . "download") (:form . "download") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "CD") (:stem . "http://www.nactem.ac.uk/GREC/")\n  (:form . "http://www.nactem.ac.uk/GREC/") (:end . 75) (:start . 46)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 84) (:start . 81)\n  (:id . 52))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 89) (:start . 85)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 99)\n  (:start . 90) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 113)\n  (:start . 103) (:id . 56))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 118) (:start . 114)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 120) (:start . 119)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s12.131) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503934@unknown@formal@none@1@S@Gene regulation and expression events@(((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 37)\n  (:start . 31) (:id . 46)))@@@1@5@((:identifiers (:sid . :s12.132) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503935@unknown@formal@none@1@S@The current annotation effort is concerned with events relating only to gene regulation or expression, i.e., events that describe any interaction which leads, either directly or indirectly, to the production of a protein.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "effort") (:form . "effort") (:end . 29)\n  (:start . 23) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "concern") (:form . "concerned") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 54)\n  (:start . 48) (:id . 49))\n ((:tag . "VBG") (:stem . "relate") (:form . "relating") (:end . 63)\n  (:start . 55) (:id . 50))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 87)\n  (:start . 77) (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 90) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 101)\n  (:start . 91) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 57))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 107) (:start . 103)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 115)\n  (:start . 109) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 120) (:start . 116)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 129)\n  (:start . 121) (:id . 62))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 133) (:start . 130)\n  (:id . 63))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 145)\n  (:start . 134) (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 151)\n  (:start . 146) (:id . 65))\n ((:tag . "VBZ") (:stem . "lead") (:form . "leads") (:end . 157)\n  (:start . 152) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 67))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 165)\n  (:start . 159) (:id . 68))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 174)\n  (:start . 166) (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 177) (:start . 175)\n  (:id . 70))\n ((:tag . "RB") (:stem . "indirectly") (:form . "indirectly") (:end . 188)\n  (:start . 178) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 192) (:start . 190)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 74))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 207)\n  (:start . 197) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 210) (:start . 208)\n  (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 212) (:start . 211)\n  (:id . 77))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 220)\n  (:start . 213) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 221) (:start . 220)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x12.133.1) (:span 159 165 175 177)))\n (:hscopes ((:id . :x12.133.1) (:span 159 188)))\n (:identifiers (:sid . :s12.133) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503936@unknown@formal@none@1@S@Annotation is restricted to sentences that contain some mechanical description of transcription, translation or post-transcriptional modifications and/or their controls.@(((:tag . "NNP") (:stem . "Annotation") (:form . "Annotation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "restrict") (:form . "restricted") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "sentence") (:form . "sentences") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 55) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "mechanical") (:form . "mechanical") (:end . 66)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "description") (:form . "description") (:end . 78)\n  (:start . 67) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 52))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 95) (:start . 82) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 54))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 108)\n  (:start . 97) (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 111) (:start . 109)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "post-transcriptional")\n  (:form . "post-transcriptional") (:end . 132) (:start . 112) (:id . 57))\n ((:tag . "NNS") (:stem . "modification") (:form . "modifications")\n  (:end . 146) (:start . 133) (:id . 58))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 153)\n  (:start . 147) (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 159)\n  (:start . 154) (:id . 60))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 168)\n  (:start . 160) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.134) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503937@unknown@formal@none@1@S@Annotators were helped by (but not restricted to) a list of verbs which we created that potentially denote gene regulation and expression events.@(((:tag . "NNS") (:stem . "annotator") (:form . "Annotators") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "help") (:form . "helped") (:end . 22) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "restricted") (:form . "restricted") (:end . 45)\n  (:start . 35) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 56) (:start . 52)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 65) (:start . 60)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 71) (:start . 66)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 74) (:start . 72)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "create") (:form . "created") (:end . 82)\n  (:start . 75) (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 87) (:start . 83)\n  (:id . 59))\n ((:tag . "RB") (:stem . "potentially") (:form . "potentially") (:end . 99)\n  (:start . 88) (:id . 60))\n ((:tag . "VB") (:stem . "denote") (:form . "denote") (:end . 106)\n  (:start . 100) (:id . 61))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 111) (:start . 107)\n  (:id . 62))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 122)\n  (:start . 112) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 64))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 137)\n  (:start . 127) (:id . 65))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 144)\n  (:start . 138) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x12.135.1) (:span 88 99)))\n (:hscopes ((:id . :x12.135.1) (:span 88 144)))\n (:identifiers (:sid . :s12.135) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503938@unknown@formal@none@1@S@These are automatically highlighted by the annotation software, WordFreak (see Software section below), in each abstract to be annotated.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "automatically") (:form . "automatically")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 35)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 38) (:start . 36)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 53)\n  (:start . 43) (:id . 48))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 62)\n  (:start . 54) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "WordFreak") (:form . "WordFreak") (:end . 73)\n  (:start . 64) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Software") (:form . "Software") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 95)\n  (:start . 88) (:id . 55))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 101) (:start . 96)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 111) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "abstract") (:form . "abstract") (:end . 120)\n  (:start . 112) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 126) (:start . 124)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 136)\n  (:start . 127) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.136) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503939@unknown@formal@none@1@S@The basis of this list was a set of 229 hand-picked gene regulation verbs provided by the European Bioinformatics Institute (EMBL-EBI).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 32) (:start . 29)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 50))\n ((:tag . "CD") (:stem . "229") (:form . "229") (:end . 39) (:start . 36)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "hand-picked") (:form . "hand-picked") (:end . 51)\n  (:start . 40) (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 56) (:start . 52)\n  (:id . 53))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 67)\n  (:start . 57) (:id . 54))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 73) (:start . 68)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 82)\n  (:start . 74) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "European") (:form . "European") (:end . 98)\n  (:start . 90) (:id . 59))\n ((:tag . "NNP") (:stem . "Bioinformatics") (:form . "Bioinformatics")\n  (:end . 113) (:start . 99) (:id . 60))\n ((:tag . "NNP") (:stem . "Institute") (:form . "Institute") (:end . 123)\n  (:start . 114) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "EMBL-EBI") (:form . "EMBL-EBI") (:end . 133)\n  (:start . 125) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.137) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503940@unknown@formal@none@1@S@We augmented this list through the automatic extraction of further verbs from an E. coli corpus.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "augment") (:form . "augmented") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "automatic") (:form . "automatic") (:end . 44)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 55)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 83) (:start . 81)\n  (:id . 55))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 88) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 95)\n  (:start . 89) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.138) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503941@unknown@formal@none@1@S@This corpus contains approximately 33,000 MEDLINE abstracts and was also provided by EMBL-EBI.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 34) (:start . 21) (:id . 45))\n ((:tag . "CD") (:stem . "33,000") (:form . "33,000") (:end . 41)\n  (:start . 35) (:id . 46))\n ((:tag . "NNP") (:stem . "MEDLINE") (:form . "MEDLINE") (:end . 49)\n  (:start . 42) (:id . 47))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 59)\n  (:start . 50) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 67) (:start . 64)\n  (:id . 50))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 72) (:start . 68)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 81)\n  (:start . 73) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 84) (:start . 82)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "EMBL-EBI") (:form . "EMBL-EBI") (:end . 93)\n  (:start . 85) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s12.139) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503942@unknown@formal@none@1@S@The automatic extraction was carried out by identifying those verbs whose syntactic arguments corresponded either to terms identified by the TerMine tool (http://www.nactem.ac.uk/software/termine/)or biological named entities identified by the GENIA tagger [55].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "automatic") (:form . "automatic") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 55)\n  (:start . 44) (:id . 49))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 61) (:start . 56)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 67) (:start . 62)\n  (:id . 51))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 73) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "syntactic") (:form . "syntactic") (:end . 83)\n  (:start . 74) (:id . 53))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 93)\n  (:start . 84) (:id . 54))\n ((:tag . "VBD") (:stem . "correspond") (:form . "corresponded") (:end . 106)\n  (:start . 94) (:id . 55))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 113)\n  (:start . 107) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 116) (:start . 114)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 122)\n  (:start . 117) (:id . 58))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 133)\n  (:start . 123) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 136) (:start . 134)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "TerMine") (:form . "TerMine") (:end . 148)\n  (:start . 141) (:id . 62))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 153) (:start . 149)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "http://www.nactem.ac.uk/software/termine/)or")\n  (:form . "http://www.nactem.ac.uk/software/termine/)or") (:end . 199)\n  (:start . 155) (:id . 65))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 210)\n  (:start . 200) (:id . 66))\n ((:tag . "VBN") (:stem . "name") (:form . "named") (:end . 216)\n  (:start . 211) (:id . 67))\n ((:tag . "NNS") (:stem . "entity") (:form . "entities") (:end . 225)\n  (:start . 217) (:id . 68))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 236)\n  (:start . 226) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 239) (:start . 237)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 243) (:start . 240)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "GENIA") (:form . "GENIA") (:end . 249)\n  (:start . 244) (:id . 72))\n ((:tag . "NN") (:stem . "tagger") (:form . "tagger") (:end . 256)\n  (:start . 250) (:id . 73))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 258) (:start . 257)\n  (:id . 74))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 260) (:start . 258)\n  (:id . 75))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 261) (:start . 260)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 262) (:start . 261)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x12.140.1) (:span 107 113 197 199)))\n (:hscopes ((:id . :x12.140.1) (:span 107 256)))\n (:identifiers (:sid . :s12.140) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503943@unknown@formal@none@1@S@The complete list was subsequently reviewed for relevance by a biology expert, resulting in a list of 353 verbs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "RB") (:stem . "subsequently") (:form . "subsequently") (:end . 34)\n  (:start . 22) (:id . 46))\n ((:tag . "VBN") (:stem . "review") (:form . "reviewed") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 48))\n ((:tag . "NN") (:stem . "relevance") (:form . "relevance") (:end . 57)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "biology") (:form . "biology") (:end . 70)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "expert") (:form . "expert") (:end . 77)\n  (:start . 71) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 88)\n  (:start . 79) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "CD") (:stem . "353") (:form . "353") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 111)\n  (:start . 106) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.141) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503944@unknown@formal@none@1@S@Semantic roles@(((:tag . "JJ") (:stem . "semantic") (:form . "Semantic") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 14) (:start . 9)\n  (:id . 43)))@@@1@2@((:identifiers (:sid . :s12.142) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503945@unknown@formal@none@1@S@Starting with the generic semantic roles proposed for VerbNet [29] and PropBank [30], we examined a large number of relevant events within MEDLINE abstracts, in consultation with biologists.@(((:tag . "VBG") (:stem . "start") (:form . "Starting") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "generic") (:form . "generic") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 40) (:start . 35)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 49)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "VerbNet") (:form . "VerbNet") (:end . 61)\n  (:start . 54) (:id . 50))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "PropBank") (:form . "PropBank") (:end . 79)\n  (:start . 71) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 84) (:start . 83)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 88) (:start . 86)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 97)\n  (:start . 89) (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 105)\n  (:start . 100) (:id . 63))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 112)\n  (:start . 106) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 124)\n  (:start . 116) (:id . 66))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 131)\n  (:start . 125) (:id . 67))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 138)\n  (:start . 132) (:id . 68))\n ((:tag . "NNP") (:stem . "MEDLINE") (:form . "MEDLINE") (:end . 146)\n  (:start . 139) (:id . 69))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 156)\n  (:start . 147) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 160) (:start . 158)\n  (:id . 72))\n ((:tag . "NN") (:stem . "consultation") (:form . "consultation") (:end . 173)\n  (:start . 161) (:id . 73))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 178) (:start . 174)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "biologist") (:form . "biologists") (:end . 189)\n  (:start . 179) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s12.143) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503946@unknown@formal@none@1@S@We concluded that arguments of gene regulation and expression events may be characterised using a subset of these general language roles, with the addition of the domain-specific CONDITION role.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "conclude") (:form . "concluded") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 46)\n  (:start . 36) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 61)\n  (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 68)\n  (:start . 62) (:id . 51))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "characterise") (:form . "characterised")\n  (:end . 89) (:start . 76) (:id . 54))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 95) (:start . 90)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n  (:id . 56))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 104)\n  (:start . 98) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 113)\n  (:start . 108) (:id . 59))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 121)\n  (:start . 114) (:id . 60))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 130)\n  (:start . 122) (:id . 61))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 136)\n  (:start . 131) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 142) (:start . 138)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 65))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 155)\n  (:start . 147) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 158) (:start . 156)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "domain-specific") (:form . "domain-specific")\n  (:end . 178) (:start . 163) (:id . 69))\n ((:tag . "NN") (:stem . "condition") (:form . "CONDITION") (:end . 188)\n  (:start . 179) (:id . 70))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 193) (:start . 189)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x12.144.1) (:span 69 72)))\n (:hscopes ((:id . :x12.144.1) (:span 18 193)))\n (:identifiers (:sid . :s12.144) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503947@unknown@formal@none@1@S@In some cases, we changed the names of the roles used in other resources in an attempt to make them more easily understandable to biologist annotators.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "change") (:form . "changed") (:end . 25)\n  (:start . 18) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "name") (:form . "names") (:end . 35) (:start . 30)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 48) (:start . 43)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 53) (:start . 49)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 62) (:start . 57)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 72)\n  (:start . 63) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 75) (:start . 73)\n  (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 78) (:start . 76)\n  (:id . 58))\n ((:tag . "NN") (:stem . "attempt") (:form . "attempt") (:end . 86)\n  (:start . 79) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 60))\n ((:tag . "VB") (:stem . "make") (:form . "make") (:end . 94) (:start . 90)\n  (:id . 61))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 99) (:start . 95)\n  (:id . 62))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 104) (:start . 100)\n  (:id . 63))\n ((:tag . "RB") (:stem . "easily") (:form . "easily") (:end . 111)\n  (:start . 105) (:id . 64))\n ((:tag . "JJ") (:stem . "understandable") (:form . "understandable")\n  (:end . 126) (:start . 112) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 129) (:start . 127)\n  (:id . 66))\n ((:tag . "NN") (:stem . "biologist") (:form . "biologist") (:end . 139)\n  (:start . 130) (:id . 67))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 150)\n  (:start . 140) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.145) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503948@unknown@formal@none@1@S@From VerbNet, we have used the roles AGENT, THEME, INSTRUMENT, LOCATION, SOURCE and DESTINATION.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "VerbNet") (:form . "VerbNet") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 36) (:start . 31)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "AGENT") (:form . "AGENT") (:end . 42) (:start . 37)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "THEME") (:form . "THEME") (:end . 49) (:start . 44)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "INSTRUMENT") (:form . "INSTRUMENT") (:end . 61)\n  (:start . 51) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "LOCATION") (:form . "LOCATION") (:end . 71)\n  (:start . 63) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "SOURCE") (:form . "SOURCE") (:end . 79)\n  (:start . 73) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "DESTINATION") (:form . "DESTINATION") (:end . 95)\n  (:start . 84) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s12.146) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503949@unknown@formal@none@1@S@Our RATE and TEMPORAL roles are based on the VerbNet EXTENT and TIME roles, respectively.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "rate") (:form . "RATE") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "temporal") (:form . "TEMPORAL") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "VerbNet") (:form . "VerbNet") (:end . 52)\n  (:start . 45) (:id . 51))\n ((:tag . "NNP") (:stem . "EXTENT") (:form . "EXTENT") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "TIME") (:form . "TIME") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 74) (:start . 69)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 56))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 88)\n  (:start . 76) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.147) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503950@unknown@formal@none@1@S@MANNER and PURPOSE come from PropBank's set of general roles that are applicable to any verb.@(((:tag . "NN") (:stem . "manner") (:form . "MANNER") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "purpose") (:form . "PURPOSE") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "VBP") (:stem . "come") (:form . "come") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "PropBank") (:form . "PropBank") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 65) (:start . 61)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "applicable") (:form . "applicable") (:end . 80)\n  (:start . 70) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "NN") (:stem . "verb") (:form . "verb") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s12.148) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503951@unknown@formal@none@1@S@We also saw a need for a role similar to the VerbNet PREDICATE role, to deal with cases such as:@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "see") (:form . "saw") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "need") (:form . "need") (:end . 18) (:start . 14)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 48))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 29) (:start . 25)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 37)\n  (:start . 30) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "VerbNet") (:form . "VerbNet") (:end . 52)\n  (:start . 45) (:id . 53))\n ((:tag . "NNP") (:stem . "PREDICATE") (:form . "PREDICATE") (:end . 62)\n  (:start . 53) (:id . 54))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 67) (:start . 63)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 57))\n ((:tag . "VB") (:stem . "deal") (:form . "deal") (:end . 76) (:start . 72)\n  (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 81) (:start . 77)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 87) (:start . 82)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 92) (:start . 88)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 95) (:start . 93)\n  (:id . 62))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 96) (:start . 95)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s12.149) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503952@unknown@formal@none@1@S@The (cAMP)-cAMP receptor protein complex functions as an activator..., where an activator corresponds to the PREDICATE role of functions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "cAMP)-cAMP") (:form . "cAMP)-cAMP") (:end . 15)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "receptor") (:form . "receptor") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "VBZ") (:stem . "function") (:form . "functions") (:end . 50)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 53) (:start . 51)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "activator") (:form . "activator") (:end . 66)\n  (:start . 57) (:id . 51))\n ((:tag . ":") (:stem . "…") (:form . "…") (:end . 66) (:start . 66)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 76) (:start . 71)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "NN") (:stem . "activator") (:form . "activator") (:end . 89)\n  (:start . 80) (:id . 56))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 101)\n  (:start . 90) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "predicate") (:form . "PREDICATE") (:end . 118)\n  (:start . 109) (:id . 60))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 126) (:start . 124)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 136)\n  (:start . 127) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s12.150) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503953@unknown@formal@none@1@S@For our own purposes, we created 2 separate roles, DESCRIPTIVE-AGENT and DESCRIPTIVE-THEME, and extended the characterisation of these roles to apply not only to predicatives, but also to any argument which describes characteristics or behaviour of either the AGENT or the THEME of the event.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "purpose") (:form . "purposes") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "create") (:form . "created") (:end . 32)\n  (:start . 25) (:id . 48))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 43)\n  (:start . 35) (:id . 50))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 49) (:start . 44)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "DESCRIPTIVE-AGENT") (:form . "DESCRIPTIVE-AGENT")\n  (:end . 68) (:start . 51) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "DESCRIPTIVE-THEME") (:form . "DESCRIPTIVE-THEME")\n  (:end . 90) (:start . 73) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "extend") (:form . "extended") (:end . 104)\n  (:start . 96) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "NN") (:stem . "characterisation") (:form . "characterisation")\n  (:end . 125) (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 128) (:start . 126)\n  (:id . 61))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 134)\n  (:start . 129) (:id . 62))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 140)\n  (:start . 135) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n  (:id . 64))\n ((:tag . "VB") (:stem . "apply") (:form . "apply") (:end . 149)\n  (:start . 144) (:id . 65))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 153) (:start . 150)\n  (:id . 66))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 158) (:start . 154)\n  (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 161) (:start . 159)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "predicative") (:form . "predicatives") (:end . 174)\n  (:start . 162) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 70))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 179) (:start . 176)\n  (:id . 71))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 184) (:start . 180)\n  (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 187) (:start . 185)\n  (:id . 73))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 191) (:start . 188)\n  (:id . 74))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 200)\n  (:start . 192) (:id . 75))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 206)\n  (:start . 201) (:id . 76))\n ((:tag . "VBZ") (:stem . "describe") (:form . "describes") (:end . 216)\n  (:start . 207) (:id . 77))\n ((:tag . "NNS") (:stem . "characteristic") (:form . "characteristics")\n  (:end . 232) (:start . 217) (:id . 78))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 235) (:start . 233)\n  (:id . 79))\n ((:tag . "NN") (:stem . "behaviour") (:form . "behaviour") (:end . 245)\n  (:start . 236) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 248) (:start . 246)\n  (:id . 81))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 255)\n  (:start . 249) (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 259) (:start . 256)\n  (:id . 83))\n ((:tag . "NN") (:stem . "agent") (:form . "AGENT") (:end . 265)\n  (:start . 260) (:id . 84))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 268) (:start . 266)\n  (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 272) (:start . 269)\n  (:id . 86))\n ((:tag . "NN") (:stem . "theme") (:form . "THEME") (:end . 278)\n  (:start . 273) (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 281) (:start . 279)\n  (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 285) (:start . 282)\n  (:id . 89))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 291)\n  (:start . 286) (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 292) (:start . 291)\n  (:id . 91)))@@@1@50@((:hcues ((:id . :x12.151.1) (:span 249 255 266 268)))\n (:hscopes ((:id . :x12.151.1) (:span 249 278)))\n (:identifiers (:sid . :s12.151) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503954@unknown@formal@none@1@S@The full set of roles is shown in Table 2.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 21) (:start . 16)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 30) (:start . 25)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 39) (:start . 34)\n  (:id . 50))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 41) (:start . 40)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s12.152) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503955@unknown@formal@none@1@S@In general, definitions of argument types normally specified as adjuncts, such as MANNER, INSTRUMENT, CONDITION and LOCATION, can be problematic to distinguish from each other.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "definition") (:form . "definitions") (:end . 23)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 50)\n  (:start . 42) (:id . 49))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "adjunct") (:form . "adjuncts") (:end . 72)\n  (:start . 64) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "MANNER") (:form . "MANNER") (:end . 88)\n  (:start . 82) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "INSTRUMENT") (:form . "INSTRUMENT") (:end . 100)\n  (:start . 90) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "CONDITION") (:form . "CONDITION") (:end . 111)\n  (:start . 102) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 115) (:start . 112)\n  (:id . 61))\n ((:tag . "NN") (:stem . "location") (:form . "LOCATION") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 63))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 129) (:start . 126)\n  (:id . 64))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "problematic") (:form . "problematic") (:end . 144)\n  (:start . 133) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 147) (:start . 145)\n  (:id . 67))\n ((:tag . "VB") (:stem . "distinguish") (:form . "distinguish") (:end . 159)\n  (:start . 148) (:id . 68))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 164) (:start . 160)\n  (:id . 69))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 169) (:start . 165)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 175)\n  (:start . 170) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x12.153.1) (:span 126 129)))\n (:hscopes ((:id . :x12.153.1) (:span 126 175)))\n (:identifiers (:sid . :s12.153) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503956@unknown@formal@none@1@S@However, our use of more biologically-oriented definitions for these cases aims to reduce discrepancies.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 24) (:start . 20)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "biologically-oriented")\n  (:form . "biologically-oriented") (:end . 46) (:start . 25) (:id . 48))\n ((:tag . "NNS") (:stem . "definition") (:form . "definitions") (:end . 58)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 68) (:start . 63)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 74) (:start . 69)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "aim") (:form . "aims") (:end . 79) (:start . 75)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "VB") (:stem . "reduce") (:form . "reduce") (:end . 89)\n  (:start . 83) (:id . 55))\n ((:tag . "NNS") (:stem . "discrepancy") (:form . "discrepancies")\n  (:end . 103) (:start . 90) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s12.154) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503957@unknown@formal@none@1@S@Semantic roles@(((:tag . "JJ") (:stem . "semantic") (:form . "Semantic") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 14) (:start . 9)\n  (:id . 43)))@@@1@2@((:identifiers (:sid . :s12.155) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5503958@unknown@formal@none@1@S@Biological concepts@(((:tag . "JJ") (:stem . "biological") (:form . "Biological") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 19)\n  (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s12.156) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503959@unknown@formal@none@1@S@Our biological concept labels are organised into hierarchies based on the Gene Regulation Ontology (GRO) [43].@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "label") (:form . "labels") (:end . 29)\n  (:start . 23) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "organise") (:form . "organised") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "hierarchy") (:form . "hierarchies") (:end . 60)\n  (:start . 49) (:id . 49))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 66) (:start . 61)\n  (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 78) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Regulation") (:form . "Regulation") (:end . 89)\n  (:start . 79) (:id . 54))\n ((:tag . "NNP") (:stem . "Ontology") (:form . "Ontology") (:end . 98)\n  (:start . 90) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 100) (:start . 99)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "GRO") (:form . "GRO") (:end . 103) (:start . 100)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.157) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503960@unknown@formal@none@1@S@This ontology, which integrates and builds on parts of other established bio-ontologies, such as Gene Ontology [56] and Sequence Ontology [57], is also included within the list of ontologies of the OBO Foundry [58].@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "ontology") (:form . "ontology") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "integrate") (:form . "integrates") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "build") (:form . "builds") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 51) (:start . 46)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "establish") (:form . "established") (:end . 72)\n  (:start . 61) (:id . 53))\n ((:tag . "NNS") (:stem . "bio-ontology") (:form . "bio-ontologies")\n  (:end . 87) (:start . 73) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Ontology") (:form . "Ontology") (:end . 110)\n  (:start . 102) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 112) (:start . 111)\n  (:id . 60))\n ((:tag . "CD") (:stem . "56") (:form . "56") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n  (:id . 63))\n ((:tag . "NN") (:stem . "sequence") (:form . "Sequence") (:end . 128)\n  (:start . 120) (:id . 64))\n ((:tag . "NNP") (:stem . "Ontology") (:form . "Ontology") (:end . 137)\n  (:start . 129) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 139) (:start . 138)\n  (:id . 66))\n ((:tag . "CD") (:stem . "57") (:form . "57") (:end . 141) (:start . 139)\n  (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 142) (:start . 141)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 69))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 146) (:start . 144)\n  (:id . 70))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 151) (:start . 147)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 160)\n  (:start . 152) (:id . 72))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 167)\n  (:start . 161) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 171) (:start . 168)\n  (:id . 74))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 176) (:start . 172)\n  (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 179) (:start . 177)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "ontology") (:form . "ontologies") (:end . 190)\n  (:start . 180) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 193) (:start . 191)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "OBO") (:form . "OBO") (:end . 201) (:start . 198)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Foundry") (:form . "Foundry") (:end . 209)\n  (:start . 202) (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 211) (:start . 210)\n  (:id . 82))\n ((:tag . "CD") (:stem . "58") (:form . "58") (:end . 213) (:start . 211)\n  (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 214) (:start . 213)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s12.158) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503961@unknown@formal@none@1@S@Our biological concept labels are arranged within 5 different hierarchies, corresponding to the following supercategories: Nucleic_Acids, Proteins, Living_Systems, Processes and Experimental.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "label") (:form . "labels") (:end . 29)\n  (:start . 23) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "arrange") (:form . "arranged") (:end . 42)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 49)\n  (:start . 43) (:id . 48))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 61)\n  (:start . 52) (:id . 50))\n ((:tag . "NNS") (:stem . "hierarchy") (:form . "hierarchies") (:end . 73)\n  (:start . 62) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 88)\n  (:start . 75) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 105)\n  (:start . 96) (:id . 56))\n ((:tag . "NNS") (:stem . "supercategory") (:form . "supercategories")\n  (:end . 121) (:start . 106) (:id . 57))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 122) (:start . 121)\n  (:id . 58))\n ((:tag . "NNPS") (:stem . "Nucleic_Acid") (:form . "Nucleic_Acids")\n  (:end . 136) (:start . 123) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 60))\n ((:tag . "NNPS") (:stem . "Protein") (:form . "Proteins") (:end . 146)\n  (:start . 138) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 62))\n ((:tag . "NNPS") (:stem . "Living_System") (:form . "Living_Systems")\n  (:end . 162) (:start . 148) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 64))\n ((:tag . "NNPS") (:stem . "Processes") (:form . "Processes") (:end . 173)\n  (:start . 164) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 177) (:start . 174)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Experimental") (:form . "Experimental")\n  (:end . 190) (:start . 178) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s12.159) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503962@unknown@formal@none@1@S@During annotation, biological concepts are identified within each semantic argument.@(((:tag . "IN") (:stem . "during") (:form . "During") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 17)\n  (:start . 7) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 53)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 60)\n  (:start . 54) (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 65) (:start . 61)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 74)\n  (:start . 66) (:id . 51))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 83)\n  (:start . 75) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s12.160) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503963@unknown@formal@none@1@S@In each case, the most specific concept category possible within the appropriate hierarchy is assigned, based on the context in which the concept occurs.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 46))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 22) (:start . 18)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 31)\n  (:start . 23) (:id . 48))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 39)\n  (:start . 32) (:id . 49))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 64)\n  (:start . 58) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 80)\n  (:start . 69) (:id . 54))\n ((:tag . "NN") (:stem . "hierarchy") (:form . "hierarchy") (:end . 90)\n  (:start . 81) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 93) (:start . 91)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 102)\n  (:start . 94) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 109)\n  (:start . 104) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 124)\n  (:start . 117) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 133)\n  (:start . 128) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 65))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 145)\n  (:start . 138) (:id . 66))\n ((:tag . "VBZ") (:stem . "occur") (:form . "occurs") (:end . 152)\n  (:start . 146) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s12.161) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503964@unknown@formal@none@1@S@The aim of this is to allow queries over extracted event instances to be performed at different levels of granularity, i.e., users could specify more general or less general concept types according to their requirements.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "aim") (:form . "aim") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 21) (:start . 19)\n  (:id . 47))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 27) (:start . 22)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "query") (:form . "queries") (:end . 35)\n  (:start . 28) (:id . 49))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 40) (:start . 36)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 50)\n  (:start . 41) (:id . 51))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 82)\n  (:start . 73) (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 95)\n  (:start . 86) (:id . 58))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 102)\n  (:start . 96) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 60))\n ((:tag . "NN") (:stem . "granularity") (:form . "granularity") (:end . 117)\n  (:start . 106) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 123) (:start . 119)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 130)\n  (:start . 125) (:id . 65))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 136)\n  (:start . 131) (:id . 66))\n ((:tag . "VB") (:stem . "specify") (:form . "specify") (:end . 144)\n  (:start . 137) (:id . 67))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 149) (:start . 145)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 157)\n  (:start . 150) (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 160) (:start . 158)\n  (:id . 70))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 165) (:start . 161)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 173)\n  (:start . 166) (:id . 72))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 181)\n  (:start . 174) (:id . 73))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 187)\n  (:start . 182) (:id . 74))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 197)\n  (:start . 188) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 200) (:start . 198)\n  (:id . 76))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 206)\n  (:start . 201) (:id . 77))\n ((:tag . "NNS") (:stem . "requirement") (:form . "requirements") (:end . 219)\n  (:start . 207) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x12.162.1) (:span 131 136)))\n (:hscopes ((:id . :x12.162.1) (:span 131 219)))\n (:identifiers (:sid . :s12.162) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503965@unknown@formal@none@1@S@Consider the following example:@(((:tag . "VB") (:stem . "consider") (:form . "Consider") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 31) (:start . 30)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s12.163) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503966@unknown@formal@none@1@S@To map the regulatory domain of Escherichia coli T-protein...@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "map") (:form . "map") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 21)\n  (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "FW") (:stem . "escherichia") (:form . "Escherichia") (:end . 43)\n  (:start . 32) (:id . 48))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "T-protein") (:form . "T-protein") (:end . 58)\n  (:start . 49) (:id . 50))\n ((:tag . ":") (:stem . "…") (:form . "…") (:end . 58) (:start . 58)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s12.164) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503967@unknown@formal@none@1@S@Here, it is possible to assign the specific concept category Domain (within the Proteins hierarchy) to the concept the regulatory domain, which is a functional part of a protein.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 20)\n  (:start . 12) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 30)\n  (:start . 24) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 43)\n  (:start . 35) (:id . 50))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 51)\n  (:start . 44) (:id . 51))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 60)\n  (:start . 52) (:id . 52))\n ((:tag . "NNP") (:stem . "Domain") (:form . "Domain") (:end . 67)\n  (:start . 61) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "NNPS") (:stem . "Protein") (:form . "Proteins") (:end . 88)\n  (:start . 80) (:id . 57))\n ((:tag . "VBP") (:stem . "hierarchy") (:form . "hierarchy") (:end . 98)\n  (:start . 89) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 114)\n  (:start . 107) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 129)\n  (:start . 119) (:id . 64))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 136)\n  (:start . 130) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 66))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 143)\n  (:start . 138) (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 146) (:start . 144)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 148) (:start . 147)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 159)\n  (:start . 149) (:id . 70))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 164) (:start . 160)\n  (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 167) (:start . 165)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 169) (:start . 168)\n  (:id . 73))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 177)\n  (:start . 170) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s12.165) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503968@unknown@formal@none@1@S@However, the following example presents a greater challenge:@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "following") (:form . "following") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "VBZ") (:stem . "present") (:form . "presents") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "challenge") (:form . "challenge") (:end . 59)\n  (:start . 50) (:id . 50))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 60) (:start . 59)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s12.166) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503969@unknown@formal@none@1@S@IHF may inhibit ompF transcription by altering how OmpR interacts with the ompF promoter.@(((:tag . "NNP") (:stem . "IHF") (:form . "IHF") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VB") (:stem . "inhibit") (:form . "inhibit") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "ompf") (:form . "ompF") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 34) (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "alter") (:form . "altering") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "OmpR") (:form . "OmpR") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "interact") (:form . "interacts") (:end . 65)\n  (:start . 56) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 70) (:start . 66)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 53))\n ((:tag . "NN") (:stem . "ompf") (:form . "ompF") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 88)\n  (:start . 80) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x12.167.1) (:span 4 7)))\n (:hscopes ((:id . :x12.167.1) (:span 4 88)))\n (:identifiers (:sid . :s12.167) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503970@unknown@formal@none@1@S@Here, IHF is clearly a repressor.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "IHF") (:form . "IHF") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 45))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 20)\n  (:start . 13) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "repressor") (:form . "repressor") (:end . 32)\n  (:start . 23) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 33) (:start . 32)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s12.168) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503971@unknown@formal@none@1@S@However, the specific category of OmpR is ambiguous from the context of the sentence between:@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "OmpR") (:form . "OmpR") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "ambiguous") (:form . "ambiguous") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 84)\n  (:start . 76) (:id . 56))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 93) (:start . 92)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.169) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503972@unknown@formal@none@1@S@• An activator of the ompF promoter.@(((:tag . "PDT") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "An") (:end . 4) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "activator") (:form . "activator") (:end . 14)\n  (:start . 5) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "ompf") (:form . "ompF") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 35)\n  (:start . 27) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 36) (:start . 35)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s12.170) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503973@unknown@formal@none@1@S@• A repressor of the ompF promoter.@(((:tag . "PDT") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 3) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "repressor") (:form . "repressor") (:end . 13)\n  (:start . 4) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "ompf") (:form . "ompF") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "promoter") (:form . "promoter") (:end . 34)\n  (:start . 26) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 35) (:start . 34)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s12.171) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503974@unknown@formal@none@1@S@Therefore, the more general category of Regulator is assigned to OmpR.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Regulator") (:form . "Regulator") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 61)\n  (:start . 53) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "OmpR") (:form . "OmpR") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.172) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503975@unknown@formal@none@1@S@Consistent annotation of text spans@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 44))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "span") (:form . "spans") (:end . 35) (:start . 30)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s12.173) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503976@unknown@formal@none@1@S@The task of annotating consistent text spans is often challenging [52], but is important to ensure a cleanly annotated corpus which is easy to understand, reuse and process.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "annotate") (:form . "annotating") (:end . 22)\n  (:start . 12) (:id . 45))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 33)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "span") (:form . "spans") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 53) (:start . 48)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "challenge") (:form . "challenging") (:end . 65)\n  (:start . 54) (:id . 51))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "CD") (:stem . "52") (:form . "52") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 78) (:start . 76)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 88)\n  (:start . 79) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 98)\n  (:start . 92) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n  (:id . 61))\n ((:tag . "RB") (:stem . "cleanly") (:form . "cleanly") (:end . 108)\n  (:start . 101) (:id . 62))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 118)\n  (:start . 109) (:id . 63))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 125)\n  (:start . 119) (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 131)\n  (:start . 126) (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 134) (:start . 132)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "easy") (:form . "easy") (:end . 139) (:start . 135)\n  (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 68))\n ((:tag . "VB") (:stem . "understand") (:form . "understand") (:end . 153)\n  (:start . 143) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 70))\n ((:tag . "NN") (:stem . "reuse") (:form . "reuse") (:end . 160)\n  (:start . 155) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n  (:id . 72))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 172)\n  (:start . 165) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s12.174) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503977@unknown@formal@none@1@S@Consider the following sentence:@(((:tag . "VB") (:stem . "consider") (:form . "Consider") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 32) (:start . 31)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s12.175) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503978@unknown@formal@none@1@S@The Klebsiella rcsA gene encoded a polypeptide of 23 kDa@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Klebsiella") (:form . "Klebsiella") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "rcsA") (:form . "rcsA") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "encode") (:form . "encoded") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "polypeptide") (:form . "polypeptide") (:end . 46)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "kda") (:form . "kDa") (:end . 56) (:start . 53)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s12.176) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503979@unknown@formal@none@1@S@The AGENT of encoded may be viewed as any of the following spans: Klebsiella rcsA, Klebsiella rcsA gene, or The Klebsiella rcsA gene.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "agent") (:form . "AGENT") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "view") (:form . "viewed") (:end . 34) (:start . 28)\n  (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 58)\n  (:start . 49) (:id . 53))\n ((:tag . "NNS") (:stem . "span") (:form . "spans") (:end . 64) (:start . 59)\n  (:id . 54))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Klebsiella") (:form . "Klebsiella") (:end . 76)\n  (:start . 66) (:id . 56))\n ((:tag . "NNP") (:stem . "rcsA") (:form . "rcsA") (:end . 81) (:start . 77)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Klebsiella") (:form . "Klebsiella") (:end . 93)\n  (:start . 83) (:id . 59))\n ((:tag . "NNP") (:stem . "rcsA") (:form . "rcsA") (:end . 98) (:start . 94)\n  (:id . 60))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 103) (:start . 99)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 107) (:start . 105)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 111) (:start . 108)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Klebsiella") (:form . "Klebsiella") (:end . 122)\n  (:start . 112) (:id . 65))\n ((:tag . "NN") (:stem . "rcsa") (:form . "rcsA") (:end . 127) (:start . 123)\n  (:id . 66))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 132) (:start . 128)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x12.177.1) (:span 21 24)))\n (:hscopes ((:id . :x12.177.1) (:span 0 132)))\n (:identifiers (:sid . :s12.177) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503980@unknown@formal@none@1@S@Similarly, the THEME could be polypeptide, a polypeptide or a polypeptide of 23 kDa.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "THEME") (:form . "THEME") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "polypeptide") (:form . "polypeptide") (:end . 41)\n  (:start . 30) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "polypeptide") (:form . "polypeptide") (:end . 56)\n  (:start . 45) (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "polypeptide") (:form . "polypeptide") (:end . 73)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "NN") (:stem . "kda") (:form . "kDa") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x12.178.1) (:span 57 59)) ((:id . :x12.178.2) (:span 21 26)))\n (:hscopes ((:id . :x12.178.1) (:span 30 83))\n  ((:id . :x12.178.2) (:span 21 83)))\n (:identifiers (:sid . :s12.178) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503981@unknown@formal@none@1@S@In order to promote consistent choice of spans, we have created a number of guidelines which are mostly based on syntactic chunks.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "promote") (:form . "promote") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 30)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "choice") (:form . "choice") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "span") (:form . "spans") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "create") (:form . "created") (:end . 63)\n  (:start . 56) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 72)\n  (:start . 66) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 86)\n  (:start . 76) (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 92) (:start . 87)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "RB") (:stem . "mostly") (:form . "mostly") (:end . 103)\n  (:start . 97) (:id . 60))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 109)\n  (:start . 104) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 112) (:start . 110)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "syntactic") (:form . "syntactic") (:end . 122)\n  (:start . 113) (:id . 63))\n ((:tag . "NNS") (:stem . "chunk") (:form . "chunks") (:end . 129)\n  (:start . 123) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.179) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503982@unknown@formal@none@1@S@Prior to annotation, chunks are automatically identified by the GENIA tagger [55].@(((:tag . "RB") (:stem . "prior") (:form . "Prior") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "chunk") (:form . "chunks") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "RB") (:stem . "automatically") (:form . "automatically")\n  (:end . 45) (:start . 32) (:id . 48))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "GENIA") (:form . "GENIA") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "tagger") (:form . "tagger") (:end . 76)\n  (:start . 70) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s12.180) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503983@unknown@formal@none@1@S@The example below illustrates the output of the tagger, in terms of the chunks identified.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "illustrate") (:form . "illustrates") (:end . 29)\n  (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "tagger") (:form . "tagger") (:end . 54)\n  (:start . 48) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 64) (:start . 59)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "chunk") (:form . "chunks") (:end . 78)\n  (:start . 72) (:id . 56))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 89)\n  (:start . 79) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.181) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503984@unknown@formal@none@1@S@Note that, according to the output of the GENIA tagger, PP chunks contain only the preposition, and not the following NP.@(((:tag . "VB") (:stem . "note") (:form . "Note") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 20)\n  (:start . 11) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 34)\n  (:start . 28) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "GENIA") (:form . "GENIA") (:end . 47) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tagger") (:form . "tagger") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "PP") (:form . "PP") (:end . 58) (:start . 56)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "chunk") (:form . "chunks") (:end . 65)\n  (:start . 59) (:id . 55))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 73)\n  (:start . 66) (:id . 56))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 78) (:start . 74)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "NN") (:stem . "preposition") (:form . "preposition") (:end . 94)\n  (:start . 83) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 61))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 103) (:start . 100)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 117)\n  (:start . 108) (:id . 64))\n ((:tag . "NNP") (:stem . "NP") (:form . "NP") (:end . 120) (:start . 118)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s12.182) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503985@unknown@formal@none@1@S@[NP The Klebsiella rcsA gene] [VP encoded ] [NP a polypeptide ] [PP of ] [NP 23 kDa]@(((:tag . "(") (:stem . "[") (:form . "[") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "NP") (:form . "NP") (:end . 3) (:start . 1)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Klebsiella") (:form . "Klebsiella") (:end . 18)\n  (:start . 8) (:id . 45))\n ((:tag . "NNP") (:stem . "rcsA") (:form . "rcsA") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 31) (:start . 30)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "VP") (:form . "VP") (:end . 33) (:start . 31)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 41)\n  (:start . 34) (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 43) (:start . 42)\n  (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 45) (:start . 44)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "NP") (:form . "NP") (:end . 47) (:start . 45)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 55))\n ((:tag . "NN") (:stem . "polypeptide") (:form . "polypeptide") (:end . 61)\n  (:start . 50) (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 63) (:start . 62)\n  (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 65) (:start . 64)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "PP") (:form . "PP") (:end . 67) (:start . 65)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 72) (:start . 71)\n  (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 74) (:start . 73)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "NP") (:form . "NP") (:end . 76) (:start . 74)\n  (:id . 63))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 79) (:start . 77)\n  (:id . 64))\n ((:tag . "NN") (:stem . "kda") (:form . "kDa") (:end . 83) (:start . 80)\n  (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 84) (:start . 83)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s12.183) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503986@unknown@formal@none@1@S@According to our guidelines, annotated text spans should normally consist of (sequences of) complete chunks, thus alleviating many issues relating to the exact words that should be included within an argument text span.@(((:tag . "VBG") (:stem . "accord") (:form . "According") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "span") (:form . "spans") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 65)\n  (:start . 57) (:id . 51))\n ((:tag . "VB") (:stem . "consist") (:form . "consist") (:end . 73)\n  (:start . 66) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 87)\n  (:start . 78) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 100)\n  (:start . 92) (:id . 58))\n ((:tag . "NNS") (:stem . "chunk") (:form . "chunks") (:end . 107)\n  (:start . 101) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "alleviate") (:form . "alleviating") (:end . 125)\n  (:start . 114) (:id . 62))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 130) (:start . 126)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "issue") (:form . "issues") (:end . 137)\n  (:start . 131) (:id . 64))\n ((:tag . "VBG") (:stem . "relate") (:form . "relating") (:end . 146)\n  (:start . 138) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 149) (:start . 147)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "exact") (:form . "exact") (:end . 159)\n  (:start . 154) (:id . 68))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 165)\n  (:start . 160) (:id . 69))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 170) (:start . 166)\n  (:id . 70))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 177)\n  (:start . 171) (:id . 71))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 180) (:start . 178)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 189)\n  (:start . 181) (:id . 73))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 196)\n  (:start . 190) (:id . 74))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 199) (:start . 197)\n  (:id . 75))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 208)\n  (:start . 200) (:id . 76))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 213) (:start . 209)\n  (:id . 77))\n ((:tag . "NN") (:stem . "span") (:form . "span") (:end . 218) (:start . 214)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x12.184.1) (:span 171 177))\n  ((:id . :x12.184.2) (:span 50 56)))\n (:hscopes ((:id . :x12.184.1) (:span 171 218))\n  ((:id . :x12.184.2) (:span 50 218)))\n (:identifiers (:sid . :s12.184) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503987@unknown@formal@none@1@S@This means that, for example, in the above sentence, the AGENT of encoded should be chosen as The Klebsiella rcsA gene, as this corresponds to a complete NP chunk.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 28)\n  (:start . 21) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 42) (:start . 37)\n  (:id . 51))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 51)\n  (:start . 43) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 54))\n ((:tag . "NN") (:stem . "agent") (:form . "AGENT") (:end . 62) (:start . 57)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 73)\n  (:start . 66) (:id . 57))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 80)\n  (:start . 74) (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 83) (:start . 81)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 90)\n  (:start . 84) (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 93) (:start . 91)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 97) (:start . 94)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Klebsiella") (:form . "Klebsiella") (:end . 108)\n  (:start . 98) (:id . 63))\n ((:tag . "NNP") (:stem . "rcsA") (:form . "rcsA") (:end . 113) (:start . 109)\n  (:id . 64))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 118) (:start . 114)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 122) (:start . 120)\n  (:id . 67))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 127) (:start . 123)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 139)\n  (:start . 128) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 144) (:start . 143)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 153)\n  (:start . 145) (:id . 72))\n ((:tag . "NNP") (:stem . "NP") (:form . "NP") (:end . 156) (:start . 154)\n  (:id . 73))\n ((:tag . "NN") (:stem . "chunk") (:form . "chunk") (:end . 162)\n  (:start . 157) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x12.185.1) (:span 74 80)))\n (:hscopes ((:id . :x12.185.1) (:span 53 118)))\n (:identifiers (:sid . :s12.185) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503988@unknown@formal@none@1@S@A further guideline stipulates that argument text spans must consist only of base NP chunks, and that additional descriptive information, usually introduced by prepositions, must be excluded from argument text spans.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "guideline") (:form . "guideline") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "stipulate") (:form . "stipulates") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "span") (:form . "spans") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "VB") (:stem . "consist") (:form . "consist") (:end . 68)\n  (:start . 61) (:id . 51))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "NN") (:stem . "base") (:form . "base") (:end . 81) (:start . 77)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "NP") (:form . "NP") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "chunk") (:form . "chunks") (:end . 91)\n  (:start . 85) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 101) (:start . 97)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 112)\n  (:start . 102) (:id . 60))\n ((:tag . "JJ") (:stem . "descriptive") (:form . "descriptive") (:end . 124)\n  (:start . 113) (:id . 61))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 136)\n  (:start . 125) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 137) (:start . 136)\n  (:id . 63))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 145)\n  (:start . 138) (:id . 64))\n ((:tag . "VBN") (:stem . "introduce") (:form . "introduced") (:end . 156)\n  (:start . 146) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 159) (:start . 157)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "preposition") (:form . "prepositions") (:end . 172)\n  (:start . 160) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 68))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 178) (:start . 174)\n  (:id . 69))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 181) (:start . 179)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 190)\n  (:start . 182) (:id . 71))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 195) (:start . 191)\n  (:id . 72))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 204)\n  (:start . 196) (:id . 73))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 209) (:start . 205)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "span") (:form . "spans") (:end . 215)\n  (:start . 210) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s12.186) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503989@unknown@formal@none@1@S@In the above sentence, application of this rule means that the THEME of encoded is only the chunk a polypeptide, whilst of 23 kDa is excluded from the argument text span.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "application") (:form . "application") (:end . 34)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "rule") (:form . "rule") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "theme") (:form . "THEME") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 79)\n  (:start . 72) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 87) (:start . 83)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "chunk") (:form . "chunk") (:end . 97) (:start . 92)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n  (:id . 61))\n ((:tag . "NN") (:stem . "polypeptide") (:form . "polypeptide") (:end . 111)\n  (:start . 100) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . "IN") (:stem . "whilst") (:form . "whilst") (:end . 119)\n  (:start . 113) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 65))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 125) (:start . 123)\n  (:id . 66))\n ((:tag . "NN") (:stem . "kda") (:form . "kDa") (:end . 129) (:start . 126)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 132) (:start . 130)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "exclude") (:form . "excluded") (:end . 141)\n  (:start . 133) (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 146) (:start . 142)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n  (:id . 71))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 159)\n  (:start . 151) (:id . 72))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 164) (:start . 160)\n  (:id . 73))\n ((:tag . "NN") (:stem . "span") (:form . "span") (:end . 169) (:start . 165)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s12.187) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503990@unknown@formal@none@1@S@Software@(((:tag . "NNP") (:stem . "Software") (:form . "Software") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s12.188) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503991@unknown@formal@none@1@S@The annotation of the GREC was performed using a Java-based annotation tool called WordFreak (http://wordfreak.sourceforge.net/[59]).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "java-based") (:form . "Java-based") (:end . 59)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 70)\n  (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 82) (:start . 76)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "WordFreak") (:form . "WordFreak") (:end . 92)\n  (:start . 83) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 56))\n ((:tag . "CD") (:stem . "http://wordfreak.sourceforge.net/[59")\n  (:form . "http://wordfreak.sourceforge.net/[59") (:end . 130) (:start . 94)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 131) (:start . 130)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.189) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503992@unknown@formal@none@1@S@The tool is designed to support many kinds of annotation of text documents, and can be adapted to new tasks fairly straightforwardly by producing new Java classes that define the task.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "support") (:form . "support") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "kind") (:form . "kinds") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 56)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "document") (:form . "documents") (:end . 74)\n  (:start . 65) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 86) (:start . 84)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "adapt") (:form . "adapted") (:end . 94)\n  (:start . 87) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 101) (:start . 98)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 107)\n  (:start . 102) (:id . 62))\n ((:tag . "RB") (:stem . "fairly") (:form . "fairly") (:end . 114)\n  (:start . 108) (:id . 63))\n ((:tag . "RB") (:stem . "straightforwardly") (:form . "straightforwardly")\n  (:end . 132) (:start . 115) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "produce") (:form . "producing") (:end . 145)\n  (:start . 136) (:id . 66))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 149) (:start . 146)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Java") (:form . "Java") (:end . 154) (:start . 150)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 162)\n  (:start . 155) (:id . 69))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 167) (:start . 163)\n  (:id . 70))\n ((:tag . "VBP") (:stem . "define") (:form . "define") (:end . 174)\n  (:start . 168) (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 72))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 183) (:start . 179)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x12.190.1) (:span 80 83)))\n (:hscopes ((:id . :x12.190.1) (:span 80 183)))\n (:identifiers (:sid . :s12.190) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503993@unknown@formal@none@1@S@Much of the work to customise WordFreak for the current task was carried out by ILC-CNR (http://www.ilc.cnr.it) in Pisa.@(((:tag . "JJ") (:stem . "much") (:form . "Much") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VB") (:stem . "customise") (:form . "customise") (:end . 29)\n  (:start . 20) (:id . 47))\n ((:tag . "NNP") (:stem . "WordFreak") (:form . "WordFreak") (:end . 39)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 72)\n  (:start . 65) (:id . 54))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 79) (:start . 77)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "ILC-CNR") (:form . "ILC-CNR") (:end . 87)\n  (:start . 80) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 58))\n ((:tag . "NN") (:stem . "http://www.ilc.cnr.it")\n  (:form . "http://www.ilc.cnr.it") (:end . 110) (:start . 89) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Pisa") (:form . "Pisa") (:end . 119) (:start . 115)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s12.191) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503994@unknown@formal@none@1@S@The customisation helps annotators to conform to the guidelines in a number of ways.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "customisation") (:form . "customisation")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "help") (:form . "helps") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 34)\n  (:start . 24) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "VB") (:stem . "conform") (:form . "conform") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 63)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 75)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "way") (:form . "ways") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.192) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503995@unknown@formal@none@1@S@For example, occurrences of biologically-relevant verbs are automatically highlighted.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "occurrence") (:form . "occurrences") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "biologically-relevant")\n  (:form . "biologically-relevant") (:end . 49) (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 55) (:start . 50)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 59) (:start . 56)\n  (:id . 49))\n ((:tag . "RB") (:stem . "automatically") (:form . "automatically")\n  (:end . 73) (:start . 60) (:id . 50))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 85)\n  (:start . 74) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s12.193) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503996@unknown@formal@none@1@S@In addition, colour-coding is used to distinguish different types of chunks, whilst certain restrictions are imposed in the tool as regards the types of chunks that can constitute different types of semantic arguments, e.g., ADVP chunks can only be labelled with the MANNER role.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "colour-coding") (:form . "colour-coding")\n  (:end . 26) (:start . 13) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "VB") (:stem . "distinguish") (:form . "distinguish") (:end . 49)\n  (:start . 38) (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 59)\n  (:start . 50) (:id . 50))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "chunk") (:form . "chunks") (:end . 75)\n  (:start . 69) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "IN") (:stem . "whilst") (:form . "whilst") (:end . 83)\n  (:start . 77) (:id . 55))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 91)\n  (:start . 84) (:id . 56))\n ((:tag . "NNS") (:stem . "restriction") (:form . "restrictions") (:end . 104)\n  (:start . 92) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 108) (:start . 105)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "impose") (:form . "imposed") (:end . 116)\n  (:start . 109) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 61))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 128) (:start . 124)\n  (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 131) (:start . 129)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "regard") (:form . "regards") (:end . 139)\n  (:start . 132) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 149)\n  (:start . 144) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "chunk") (:form . "chunks") (:end . 159)\n  (:start . 153) (:id . 68))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 164) (:start . 160)\n  (:id . 69))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 168) (:start . 165)\n  (:id . 70))\n ((:tag . "VB") (:stem . "constitute") (:form . "constitute") (:end . 179)\n  (:start . 169) (:id . 71))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 189)\n  (:start . 180) (:id . 72))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 195)\n  (:start . 190) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 198) (:start . 196)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 207)\n  (:start . 199) (:id . 75))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 217)\n  (:start . 208) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 218) (:start . 217)\n  (:id . 77))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 223) (:start . 219)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 224) (:start . 223)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "ADVP") (:form . "ADVP") (:end . 229) (:start . 225)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "chunk") (:form . "chunks") (:end . 236)\n  (:start . 230) (:id . 81))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 240) (:start . 237)\n  (:id . 82))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 245) (:start . 241)\n  (:id . 83))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 248) (:start . 246)\n  (:id . 84))\n ((:tag . "VBN") (:stem . "label") (:form . "labelled") (:end . 257)\n  (:start . 249) (:id . 85))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 262) (:start . 258)\n  (:id . 86))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 266) (:start . 263)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "MANNER") (:form . "MANNER") (:end . 273)\n  (:start . 267) (:id . 88))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 278) (:start . 274)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 279) (:start . 278)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s12.194) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503997@unknown@formal@none@1@S@Annotators and training@(((:tag . "NNS") (:stem . "annotator") (:form . "Annotators") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 23)\n  (:start . 15) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.195) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5503998@unknown@formal@none@1@S@Due to the requirement for biological knowledge and complete understanding of the abstracts, annotation was undertaken by 6 biology PhD students with native or near-native competency in English.@(((:tag . "JJ") (:stem . "due") (:form . "Due") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "requirement") (:form . "requirement") (:end . 22)\n  (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 60)\n  (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "understanding") (:form . "understanding")\n  (:end . 74) (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 91)\n  (:start . 82) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 55))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 103)\n  (:start . 93) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 107) (:start . 104)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "undertake") (:form . "undertaken") (:end . 118)\n  (:start . 108) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 121) (:start . 119)\n  (:id . 59))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 123) (:start . 122)\n  (:id . 60))\n ((:tag . "NN") (:stem . "biology") (:form . "biology") (:end . 131)\n  (:start . 124) (:id . 61))\n ((:tag . "NN") (:stem . "phd") (:form . "PhD") (:end . 135) (:start . 132)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "student") (:form . "students") (:end . 144)\n  (:start . 136) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 149) (:start . 145)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 156)\n  (:start . 150) (:id . 65))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 159) (:start . 157)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "near-native") (:form . "near-native") (:end . 171)\n  (:start . 160) (:id . 67))\n ((:tag . "NN") (:stem . "competency") (:form . "competency") (:end . 182)\n  (:start . 172) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 185) (:start . 183)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "English") (:form . "English") (:end . 193)\n  (:start . 186) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s12.196) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5503999@unknown@formal@none@1@S@It was also required that annotators had at least some experience in gene regulation.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 36)\n  (:start . 26) (:id . 47))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "experience") (:form . "experience") (:end . 65)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 84)\n  (:start . 74) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.197) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504000@unknown@formal@none@1@S@Linguistic expertise would be acquired through the training programme and through study of the annotation guidelines.@(((:tag . "JJ") (:stem . "linguistic") (:form . "Linguistic") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "expertise") (:form . "expertise") (:end . 20)\n  (:start . 11) (:id . 43))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 26) (:start . 21)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "acquire") (:form . "acquired") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 46)\n  (:start . 39) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 59)\n  (:start . 51) (:id . 49))\n ((:tag . "NN") (:stem . "programme") (:form . "programme") (:end . 69)\n  (:start . 60) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 51))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 81)\n  (:start . 74) (:id . 52))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 87) (:start . 82)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 55))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 105)\n  (:start . 95) (:id . 56))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 116)\n  (:start . 106) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x12.198.1) (:span 21 26)))\n (:hscopes ((:id . :x12.198.1) (:span 0 116)))\n (:identifiers (:sid . :s12.198) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504001@unknown@formal@none@1@S@As the annotation was carried out as part of the EC BOOTStrep project (http://www.bootstrep.org), it was subject to strict time constraints, with the amount of time to complete the annotation work being limited to three months.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "EC") (:form . "EC") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "BOOTStrep") (:form . "BOOTStrep") (:end . 61)\n  (:start . 52) (:id . 53))\n ((:tag . "NN") (:stem . "project") (:form . "project") (:end . 69)\n  (:start . 62) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "http://www.bootstrep.org")\n  (:form . "http://www.bootstrep.org") (:end . 95) (:start . 71) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "subject") (:form . "subject") (:end . 112)\n  (:start . 105) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "VB") (:stem . "strict") (:form . "strict") (:end . 122)\n  (:start . 116) (:id . 63))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 127) (:start . 123)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "constraint") (:form . "constraints") (:end . 139)\n  (:start . 128) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 145) (:start . 141)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 149) (:start . 146)\n  (:id . 68))\n ((:tag . "NN") (:stem . "amount") (:form . "amount") (:end . 156)\n  (:start . 150) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 159) (:start . 157)\n  (:id . 70))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 164) (:start . 160)\n  (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 167) (:start . 165)\n  (:id . 72))\n ((:tag . "VB") (:stem . "complete") (:form . "complete") (:end . 176)\n  (:start . 168) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 180) (:start . 177)\n  (:id . 74))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 191)\n  (:start . 181) (:id . 75))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 196) (:start . 192)\n  (:id . 76))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 202) (:start . 197)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 210)\n  (:start . 203) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 213) (:start . 211)\n  (:id . 79))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 219)\n  (:start . 214) (:id . 80))\n ((:tag . "NNS") (:stem . "month") (:form . "months") (:end . 226)\n  (:start . 220) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s12.199) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504002@unknown@formal@none@1@S@This time constraint firstly meant that we were unable to recruit annotators who all had a similarly high level of knowledge of gene regulation and expression.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "constraint") (:form . "constraint") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "RB") (:stem . "firstly") (:form . "firstly") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . "VBD") (:stem . "mean") (:form . "meant") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "unable") (:form . "unable") (:end . 54)\n  (:start . 48) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "VB") (:stem . "recruit") (:form . "recruit") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 76)\n  (:start . 66) (:id . 53))\n ((:tag . "WP") (:stem . "who") (:form . "who") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "RB") (:stem . "similarly") (:form . "similarly") (:end . 100)\n  (:start . 91) (:id . 58))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 111)\n  (:start . 106) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 114) (:start . 112)\n  (:id . 61))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 124)\n  (:start . 115) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 132) (:start . 128)\n  (:id . 64))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 143)\n  (:start . 133) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n  (:id . 66))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 158)\n  (:start . 148) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s12.200) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504003@unknown@formal@none@1@S@In addition, due to the envisaged steep learning curve for annotators, it was decided to devote the majority of the time available to annotator training.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "due") (:form . "due") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "envisage") (:form . "envisaged") (:end . 33)\n  (:start . 24) (:id . 48))\n ((:tag . "JJ") (:stem . "steep") (:form . "steep") (:end . 39) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "learning") (:form . "learning") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "curve") (:form . "curve") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "decide") (:form . "decided") (:end . 85)\n  (:start . 78) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . "VB") (:stem . "devote") (:form . "devote") (:end . 95)\n  (:start . 89) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 60))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 108)\n  (:start . 100) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 63))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 120) (:start . 116)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 130)\n  (:start . 121) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 133) (:start . 131)\n  (:id . 66))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 143)\n  (:start . 134) (:id . 67))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 152)\n  (:start . 144) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.201) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504004@unknown@formal@none@1@S@The employment of 6 annotators, however, allowed a medium-sized final GREC to be annotated in a relatively short space of time.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "employment") (:form . "employment") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 30)\n  (:start . 20) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "allow") (:form . "allowed") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "medium-sized") (:form . "medium-sized") (:end . 63)\n  (:start . 51) (:id . 52))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 90)\n  (:start . 81) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 106)\n  (:start . 96) (:id . 60))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 112)\n  (:start . 107) (:id . 61))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 118)\n  (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 63))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 126) (:start . 122)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.202) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504005@unknown@formal@none@1@S@Initial training sessions introduced the annotation tool and the task, with a particular emphasis being placed on clear positive and negative examples of gene regulation and expression events.@(((:tag . "JJ") (:stem . "initial") (:form . "Initial") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "session") (:form . "sessions") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "VBD") (:stem . "introduce") (:form . "introduced") (:end . 36)\n  (:start . 26) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 46))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 51)\n  (:start . 41) (:id . 47))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 56) (:start . 52)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 50))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 88)\n  (:start . 78) (:id . 55))\n ((:tag . "NN") (:stem . "emphasis") (:form . "emphasis") (:end . 97)\n  (:start . 89) (:id . 56))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 103) (:start . 98)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "place") (:form . "placed") (:end . 110)\n  (:start . 104) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 113) (:start . 111)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 119)\n  (:start . 114) (:id . 60))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 128)\n  (:start . 120) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 141)\n  (:start . 133) (:id . 63))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 150)\n  (:start . 142) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 153) (:start . 151)\n  (:id . 65))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 158) (:start . 154)\n  (:id . 66))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 169)\n  (:start . 159) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 173) (:start . 170)\n  (:id . 68))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 184)\n  (:start . 174) (:id . 69))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 191)\n  (:start . 185) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s12.203) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504006@unknown@formal@none@1@S@This was considered particularly important for those annotators with less experience in gene regulation and expression.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 32)\n  (:start . 20) (:id . 45))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 42)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 46) (:start . 43)\n  (:id . 47))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 52) (:start . 47)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 63)\n  (:start . 53) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 68) (:start . 64)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 73) (:start . 69)\n  (:id . 51))\n ((:tag . "NN") (:stem . "experience") (:form . "experience") (:end . 84)\n  (:start . 74) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 53))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 92) (:start . 88)\n  (:id . 54))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 103)\n  (:start . 93) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 56))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 118)\n  (:start . 108) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.204) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504007@unknown@formal@none@1@S@The initial training sessions were followed up by 5 fortnightly cycles, during which abstracts were firstly annotated by the annotators and then examined by 2 of the authors (one with biological expertise and the other with linguistic expertise), who produced individual feedback reports for each annotator prior to the start of the next cycle of annotation.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "session") (:form . "sessions") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 46) (:start . 44)\n  (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "RB") (:stem . "fortnightly") (:form . "fortnightly") (:end . 63)\n  (:start . 52) (:id . 51))\n ((:tag . "NNS") (:stem . "cycle") (:form . "cycles") (:end . 70)\n  (:start . 64) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 78)\n  (:start . 72) (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 84) (:start . 79)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 94)\n  (:start . 85) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 99) (:start . 95)\n  (:id . 57))\n ((:tag . "RB") (:stem . "firstly") (:form . "firstly") (:end . 107)\n  (:start . 100) (:id . 58))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 117)\n  (:start . 108) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 120) (:start . 118)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 135)\n  (:start . 125) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 63))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 144) (:start . 140)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 153)\n  (:start . 145) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 156) (:start . 154)\n  (:id . 66))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 158) (:start . 157)\n  (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 161) (:start . 159)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "author") (:form . "authors") (:end . 173)\n  (:start . 166) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 175) (:start . 174)\n  (:id . 71))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 178) (:start . 175)\n  (:id . 72))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 183) (:start . 179)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 194)\n  (:start . 184) (:id . 74))\n ((:tag . "NN") (:stem . "expertise") (:form . "expertise") (:end . 204)\n  (:start . 195) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 208) (:start . 205)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 212) (:start . 209)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 218)\n  (:start . 213) (:id . 78))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 223) (:start . 219)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "linguistic") (:form . "linguistic") (:end . 234)\n  (:start . 224) (:id . 80))\n ((:tag . "NN") (:stem . "expertise") (:form . "expertise") (:end . 244)\n  (:start . 235) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 245) (:start . 244)\n  (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 246) (:start . 245)\n  (:id . 83))\n ((:tag . "WP") (:stem . "who") (:form . "who") (:end . 250) (:start . 247)\n  (:id . 84))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 259)\n  (:start . 251) (:id . 85))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 270)\n  (:start . 260) (:id . 86))\n ((:tag . "NN") (:stem . "feedback") (:form . "feedback") (:end . 279)\n  (:start . 271) (:id . 87))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 287)\n  (:start . 280) (:id . 88))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 291) (:start . 288)\n  (:id . 89))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 296) (:start . 292)\n  (:id . 90))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 306)\n  (:start . 297) (:id . 91))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 312)\n  (:start . 307) (:id . 92))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 315) (:start . 313)\n  (:id . 93))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 319) (:start . 316)\n  (:id . 94))\n ((:tag . "NN") (:stem . "start") (:form . "start") (:end . 325)\n  (:start . 320) (:id . 95))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 328) (:start . 326)\n  (:id . 96))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 332) (:start . 329)\n  (:id . 97))\n ((:tag . "JJ") (:stem . "next") (:form . "next") (:end . 337) (:start . 333)\n  (:id . 98))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 343)\n  (:start . 338) (:id . 99))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 346) (:start . 344)\n  (:id . 100))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 357)\n  (:start . 347) (:id . 101))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 358) (:start . 357)\n  (:id . 102)))@@@1@61@((:identifiers (:sid . :s12.205) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504008@unknown@formal@none@1@S@Additional regular group sessions allowed problems to be discussed in more detail.@(((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 18)\n  (:start . 11) (:id . 43))\n ((:tag . "NN") (:stem . "group") (:form . "group") (:end . 24) (:start . 19)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "session") (:form . "sessions") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "VBD") (:stem . "allow") (:form . "allowed") (:end . 41)\n  (:start . 34) (:id . 46))\n ((:tag . "NNS") (:stem . "problem") (:form . "problems") (:end . 50)\n  (:start . 42) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 53) (:start . 51)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 56) (:start . 54)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "discuss") (:form . "discussed") (:end . 66)\n  (:start . 57) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "detail") (:form . "detail") (:end . 81)\n  (:start . 75) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.206) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504009@unknown@formal@none@1@S@The calculation of IAA scores after each training cycle provided a quantitative measure of improvement during the training period.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "calculation") (:form . "calculation") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "IAA") (:form . "IAA") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "provide") (:form . "provided") (:end . 64)\n  (:start . 56) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 79)\n  (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "measure") (:form . "measure") (:end . 87)\n  (:start . 80) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "improvement") (:form . "improvement") (:end . 102)\n  (:start . 91) (:id . 56))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 109)\n  (:start . 103) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 58))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 122)\n  (:start . 114) (:id . 59))\n ((:tag . "NN") (:stem . "period") (:form . "period") (:end . 129)\n  (:start . 123) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s12.207) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504010@unknown@formal@none@1@S@Prior to providing these scores, we first describe our method of calculating agreement.@(((:tag . "RB") (:stem . "prior") (:form . "Prior") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "provide") (:form . "providing") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 41) (:start . 36)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 50)\n  (:start . 42) (:id . 50))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "calculate") (:form . "calculating") (:end . 76)\n  (:start . 65) (:id . 54))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 86)\n  (:start . 77) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.208) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504011@unknown@formal@none@1@S@Calculating inter-annotator agreement@(((:tag . "VBG") (:stem . "calculate") (:form . "Calculating") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "inter-annotator") (:form . "inter-annotator")\n  (:end . 27) (:start . 12) (:id . 43))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 37)\n  (:start . 28) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.209) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504012@unknown@formal@none@1@S@We have defined a novel evaluation methodology which calculates IAA for a number of separate subtasks of the annotation process.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 34)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "methodology") (:form . "methodology") (:end . 46)\n  (:start . 35) (:id . 48))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "calculate") (:form . "calculates") (:end . 63)\n  (:start . 53) (:id . 50))\n ((:tag . "NNP") (:stem . "IAA") (:form . "IAA") (:end . 67) (:start . 64)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 80)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 83) (:start . 81)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . "NNS") (:stem . "subtask") (:form . "subtasks") (:end . 101)\n  (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 119)\n  (:start . 109) (:id . 60))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 127)\n  (:start . 120) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.210) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504013@unknown@formal@none@1@S@These subtasks are as follows:@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "subtask") (:form . "subtasks") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 30) (:start . 29)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s12.211) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504014@unknown@formal@none@1@S@• Event identification (how frequently annotators agree on which events to annotate).@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Event") (:form . "Event") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 22) (:start . 8) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 49)\n  (:start . 39) (:id . 48))\n ((:tag . "VBP") (:stem . "agree") (:form . "agree") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 64) (:start . 59)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 71)\n  (:start . 65) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "VB") (:stem . "annotate") (:form . "annotate") (:end . 83)\n  (:start . 75) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 85) (:start . 84)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.212) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504015@unknown@formal@none@1@S@• Argument identification (for agreed events, how frequently the same arguments are chosen by each annotator).@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Argument") (:form . "Argument") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 25) (:start . 11) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "agree") (:form . "agreed") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 60)\n  (:start . 50) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 79)\n  (:start . 70) (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 90)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 98) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 108)\n  (:start . 99) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 109) (:start . 108)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s12.213) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504016@unknown@formal@none@1@S@For this task, we calculate separate agreement rates corresponding to:@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "calculate") (:form . "calculate") (:end . 27)\n  (:start . 18) (:id . 47))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 66)\n  (:start . 53) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 70) (:start . 69)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s12.214) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504017@unknown@formal@none@1@S@a. Relaxed span matches, where argument text spans identified by a pair of annotators at least overlap with each other, but do not necessarily match exactly.@(((:tag . "LS") (:stem . "a.") (:form . "a.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "relax") (:form . "Relaxed") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "span") (:form . "span") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "span") (:form . "spans") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 61)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 85)\n  (:start . 75) (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 94) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "overlap") (:form . "overlap") (:end . 102)\n  (:start . 95) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 107) (:start . 103)\n  (:id . 60))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 112) (:start . 108)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 118)\n  (:start . 113) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 63))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 123) (:start . 120)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 126) (:start . 124)\n  (:id . 65))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 130) (:start . 127)\n  (:id . 66))\n ((:tag . "RB") (:stem . "necessarily") (:form . "necessarily") (:end . 142)\n  (:start . 131) (:id . 67))\n ((:tag . "VB") (:stem . "match") (:form . "match") (:end . 148)\n  (:start . 143) (:id . 68))\n ((:tag . "RB") (:stem . "exactly") (:form . "exactly") (:end . 156)\n  (:start . 149) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s12.215) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504018@unknown@formal@none@1@S@b. Exact span matches, where argument text spans identified by a pair of annotators match exactly.@(((:tag . "LS") (:stem . "b.") (:form . "b.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Exact") (:form . "Exact") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "span") (:form . "span") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "span") (:form . "spans") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 59)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 69) (:start . 65)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 83)\n  (:start . 73) (:id . 56))\n ((:tag . "VBP") (:stem . "match") (:form . "match") (:end . 89) (:start . 84)\n  (:id . 57))\n ((:tag . "RB") (:stem . "exactly") (:form . "exactly") (:end . 97)\n  (:start . 90) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s12.216) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504019@unknown@formal@none@1@S@This statistic helps us to evaluate the effectiveness of our rules for consistent span annotation.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "statistic") (:form . "statistic") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "help") (:form . "helps") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "effectiveness") (:form . "effectiveness")\n  (:end . 53) (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "rule") (:form . "rules") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 81)\n  (:start . 71) (:id . 54))\n ((:tag . "NN") (:stem . "span") (:form . "span") (:end . 86) (:start . 82)\n  (:id . 55))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 97)\n  (:start . 87) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s12.217) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504020@unknown@formal@none@1@S@• Semantic role assignment (for agreed arguments, how often the same semantic roles are assigned by each annotator).@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "semantic") (:form . "Semantic") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "agree") (:form . "agreed") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 48)\n  (:start . 39) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 77)\n  (:start . 69) (:id . 55))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 83) (:start . 78)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 96)\n  (:start . 88) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 99) (:start . 97)\n  (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 104) (:start . 100)\n  (:id . 60))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 114)\n  (:start . 105) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s12.218) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504021@unknown@formal@none@1@S@• Biological concept identification (within agreed arguments, how often annotators identify the same biological concepts).@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "biological") (:form . "Biological") (:end . 12)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 35) (:start . 21) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 46))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 43)\n  (:start . 37) (:id . 47))\n ((:tag . "VBN") (:stem . "agree") (:form . "agreed") (:end . 50)\n  (:start . 44) (:id . 48))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 50))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 71) (:start . 66)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 82)\n  (:start . 72) (:id . 53))\n ((:tag . "VBP") (:stem . "identify") (:form . "identify") (:end . 91)\n  (:start . 83) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 100) (:start . 96)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 111)\n  (:start . 101) (:id . 57))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 120)\n  (:start . 112) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 121) (:start . 120)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.219) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504022@unknown@formal@none@1@S@• Biological concept category assignment (for agreed biological concepts, how often the assigned categories are agreed upon by each annotator).@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "biological") (:form . "Biological") (:end . 12)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 40)\n  (:start . 30) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "agree") (:form . "agreed") (:end . 52)\n  (:start . 46) (:id . 49))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 63)\n  (:start . 53) (:id . 50))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 72)\n  (:start . 64) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 52))\n ((:tag . "WRB") (:stem . "how") (:form . "how") (:end . 77) (:start . 74)\n  (:id . 53))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 83) (:start . 78)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 96)\n  (:start . 88) (:id . 56))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 107)\n  (:start . 97) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 111) (:start . 108)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "agree") (:form . "agreed") (:end . 118)\n  (:start . 112) (:id . 59))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 123) (:start . 119)\n  (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 126) (:start . 124)\n  (:id . 61))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 131) (:start . 127)\n  (:id . 62))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 141)\n  (:start . 132) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.220) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504023@unknown@formal@none@1@S@For this task, we calculate 3 different agreement rates, i.e.,@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "calculate") (:form . "calculate") (:end . 27)\n  (:start . 18) (:id . 47))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 39)\n  (:start . 30) (:id . 49))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 49)\n  (:start . 40) (:id . 50))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 55) (:start . 50)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.221) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504024@unknown@formal@none@1@S@a. Exact category matches, where each annotator has assigned exactly the same concept label.@(((:tag . "RB") (:stem . "a.") (:form . "a.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Exact") (:form . "Exact") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 60)\n  (:start . 52) (:id . 51))\n ((:tag . "RB") (:stem . "exactly") (:form . "exactly") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 85)\n  (:start . 78) (:id . 55))\n ((:tag . "NN") (:stem . "label") (:form . "label") (:end . 91) (:start . 86)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 92) (:start . 91)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s12.222) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504025@unknown@formal@none@1@S@b. Matches including parent, where we also consider as matches those cases where the category assigned by one annotator is the parent concept of the category assigned by the other annotator.@(((:tag . "LS") (:stem . "b.") (:form . "b.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Match") (:form . "Matches") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "parent") (:form . "parent") (:end . 27)\n  (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 34) (:start . 29)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 51)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 80) (:start . 75)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 93)\n  (:start . 85) (:id . 57))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 102)\n  (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 105) (:start . 103)\n  (:id . 59))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 119)\n  (:start . 110) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 63))\n ((:tag . "NN") (:stem . "parent") (:form . "parent") (:end . 133)\n  (:start . 127) (:id . 64))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 141)\n  (:start . 134) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 67))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 157)\n  (:start . 149) (:id . 68))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 166)\n  (:start . 158) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 169) (:start . 167)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 173) (:start . 170)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 179)\n  (:start . 174) (:id . 72))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 189)\n  (:start . 180) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s12.223) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504026@unknown@formal@none@1@S@c. Supercategory assignment, where we consider only whether each annotator has assigned a concept within the same top level superclass, i.e., Nucleic_Acids, Proteins, Living_Systems, Processes and Experimental.@(((:tag . "LS") (:stem . "c.") (:form . "c.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Supercategory") (:form . "Supercategory")\n  (:end . 16) (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 27)\n  (:start . 17) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 45))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 51) (:start . 47)\n  (:id . 49))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 74)\n  (:start . 65) (:id . 52))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 97)\n  (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 104)\n  (:start . 98) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 113) (:start . 109)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 117) (:start . 114)\n  (:id . 60))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 123)\n  (:start . 118) (:id . 61))\n ((:tag . "NN") (:stem . "superclass") (:form . "superclass") (:end . 134)\n  (:start . 124) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 63))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 140) (:start . 136)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 65))\n ((:tag . "NNPS") (:stem . "Nucleic_Acids") (:form . "Nucleic_Acids")\n  (:end . 155) (:start . 142) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 67))\n ((:tag . "NNPS") (:stem . "Proteins") (:form . "Proteins") (:end . 165)\n  (:start . 157) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 69))\n ((:tag . "NNPS") (:stem . "Living_Systems") (:form . "Living_Systems")\n  (:end . 181) (:start . 167) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 182) (:start . 181)\n  (:id . 71))\n ((:tag . "NNPS") (:stem . "Processes") (:form . "Processes") (:end . 192)\n  (:start . 183) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 196) (:start . 193)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "Experimental") (:form . "Experimental")\n  (:end . 209) (:start . 197) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s12.224) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504027@unknown@formal@none@1@S@Whilst the Kappa statistic [60] has become a standard way of calculating IAA for classification tasks, it is problematic for most of the annotation subtasks outlined above, as it requires classifications to correspond to mutually exclusive and discrete categories.@(((:tag . "IN") (:stem . "whilst") (:form . "Whilst") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Kappa") (:form . "Kappa") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "statistic") (:form . "statistic") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "become") (:form . "become") (:end . 42)\n  (:start . 36) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 53)\n  (:start . 45) (:id . 52))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "calculate") (:form . "calculating") (:end . 72)\n  (:start . 61) (:id . 55))\n ((:tag . "NNP") (:stem . "IAA") (:form . "IAA") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "NN") (:stem . "classification") (:form . "classification")\n  (:end . 95) (:start . 81) (:id . 58))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 108) (:start . 106)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "problematic") (:form . "problematic") (:end . 120)\n  (:start . 109) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 124) (:start . 121)\n  (:id . 64))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 129) (:start . 125)\n  (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 67))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 147)\n  (:start . 137) (:id . 68))\n ((:tag . "NNS") (:stem . "subtask") (:form . "subtasks") (:end . 156)\n  (:start . 148) (:id . 69))\n ((:tag . "VBN") (:stem . "outline") (:form . "outlined") (:end . 165)\n  (:start . 157) (:id . 70))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 171)\n  (:start . 166) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 72))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 175) (:start . 173)\n  (:id . 73))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 178) (:start . 176)\n  (:id . 74))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 187)\n  (:start . 179) (:id . 75))\n ((:tag . "NNS") (:stem . "classification") (:form . "classifications")\n  (:end . 203) (:start . 188) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 206) (:start . 204)\n  (:id . 77))\n ((:tag . "VB") (:stem . "correspond") (:form . "correspond") (:end . 217)\n  (:start . 207) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 220) (:start . 218)\n  (:id . 79))\n ((:tag . "RB") (:stem . "mutually") (:form . "mutually") (:end . 229)\n  (:start . 221) (:id . 80))\n ((:tag . "JJ") (:stem . "exclusive") (:form . "exclusive") (:end . 239)\n  (:start . 230) (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 243) (:start . 240)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "discrete") (:form . "discrete") (:end . 252)\n  (:start . 244) (:id . 83))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 263)\n  (:start . 253) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 264) (:start . 263)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s12.225) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504028@unknown@formal@none@1@S@The only subtask which fits neatly into this category is the semantic role assignment subtask.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "subtask") (:form . "subtask") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "fit") (:form . "fits") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "RB") (:stem . "neatly") (:form . "neatly") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 44) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 69)\n  (:start . 61) (:id . 53))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 85)\n  (:start . 75) (:id . 55))\n ((:tag . "NN") (:stem . "subtask") (:form . "subtask") (:end . 93)\n  (:start . 86) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s12.226) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504029@unknown@formal@none@1@S@We have thus chosen to follow [61] in choosing the F-Score to calculate IAA, as it can be applied straightforwardly to all of the above annotation subtasks.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "VB") (:stem . "follow") (:form . "follow") (:end . 29)\n  (:start . 23) (:id . 47))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "CD") (:stem . "61") (:form . "61") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 34) (:start . 33)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "choose") (:form . "choosing") (:end . 46)\n  (:start . 38) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 53))\n ((:tag . "NN") (:stem . "f-score") (:form . "F-Score") (:end . 58)\n  (:start . 51) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 55))\n ((:tag . "VB") (:stem . "calculate") (:form . "calculate") (:end . 71)\n  (:start . 62) (:id . 56))\n ((:tag . "NNP") (:stem . "IAA") (:form . "IAA") (:end . 75) (:start . 72)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 79) (:start . 77)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 82) (:start . 80)\n  (:id . 60))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 86) (:start . 83)\n  (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 89) (:start . 87)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 97)\n  (:start . 90) (:id . 63))\n ((:tag . "RB") (:stem . "straightforwardly") (:form . "straightforwardly")\n  (:end . 115) (:start . 98) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 118) (:start . 116)\n  (:id . 65))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 122) (:start . 119)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 135)\n  (:start . 130) (:id . 69))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 146)\n  (:start . 136) (:id . 70))\n ((:tag . "NNS") (:stem . "subtask") (:form . "subtasks") (:end . 155)\n  (:start . 147) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s12.227) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504030@unknown@formal@none@1@S@The F-Score is the harmonic mean of precision and recall scores, which are normally calculated to compare the performance of an information retrieval or extraction system to a gold standard.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "f-score") (:form . "F-Score") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "harmonic") (:form . "harmonic") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "mean") (:form . "mean") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "precision") (:form . "precision") (:end . 45)\n  (:start . 36) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "recall") (:form . "recall") (:end . 56)\n  (:start . 50) (:id . 51))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 70) (:start . 65)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 83)\n  (:start . 75) (:id . 56))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 94)\n  (:start . 84) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 105)\n  (:start . 98) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 121)\n  (:start . 110) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 62))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 139)\n  (:start . 128) (:id . 64))\n ((:tag . "NN") (:stem . "retrieval") (:form . "retrieval") (:end . 149)\n  (:start . 140) (:id . 65))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 152) (:start . 150)\n  (:id . 66))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 163)\n  (:start . 153) (:id . 67))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 170)\n  (:start . 164) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 173) (:start . 171)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 175) (:start . 174)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "gold") (:form . "gold") (:end . 180) (:start . 176)\n  (:id . 71))\n ((:tag . "NN") (:stem . "standard") (:form . "standard") (:end . 189)\n  (:start . 181) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s12.228) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504031@unknown@formal@none@1@S@For the purposes of calculating IAA, precision and recall between two annotators can be calculated by treating one set of annotations as the gold standard.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "purpose") (:form . "purposes") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "calculate") (:form . "calculating") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "NNP") (:stem . "IAA") (:form . "IAA") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "precision") (:form . "precision") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "recall") (:form . "recall") (:end . 57)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 80)\n  (:start . 70) (:id . 54))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 98)\n  (:start . 88) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 101) (:start . 99)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "treat") (:form . "treating") (:end . 110)\n  (:start . 102) (:id . 59))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 114) (:start . 111)\n  (:id . 60))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 118) (:start . 115)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "annotation") (:form . "annotations") (:end . 133)\n  (:start . 122) (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 136) (:start . 134)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "gold") (:form . "gold") (:end . 145) (:start . 141)\n  (:id . 66))\n ((:tag . "NN") (:stem . "standard") (:form . "standard") (:end . 154)\n  (:start . 146) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s12.229) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504032@unknown@formal@none@1@S@The F-score is the same whichever set of annotations is used as the gold standard [62].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "f-score") (:form . "F-score") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "WDT") (:stem . "whichever") (:form . "whichever") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "annotation") (:form . "annotations") (:end . 52)\n  (:start . 41) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 54))\n ((:tag . "NN") (:stem . "gold") (:form . "gold") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "standard") (:form . "standard") (:end . 81)\n  (:start . 73) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "CD") (:stem . "62") (:form . "62") (:end . 85) (:start . 83)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 86) (:start . 85)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.230) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504033@unknown@formal@none@1@S@Agreement during training@(((:tag . "NN") (:stem . "agreement") (:form . "Agreement") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 16)\n  (:start . 10) (:id . 43))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 25)\n  (:start . 17) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.231) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504034@unknown@formal@none@1@S@Table 3 reports the changes in the IAA rates as the training period progressed.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "change") (:form . "changes") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "IAA") (:form . "IAA") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 44) (:start . 39)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 60)\n  (:start . 52) (:id . 53))\n ((:tag . "NN") (:stem . "period") (:form . "period") (:end . 67)\n  (:start . 61) (:id . 54))\n ((:tag . "VBD") (:stem . "progress") (:form . "progressed") (:end . 78)\n  (:start . 68) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.232) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504035@unknown@formal@none@1@S@Four of the cycles (C1 - C4) concerned E. coli abstracts, whilst the final cycle (C5) switched to annotation of human abstracts.@(((:tag . "CD") (:stem . "four") (:form . "Four") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "cycle") (:form . "cycles") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "C1") (:form . "C1") (:end . 22) (:start . 20)\n  (:id . 47))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 24) (:start . 23)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "C4") (:form . "C4") (:end . 27) (:start . 25)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 28) (:start . 27)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "concerned") (:form . "concerned") (:end . 38)\n  (:start . 29) (:id . 51))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 41) (:start . 39)\n  (:id . 52))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 46) (:start . 42)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 56)\n  (:start . 47) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 55))\n ((:tag . "IN") (:stem . "whilst") (:form . "whilst") (:end . 64)\n  (:start . 58) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 74) (:start . 69)\n  (:id . 58))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 80) (:start . 75)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "C5") (:form . "C5") (:end . 84) (:start . 82)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 85) (:start . 84)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "switch") (:form . "switched") (:end . 94)\n  (:start . 86) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 64))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 108)\n  (:start . 98) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 117)\n  (:start . 112) (:id . 67))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 127)\n  (:start . 118) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.233) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504036@unknown@formal@none@1@S@As the final corpus would consist of both E. coli and human abstracts, we wanted to verify to what extent annotation quality could be maintained if the species referred to in the abstracts is changed.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VB") (:stem . "consist") (:form . "consist") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 41) (:start . 37)\n  (:id . 49))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 49) (:start . 45)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 59) (:start . 54)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 69)\n  (:start . 60) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "want") (:form . "wanted") (:end . 80) (:start . 74)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n  (:id . 58))\n ((:tag . "VB") (:stem . "verify") (:form . "verify") (:end . 90)\n  (:start . 84) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . "WP") (:stem . "what") (:form . "what") (:end . 98) (:start . 94)\n  (:id . 61))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 105)\n  (:start . 99) (:id . 62))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 116)\n  (:start . 106) (:id . 63))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 124)\n  (:start . 117) (:id . 64))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 130)\n  (:start . 125) (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 133) (:start . 131)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "maintain") (:form . "maintained") (:end . 144)\n  (:start . 134) (:id . 67))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 147) (:start . 145)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 159)\n  (:start . 152) (:id . 70))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 168)\n  (:start . 160) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 171) (:start . 169)\n  (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 174) (:start . 172)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 188)\n  (:start . 179) (:id . 75))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 191) (:start . 189)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "change") (:form . "changed") (:end . 199)\n  (:start . 192) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s12.234) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504037@unknown@formal@none@1@S@Inter-annotator agreement during training@(((:tag . "NNP") (:stem . "Inter-annotator") (:form . "Inter-annotator")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 25)\n  (:start . 16) (:id . 43))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 32)\n  (:start . 26) (:id . 44))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 41)\n  (:start . 33) (:id . 45)))@@@1@4@((:identifiers (:sid . :s12.235) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504038@unknown@formal@none@1@S@The general trend was for the agreement rates to rise gradually between training cycles C1 and C4.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "trend") (:form . "trend") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 39)\n  (:start . 30) (:id . 48))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "VB") (:stem . "rise") (:form . "rise") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "RB") (:stem . "gradually") (:form . "gradually") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 71)\n  (:start . 64) (:id . 53))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 80)\n  (:start . 72) (:id . 54))\n ((:tag . "NNS") (:stem . "cycle") (:form . "cycles") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . "NNP") (:stem . "C1") (:form . "C1") (:end . 90) (:start . 88)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 57))\n ((:tag . "NN") (:stem . "c4") (:form . "C4") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s12.236) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504039@unknown@formal@none@1@S@In addition, the discrepancy between relaxed and exact span matches narrowed as the training progressed.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "discrepancy") (:form . "discrepancy") (:end . 28)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "JJ") (:stem . "relaxed") (:form . "relaxed") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "exact") (:form . "exact") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "span") (:form . "span") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "match") (:form . "matches") (:end . 67)\n  (:start . 60) (:id . 52))\n ((:tag . "VBN") (:stem . "narrow") (:form . "narrowed") (:end . 76)\n  (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . "VBD") (:stem . "progress") (:form . "progressed") (:end . 103)\n  (:start . 93) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.237) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504040@unknown@formal@none@1@S@For most tasks, the agreement rates peaked at the end of cycle C4, with most agreement levels falling in the range 70% - 90%, which we consider to be acceptable [47].@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 29)\n  (:start . 20) (:id . 47))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "peak") (:form . "peaked") (:end . 42) (:start . 36)\n  (:id . 49))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 62) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "c4") (:form . "C4") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 71) (:start . 67)\n  (:id . 57))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 76) (:start . 72)\n  (:id . 58))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 86)\n  (:start . 77) (:id . 59))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 93)\n  (:start . 87) (:id . 60))\n ((:tag . "VBG") (:stem . "fall") (:form . "falling") (:end . 101)\n  (:start . 94) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 63))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 114)\n  (:start . 109) (:id . 64))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 117) (:start . 115)\n  (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 118) (:start . 117)\n  (:id . 66))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 120) (:start . 119)\n  (:id . 67))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 123) (:start . 121)\n  (:id . 68))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 124) (:start . 123)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 70))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 131)\n  (:start . 126) (:id . 71))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 134) (:start . 132)\n  (:id . 72))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 143)\n  (:start . 135) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 146) (:start . 144)\n  (:id . 74))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 149) (:start . 147)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "acceptable") (:form . "acceptable") (:end . 160)\n  (:start . 150) (:id . 76))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 162) (:start . 161)\n  (:id . 77))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 164) (:start . 162)\n  (:id . 78))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 165) (:start . 164)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s12.238) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504041@unknown@formal@none@1@S@When the species referred to in the abstract was changed (from E. coli to human), this resulted in a drop in agreement rates for most tasks, particularly bio-concept assignment, suggesting that a period of adjustment is required when switching to a new species.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "abstract") (:form . "abstract") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "change") (:form . "changed") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 70) (:start . 66)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 79) (:start . 74)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 59))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 86) (:start . 82)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 95)\n  (:start . 87) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n  (:id . 63))\n ((:tag . "NN") (:stem . "drop") (:form . "drop") (:end . 105) (:start . 101)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 65))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 118)\n  (:start . 109) (:id . 66))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 124)\n  (:start . 119) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 128) (:start . 125)\n  (:id . 68))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 133) (:start . 129)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 139)\n  (:start . 134) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 71))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 153)\n  (:start . 141) (:id . 72))\n ((:tag . "JJ") (:stem . "bio-concept") (:form . "bio-concept") (:end . 165)\n  (:start . 154) (:id . 73))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 176)\n  (:start . 166) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 188)\n  (:start . 178) (:id . 76))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 193) (:start . 189)\n  (:id . 77))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 195) (:start . 194)\n  (:id . 78))\n ((:tag . "NN") (:stem . "period") (:form . "period") (:end . 202)\n  (:start . 196) (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n  (:id . 80))\n ((:tag . "NN") (:stem . "adjustment") (:form . "adjustment") (:end . 216)\n  (:start . 206) (:id . 81))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 219) (:start . 217)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 228)\n  (:start . 220) (:id . 83))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 233) (:start . 229)\n  (:id . 84))\n ((:tag . "VBG") (:stem . "switch") (:form . "switching") (:end . 243)\n  (:start . 234) (:id . 85))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 246) (:start . 244)\n  (:id . 86))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 248) (:start . 247)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 252) (:start . 249)\n  (:id . 88))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 260)\n  (:start . 253) (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 261) (:start . 260)\n  (:id . 90)))@@@1@49@((:hcues ((:id . :x12.239.1) (:span 178 188)))\n (:hscopes ((:id . :x12.239.1) (:span 178 260)))\n (:identifiers (:sid . :s12.239) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504042@unknown@formal@none@1@S@Two tasks, however, i.e., semantic role assignment and argument identification, seem more domain-independent, in that the agreement rates stayed constant, or even continued to rise slightly, when the species referred to in the text was changed.@(((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 18)\n  (:start . 11) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 24) (:start . 20)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 34)\n  (:start . 26) (:id . 49))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 39) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 50)\n  (:start . 40) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 63)\n  (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 78) (:start . 64) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "seem") (:form . "seem") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 89) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "domain-independent") (:form . "domain-independent")\n  (:end . 108) (:start . 90) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 112) (:start . 110)\n  (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 117) (:start . 113)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 131)\n  (:start . 122) (:id . 63))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 137)\n  (:start . 132) (:id . 64))\n ((:tag . "VBD") (:stem . "stay") (:form . "stayed") (:end . 144)\n  (:start . 138) (:id . 65))\n ((:tag . "JJ") (:stem . "constant") (:form . "constant") (:end . 153)\n  (:start . 145) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 157) (:start . 155)\n  (:id . 68))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 162) (:start . 158)\n  (:id . 69))\n ((:tag . "VBD") (:stem . "continue") (:form . "continued") (:end . 172)\n  (:start . 163) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "VB") (:stem . "rise") (:form . "rise") (:end . 180) (:start . 176)\n  (:id . 72))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 189)\n  (:start . 181) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n  (:id . 74))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 195) (:start . 191)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 199) (:start . 196)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 207)\n  (:start . 200) (:id . 77))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 216)\n  (:start . 208) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 219) (:start . 217)\n  (:id . 79))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 222) (:start . 220)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 226) (:start . 223)\n  (:id . 81))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 231) (:start . 227)\n  (:id . 82))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 235) (:start . 232)\n  (:id . 83))\n ((:tag . "VBN") (:stem . "change") (:form . "changed") (:end . 243)\n  (:start . 236) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x12.240.1) (:span 155 157))\n  ((:id . :x12.240.2) (:span 80 84)))\n (:hscopes ((:id . :x12.240.1) (:span 138 189))\n  ((:id . :x12.240.2) (:span 0 108)))\n (:identifiers (:sid . :s12.240) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504043@unknown@formal@none@1@S@The main exception to the general trend for improvement is in the assignment of biological concept categories, for which there was no discernible improvement during the training period.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "main") (:form . "main") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "exception") (:form . "exception") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "trend") (:form . "trend") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "improvement") (:form . "improvement") (:end . 55)\n  (:start . 44) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 76)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 90)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 98)\n  (:start . 91) (:id . 57))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 109)\n  (:start . 99) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 114) (:start . 111)\n  (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 120)\n  (:start . 115) (:id . 61))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 126)\n  (:start . 121) (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 133) (:start . 131)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "discernible") (:form . "discernible") (:end . 145)\n  (:start . 134) (:id . 65))\n ((:tag . "NN") (:stem . "improvement") (:form . "improvement") (:end . 157)\n  (:start . 146) (:id . 66))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 164)\n  (:start . 158) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 68))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 177)\n  (:start . 169) (:id . 69))\n ((:tag . "NN") (:stem . "period") (:form . "period") (:end . 184)\n  (:start . 178) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s12.241) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504044@unknown@formal@none@1@S@Differing levels of experience in gene regulation may have caused annotators to vary in their ability to accurately assign fine-grained biological concept categories.@(((:tag . "VBG") (:stem . "differ") (:form . "Differing") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 16)\n  (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "NN") (:stem . "experience") (:form . "experience") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 49)\n  (:start . 39) (:id . 48))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 65)\n  (:start . 59) (:id . 51))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 76)\n  (:start . 66) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "VB") (:stem . "vary") (:form . "vary") (:end . 84) (:start . 80)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 93)\n  (:start . 88) (:id . 56))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 101)\n  (:start . 94) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "RB") (:stem . "accurately") (:form . "accurately") (:end . 115)\n  (:start . 105) (:id . 59))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 122)\n  (:start . 116) (:id . 60))\n ((:tag . "JJ") (:stem . "fine-grained") (:form . "fine-grained") (:end . 135)\n  (:start . 123) (:id . 61))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 146)\n  (:start . 136) (:id . 62))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 154)\n  (:start . 147) (:id . 63))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 165)\n  (:start . 155) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x12.242.1) (:span 50 53)))\n (:hscopes ((:id . :x12.242.1) (:span 50 165)))\n (:identifiers (:sid . :s12.242) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504045@unknown@formal@none@1@S@However, higher levels of agreement are achieved if we take the hierarchical structure of the concept categories into account, and look at cases where the category assigned by one annotator is the parent of the term assigned by the other.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "take") (:form . "take") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "hierarchical") (:form . "hierarchical") (:end . 76)\n  (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 86)\n  (:start . 77) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 101)\n  (:start . 94) (:id . 58))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 112)\n  (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 117) (:start . 113)\n  (:id . 60))\n ((:tag . "NN") (:stem . "account") (:form . "account") (:end . 125)\n  (:start . 118) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "VB") (:stem . "look") (:form . "look") (:end . 135) (:start . 131)\n  (:id . 64))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 138) (:start . 136)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 144)\n  (:start . 139) (:id . 66))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 150)\n  (:start . 145) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 68))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 163)\n  (:start . 155) (:id . 69))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 172)\n  (:start . 164) (:id . 70))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 179) (:start . 176)\n  (:id . 72))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 189)\n  (:start . 180) (:id . 73))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 192) (:start . 190)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 75))\n ((:tag . "NN") (:stem . "parent") (:form . "parent") (:end . 203)\n  (:start . 197) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 206) (:start . 204)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 210) (:start . 207)\n  (:id . 78))\n ((:tag . "NN") (:stem . "term") (:form . "term") (:end . 215) (:start . 211)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 224)\n  (:start . 216) (:id . 80))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 227) (:start . 225)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 231) (:start . 228)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 237)\n  (:start . 232) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s12.243) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504046@unknown@formal@none@1@S@If we map all concept categories to their top level supercategories, then agreement rates of up to 90% (after cycle C4) are achieved.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "map") (:form . "map") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 21)\n  (:start . 14) (:id . 46))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 32)\n  (:start . 22) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 41)\n  (:start . 36) (:id . 49))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "supercategory") (:form . "supercategories")\n  (:end . 67) (:start . 52) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 83)\n  (:start . 74) (:id . 55))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 89) (:start . 84)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "IN") (:stem . "up") (:form . "up") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 101) (:start . 99)\n  (:id . 60))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 109)\n  (:start . 104) (:id . 63))\n ((:tag . "NN") (:stem . "cycle") (:form . "cycle") (:end . 115)\n  (:start . 110) (:id . 64))\n ((:tag . "NN") (:stem . "c4") (:form . "C4") (:end . 118) (:start . 116)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 123) (:start . 120)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 132)\n  (:start . 124) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.244) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504047@unknown@formal@none@1@S@Results and discussion@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "discussion") (:form . "discussion") (:end . 22)\n  (:start . 12) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.245) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504048@unknown@formal@none@1@S@Following the training period, the final annotated GREC was produced.@(((:tag . "VBG") (:stem . "follow") (:form . "Following") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "period") (:form . "period") (:end . 29)\n  (:start . 23) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "produce") (:form . "produced") (:end . 68)\n  (:start . 60) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s12.246) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504049@unknown@formal@none@1@S@In this section, we provide details, statistics and analysis of this corpus.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 27)\n  (:start . 20) (:id . 47))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 47)\n  (:start . 37) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 60)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 76) (:start . 75)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.247) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504050@unknown@formal@none@1@S@Following some initial general statistics regarding the corpus, we move on to examine the most commonly annotated verbs and nominalised verbs on which events are centred.@(((:tag . "VBG") (:stem . "follow") (:form . "Following") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 41)\n  (:start . 31) (:id . 46))\n ((:tag . "VBG") (:stem . "regard") (:form . "regarding") (:end . 51)\n  (:start . 42) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 48))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 62)\n  (:start . 56) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "move") (:form . "move") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "RP") (:stem . "on") (:form . "on") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 85)\n  (:start . 78) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 94) (:start . 90)\n  (:id . 57))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 103)\n  (:start . 95) (:id . 58))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 113)\n  (:start . 104) (:id . 59))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 119)\n  (:start . 114) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 135)\n  (:start . 124) (:id . 62))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 141)\n  (:start . 136) (:id . 63))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 150)\n  (:start . 145) (:id . 65))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 157)\n  (:start . 151) (:id . 66))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 161) (:start . 158)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "centre") (:form . "centred") (:end . 169)\n  (:start . 162) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.248) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504051@unknown@formal@none@1@S@Subsequently, we examine in more detail the arguments of events, including an analysis of the numbers of arguments that occur in different events, the distribution of different semantic argument types, and the most commonly occurring patterns of arguments.@(((:tag . "RB") (:stem . "subsequently") (:form . "Subsequently") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "examine") (:form . "examine") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "detail") (:form . "detail") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 74)\n  (:start . 65) (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 101)\n  (:start . 94) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 114)\n  (:start . 105) (:id . 61))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 119) (:start . 115)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 125)\n  (:start . 120) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 128) (:start . 126)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 138)\n  (:start . 129) (:id . 65))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 145)\n  (:start . 139) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 150) (:start . 147)\n  (:id . 68))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 163)\n  (:start . 151) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 166) (:start . 164)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 176)\n  (:start . 167) (:id . 71))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 185)\n  (:start . 177) (:id . 72))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 194)\n  (:start . 186) (:id . 73))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 200)\n  (:start . 195) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 201) (:start . 200)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 205) (:start . 202)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n  (:id . 77))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 214) (:start . 210)\n  (:id . 78))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 223)\n  (:start . 215) (:id . 79))\n ((:tag . "VBG") (:stem . "occur") (:form . "occurring") (:end . 233)\n  (:start . 224) (:id . 80))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 242)\n  (:start . 234) (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 245) (:start . 243)\n  (:id . 82))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 255)\n  (:start . 246) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 256) (:start . 255)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s12.249) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504052@unknown@formal@none@1@S@Biological concept assignment is then covered, including the distribution of the assigned concepts amongst the five different supercategories, together with an analysis of the most commonly assigned concepts.@(((:tag . "JJ") (:stem . "biological") (:form . "Biological") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 18)\n  (:start . 11) (:id . 43))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 29)\n  (:start . 19) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 32) (:start . 30)\n  (:id . 45))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 56)\n  (:start . 47) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 73)\n  (:start . 61) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 98)\n  (:start . 90) (:id . 55))\n ((:tag . "IN") (:stem . "amongst") (:form . "amongst") (:end . 106)\n  (:start . 99) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 57))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 115) (:start . 111)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 125)\n  (:start . 116) (:id . 59))\n ((:tag . "NNS") (:stem . "supercategory") (:form . "supercategories")\n  (:end . 141) (:start . 126) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 142) (:start . 141)\n  (:id . 61))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 151)\n  (:start . 143) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 156) (:start . 152)\n  (:id . 63))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 159) (:start . 157)\n  (:id . 64))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 168)\n  (:start . 160) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 171) (:start . 169)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 175) (:start . 172)\n  (:id . 67))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 180) (:start . 176)\n  (:id . 68))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 189)\n  (:start . 181) (:id . 69))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 198)\n  (:start . 190) (:id . 70))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 207)\n  (:start . 199) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s12.250) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504053@unknown@formal@none@1@S@Finally, we consider quality control of the GREC, including both IAA scores and annotator discrepancies that were found through manual examination of the corpus.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 59)\n  (:start . 50) (:id . 52))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "IAA") (:form . "IAA") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 89)\n  (:start . 80) (:id . 57))\n ((:tag . "NNS") (:stem . "discrepancy") (:form . "discrepancies")\n  (:end . 103) (:start . 90) (:id . 58))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 113) (:start . 109)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 119)\n  (:start . 114) (:id . 61))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 127)\n  (:start . 120) (:id . 62))\n ((:tag . "JJ") (:stem . "manual") (:form . "manual") (:end . 134)\n  (:start . 128) (:id . 63))\n ((:tag . "NN") (:stem . "examination") (:form . "examination") (:end . 146)\n  (:start . 135) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 66))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 160)\n  (:start . 154) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s12.251) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504054@unknown@formal@none@1@S@Corpus characteristics and statistics@(((:tag . "NN") (:stem . "corpus") (:form . "Corpus") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "characteristic") (:form . "characteristics")\n  (:end . 22) (:start . 7) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 37)\n  (:start . 27) (:id . 45)))@@@1@4@((:identifiers (:sid . :s12.252) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504055@unknown@formal@none@1@S@Candidate abstracts for annotation for the final GREC were selected from species-specific corpora of MEDLINE abstracts collected by EMBL-EBI, who chose abstracts relevant to the E. coli and human species using their own rule-based species-filtering methods.@(((:tag . "NN") (:stem . "candidate") (:form . "Candidate") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 19)\n  (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 23) (:start . 20)\n  (:id . 44))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 34)\n  (:start . 24) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 48) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 53) (:start . 49)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 67)\n  (:start . 59) (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "species-specific") (:form . "species-specific")\n  (:end . 89) (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 97)\n  (:start . 90) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "MEDLINE") (:form . "MEDLINE") (:end . 108)\n  (:start . 101) (:id . 56))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 118)\n  (:start . 109) (:id . 57))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 128)\n  (:start . 119) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 131) (:start . 129)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "EMBL-EBI") (:form . "EMBL-EBI") (:end . 140)\n  (:start . 132) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 61))\n ((:tag . "WP") (:stem . "who") (:form . "who") (:end . 145) (:start . 142)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 151)\n  (:start . 146) (:id . 63))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 161)\n  (:start . 152) (:id . 64))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 170)\n  (:start . 162) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 173) (:start . 171)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 67))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 180) (:start . 178)\n  (:id . 68))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 185) (:start . 181)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 189) (:start . 186)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 195)\n  (:start . 190) (:id . 71))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 203)\n  (:start . 196) (:id . 72))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 209) (:start . 204)\n  (:id . 73))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 215)\n  (:start . 210) (:id . 74))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 219) (:start . 216)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "rule-based") (:form . "rule-based") (:end . 230)\n  (:start . 220) (:id . 76))\n ((:tag . "JJ") (:stem . "species-filtering") (:form . "species-filtering")\n  (:end . 248) (:start . 231) (:id . 77))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 256)\n  (:start . 249) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s12.253) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504056@unknown@formal@none@1@S@The candidate abstracts were further screened for relevance to gene regulation by one of the authors with biological expertise.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 28) (:start . 24)\n  (:id . 45))\n ((:tag . "RB") (:stem . "further") (:form . "further") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "VBN") (:stem . "screen") (:form . "screened") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "NN") (:stem . "relevance") (:form . "relevance") (:end . 59)\n  (:start . 50) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n  (:id . 50))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 78)\n  (:start . 68) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "author") (:form . "authors") (:end . 100)\n  (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 105) (:start . 101)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 116)\n  (:start . 106) (:id . 59))\n ((:tag . "NN") (:stem . "expertise") (:form . "expertise") (:end . 126)\n  (:start . 117) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s12.254) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504057@unknown@formal@none@1@S@General statistics regarding the GREC are shown in Table 4.@(((:tag . "JJ") (:stem . "general") (:form . "General") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 18)\n  (:start . 8) (:id . 43))\n ((:tag . "VBG") (:stem . "regard") (:form . "regarding") (:end . 28)\n  (:start . 19) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 47) (:start . 42)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 56) (:start . 51)\n  (:id . 50))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s12.255) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504058@unknown@formal@none@1@S@The effort expended by the 6 annotators amounted to a total of 876 person hours (equivalent to 6.4 person months).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "effort") (:form . "effort") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "expend") (:form . "expended") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 39)\n  (:start . 29) (:id . 48))\n ((:tag . "VBD") (:stem . "amounte") (:form . "amounted") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "NN") (:stem . "total") (:form . "total") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "CD") (:stem . "876") (:form . "876") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "NN") (:stem . "person") (:form . "person") (:end . 73)\n  (:start . 67) (:id . 55))\n ((:tag . "NNS") (:stem . "hour") (:form . "hours") (:end . 79) (:start . 74)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "equivalent") (:form . "equivalent") (:end . 91)\n  (:start . 81) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 59))\n ((:tag . "CD") (:stem . "6.4") (:form . "6.4") (:end . 98) (:start . 95)\n  (:id . 60))\n ((:tag . "NN") (:stem . "person") (:form . "person") (:end . 105)\n  (:start . 99) (:id . 61))\n ((:tag . "NNS") (:stem . "month") (:form . "months") (:end . 112)\n  (:start . 106) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s12.256) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504059@unknown@formal@none@1@S@General corpus statistics@(((:tag . "JJ") (:stem . "general") (:form . "General") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 25)\n  (:start . 15) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.257) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504060@unknown@formal@none@1@S@The statistics in Table 4 reinforce the importance of considering events that are described by nominalised verbs as well as those that are described by verbs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "reinforce") (:form . "reinforce") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 50)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "consider") (:form . "considering") (:end . 65)\n  (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 72)\n  (:start . 66) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 91)\n  (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 106)\n  (:start . 95) (:id . 57))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 112)\n  (:start . 107) (:id . 58))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 115) (:start . 113)\n  (:id . 59))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 120) (:start . 116)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 123) (:start . 121)\n  (:id . 61))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 129)\n  (:start . 124) (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 134) (:start . 130)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 138) (:start . 135)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 148)\n  (:start . 139) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 151) (:start . 149)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 157)\n  (:start . 152) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s12.258) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504061@unknown@formal@none@1@S@In the E. coli corpus, events that are centred on nominalised verbs are almost as common as those centred on verbs, although the range of different words that are used to describe events is much greater for verbs than for nominalised verbs.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 14) (:start . 10)\n  (:id . 45))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 21)\n  (:start . 15) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 29)\n  (:start . 23) (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 38) (:start . 35)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "centre") (:form . "centred") (:end . 46)\n  (:start . 39) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 49) (:start . 47)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 61)\n  (:start . 50) (:id . 53))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 78)\n  (:start . 72) (:id . 56))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 88)\n  (:start . 82) (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 97) (:start . 92)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "centre") (:form . "centred") (:end . 105)\n  (:start . 98) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 108) (:start . 106)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 114)\n  (:start . 109) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 64))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 124)\n  (:start . 116) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 128) (:start . 125)\n  (:id . 66))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 134)\n  (:start . 129) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 147)\n  (:start . 138) (:id . 69))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 153)\n  (:start . 148) (:id . 70))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 158) (:start . 154)\n  (:id . 71))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 162) (:start . 159)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 167) (:start . 163)\n  (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 170) (:start . 168)\n  (:id . 74))\n ((:tag . "VB") (:stem . "describe") (:form . "describe") (:end . 179)\n  (:start . 171) (:id . 75))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 186)\n  (:start . 180) (:id . 76))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 189) (:start . 187)\n  (:id . 77))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 194) (:start . 190)\n  (:id . 78))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 202)\n  (:start . 195) (:id . 79))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 206) (:start . 203)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 212)\n  (:start . 207) (:id . 81))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 217) (:start . 213)\n  (:id . 82))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 221) (:start . 218)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 233)\n  (:start . 222) (:id . 84))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 239)\n  (:start . 234) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 240) (:start . 239)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s12.259) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504062@unknown@formal@none@1@S@Verbs and nominalised verbs expressing events@(((:tag . "NNS") (:stem . "verb") (:form . "Verbs") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "express") (:form . "expressing") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 45)\n  (:start . 39) (:id . 47)))@@@1@6@((:identifiers (:sid . :s12.260) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504063@unknown@formal@none@1@S@Table 5 shows the top 10 most common words (verbs and nominalised verbs) which express events, both in the corpus as a whole, and separately for the E. coli and human parts of the corpus.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 29) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 36)\n  (:start . 30) (:id . 49))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 42) (:start . 37)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 49) (:start . 44)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 65)\n  (:start . 54) (:id . 54))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 71) (:start . 66)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 78) (:start . 73)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "express") (:form . "express") (:end . 86)\n  (:start . 79) (:id . 58))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 93)\n  (:start . 87) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 60))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 99) (:start . 95)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 63))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 113)\n  (:start . 107) (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 116) (:start . 114)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 118) (:start . 117)\n  (:id . 66))\n ((:tag . "NN") (:stem . "whole") (:form . "whole") (:end . 124)\n  (:start . 119) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 69))\n ((:tag . "RB") (:stem . "separately") (:form . "separately") (:end . 140)\n  (:start . 130) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 144) (:start . 141)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 72))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 151) (:start . 149)\n  (:id . 73))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 156) (:start . 152)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 166)\n  (:start . 161) (:id . 76))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 172)\n  (:start . 167) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 175) (:start . 173)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 79))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 186)\n  (:start . 180) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s12.261) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504064@unknown@formal@none@1@S@In each case, events centred on these 10 words constitute 45 - 50% of the total events annotated, suggesting that the majority of relevant events are centred on a relatively small set of words.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 20)\n  (:start . 14) (:id . 46))\n ((:tag . "VBN") (:stem . "centre") (:form . "centred") (:end . 28)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 46) (:start . 41)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "constitute") (:form . "constitute") (:end . 57)\n  (:start . 47) (:id . 52))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 66) (:start . 65)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 79) (:start . 74)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 86)\n  (:start . 80) (:id . 60))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 96)\n  (:start . 87) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "suggest") (:form . "suggesting") (:end . 108)\n  (:start . 98) (:id . 63))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 113) (:start . 109)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 65))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 126)\n  (:start . 118) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 138)\n  (:start . 130) (:id . 68))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 145)\n  (:start . 139) (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 149) (:start . 146)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "centre") (:form . "centred") (:end . 157)\n  (:start . 150) (:id . 71))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 160) (:start . 158)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 162) (:start . 161)\n  (:id . 73))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 173)\n  (:start . 163) (:id . 74))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 179)\n  (:start . 174) (:id . 75))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 183) (:start . 180)\n  (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 186) (:start . 184)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 192)\n  (:start . 187) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x12.262.1) (:span 98 108)))\n (:hscopes ((:id . :x12.262.1) (:span 98 192)))\n (:identifiers (:sid . :s12.262) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504065@unknown@formal@none@1@S@Indeed, in the corpus as a whole, only 55 words (either verbs or nominalised verbs) have been used to annotate 10 or more events.@(((:tag . "RB") (:stem . "indeed") (:form . "Indeed") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 21)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . "whole") (:form . "whole") (:end . 32) (:start . 27)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 50))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 38) (:start . 34)\n  (:id . 51))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 41) (:start . 39)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 47) (:start . 42)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 54))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 55)\n  (:start . 49) (:id . 55))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 61) (:start . 56)\n  (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 64) (:start . 62)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 76)\n  (:start . 65) (:id . 58))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 82) (:start . 77)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 88) (:start . 84)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 93) (:start . 89)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 98) (:start . 94)\n  (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 64))\n ((:tag . "VB") (:stem . "annotate") (:form . "annotate") (:end . 110)\n  (:start . 102) (:id . 65))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 113) (:start . 111)\n  (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 116) (:start . 114)\n  (:id . 67))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 121) (:start . 117)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 128)\n  (:start . 122) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s12.263) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504066@unknown@formal@none@1@S@Most common words describing events@(((:tag . "JJS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "describe") (:form . "describing") (:end . 28)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 35)\n  (:start . 29) (:id . 46)))@@@1@5@((:identifiers (:sid . :s12.264) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504067@unknown@formal@none@1@S@Most of the words in Table 5 correspond to important biological processes.@(((:tag . "JJS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "word") (:form . "words") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 26) (:start . 21)\n  (:id . 47))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "correspond") (:form . "correspond") (:end . 39)\n  (:start . 29) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 52)\n  (:start . 43) (:id . 51))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 63)\n  (:start . 53) (:id . 52))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 73)\n  (:start . 64) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.265) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504068@unknown@formal@none@1@S@For some of these processes, occurrences of both the verbal and nominalised forms are quite common, e.g., regulate/regulation, bind/binding, repress/repression, activate/activation.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "occurrence") (:form . "occurrences") (:end . 40)\n  (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "verbal") (:form . "verbal") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 75)\n  (:start . 64) (:id . 54))\n ((:tag . "NNS") (:stem . "form") (:form . "forms") (:end . 81) (:start . 76)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "RB") (:stem . "quite") (:form . "quite") (:end . 91) (:start . 86)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 98)\n  (:start . 92) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 104) (:start . 100)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 61))\n ((:tag . "NN") (:stem . "regulate/regulation")\n  (:form . "regulate/regulation") (:end . 125) (:start . 106) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 63))\n ((:tag . "NN") (:stem . "bind/binding") (:form . "bind/binding") (:end . 139)\n  (:start . 127) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 65))\n ((:tag . "NN") (:stem . "repress/repression") (:form . "repress/repression")\n  (:end . 159) (:start . 141) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 67))\n ((:tag . "NN") (:stem . "activate/activation")\n  (:form . "activate/activation") (:end . 180) (:start . 161) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.266) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504069@unknown@formal@none@1@S@In other cases, there appears to be a stronger preference for either the verb or the nominalised verb.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 21) (:start . 16)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "appear") (:form . "appears") (:end . 29)\n  (:start . 22) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "strong") (:form . "stronger") (:end . 46)\n  (:start . 38) (:id . 51))\n ((:tag . "NN") (:stem . "preference") (:form . "preference") (:end . 57)\n  (:start . 47) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 68)\n  (:start . 62) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . "NN") (:stem . "verb") (:form . "verb") (:end . 77) (:start . 73)\n  (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 96)\n  (:start . 85) (:id . 59))\n ((:tag . "NN") (:stem . "verb") (:form . "verb") (:end . 101) (:start . 97)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x12.267.1) (:span 62 68 78 80))\n  ((:id . :x12.267.2) (:span 22 29)))\n (:hscopes ((:id . :x12.267.1) (:span 62 101))\n  ((:id . :x12.267.2) (:span 22 101)))\n (:identifiers (:sid . :s12.267) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504070@unknown@formal@none@1@S@In the E. coli portion of the corpus, for example, twice as many events are centred on the nominalised verb expression than any other word.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 14) (:start . 10)\n  (:id . 45))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 22)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 36)\n  (:start . 30) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 41) (:start . 38)\n  (:id . 51))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 49)\n  (:start . 42) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 53))\n ((:tag . "RB") (:stem . "twice") (:form . "twice") (:end . 56) (:start . 51)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 59) (:start . 57)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 64) (:start . 60)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 71)\n  (:start . 65) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 75) (:start . 72)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "centre") (:form . "centred") (:end . 83)\n  (:start . 76) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 86) (:start . 84)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 102)\n  (:start . 91) (:id . 62))\n ((:tag . "NN") (:stem . "verb") (:form . "verb") (:end . 107) (:start . 103)\n  (:id . 63))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 118)\n  (:start . 108) (:id . 64))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 123) (:start . 119)\n  (:id . 65))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 127) (:start . 124)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 133)\n  (:start . 128) (:id . 67))\n ((:tag . "NN") (:stem . "word") (:form . "word") (:end . 138) (:start . 134)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.268) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504071@unknown@formal@none@1@S@Transcription is also rarely used in its verbal form, i.e. transcribe (16 times in the complete corpus), whilst encode is only ever used in its verbal form.@(((:tag . "NNP") (:stem . "Transcription") (:form . "Transcription")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "RB") (:stem . "rarely") (:form . "rarely") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "verbal") (:form . "verbal") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "FW") (:stem . "transcribe") (:form . "transcribe") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 79) (:start . 74)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "complete") (:form . "complete") (:end . 95)\n  (:start . 87) (:id . 59))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 102)\n  (:start . 96) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "IN") (:stem . "whilst") (:form . "whilst") (:end . 111)\n  (:start . 105) (:id . 63))\n ((:tag . "NN") (:stem . "encode") (:form . "encode") (:end . 118)\n  (:start . 112) (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 121) (:start . 119)\n  (:id . 65))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 126) (:start . 122)\n  (:id . 66))\n ((:tag . "RB") (:stem . "ever") (:form . "ever") (:end . 131) (:start . 127)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 136) (:start . 132)\n  (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 139) (:start . 137)\n  (:id . 69))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 143) (:start . 140)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "verbal") (:form . "verbal") (:end . 150)\n  (:start . 144) (:id . 71))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 155) (:start . 151)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s12.269) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504072@unknown@formal@none@1@S@Event arguments@(((:tag . "NN") (:stem . "event") (:form . "Event") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 15)\n  (:start . 6) (:id . 43)))@@@1@2@((:identifiers (:sid . :s12.270) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504073@unknown@formal@none@1@S@In this section, we provide some statistics regarding annotated event arguments.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 27)\n  (:start . 20) (:id . 47))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 43)\n  (:start . 33) (:id . 49))\n ((:tag . "VBG") (:stem . "regard") (:form . "regarding") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 63)\n  (:start . 54) (:id . 51))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 79)\n  (:start . 70) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.271) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504074@unknown@formal@none@1@S@Firstly, Figure 1 provides an analysis of the numbers of arguments that were identified for different events.@(((:tag . "RB") (:stem . "firstly") (:form . "Firstly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 15)\n  (:start . 9) (:id . 44))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 38)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 53)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 71) (:start . 67)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 87)\n  (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 91) (:start . 88)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 101)\n  (:start . 92) (:id . 58))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 108)\n  (:start . 102) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.272) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504075@unknown@formal@none@1@S@Distribution of event argument counts.@(((:tag . "NN") (:stem . "distribution") (:form . "Distribution") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "NNS") (:stem . "count") (:form . "counts") (:end . 37)\n  (:start . 31) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 38) (:start . 37)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s12.273) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504076@unknown@formal@none@1@S@Each section of the chart shows the percentage of events in the GREC that have been annotated with the indicated number of arguments.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "chart") (:form . "chart") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 46)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 56)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 73) (:start . 69)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 78) (:start . 74)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 93)\n  (:start . 84) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 98) (:start . 94)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 112)\n  (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 119)\n  (:start . 113) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 132)\n  (:start . 123) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.274) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504077@unknown@formal@none@1@S@Whilst it is most common for 1 or 2 arguments to be specified, 15% of events specify 3 or more arguments.@(((:tag . "IN") (:stem . "whilst") (:form . "Whilst") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 35) (:start . 34)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 45)\n  (:start . 36) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 48) (:start . 46)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 51) (:start . 49)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 61)\n  (:start . 52) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 65) (:start . 63)\n  (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 66) (:start . 65)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 76)\n  (:start . 70) (:id . 59))\n ((:tag . "VBP") (:stem . "specify") (:form . "specify") (:end . 84)\n  (:start . 77) (:id . 60))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 86) (:start . 85)\n  (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 89) (:start . 87)\n  (:id . 62))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 94) (:start . 90)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 104)\n  (:start . 95) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.275) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504078@unknown@formal@none@1@S@However, as Figure 1 shows, it is extremely rare in our corpus for 4 or more arguments to be specified.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "show") (:form . "shows") (:end . 26) (:start . 21)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 33) (:start . 31)\n  (:id . 50))\n ((:tag . "RB") (:stem . "extremely") (:form . "extremely") (:end . 43)\n  (:start . 34) (:id . 51))\n ((:tag . "JJ") (:stem . "rare") (:form . "rare") (:end . 48) (:start . 44)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 53))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 55) (:start . 52)\n  (:id . 54))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 62)\n  (:start . 56) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 66) (:start . 63)\n  (:id . 56))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 68) (:start . 67)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 71) (:start . 69)\n  (:id . 58))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 76) (:start . 72)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 86)\n  (:start . 77) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 92) (:start . 90)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 102)\n  (:start . 93) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s12.276) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504079@unknown@formal@none@1@S@Table 6 provides statistics regarding the semantic roles that were assigned to arguments.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . "VBG") (:stem . "regard") (:form . "regarding") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 56) (:start . 51)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 66) (:start . 62)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 75)\n  (:start . 67) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 88)\n  (:start . 79) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s12.277) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504080@unknown@formal@none@1@S@Semantic role occurrences@(((:tag . "JJ") (:stem . "semantic") (:form . "Semantic") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "occurrence") (:form . "occurrences") (:end . 25)\n  (:start . 14) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.278) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504081@unknown@formal@none@1@S@In addition to the 13 roles already introduced, there is a further role named Underspecified, which was to be assigned by annotators to arguments that could not be characterised by one of the 13 defined roles.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "VBN") (:stem . "introduce") (:form . "introduced") (:end . 46)\n  (:start . 36) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 66)\n  (:start . 59) (:id . 54))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 71) (:start . 67)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "name") (:form . "named") (:end . 77) (:start . 72)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Underspecified") (:form . "Underspecified")\n  (:end . 92) (:start . 78) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 99) (:start . 94)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 118)\n  (:start . 110) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 121) (:start . 119)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 132)\n  (:start . 122) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 145)\n  (:start . 136) (:id . 67))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 150) (:start . 146)\n  (:id . 68))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 156)\n  (:start . 151) (:id . 69))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 160) (:start . 157)\n  (:id . 70))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 163) (:start . 161)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "characterise") (:form . "characterised")\n  (:end . 177) (:start . 164) (:id . 72))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 180) (:start . 178)\n  (:id . 73))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 184) (:start . 181)\n  (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n  (:id . 76))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 194) (:start . 192)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 202)\n  (:start . 195) (:id . 78))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 208)\n  (:start . 203) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 209) (:start . 208)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s12.279) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504082@unknown@formal@none@1@S@However, the fact that the Underspecified role was only assigned 11 times in the whole corpus suggests that our originally-defined role set is sufficient to characterise the vast majority of semantic arguments.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "underspecified") (:form . "Underspecified")\n  (:end . 41) (:start . 27) (:id . 48))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 86) (:start . 81)\n  (:id . 57))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 93)\n  (:start . 87) (:id . 58))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 107) (:start . 103)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 111) (:start . 108)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "originally-defined") (:form . "originally-defined")\n  (:end . 130) (:start . 112) (:id . 62))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 135) (:start . 131)\n  (:id . 63))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 139) (:start . 136)\n  (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 142) (:start . 140)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "sufficient") (:form . "sufficient") (:end . 153)\n  (:start . 143) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 156) (:start . 154)\n  (:id . 67))\n ((:tag . "VB") (:stem . "characterise") (:form . "characterise") (:end . 169)\n  (:start . 157) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 173) (:start . 170)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "vast") (:form . "vast") (:end . 178) (:start . 174)\n  (:id . 70))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 187)\n  (:start . 179) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 190) (:start . 188)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 199)\n  (:start . 191) (:id . 73))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 209)\n  (:start . 200) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x12.280.1) (:span 94 102)))\n (:hscopes ((:id . :x12.280.1) (:span 94 209)))\n (:identifiers (:sid . :s12.280) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504083@unknown@formal@none@1@S@The AGENT and THEME roles, which provide the most fundamental information about events, are by far the most commonly assigned.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "AGENT") (:form . "AGENT") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "THEME") (:form . "THEME") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 40)\n  (:start . 33) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 49) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "fundamental") (:form . "fundamental") (:end . 61)\n  (:start . 50) (:id . 52))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 73)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 86)\n  (:start . 80) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 91) (:start . 88)\n  (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 107) (:start . 103)\n  (:id . 61))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 116)\n  (:start . 108) (:id . 62))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 125)\n  (:start . 117) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s12.281) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504084@unknown@formal@none@1@S@Whilst it may seem surprising that only about half of the events specify an AGENT, this can partly be explained by the relatively high occurrence of events that are centred on nominalised verbs (42% of all events) and passive constructions (14% of events).@(((:tag . "IN") (:stem . "whilst") (:form . "Whilst") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "VB") (:stem . "seem") (:form . "seem") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "surprising") (:form . "surprising") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "RB") (:stem . "about") (:form . "about") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "half") (:form . "half") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 64)\n  (:start . 58) (:id . 53))\n ((:tag . "VBP") (:stem . "specify") (:form . "specify") (:end . 72)\n  (:start . 65) (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AGENT") (:form . "AGENT") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 87) (:start . 83)\n  (:id . 58))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "RB") (:stem . "partly") (:form . "partly") (:end . 98)\n  (:start . 92) (:id . 60))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 101) (:start . 99)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "explain") (:form . "explained") (:end . 111)\n  (:start . 102) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 114) (:start . 112)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 64))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 129)\n  (:start . 119) (:id . 65))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 134) (:start . 130)\n  (:id . 66))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 145)\n  (:start . 135) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 155)\n  (:start . 149) (:id . 69))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 160) (:start . 156)\n  (:id . 70))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 164) (:start . 161)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "centre") (:form . "centred") (:end . 172)\n  (:start . 165) (:id . 72))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 175) (:start . 173)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 187)\n  (:start . 176) (:id . 74))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 193)\n  (:start . 188) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 195) (:start . 194)\n  (:id . 76))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 197) (:start . 195)\n  (:id . 77))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 198) (:start . 197)\n  (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 201) (:start . 199)\n  (:id . 79))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 205) (:start . 202)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 212)\n  (:start . 206) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 213) (:start . 212)\n  (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 217) (:start . 214)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "passive") (:form . "passive") (:end . 225)\n  (:start . 218) (:id . 84))\n ((:tag . "NNS") (:stem . "construction") (:form . "constructions")\n  (:end . 239) (:start . 226) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 241) (:start . 240)\n  (:id . 86))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 243) (:start . 241)\n  (:id . 87))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 244) (:start . 243)\n  (:id . 88))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 247) (:start . 245)\n  (:id . 89))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 254)\n  (:start . 248) (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 255) (:start . 254)\n  (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 256) (:start . 255)\n  (:id . 92)))@@@1@51@((:hcues ((:id . :x12.282.1) (:span 88 91)) ((:id . :x12.282.2) (:span 10 13)))\n (:hscopes ((:id . :x12.282.1) (:span 83 255))\n  ((:id . :x12.282.2) (:span 10 81)))\n (:identifiers (:sid . :s12.282) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504085@unknown@formal@none@1@S@According to our corpus, only around 20% of events centred on nominalised verbs and 50% of events using passive verb constructions specify an AGENT.@(((:tag . "VBG") (:stem . "accord") (:form . "According") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 50)\n  (:start . 44) (:id . 52))\n ((:tag . "VBN") (:stem . "centre") (:form . "centred") (:end . 58)\n  (:start . 51) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 61) (:start . 59)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 73)\n  (:start . 62) (:id . 55))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 79) (:start . 74)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 57))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 86) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 87) (:start . 86)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 97)\n  (:start . 91) (:id . 61))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 103) (:start . 98)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "passive") (:form . "passive") (:end . 111)\n  (:start . 104) (:id . 63))\n ((:tag . "NN") (:stem . "verb") (:form . "verb") (:end . 116) (:start . 112)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "construction") (:form . "constructions")\n  (:end . 130) (:start . 117) (:id . 65))\n ((:tag . "VBP") (:stem . "specify") (:form . "specify") (:end . 138)\n  (:start . 131) (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 141) (:start . 139)\n  (:id . 67))\n ((:tag . "NN") (:stem . "agent") (:form . "AGENT") (:end . 147)\n  (:start . 142) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.283) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504086@unknown@formal@none@1@S@Several other roles feature fairly prominently in the events, particularly MANNER, LOCATION, DESTINATION and CONDITION, which is in line with observations made by [20].@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "feature") (:form . "feature") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "RB") (:stem . "fairly") (:form . "fairly") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . "RB") (:stem . "prominently") (:form . "prominently") (:end . 46)\n  (:start . 35) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 60)\n  (:start . 54) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 51))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 74)\n  (:start . 62) (:id . 52))\n ((:tag . "NNP") (:stem . "MANNER") (:form . "MANNER") (:end . 81)\n  (:start . 75) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "LOCATION") (:form . "LOCATION") (:end . 91)\n  (:start . 83) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 92) (:start . 91)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "DESTINATION") (:form . "DESTINATION") (:end . 104)\n  (:start . 93) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 108) (:start . 105)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "CONDITION") (:form . "CONDITION") (:end . 118)\n  (:start . 109) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 125)\n  (:start . 120) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 131) (:start . 129)\n  (:id . 63))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 136) (:start . 132)\n  (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 141) (:start . 137)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "observation") (:form . "observations") (:end . 154)\n  (:start . 142) (:id . 66))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 159) (:start . 155)\n  (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 162) (:start . 160)\n  (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 164) (:start . 163)\n  (:id . 69))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 166) (:start . 164)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s12.284) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504087@unknown@formal@none@1@S@In Table 7, the most common patterns semantic roles assigned to event arguments are shown.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 46))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 20) (:start . 16)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 27)\n  (:start . 21) (:id . 48))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 36)\n  (:start . 28) (:id . 49))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 45)\n  (:start . 37) (:id . 50))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 60)\n  (:start . 52) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 79)\n  (:start . 70) (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 89) (:start . 84)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.285) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504088@unknown@formal@none@1@S@The most common pattern is for only an AGENT and a THEME to be a specified, constituting almost a third of all events.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "agent") (:form . "AGENT") (:end . 44) (:start . 39)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n  (:id . 52))\n ((:tag . "NN") (:stem . "theme") (:form . "THEME") (:end . 56) (:start . 51)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 62) (:start . 60)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 74)\n  (:start . 65) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "constitute") (:form . "constituting") (:end . 88)\n  (:start . 76) (:id . 59))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 95)\n  (:start . 89) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 103) (:start . 98)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 63))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 110) (:start . 107)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 117)\n  (:start . 111) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s12.286) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504089@unknown@formal@none@1@S@When events do specify a third argument, it is most common for the AGENT and THEME, plus one additional type of argument, to be present.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "VB") (:stem . "specify") (:form . "specify") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "third") (:form . "third") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 39)\n  (:start . 31) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 43) (:start . 41)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 46) (:start . 44)\n  (:id . 51))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 51) (:start . 47)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 58)\n  (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "AGENT") (:form . "AGENT") (:end . 72) (:start . 67)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "THEME") (:form . "THEME") (:end . 82) (:start . 77)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 59))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 88) (:start . 84)\n  (:id . 60))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 92) (:start . 89)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 103)\n  (:start . 93) (:id . 62))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 108) (:start . 104)\n  (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 64))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 120)\n  (:start . 112) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 124) (:start . 122)\n  (:id . 67))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 127) (:start . 125)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 135)\n  (:start . 128) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s12.287) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504090@unknown@formal@none@1@S@Most common semantic role patterns@(((:tag . "RBS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 34)\n  (:start . 26) (:id . 46)))@@@1@5@((:identifiers (:sid . :s12.288) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504091@unknown@formal@none@1@S@Biological concepts@(((:tag . "JJ") (:stem . "biological") (:form . "Biological") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 19)\n  (:start . 11) (:id . 43)))@@@1@2@((:identifiers (:sid . :s12.289) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504092@unknown@formal@none@1@S@In the corpus as a whole, 5026 biological concepts were identified.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "whole") (:form . "whole") (:end . 24) (:start . 19)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 48))\n ((:tag . "CD") (:stem . "5026") (:form . "5026") (:end . 30) (:start . 26)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 41)\n  (:start . 31) (:id . 50))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 66)\n  (:start . 56) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.290) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504093@unknown@formal@none@1@S@The distribution of the categories assigned to these concepts amongst the five supercategories is shown in Figure 2.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 46) (:start . 44)\n  (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "amongst") (:form . "amongst") (:end . 69)\n  (:start . 62) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 52))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 78) (:start . 74)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "supercategory") (:form . "supercategories")\n  (:end . 94) (:start . 79) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 97) (:start . 95)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 103) (:start . 98)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 113)\n  (:start . 107) (:id . 58))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 115) (:start . 114)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.291) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504094@unknown@formal@none@1@S@Distribution of biological concept supercategories.@(((:tag . "NN") (:stem . "distribution") (:form . "Distribution") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 26)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 34)\n  (:start . 27) (:id . 45))\n ((:tag . "NNS") (:stem . "supercategory") (:form . "supercategories")\n  (:end . 50) (:start . 35) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 51) (:start . 50)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s12.292) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504095@unknown@formal@none@1@S@Each section of the chart shows the percentage of annotated biological concepts in the GREC that have been assigned a concept class belonging to the indicated supercategory.@(((:tag . "DT") (:stem . "each") (:form . "Each") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "chart") (:form . "chart") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 46)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "annotated") (:form . "annotated") (:end . 59)\n  (:start . 50) (:id . 51))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 70)\n  (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 115)\n  (:start . 107) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 125)\n  (:start . 118) (:id . 62))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 131)\n  (:start . 126) (:id . 63))\n ((:tag . "VBG") (:stem . "belong") (:form . "belonging") (:end . 141)\n  (:start . 132) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 158)\n  (:start . 149) (:id . 67))\n ((:tag . "NN") (:stem . "supercategory") (:form . "supercategory")\n  (:end . 172) (:start . 159) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.293) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504096@unknown@formal@none@1@S@The supercategories Nucleic_Acids and Proteins are so dominant because most gene regulation and expression events describe some kind of relationship between entities of these two types.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "supercategory") (:form . "supercategories")\n  (:end . 19) (:start . 4) (:id . 43))\n ((:tag . "NNPS") (:stem . "Nucleic_Acid") (:form . "Nucleic_Acids")\n  (:end . 33) (:start . 20) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 45))\n ((:tag . "NNPS") (:stem . "Protein") (:form . "Proteins") (:end . 46)\n  (:start . 38) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n  (:id . 47))\n ((:tag . "RB") (:stem . "so") (:form . "so") (:end . 53) (:start . 51)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "dominant") (:form . "dominant") (:end . 62)\n  (:start . 54) (:id . 49))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 70)\n  (:start . 63) (:id . 50))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 75) (:start . 71)\n  (:id . 51))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 80) (:start . 76)\n  (:id . 52))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 91)\n  (:start . 81) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 54))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 106)\n  (:start . 96) (:id . 55))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 113)\n  (:start . 107) (:id . 56))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 122)\n  (:start . 114) (:id . 57))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 127) (:start . 123)\n  (:id . 58))\n ((:tag . "NN") (:stem . "kind") (:form . "kind") (:end . 132) (:start . 128)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 135) (:start . 133)\n  (:id . 60))\n ((:tag . "NN") (:stem . "relationship") (:form . "relationship") (:end . 148)\n  (:start . 136) (:id . 61))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 156)\n  (:start . 149) (:id . 62))\n ((:tag . "NNS") (:stem . "entity") (:form . "entities") (:end . 165)\n  (:start . 157) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n  (:id . 64))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 174)\n  (:start . 169) (:id . 65))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 178) (:start . 175)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 184)\n  (:start . 179) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s12.294) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504097@unknown@formal@none@1@S@The Processes supercategory is also very common, as concepts assigned to this correspond to "embedded" events that describe a mechanistic link between Nucleic_Acid and Proteins, e.g.:@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Processes") (:form . "Processes") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "supercategory") (:form . "supercategory")\n  (:end . 27) (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 47)\n  (:start . 41) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 60)\n  (:start . 52) (:id . 51))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 69)\n  (:start . 61) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 77) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "correspond") (:form . "correspond") (:end . 88)\n  (:start . 78) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 93) (:start . 92)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "embed") (:form . "embedded") (:end . 101)\n  (:start . 93) (:id . 58))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 109)\n  (:start . 103) (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 114) (:start . 110)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 123)\n  (:start . 115) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 125) (:start . 124)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "mechanistic") (:form . "mechanistic") (:end . 137)\n  (:start . 126) (:id . 64))\n ((:tag . "NN") (:stem . "link") (:form . "link") (:end . 142) (:start . 138)\n  (:id . 65))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 150)\n  (:start . 143) (:id . 66))\n ((:tag . "NNP") (:stem . "Nucleic_Acid") (:form . "Nucleic_Acid")\n  (:end . 163) (:start . 151) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 68))\n ((:tag . "NNPS") (:stem . "Protein") (:form . "Proteins") (:end . 176)\n  (:start . 168) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 70))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 182) (:start . 178)\n  (:id . 71))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 183) (:start . 182)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s12.295) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504098@unknown@formal@none@1@S@Expression of the ompF and ompC genes is affected in a reciprocal manner by the osmolarity of the growth medium.@(((:tag . "NN") (:stem . "expression") (:form . "Expression") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "ompf") (:form . "ompF") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "ompc") (:form . "ompC") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "affect") (:form . "affected") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "reciprocal") (:form . "reciprocal") (:end . 65)\n  (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 72)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "NN") (:stem . "osmolarity") (:form . "osmolarity") (:end . 90)\n  (:start . 80) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "growth") (:form . "growth") (:end . 104)\n  (:start . 98) (:id . 60))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 111)\n  (:start . 105) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.296) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504099@unknown@formal@none@1@S@Annotators were instructed to assign the most specific concept possible in the hierarchy; the results show that 66.91% of assignments indeed constitute the most specific concepts.@(((:tag . "NNS") (:stem . "annotator") (:form . "Annotators") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "instruct") (:form . "instructed") (:end . 26)\n  (:start . 16) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 36)\n  (:start . 30) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 62)\n  (:start . 55) (:id . 50))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 71)\n  (:start . 63) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "NN") (:stem . "hierarchy") (:form . "hierarchy") (:end . 88)\n  (:start . 79) (:id . 54))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 101)\n  (:start . 94) (:id . 57))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 106) (:start . 102)\n  (:id . 58))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 111) (:start . 107)\n  (:id . 59))\n ((:tag . "CD") (:stem . "66.91") (:form . "66.91") (:end . 117)\n  (:start . 112) (:id . 60))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 133)\n  (:start . 122) (:id . 63))\n ((:tag . "RB") (:stem . "indeed") (:form . "indeed") (:end . 140)\n  (:start . 134) (:id . 64))\n ((:tag . "VBP") (:stem . "constitute") (:form . "constitute") (:end . 151)\n  (:start . 141) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 66))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 160) (:start . 156)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 169)\n  (:start . 161) (:id . 68))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 178)\n  (:start . 170) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s12.297) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504100@unknown@formal@none@1@S@Table 8 compares the most commonly assigned concepts in the E. coli and human parts of the corpus.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "compare") (:form . "compares") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 83) (:start . 78)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 97)\n  (:start . 91) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.298) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504101@unknown@formal@none@1@S@Comparison of concept assignments in E. coli and human abstracts@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 33)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 64)\n  (:start . 55) (:id . 51)))@@@1@10@((:identifiers (:sid . :s12.299) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504102@unknown@formal@none@1@S@Gene constitutes the most commonly assigned concept in both parts of the corpus.@(((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "constitute") (:form . "constitutes") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 43)\n  (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 51)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 79)\n  (:start . 73) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s12.300) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504103@unknown@formal@none@1@S@It is a general, rather than a specific concept in the Nucleic_Acids hierarchy.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 7) (:start . 6)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 15)\n  (:start . 8) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 23)\n  (:start . 17) (:id . 47))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 39)\n  (:start . 31) (:id . 50))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 47)\n  (:start . 40) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Nucleic_Acids") (:form . "Nucleic_Acids")\n  (:end . 68) (:start . 55) (:id . 54))\n ((:tag . "NN") (:stem . "hierarchy") (:form . "hierarchy") (:end . 78)\n  (:start . 69) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.301) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504104@unknown@formal@none@1@S@However, the frequency of assignments of its specific subtypes, i.e., Mutant_Gene, ORF and Allele is very low, with 19, 10 and 1 assignment, respectively.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "NNS") (:stem . "subtype") (:form . "subtypes") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Mutant_Gene") (:form . "Mutant_Gene") (:end . 81)\n  (:start . 70) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "ORF") (:form . "ORF") (:end . 86) (:start . 83)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Allele") (:form . "Allele") (:end . 97)\n  (:start . 91) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 100) (:start . 98)\n  (:id . 60))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 105) (:start . 101)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 115) (:start . 111)\n  (:id . 64))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 118) (:start . 116)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 66))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 122) (:start . 120)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 68))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 128) (:start . 127)\n  (:id . 69))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 139)\n  (:start . 129) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 71))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 153)\n  (:start . 141) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s12.302) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504105@unknown@formal@none@1@S@This suggests that more specific concept type assignment for genes can be problematic.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 66) (:start . 61)\n  (:id . 51))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "problematic") (:form . "problematic") (:end . 85)\n  (:start . 74) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 55)))@@@1@14@((:hcues ((:id . :x12.303.1) (:span 67 70)) ((:id . :x12.303.2) (:span 5 13)))\n (:hscopes ((:id . :x12.303.1) (:span 19 85))\n  ((:id . :x12.303.2) (:span 5 85)))\n (:identifiers (:sid . :s12.303) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504106@unknown@formal@none@1@S@The category Transcription_Factor also has far more assignments than its sub-categories, Repressor and Activator in the human part of the corpus.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "transcription_factor")\n  (:form . "Transcription_Factor") (:end . 33) (:start . 13) (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 38) (:start . 34)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 42) (:start . 39)\n  (:id . 46))\n ((:tag . "RB") (:stem . "far") (:form . "far") (:end . 46) (:start . 43)\n  (:id . 47))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 63)\n  (:start . 52) (:id . 49))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 68) (:start . 64)\n  (:id . 50))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "sub-category") (:form . "sub-categories")\n  (:end . 87) (:start . 73) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Repressor") (:form . "Repressor") (:end . 98)\n  (:start . 89) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Activator") (:form . "Activator") (:end . 112)\n  (:start . 103) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 125)\n  (:start . 120) (:id . 59))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 130) (:start . 126)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 62))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 144)\n  (:start . 138) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s12.304) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504107@unknown@formal@none@1@S@However, Transcription_Factor is not nearly as frequent in E. coli abstracts as in human corpus (see Table 7).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "transcription_factor")\n  (:form . "Transcription_Factor") (:end . 29) (:start . 9) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 32) (:start . 30)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "RB") (:stem . "nearly") (:form . "nearly") (:end . 43)\n  (:start . 37) (:id . 47))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 46) (:start . 44)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 76)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 88) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 95)\n  (:start . 89) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 100) (:start . 97)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s12.305) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504108@unknown@formal@none@1@S@These differences represent important biological information: due to the relative complexity of eukaryotic systems, transcription factors play a very important role in gene regulation compared to prokaryotes, like E. coli.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 17)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 27)\n  (:start . 18) (:id . 44))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 37)\n  (:start . 28) (:id . 45))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 48)\n  (:start . 38) (:id . 46))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 60)\n  (:start . 49) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 61) (:start . 60)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 65) (:start . 62)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 81)\n  (:start . 73) (:id . 52))\n ((:tag . "NN") (:stem . "complexity") (:form . "complexity") (:end . 92)\n  (:start . 82) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "eukaryotic") (:form . "eukaryotic") (:end . 106)\n  (:start . 96) (:id . 55))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 114)\n  (:start . 107) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 57))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 129) (:start . 116) (:id . 58))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 137)\n  (:start . 130) (:id . 59))\n ((:tag . "VBP") (:stem . "play") (:form . "play") (:end . 142) (:start . 138)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 144) (:start . 143)\n  (:id . 61))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 149) (:start . 145)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 159)\n  (:start . 150) (:id . 63))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 164) (:start . 160)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 167) (:start . 165)\n  (:id . 65))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 172) (:start . 168)\n  (:id . 66))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 183)\n  (:start . 173) (:id . 67))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 192)\n  (:start . 184) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 195) (:start . 193)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "prokaryote") (:form . "prokaryotes") (:end . 207)\n  (:start . 196) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 208) (:start . 207)\n  (:id . 71))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 213) (:start . 209)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "E.") (:form . "E.") (:end . 216) (:start . 214)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "coli") (:form . "coli") (:end . 221) (:start . 217)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s12.306) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504109@unknown@formal@none@1@S@Quality control@(((:tag . "NN") (:stem . "quality") (:form . "Quality") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 15)\n  (:start . 8) (:id . 43)))@@@1@2@((:identifiers (:sid . :s12.307) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504110@unknown@formal@none@1@S@Previously, we showed that good rates of agreement were achieved by the end of the training period.@(((:tag . "RB") (:stem . "previously") (:form . "Previously") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 21) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "good") (:form . "good") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 37) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 50)\n  (:start . 41) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 67) (:start . 65)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 91)\n  (:start . 83) (:id . 58))\n ((:tag . "NN") (:stem . "period") (:form . "period") (:end . 98)\n  (:start . 92) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.308) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504111@unknown@formal@none@1@S@To ensure annotation quality was maintained in the final GREC, approximately one quarter of the abstracts was annotated by all annotators.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "maintain") (:form . "maintained") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 56) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 76) (:start . 63) (:id . 53))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "quarter") (:form . "quarter") (:end . 88)\n  (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 105)\n  (:start . 96) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 119)\n  (:start . 110) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 126) (:start . 123)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 137)\n  (:start . 127) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s12.309) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504112@unknown@formal@none@1@S@In this section, we firstly present some general agreement statistics relating to the whole corpus, followed by more detailed statistics regarding semantic role and biological concept assignment.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "RB") (:stem . "firstly") (:form . "firstly") (:end . 27)\n  (:start . 20) (:id . 47))\n ((:tag . "VBP") (:stem . "present") (:form . "present") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 69)\n  (:start . 59) (:id . 52))\n ((:tag . "VBG") (:stem . "relate") (:form . "relating") (:end . 78)\n  (:start . 70) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 91) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 98)\n  (:start . 92) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "follow") (:form . "followed") (:end . 108)\n  (:start . 100) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 116) (:start . 112)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 125)\n  (:start . 117) (:id . 62))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 136)\n  (:start . 126) (:id . 63))\n ((:tag . "VBG") (:stem . "regard") (:form . "regarding") (:end . 146)\n  (:start . 137) (:id . 64))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 155)\n  (:start . 147) (:id . 65))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 160) (:start . 156)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 164) (:start . 161)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 175)\n  (:start . 165) (:id . 68))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 183)\n  (:start . 176) (:id . 69))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 194)\n  (:start . 184) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s12.310) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504113@unknown@formal@none@1@S@Finally, we examine some types of annotator discrepancies that were found through manual examination of the corpus.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "examine") (:form . "examine") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "NNS") (:stem . "discrepancy") (:form . "discrepancies") (:end . 57)\n  (:start . 44) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 73) (:start . 68)\n  (:id . 53))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 81)\n  (:start . 74) (:id . 54))\n ((:tag . "JJ") (:stem . "manual") (:form . "manual") (:end . 88)\n  (:start . 82) (:id . 55))\n ((:tag . "NN") (:stem . "examination") (:form . "examination") (:end . 100)\n  (:start . 89) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 114)\n  (:start . 108) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.311) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504114@unknown@formal@none@1@S@General agreement statistics@(((:tag . "JJ") (:stem . "general") (:form . "General") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 28)\n  (:start . 18) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.312) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504115@unknown@formal@none@1@S@Average agreement rates for the final corpus were calculated in the same way and for the same annotation subtasks as during the training period.@(((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 104)\n  (:start . 94) (:id . 59))\n ((:tag . "NNS") (:stem . "subtask") (:form . "subtasks") (:end . 113)\n  (:start . 105) (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 116) (:start . 114)\n  (:id . 61))\n ((:tag . "IN") (:stem . "during") (:form . "during") (:end . 123)\n  (:start . 117) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 136)\n  (:start . 128) (:id . 64))\n ((:tag . "NN") (:stem . "period") (:form . "period") (:end . 143)\n  (:start . 137) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s12.313) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504116@unknown@formal@none@1@S@These are reported in Table 9, categorised according to abstract subject.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "categorise") (:form . "categorised") (:end . 42)\n  (:start . 31) (:id . 49))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "VB") (:stem . "abstract") (:form . "abstract") (:end . 64)\n  (:start . 56) (:id . 52))\n ((:tag . "NN") (:stem . "subject") (:form . "subject") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s12.314) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504117@unknown@formal@none@1@S@In most cases, agreement rates are maintain the same level, or in some cases exceed those attained by the end of the training period.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 24)\n  (:start . 15) (:id . 46))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "VB") (:stem . "maintain") (:form . "maintain") (:end . 43)\n  (:start . 35) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 55))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 70) (:start . 66)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 76) (:start . 71)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "exceed") (:form . "exceed") (:end . 83)\n  (:start . 77) (:id . 58))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 89) (:start . 84)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "attain") (:form . "attained") (:end . 98)\n  (:start . 90) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 101) (:start . 99)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 62))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 109) (:start . 106)\n  (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 65))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 125)\n  (:start . 117) (:id . 66))\n ((:tag . "NN") (:stem . "period") (:form . "period") (:end . 132)\n  (:start . 126) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s12.315) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504118@unknown@formal@none@1@S@General agreement statistics in the GREC@(((:tag . "JJ") (:stem . "general") (:form . "General") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 28)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 40) (:start . 36)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s12.316) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504119@unknown@formal@none@1@S@Particularly high levels of agreement (88% or above) are achieved for both the identification of semantic arguments and the assignment of semantic roles to these arguments.@(((:tag . "RB") (:stem . "particularly") (:form . "Particularly") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 17) (:start . 13)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 24)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 47))\n ((:tag . "CD") (:stem . "88") (:form . "88") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 52) (:start . 51)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 56) (:start . 53)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 65)\n  (:start . 57) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 74) (:start . 70)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 57))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 93) (:start . 79) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 105)\n  (:start . 97) (:id . 60))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 115)\n  (:start . 106) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 134)\n  (:start . 124) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 137) (:start . 135)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 146)\n  (:start . 138) (:id . 66))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 152)\n  (:start . 147) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 155) (:start . 153)\n  (:id . 68))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 161)\n  (:start . 156) (:id . 69))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 171)\n  (:start . 162) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s12.317) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504120@unknown@formal@none@1@S@As these are the subtasks that we originally identified as being more linguistically-oriented than others, our results suggest that a detailed set of guidelines, together with an intensive training programme, allow these tasks to be carried out by biologists to a high degree of accuracy.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "subtask") (:form . "subtasks") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "RB") (:stem . "originally") (:form . "originally") (:end . 44)\n  (:start . 34) (:id . 49))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 55)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 64) (:start . 59)\n  (:id . 52))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "linguistically-oriented")\n  (:form . "linguistically-oriented") (:end . 93) (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 98) (:start . 94)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 105)\n  (:start . 99) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 57))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 110) (:start . 107)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 118)\n  (:start . 111) (:id . 59))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 126)\n  (:start . 119) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 131) (:start . 127)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 133) (:start . 132)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 142)\n  (:start . 134) (:id . 63))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 146) (:start . 143)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 160)\n  (:start . 150) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 67))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 170)\n  (:start . 162) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 175) (:start . 171)\n  (:id . 69))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 178) (:start . 176)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "intensive") (:form . "intensive") (:end . 188)\n  (:start . 179) (:id . 71))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 197)\n  (:start . 189) (:id . 72))\n ((:tag . "NN") (:stem . "programme") (:form . "programme") (:end . 207)\n  (:start . 198) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 208) (:start . 207)\n  (:id . 74))\n ((:tag . "VBP") (:stem . "allow") (:form . "allow") (:end . 214)\n  (:start . 209) (:id . 75))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 220)\n  (:start . 215) (:id . 76))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 226)\n  (:start . 221) (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 229) (:start . 227)\n  (:id . 78))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 232) (:start . 230)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 240)\n  (:start . 233) (:id . 80))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 244) (:start . 241)\n  (:id . 81))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 247) (:start . 245)\n  (:id . 82))\n ((:tag . "NNS") (:stem . "biologist") (:form . "biologists") (:end . 258)\n  (:start . 248) (:id . 83))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 261) (:start . 259)\n  (:id . 84))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 263) (:start . 262)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 268) (:start . 264)\n  (:id . 86))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 275)\n  (:start . 269) (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 278) (:start . 276)\n  (:id . 88))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 287)\n  (:start . 279) (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 288) (:start . 287)\n  (:id . 90)))@@@1@49@((:hcues ((:id . :x12.318.1) (:span 119 126)))\n (:hscopes ((:id . :x12.318.1) (:span 119 287)))\n (:identifiers (:sid . :s12.318) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504121@unknown@formal@none@1@S@Semantic role assignment@(((:tag . "JJ") (:stem . "semantic") (:form . "Semantic") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 24)\n  (:start . 14) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.319) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504122@unknown@formal@none@1@S@Table 10 provides more detailed agreement rates for semantic role assignment.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 47) (:start . 42)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 51) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 60)\n  (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 76)\n  (:start . 66) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s12.320) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504123@unknown@formal@none@1@S@High levels of agreement (over 84%) are achieved amongst many of the most commonly occurring roles, including AGENT, THEME, MANNER, LOCATION, DESTINATION and SOURCE.@(((:tag . "JJ") (:stem . "high") (:form . "High") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "CD") (:stem . "84") (:form . "84") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 35) (:start . 34)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 48)\n  (:start . 40) (:id . 52))\n ((:tag . "IN") (:stem . "amongst") (:form . "amongst") (:end . 56)\n  (:start . 49) (:id . 53))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 56))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 73) (:start . 69)\n  (:id . 57))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 82)\n  (:start . 74) (:id . 58))\n ((:tag . "VBG") (:stem . "occur") (:form . "occurring") (:end . 92)\n  (:start . 83) (:id . 59))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 98) (:start . 93)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 109)\n  (:start . 100) (:id . 62))\n ((:tag . "NNP") (:stem . "AGENT") (:form . "AGENT") (:end . 115)\n  (:start . 110) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "THEME") (:form . "THEME") (:end . 122)\n  (:start . 117) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "MANNER") (:form . "MANNER") (:end . 130)\n  (:start . 124) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "LOCATION") (:form . "LOCATION") (:end . 140)\n  (:start . 132) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "DESTINATION") (:form . "DESTINATION") (:end . 153)\n  (:start . 142) (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "SOURCE") (:form . "SOURCE") (:end . 164)\n  (:start . 158) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s12.321) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504124@unknown@formal@none@1@S@However, CONDITION and DESCRIPTIVE-THEME are also fairly common, but have lower rates of agreement.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNP") (:stem . "CONDITION") (:form . "CONDITION") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "DESCRIPTIVE-THEME") (:form . "DESCRIPTIVE-THEME")\n  (:end . 40) (:start . 23) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 44) (:start . 41)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "RB") (:stem . "fairly") (:form . "fairly") (:end . 56)\n  (:start . 50) (:id . 49))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 63)\n  (:start . 57) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 51))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 85) (:start . 80)\n  (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 98)\n  (:start . 89) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 99) (:start . 98)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.322) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504125@unknown@formal@none@1@S@Discrepancies have been examined and are further discussed in the Annotator Discrepancies section below.@(((:tag . "NNS") (:stem . "discrepancy") (:form . "Discrepancies") (:end . 13)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 18) (:start . 14)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 23) (:start . 19)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "examine") (:form . "examined") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "VBN") (:stem . "discuss") (:form . "discussed") (:end . 58)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Annotator") (:form . "Annotator") (:end . 75)\n  (:start . 66) (:id . 52))\n ((:tag . "NNP") (:stem . "Discrepancies") (:form . "Discrepancies")\n  (:end . 89) (:start . 76) (:id . 53))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 97)\n  (:start . 90) (:id . 54))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 103) (:start . 98)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.323) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504126@unknown@formal@none@1@S@Most of the other role types occur much less frequently in the corpus (varying between 1-5% of events), meaning that the agreement rates shown may be less reliable.@(((:tag . "JJS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 34) (:start . 29)\n  (:id . 48))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 55)\n  (:start . 45) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 69)\n  (:start . 63) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "vary") (:form . "varying") (:end . 78)\n  (:start . 71) (:id . 56))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 86)\n  (:start . 79) (:id . 57))\n ((:tag . "CD") (:stem . "1-5") (:form . "1-5") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 101)\n  (:start . 95) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "mean") (:form . "meaning") (:end . 111)\n  (:start . 104) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 66))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 130)\n  (:start . 121) (:id . 67))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 136)\n  (:start . 131) (:id . 68))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 142)\n  (:start . 137) (:id . 69))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 146) (:start . 143)\n  (:id . 70))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 149) (:start . 147)\n  (:id . 71))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 154) (:start . 150)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "reliable") (:form . "reliable") (:end . 163)\n  (:start . 155) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x12.324.1) (:span 143 146)))\n (:hscopes ((:id . :x12.324.1) (:span 143 163)))\n (:identifiers (:sid . :s12.324) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504127@unknown@formal@none@1@S@Individual role agreement statistics@(((:tag . "JJ") (:stem . "individual") (:form . "Individual") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 36)\n  (:start . 26) (:id . 45)))@@@1@4@((:identifiers (:sid . :s12.325) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504128@unknown@formal@none@1@S@Biological concept assignment@(((:tag . "JJ") (:stem . "biological") (:form . "Biological") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 18)\n  (:start . 11) (:id . 43))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 29)\n  (:start . 19) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.326) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504129@unknown@formal@none@1@S@Whilst Table 9 showed that coarse-grained biological category assignment achieved around 95% agreement, the assignment of finer-grained categories achieved the lowest agreement rates amongst all annotation subtasks.@(((:tag . "NNP") (:stem . "Whilst") (:form . "Whilst") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Table") (:form . "Table") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 21) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "coarse-grained") (:form . "coarse-grained")\n  (:end . 41) (:start . 27) (:id . 47))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 52)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 61)\n  (:start . 53) (:id . 49))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 72)\n  (:start . 62) (:id . 50))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 81)\n  (:start . 73) (:id . 51))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 88)\n  (:start . 82) (:id . 52))\n ((:tag . "CD") (:stem . "95") (:form . "95") (:end . 91) (:start . 89)\n  (:id . 53))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 92) (:start . 91)\n  (:id . 54))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 102)\n  (:start . 93) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 57))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 118)\n  (:start . 108) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "finer-grained") (:form . "finer-grained")\n  (:end . 135) (:start . 122) (:id . 60))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 146)\n  (:start . 136) (:id . 61))\n ((:tag . "VBD") (:stem . "achieve") (:form . "achieved") (:end . 155)\n  (:start . 147) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 63))\n ((:tag . "JJS") (:stem . "low") (:form . "lowest") (:end . 166)\n  (:start . 160) (:id . 64))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 176)\n  (:start . 167) (:id . 65))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 182)\n  (:start . 177) (:id . 66))\n ((:tag . "IN") (:stem . "amongst") (:form . "amongst") (:end . 190)\n  (:start . 183) (:id . 67))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 194) (:start . 191)\n  (:id . 68))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 205)\n  (:start . 195) (:id . 69))\n ((:tag . "NNS") (:stem . "subtask") (:form . "subtasks") (:end . 214)\n  (:start . 206) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 215) (:start . 214)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s12.327) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504130@unknown@formal@none@1@S@Table 11 shows the most commonly assigned categories in each portion of the corpus, together with their agreement rates.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 60) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "portion") (:form . "portion") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 82)\n  (:start . 76) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 92)\n  (:start . 84) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 97) (:start . 93)\n  (:id . 58))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 103)\n  (:start . 98) (:id . 59))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 113)\n  (:start . 104) (:id . 60))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 119)\n  (:start . 114) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s12.328) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504131@unknown@formal@none@1@S@Individual biological concept category agreement statistics@(((:tag . "JJ") (:stem . "individual") (:form . "Individual") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 29)\n  (:start . 22) (:id . 44))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 38)\n  (:start . 30) (:id . 45))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 48)\n  (:start . 39) (:id . 46))\n ((:tag . "NNS") (:stem . "statistic") (:form . "statistics") (:end . 59)\n  (:start . 49) (:id . 47)))@@@1@6@((:identifiers (:sid . :s12.329) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504132@unknown@formal@none@1@S@Table 11 illustrates that there are several differences in the most commonly assigned concepts according to the species referred to in the abstract (i.e., E. coli or human).@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "illustrate") (:form . "illustrates") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 55)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 76)\n  (:start . 68) (:id . 53))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 85)\n  (:start . 77) (:id . 54))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 94)\n  (:start . 86) (:id . 55))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 104)\n  (:start . 95) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 107) (:start . 105)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "specie") (:form . "species") (:end . 119)\n  (:start . 112) (:id . 59))\n ((:tag . "VBN") (:stem . "refer") (:form . "referred") (:end . 128)\n  (:start . 120) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 131) (:start . 129)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 63))\n ((:tag . "NN") (:stem . "abstract") (:form . "abstract") (:end . 147)\n  (:start . 139) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 149) (:start . 148)\n  (:id . 65))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 153) (:start . 149)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 67))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 157) (:start . 155)\n  (:id . 68))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 162) (:start . 158)\n  (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 165) (:start . 163)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 171)\n  (:start . 166) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 172) (:start . 171)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s12.330) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504133@unknown@formal@none@1@S@There are also large differences in the rates of agreement for different categories, which are not correlated with their frequency of occurrence.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 32)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 72)\n  (:start . 63) (:id . 53))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 83)\n  (:start . 73) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 90) (:start . 85)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 94) (:start . 91)\n  (:id . 57))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 98) (:start . 95)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "correlate") (:form . "correlated") (:end . 109)\n  (:start . 99) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 114) (:start . 110)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 120)\n  (:start . 115) (:id . 61))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 130)\n  (:start . 121) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 63))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 144)\n  (:start . 134) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.331) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504134@unknown@formal@none@1@S@High levels of agreement (over 75%) are achieved for a number of these categories, most notably Transcription, Cells, Regulation, Promoter, Gene and Enzyme.@(((:tag . "JJ") (:stem . "high") (:form . "High") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "CD") (:stem . "75") (:form . "75") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 35) (:start . 34)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 48)\n  (:start . 40) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 52) (:start . 49)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 54))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 61)\n  (:start . 55) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 56))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 70) (:start . 65)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 81)\n  (:start . 71) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 59))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 87) (:start . 83)\n  (:id . 60))\n ((:tag . "RB") (:stem . "notably") (:form . "notably") (:end . 95)\n  (:start . 88) (:id . 61))\n ((:tag . "NNP") (:stem . "Transcription") (:form . "Transcription")\n  (:end . 109) (:start . 96) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Cells") (:form . "Cells") (:end . 116)\n  (:start . 111) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Regulation") (:form . "Regulation") (:end . 128)\n  (:start . 118) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Promoter") (:form . "Promoter") (:end . 138)\n  (:start . 130) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 144) (:start . 140)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Enzyme") (:form . "Enzyme") (:end . 155)\n  (:start . 149) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s12.332) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504135@unknown@formal@none@1@S@In general, the classes with the highest agreement seem to be those that do not have very specific interpretations, i.e., those concepts with broader interpretations which are understandable by biologists with different backgrounds.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 40)\n  (:start . 33) (:id . 49))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 50)\n  (:start . 41) (:id . 50))\n ((:tag . "VBP") (:stem . "seem") (:form . "seem") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 75) (:start . 73)\n  (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 79) (:start . 76)\n  (:id . 57))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 84) (:start . 80)\n  (:id . 58))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 89) (:start . 85)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 98)\n  (:start . 90) (:id . 60))\n ((:tag . "NNS") (:stem . "interpretation") (:form . "interpretations")\n  (:end . 114) (:start . 99) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 120) (:start . 116)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 127)\n  (:start . 122) (:id . 65))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 136)\n  (:start . 128) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 141) (:start . 137)\n  (:id . 67))\n ((:tag . "JJR") (:stem . "broad") (:form . "broader") (:end . 149)\n  (:start . 142) (:id . 68))\n ((:tag . "NNS") (:stem . "interpretation") (:form . "interpretations")\n  (:end . 165) (:start . 150) (:id . 69))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 171)\n  (:start . 166) (:id . 70))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 175) (:start . 172)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "understandable") (:form . "understandable")\n  (:end . 190) (:start . 176) (:id . 72))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 193) (:start . 191)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "biologist") (:form . "biologists") (:end . 204)\n  (:start . 194) (:id . 74))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 209) (:start . 205)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 219)\n  (:start . 210) (:id . 76))\n ((:tag . "NNS") (:stem . "background") (:form . "backgrounds") (:end . 231)\n  (:start . 220) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s12.333) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504136@unknown@formal@none@1@S@This means that the highest levels of agreement have been reached when the context dictates that a very specific concept cannot be assigned.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 27)\n  (:start . 20) (:id . 46))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "reach") (:form . "reached") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 70) (:start . 66)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 82)\n  (:start . 75) (:id . 55))\n ((:tag . "VBZ") (:stem . "dictate") (:form . "dictates") (:end . 91)\n  (:start . 83) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 98) (:start . 97)\n  (:id . 58))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 103) (:start . 99)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 112)\n  (:start . 104) (:id . 60))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 120)\n  (:start . 113) (:id . 61))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 127)\n  (:start . 121) (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 130) (:start . 128)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 139)\n  (:start . 131) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.334) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504137@unknown@formal@none@1@S@Less agreement is achieved for categories that are more specific to the context of gene regulation and expression, such as Activator, Repressor, Transcription_Factor, etc.@(((:tag . "NN") (:stem . "less") (:form . "Less") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 64)\n  (:start . 56) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 87) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 98)\n  (:start . 88) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 113)\n  (:start . 103) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 119) (:start . 115)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Activator") (:form . "Activator") (:end . 132)\n  (:start . 123) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Repressor") (:form . "Repressor") (:end . 143)\n  (:start . 134) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Transcription_Factor")\n  (:form . "Transcription_Factor") (:end . 165) (:start . 145) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 68))\n ((:tag . "NN") (:stem . "etc") (:form . "etc") (:end . 170) (:start . 167)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s12.335) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504138@unknown@formal@none@1@S@Annotator discrepancies@(((:tag . "NNP") (:stem . "Annotator") (:form . "Annotator") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "discrepancy") (:form . "discrepancies") (:end . 23)\n  (:start . 10) (:id . 43)))@@@1@2@((:identifiers (:sid . :s12.336) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504139@unknown@formal@none@1@S@Certain discrepancies between annotators exist in the final corpus, of which a number are highlighted in this section.@(((:tag . "JJ") (:stem . "certain") (:form . "Certain") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "discrepancy") (:form . "discrepancies") (:end . 21)\n  (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 29)\n  (:start . 22) (:id . 44))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 40)\n  (:start . 30) (:id . 45))\n ((:tag . "VBP") (:stem . "exist") (:form . "exist") (:end . 46) (:start . 41)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 59) (:start . 54)\n  (:id . 49))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 66)\n  (:start . 60) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 76) (:start . 71)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 78) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 85)\n  (:start . 79) (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "highlight") (:form . "highlighted") (:end . 101)\n  (:start . 90) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 109) (:start . 105)\n  (:id . 59))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 117)\n  (:start . 110) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s12.337) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504140@unknown@formal@none@1@S@Whilst the identification of these discrepancies will help to refine the guidelines for future phases of annotation, it was also found that certain errors were being made which were already covered in the guidelines.@(((:tag . "IN") (:stem . "whilst") (:form . "Whilst") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 25) (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "discrepancy") (:form . "discrepancies") (:end . 48)\n  (:start . 35) (:id . 47))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 53) (:start . 49)\n  (:id . 48))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 58) (:start . 54)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "VB") (:stem . "refine") (:form . "refine") (:end . 68)\n  (:start . 62) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 83)\n  (:start . 73) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 87) (:start . 84)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "future") (:form . "future") (:end . 94)\n  (:start . 88) (:id . 55))\n ((:tag . "NNS") (:stem . "phase") (:form . "phases") (:end . 101)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 57))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 115)\n  (:start . 105) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 119) (:start . 117)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 123) (:start . 120)\n  (:id . 61))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 128) (:start . 124)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 134)\n  (:start . 129) (:id . 63))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 139) (:start . 135)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 147)\n  (:start . 140) (:id . 65))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 154)\n  (:start . 148) (:id . 66))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 159) (:start . 155)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 165) (:start . 160)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 170) (:start . 166)\n  (:id . 69))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 176)\n  (:start . 171) (:id . 70))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 181) (:start . 177)\n  (:id . 71))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 189)\n  (:start . 182) (:id . 72))\n ((:tag . "VBN") (:stem . "cover") (:form . "covered") (:end . 197)\n  (:start . 190) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 200) (:start . 198)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 204) (:start . 201)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 215)\n  (:start . 205) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s12.338) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504141@unknown@formal@none@1@S@Thus, there may be a need to more carefully balance conciseness with comprehensiveness in the guidelines.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "need") (:form . "need") (:end . 25) (:start . 21)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n  (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 33) (:start . 29)\n  (:id . 50))\n ((:tag . "RB") (:stem . "carefully") (:form . "carefully") (:end . 43)\n  (:start . 34) (:id . 51))\n ((:tag . "NN") (:stem . "balance") (:form . "balance") (:end . 51)\n  (:start . 44) (:id . 52))\n ((:tag . "NN") (:stem . "conciseness") (:form . "conciseness") (:end . 63)\n  (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "NN") (:stem . "comprehensiveness") (:form . "comprehensiveness")\n  (:end . 86) (:start . 69) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 104)\n  (:start . 94) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x12.339.1) (:span 12 15)))\n (:hscopes ((:id . :x12.339.1) (:span 12 104)))\n (:identifiers (:sid . :s12.339) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504142@unknown@formal@none@1@S@Event identification@(((:tag . "NNP") (:stem . "Event") (:form . "Event") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 20) (:start . 6) (:id . 43)))@@@1@2@((:identifiers (:sid . :s12.340) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504143@unknown@formal@none@1@S@The majority of discrepancies in event identification concern nominalised verbs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "discrepancy") (:form . "discrepancies") (:end . 29)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 53) (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "concern") (:form . "concern") (:end . 61)\n  (:start . 54) (:id . 49))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 73)\n  (:start . 62) (:id . 50))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 79) (:start . 74)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 80) (:start . 79)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s12.341) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504144@unknown@formal@none@1@S@A particular example is the word mutation, which can be used either as a nominalised verb (i.e., the action of mutating), or as an entity (e.g., a mutated gene).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 12)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "word") (:form . "word") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 60) (:start . 56)\n  (:id . 53))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 67)\n  (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 84)\n  (:start . 73) (:id . 57))\n ((:tag . "NN") (:stem . "verb") (:form . "verb") (:end . 89) (:start . 85)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 95) (:start . 91)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 62))\n ((:tag . "NN") (:stem . "action") (:form . "action") (:end . 107)\n  (:start . 101) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "mutate") (:form . "mutating") (:end . 119)\n  (:start . 111) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 124) (:start . 122)\n  (:id . 68))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 127) (:start . 125)\n  (:id . 69))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 130) (:start . 128)\n  (:id . 70))\n ((:tag . "NN") (:stem . "entity") (:form . "entity") (:end . 137)\n  (:start . 131) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 139) (:start . 138)\n  (:id . 72))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 143) (:start . 139)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 146) (:start . 145)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 154)\n  (:start . 147) (:id . 76))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 159) (:start . 155)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 160) (:start . 159)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x12.342.1) (:span 61 67 122 124)))\n (:hscopes ((:id . :x12.342.1) (:span 61 160)))\n (:identifiers (:sid . :s12.342) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504145@unknown@formal@none@1@S@However, the distinction can sometimes be problematic.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "distinction") (:form . "distinction") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "RB") (:stem . "sometimes") (:form . "sometimes") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "problematic") (:form . "problematic") (:end . 53)\n  (:start . 42) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n  (:id . 50)))@@@1@9@((:hcues ((:id . :x12.343.1) (:span 25 28)))\n (:hscopes ((:id . :x12.343.1) (:span 25 53)))\n (:identifiers (:sid . :s12.343) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504146@unknown@formal@none@1@S@Consider the following examples:@(((:tag . "VB") (:stem . "consider") (:form . "Consider") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "following") (:form . "following") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 32) (:start . 31)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s12.344) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504147@unknown@formal@none@1@S@1) In addition, the pleiotropic phenotypes conferred by a particular envZ mutation (envZ473) required the presence of functional OmpR protein.@(((:tag . "LS") (:stem . "1") (:form . "1") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "In") (:end . 5) (:start . 3)\n  (:id . 44))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 14)\n  (:start . 6) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "pleiotropic") (:form . "pleiotropic") (:end . 31)\n  (:start . 20) (:id . 48))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 42)\n  (:start . 32) (:id . 49))\n ((:tag . "VBN") (:stem . "confer") (:form . "conferred") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 68)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "envz") (:form . "envZ") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 82)\n  (:start . 74) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "envz473") (:form . "envZ473") (:end . 91)\n  (:start . 84) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "require") (:form . "required") (:end . 101)\n  (:start . 93) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 114)\n  (:start . 106) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 128)\n  (:start . 118) (:id . 63))\n ((:tag . "NN") (:stem . "ompr") (:form . "OmpR") (:end . 133) (:start . 129)\n  (:id . 64))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 141)\n  (:start . 134) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s12.345) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504148@unknown@formal@none@1@S@2) Therefore, OmpF reduction resulted in a mutation in the marA region.@(((:tag . "LS") (:stem . "2") (:form . "2") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 12)\n  (:start . 3) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "OmpF") (:form . "OmpF") (:end . 18) (:start . 14)\n  (:id . 46))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 28)\n  (:start . 19) (:id . 47))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 51)\n  (:start . 43) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "mara") (:form . "marA") (:end . 63) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 70)\n  (:start . 64) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.346) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504149@unknown@formal@none@1@S@In sentence 1), a particular envZ mutation seems to describe a mutated entity rather than the action of mutation.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 28)\n  (:start . 18) (:id . 48))\n ((:tag . "NN") (:stem . "envz") (:form . "envZ") (:end . 33) (:start . 29)\n  (:id . 49))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 42)\n  (:start . 34) (:id . 50))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 48) (:start . 43)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 52))\n ((:tag . "VB") (:stem . "describe") (:form . "describe") (:end . 60)\n  (:start . 52) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 70)\n  (:start . 63) (:id . 55))\n ((:tag . "NN") (:stem . "entity") (:form . "entity") (:end . 77)\n  (:start . 71) (:id . 56))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 84)\n  (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 89) (:start . 85)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "NN") (:stem . "action") (:form . "action") (:end . 100)\n  (:start . 94) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 61))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 112)\n  (:start . 104) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x12.347.1) (:span 43 48)))\n (:hscopes ((:id . :x12.347.1) (:span 16 112)))\n (:identifiers (:sid . :s12.347) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504150@unknown@formal@none@1@S@In contrast, the mutation in sentence 2) describes the action of marA being mutated due to reduction of OmpF.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 25)\n  (:start . 17) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "describe") (:form . "describes") (:end . 50)\n  (:start . 41) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "action") (:form . "action") (:end . 61)\n  (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "marA") (:form . "marA") (:end . 69) (:start . 65)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 75) (:start . 70)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 83)\n  (:start . 76) (:id . 57))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "reduction") (:form . "reduction") (:end . 100)\n  (:start . 91) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "OmpF") (:form . "OmpF") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s12.348) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504151@unknown@formal@none@1@S@Argument identification@(((:tag . "NN") (:stem . "argument") (:form . "Argument") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 23) (:start . 9) (:id . 43)))@@@1@2@((:identifiers (:sid . :s12.349) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504152@unknown@formal@none@1@S@Argument identification discrepancies often occurred in more complex sentences, in which a "double layer" of annotation was sometimes required.@(((:tag . "NN") (:stem . "argument") (:form . "Argument") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 23) (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "discrepancy") (:form . "discrepancies") (:end . 37)\n  (:start . 24) (:id . 44))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 43) (:start . 38)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "occur") (:form . "occurred") (:end . 52)\n  (:start . 44) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 47))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 60) (:start . 56)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 68)\n  (:start . 61) (:id . 49))\n ((:tag . "NNS") (:stem . "sentence") (:form . "sentences") (:end . 78)\n  (:start . 69) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 88) (:start . 83)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 90) (:start . 89)\n  (:id . 54))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 92) (:start . 91)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "double") (:form . "double") (:end . 98)\n  (:start . 92) (:id . 56))\n ((:tag . "NN") (:stem . "layer") (:form . "layer") (:end . 104) (:start . 99)\n  (:id . 57))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 119)\n  (:start . 109) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 123) (:start . 120)\n  (:id . 61))\n ((:tag . "RB") (:stem . "sometimes") (:form . "sometimes") (:end . 133)\n  (:start . 124) (:id . 62))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 142)\n  (:start . 134) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s12.350) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504153@unknown@formal@none@1@S@In the following sentence, Alpha interferon should be seen as the AGENT of converting as well as the AGENT of stimulates:@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Alpha") (:form . "Alpha") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "interferon") (:form . "interferon") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "agent") (:form . "AGENT") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "convert") (:form . "converting") (:end . 85)\n  (:start . 75) (:id . 56))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 96) (:start . 94)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "NN") (:stem . "agent") (:form . "AGENT") (:end . 106)\n  (:start . 101) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "stimulate") (:form . "stimulates") (:end . 120)\n  (:start . 110) (:id . 63))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 121) (:start . 120)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x12.351.1) (:span 44 50)))\n (:hscopes ((:id . :x12.351.1) (:span 27 120)))\n (:identifiers (:sid . :s12.351) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504154@unknown@formal@none@1@S@Alpha interferon stimulates transcription by converting the positive transcriptional regulator ISGF3 from a latent to an active form.@(((:tag . "NNP") (:stem . "Alpha") (:form . "Alpha") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "interferon") (:form . "interferon") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "VBZ") (:stem . "stimulate") (:form . "stimulates") (:end . 27)\n  (:start . 17) (:id . 44))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 41) (:start . 28) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 44) (:start . 42)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "convert") (:form . "converting") (:end . 55)\n  (:start . 45) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 68)\n  (:start . 60) (:id . 49))\n ((:tag . "JJ") (:stem . "transcriptional") (:form . "transcriptional")\n  (:end . 84) (:start . 69) (:id . 50))\n ((:tag . "NN") (:stem . "regulator") (:form . "regulator") (:end . 94)\n  (:start . 85) (:id . 51))\n ((:tag . "NN") (:stem . "isgf3") (:form . "ISGF3") (:end . 100) (:start . 95)\n  (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 105) (:start . 101)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 107) (:start . 106)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "latent") (:form . "latent") (:end . 114)\n  (:start . 108) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n  (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 120) (:start . 118)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 127)\n  (:start . 121) (:id . 58))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 132) (:start . 128)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.352) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504155@unknown@formal@none@1@S@LOCATION arguments can also be problematic in sentences containing multiple events.@(((:tag . "NN") (:stem . "location") (:form . "LOCATION") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "problematic") (:form . "problematic") (:end . 42)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "sentence") (:form . "sentences") (:end . 55)\n  (:start . 46) (:id . 49))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 66)\n  (:start . 56) (:id . 50))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 75)\n  (:start . 67) (:id . 51))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 82)\n  (:start . 76) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 53)))@@@1@12@((:hcues ((:id . :x12.353.1) (:span 19 22)))\n (:hscopes ((:id . :x12.353.1) (:span 19 82)))\n (:identifiers (:sid . :s12.353) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504156@unknown@formal@none@1@S@In the following sentence, for example, different annotators associated the LOCATION in Escherichia coli K-12 with either the event described by the verb control or the nominalised verb expression.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 49)\n  (:start . 40) (:id . 50))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 60)\n  (:start . 50) (:id . 51))\n ((:tag . "VBD") (:stem . "associate") (:form . "associated") (:end . 71)\n  (:start . 61) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "location") (:form . "LOCATION") (:end . 84)\n  (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "FW") (:stem . "escherichia") (:form . "Escherichia") (:end . 99)\n  (:start . 88) (:id . 56))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 104) (:start . 100)\n  (:id . 57))\n ((:tag . "NN") (:stem . "k-12") (:form . "K-12") (:end . 109) (:start . 105)\n  (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 114) (:start . 110)\n  (:id . 59))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 121)\n  (:start . 115) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 61))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 131)\n  (:start . 126) (:id . 62))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 141)\n  (:start . 132) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 65))\n ((:tag . "NN") (:stem . "verb") (:form . "verb") (:end . 153) (:start . 149)\n  (:id . 66))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 161)\n  (:start . 154) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 164) (:start . 162)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "nominalised") (:form . "nominalised") (:end . 180)\n  (:start . 169) (:id . 70))\n ((:tag . "NN") (:stem . "verb") (:form . "verb") (:end . 185) (:start . 181)\n  (:id . 71))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 196)\n  (:start . 186) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s12.354) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504157@unknown@formal@none@1@S@EnvZ functions through OmpR to control porin gene expression in Escherichia coli K-12.@(((:tag . "NNP") (:stem . "EnvZ") (:form . "EnvZ") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "function") (:form . "functions") (:end . 14)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "NNP") (:stem . "OmpR") (:form . "OmpR") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "VB") (:stem . "control") (:form . "control") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "porin") (:form . "porin") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "FW") (:stem . "escherichia") (:form . "Escherichia") (:end . 75)\n  (:start . 64) (:id . 52))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 80) (:start . 76)\n  (:id . 53))\n ((:tag . "NN") (:stem . "k-12") (:form . "K-12") (:end . 85) (:start . 81)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s12.355) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504158@unknown@formal@none@1@S@Semantic role assignment@(((:tag . "JJ") (:stem . "semantic") (:form . "Semantic") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 24)\n  (:start . 14) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.356) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504159@unknown@formal@none@1@S@Amongst the most important semantic roles, both in terms of frequency of occurrence and according to [20], CONDITION is the one with the lowest rates of agreement.@(((:tag . "IN") (:stem . "amongst") (:form . "Amongst") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 35)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 69)\n  (:start . 60) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 83)\n  (:start . 73) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 97)\n  (:start . 88) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 105) (:start . 104)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "CONDITION") (:form . "CONDITION") (:end . 116)\n  (:start . 107) (:id . 63))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 119) (:start . 117)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 65))\n ((:tag . "NN") (:stem . "one") (:form . "one") (:end . 127) (:start . 124)\n  (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 132) (:start . 128)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 68))\n ((:tag . "JJS") (:stem . "low") (:form . "lowest") (:end . 143)\n  (:start . 137) (:id . 69))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 149)\n  (:start . 144) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n  (:id . 71))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 162)\n  (:start . 153) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s12.357) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504160@unknown@formal@none@1@S@We thus examined more closely the types of disagreements that occur.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "disagreement") (:form . "disagreements")\n  (:end . 56) (:start . 43) (:id . 50))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s12.358) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504161@unknown@formal@none@1@S@According to our study, the most common confusions are with the MANNER and TEMPORAL roles.@(((:tag . "VBG") (:stem . "accord") (:form . "According") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 39)\n  (:start . 33) (:id . 49))\n ((:tag . "NNS") (:stem . "confusion") (:form . "confusions") (:end . 50)\n  (:start . 40) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 59) (:start . 55)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "MANNER") (:form . "MANNER") (:end . 70)\n  (:start . 64) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "TEMPORAL") (:form . "TEMPORAL") (:end . 83)\n  (:start . 75) (:id . 56))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 89) (:start . 84)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.359) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504162@unknown@formal@none@1@S@Typical examples include the following:@(((:tag . "JJ") (:stem . "typical") (:form . "Typical") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "following") (:form . "following") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 39) (:start . 38)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s12.360) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504163@unknown@formal@none@1@S@1) In contrast, the anaerobic repression of ethanol dehydrogenase by nitrate does not require the narL product.@(((:tag . "LS") (:stem . "1") (:form . "1") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "In") (:end . 5) (:start . 3)\n  (:id . 44))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 14)\n  (:start . 6) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "anaerobic") (:form . "anaerobic") (:end . 29)\n  (:start . 20) (:id . 48))\n ((:tag . "NN") (:stem . "repression") (:form . "repression") (:end . 40)\n  (:start . 30) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "ethanol") (:form . "ethanol") (:end . 51)\n  (:start . 44) (:id . 51))\n ((:tag . "NN") (:stem . "dehydrogenase") (:form . "dehydrogenase")\n  (:end . 65) (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "nitrate") (:form . "nitrate") (:end . 76)\n  (:start . 69) (:id . 54))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "VB") (:stem . "require") (:form . "require") (:end . 93)\n  (:start . 86) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "NN") (:stem . "narl") (:form . "narL") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 110)\n  (:start . 103) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s12.361) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504164@unknown@formal@none@1@S@2) Nitrate repression, however, was significantly enhanced (sevenfold) when the cells were cultured in minimal medium.@(((:tag . "LS") (:stem . "2") (:form . "2") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "VB") (:stem . "nitrate") (:form . "Nitrate") (:end . 10)\n  (:start . 3) (:id . 44))\n ((:tag . "NN") (:stem . "repression") (:form . "repression") (:end . 21)\n  (:start . 11) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 30)\n  (:start . 23) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 49) (:start . 36) (:id . 50))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 58)\n  (:start . 50) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 52))\n ((:tag . "RB") (:stem . "sevenfold") (:form . "sevenfold") (:end . 69)\n  (:start . 60) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 75) (:start . 71)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 85) (:start . 80)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 90) (:start . 86)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 99)\n  (:start . 91) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "minimal") (:form . "minimal") (:end . 110)\n  (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 117)\n  (:start . 111) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s12.362) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504165@unknown@formal@none@1@S@For the repression event in sentence 1), anaerobic was confused between MANNER and CONDITION.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "repression") (:form . "repression") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "anaerobic") (:form . "anaerobic") (:end . 50)\n  (:start . 41) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "confuse") (:form . "confused") (:end . 63)\n  (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 71)\n  (:start . 64) (:id . 54))\n ((:tag . "NNP") (:stem . "MANNER") (:form . "MANNER") (:end . 78)\n  (:start . 72) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "CONDITION") (:form . "CONDITION") (:end . 92)\n  (:start . 83) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.363) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504166@unknown@formal@none@1@S@The confusion may occur because anaerobic can be used in the description of environmental conditions in a phrase such as under anaerobic conditions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "confusion") (:form . "confusion") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VB") (:stem . "occur") (:form . "occur") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "anaerobic") (:form . "anaerobic") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NN") (:stem . "description") (:form . "description") (:end . 72)\n  (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "environmental") (:form . "environmental")\n  (:end . 89) (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 100)\n  (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "phrase") (:form . "phrase") (:end . 112)\n  (:start . 106) (:id . 59))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 117) (:start . 113)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 120) (:start . 118)\n  (:id . 61))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 126)\n  (:start . 121) (:id . 62))\n ((:tag . "JJ") (:stem . "anaerobic") (:form . "anaerobic") (:end . 136)\n  (:start . 127) (:id . 63))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 147)\n  (:start . 137) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x12.364.1) (:span 42 45)) ((:id . :x12.364.2) (:span 14 17)))\n (:hscopes ((:id . :x12.364.1) (:span 32 147))\n  ((:id . :x12.364.2) (:span 14 147)))\n (:identifiers (:sid . :s12.364) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504167@unknown@formal@none@1@S@Here, however, it is being used to describe the method of repression, and hence the MANNER role is most appropriate.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 13)\n  (:start . 6) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 26) (:start . 21)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 31) (:start . 27)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 50))\n ((:tag . "VB") (:stem . "describe") (:form . "describe") (:end . 43)\n  (:start . 35) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 54)\n  (:start . 48) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 54))\n ((:tag . "NN") (:stem . "repression") (:form . "repression") (:end . 68)\n  (:start . 58) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 57))\n ((:tag . "RB") (:stem . "hence") (:form . "hence") (:end . 79) (:start . 74)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 59))\n ((:tag . "NN") (:stem . "manner") (:form . "MANNER") (:end . 90)\n  (:start . 84) (:id . 60))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 95) (:start . 91)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 98) (:start . 96)\n  (:id . 62))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 103) (:start . 99)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 115)\n  (:start . 104) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s12.365) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504168@unknown@formal@none@1@S@In sentence 2), the phrase the cells were cultured in minimal medium was annotated either as a CONDITION or as a TEMPORAL argument of the enhanced event.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sentence") (:form . "sentence") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 47))\n ((:tag . "NN") (:stem . "phrase") (:form . "phrase") (:end . 26)\n  (:start . 20) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 36) (:start . 31)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 41) (:start . 37)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "culture") (:form . "cultured") (:end . 50)\n  (:start . 42) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "minimal") (:form . "minimal") (:end . 61)\n  (:start . 54) (:id . 54))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 68)\n  (:start . 62) (:id . 55))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 82)\n  (:start . 73) (:id . 57))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 89)\n  (:start . 83) (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "CONDITION") (:form . "CONDITION") (:end . 104)\n  (:start . 95) (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 107) (:start . 105)\n  (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 110) (:start . 108)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "temporal") (:form . "TEMPORAL") (:end . 121)\n  (:start . 113) (:id . 65))\n ((:tag . "NN") (:stem . "argument") (:form . "argument") (:end . 130)\n  (:start . 122) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "enhance") (:form . "enhanced") (:end . 146)\n  (:start . 138) (:id . 69))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 152)\n  (:start . 147) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s12.366) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504169@unknown@formal@none@1@S@Whilst this would normally be interpreted as a CONDITION, the confusion may have arisen due to the use of when at the beginning of the phrase.@(((:tag . "IN") (:stem . "whilst") (:form . "Whilst") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 17) (:start . 12)\n  (:id . 44))\n ((:tag . "RB") (:stem . "normally") (:form . "normally") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "interpret") (:form . "interpreted") (:end . 41)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "CONDITION") (:form . "CONDITION") (:end . 56)\n  (:start . 47) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "confusion") (:form . "confusion") (:end . 71)\n  (:start . 62) (:id . 53))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "arise") (:form . "arisen") (:end . 87)\n  (:start . 81) (:id . 56))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 91) (:start . 88)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 110) (:start . 106)\n  (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 113) (:start . 111)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 64))\n ((:tag . "NN") (:stem . "beginning") (:form . "beginning") (:end . 127)\n  (:start . 118) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n  (:id . 67))\n ((:tag . "NN") (:stem . "phrase") (:form . "phrase") (:end . 141)\n  (:start . 135) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x12.367.1) (:span 72 75)) ((:id . :x12.367.2) (:span 12 17)))\n (:hscopes ((:id . :x12.367.1) (:span 72 141))\n  ((:id . :x12.367.2) (:span 7 56)))\n (:identifiers (:sid . :s12.367) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504170@unknown@formal@none@1@S@Regarding the DESCRIPTIVE-THEME role, the most common type of confusion is with THEME.@(((:tag . "VBG") (:stem . "regard") (:form . "Regarding") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "DESCRIPTIVE-THEME") (:form . "DESCRIPTIVE-THEME")\n  (:end . 31) (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 36) (:start . 32)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "confusion") (:form . "confusion") (:end . 71)\n  (:start . 62) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "THEME") (:form . "THEME") (:end . 85) (:start . 80)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s12.368) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504171@unknown@formal@none@1@S@According to the guidelines, one of the situations in which DESCRIPTIVE-THEME should be assigned is to objects of verbs that describe states rather than actions e.g., The fru operon contains the genes for IIFru.@(((:tag . "VBG") (:stem . "accord") (:form . "According") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "situation") (:form . "situations") (:end . 50)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "DESCRIPTIVE-THEME") (:form . "DESCRIPTIVE-THEME")\n  (:end . 77) (:start . 60) (:id . 53))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 84)\n  (:start . 78) (:id . 54))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 96)\n  (:start . 88) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 102) (:start . 100)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "object") (:form . "objects") (:end . 110)\n  (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 119)\n  (:start . 114) (:id . 61))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 124) (:start . 120)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 133)\n  (:start . 125) (:id . 63))\n ((:tag . "NNS") (:stem . "state") (:form . "states") (:end . 140)\n  (:start . 134) (:id . 64))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 147)\n  (:start . 141) (:id . 65))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 152) (:start . 148)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "action") (:form . "actions") (:end . 160)\n  (:start . 153) (:id . 67))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 165) (:start . 161)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 170) (:start . 167)\n  (:id . 70))\n ((:tag . "NN") (:stem . "fru") (:form . "fru") (:end . 174) (:start . 171)\n  (:id . 71))\n ((:tag . "NN") (:stem . "operon") (:form . "operon") (:end . 181)\n  (:start . 175) (:id . 72))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 190)\n  (:start . 182) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 194) (:start . 191)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 200)\n  (:start . 195) (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 204) (:start . 201)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "IIFru") (:form . "IIFru") (:end . 210)\n  (:start . 205) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x12.369.1) (:span 78 84)))\n (:hscopes ((:id . :x12.369.1) (:span 60 210)))\n (:identifiers (:sid . :s12.369) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504172@unknown@formal@none@1@S@Here, there is no action and hence no AGENT.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 11) (:start . 6)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "action") (:form . "action") (:end . 24)\n  (:start . 18) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "RB") (:stem . "hence") (:form . "hence") (:end . 34) (:start . 29)\n  (:id . 49))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 37) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "agent") (:form . "AGENT") (:end . 43) (:start . 38)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 44) (:start . 43)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s12.370) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504173@unknown@formal@none@1@S@Thus, the fru operon is the THEME and the genes for IIFru is the DESCRIPTIVE-THEME.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "NN") (:stem . "fru") (:form . "fru") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "NN") (:stem . "operon") (:form . "operon") (:end . 20)\n  (:start . 14) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "THEME") (:form . "THEME") (:end . 33) (:start . 28)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 47) (:start . 42)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 51) (:start . 48)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "IIFru") (:form . "IIFru") (:end . 57) (:start . 52)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 56))\n ((:tag . "NN") (:stem . "descriptive-theme") (:form . "DESCRIPTIVE-THEME")\n  (:end . 82) (:start . 65) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s12.371) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504174@unknown@formal@none@1@S@However, problems sometimes arose for certain verbs such as exhibit, where there may be some confusion as to whether a "state" or "active" interpretation should be taken, e.g., The wild-type and mutant ompR genes exhibit different phenotypes of osmoregulation...@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "problem") (:form . "problems") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "RB") (:stem . "sometimes") (:form . "sometimes") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "VBD") (:stem . "arise") (:form . "arose") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "verb") (:form . "verbs") (:end . 51) (:start . 46)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "exhibit") (:form . "exhibit") (:end . 67)\n  (:start . 60) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 80) (:start . 75)\n  (:id . 55))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . "NN") (:stem . "confusion") (:form . "confusion") (:end . 102)\n  (:start . 93) (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 105) (:start . 103)\n  (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 61))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 116)\n  (:start . 109) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 118) (:start . 117)\n  (:id . 63))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 120) (:start . 119)\n  (:id . 64))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 125)\n  (:start . 120) (:id . 65))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 126) (:start . 125)\n  (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 129) (:start . 127)\n  (:id . 67))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 131) (:start . 130)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 137)\n  (:start . 131) (:id . 69))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 138) (:start . 137)\n  (:id . 70))\n ((:tag . "NN") (:stem . "interpretation") (:form . "interpretation")\n  (:end . 153) (:start . 139) (:id . 71))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 160)\n  (:start . 154) (:id . 72))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 163) (:start . 161)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 169)\n  (:start . 164) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 170) (:start . 169)\n  (:id . 75))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 175) (:start . 171)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 176) (:start . 175)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 180) (:start . 177)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 190)\n  (:start . 181) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 201)\n  (:start . 195) (:id . 81))\n ((:tag . "NNP") (:stem . "ompR") (:form . "ompR") (:end . 206) (:start . 202)\n  (:id . 82))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 212)\n  (:start . 207) (:id . 83))\n ((:tag . "VBP") (:stem . "exhibit") (:form . "exhibit") (:end . 220)\n  (:start . 213) (:id . 84))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 230)\n  (:start . 221) (:id . 85))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 241)\n  (:start . 231) (:id . 86))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 244) (:start . 242)\n  (:id . 87))\n ((:tag . "NN") (:stem . "osmoregulation") (:form . "osmoregulation")\n  (:end . 259) (:start . 245) (:id . 88))\n ((:tag . ":") (:stem . "…") (:form . "…") (:end . 259) (:start . 259)\n  (:id . 89)))@@@1@48@((:hcues ((:id . :x12.372.2) (:span 154 160))\n  ((:id . :x12.372.1) (:span 127 129)) ((:id . :x12.372.3) (:span 109 116))\n  ((:id . :x12.372.4) (:span 81 84)))\n (:hscopes ((:id . :x12.372.1) (:span 119 138))\n  ((:id . :x12.372.2) (:span 117 169)) ((:id . :x12.372.3) (:span 109 169))\n  ((:id . :x12.372.4) (:span 81 169)))\n (:identifiers (:sid . :s12.372) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504175@unknown@formal@none@1@S@The interpretation taken by the annotator determines whether different phenotypes is assigned the role THEME or DESCRIPTIVE-THEME (and also whether The wild-type and mutant ompR genes is assigned AGENT or THEME).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "interpretation") (:form . "interpretation")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 24) (:start . 19)\n  (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "determine") (:form . "determines") (:end . 52)\n  (:start . 42) (:id . 48))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 60)\n  (:start . 53) (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 70)\n  (:start . 61) (:id . 50))\n ((:tag . "NNS") (:stem . "phenotype") (:form . "phenotypes") (:end . 81)\n  (:start . 71) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 84) (:start . 82)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 93)\n  (:start . 85) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 54))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 102) (:start . 98)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "THEME") (:form . "THEME") (:end . 108)\n  (:start . 103) (:id . 56))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 111) (:start . 109)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "DESCRIPTIVE-THEME") (:form . "DESCRIPTIVE-THEME")\n  (:end . 129) (:start . 112) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 60))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 139) (:start . 135)\n  (:id . 61))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 147)\n  (:start . 140) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 151) (:start . 148)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "wild-type") (:form . "wild-type") (:end . 161)\n  (:start . 152) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "mutant") (:form . "mutant") (:end . 172)\n  (:start . 166) (:id . 66))\n ((:tag . "NNP") (:stem . "ompR") (:form . "ompR") (:end . 177) (:start . 173)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "gene") (:form . "genes") (:end . 183)\n  (:start . 178) (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 186) (:start . 184)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 195)\n  (:start . 187) (:id . 70))\n ((:tag . "NNP") (:stem . "AGENT") (:form . "AGENT") (:end . 201)\n  (:start . 196) (:id . 71))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 204) (:start . 202)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "THEME") (:form . "THEME") (:end . 210)\n  (:start . 205) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 211) (:start . 210)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x12.373.1) (:span 202 204))\n  ((:id . :x12.373.2) (:span 140 147)) ((:id . :x12.373.3) (:span 109 111))\n  ((:id . :x12.373.4) (:span 53 60)))\n (:hscopes ((:id . :x12.373.1) (:span 196 210))\n  ((:id . :x12.373.2) (:span 140 211)) ((:id . :x12.373.3) (:span 103 129))\n  ((:id . :x12.373.4) (:span 53 129)))\n (:identifiers (:sid . :s12.373) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504176@unknown@formal@none@1@S@In general, DESCRIPTIVE-THEME and DESCRIPTIVE-AGENT have less strict definitions than other roles, in that the only restriction imposed is that they should be assigned to arguments that describe characteristics or behaviour of the AGENT or THEME.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "DESCRIPTIVE-THEME") (:form . "DESCRIPTIVE-THEME")\n  (:end . 29) (:start . 12) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "DESCRIPTIVE-AGENT") (:form . "DESCRIPTIVE-AGENT")\n  (:end . 51) (:start . 34) (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 56) (:start . 52)\n  (:id . 48))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 61) (:start . 57)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "strict") (:form . "strict") (:end . 68)\n  (:start . 62) (:id . 50))\n ((:tag . "NNS") (:stem . "definition") (:form . "definitions") (:end . 80)\n  (:start . 69) (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 85) (:start . 81)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 91) (:start . 86)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 97) (:start . 92)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 101) (:start . 99)\n  (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 106) (:start . 102)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . "NN") (:stem . "restriction") (:form . "restriction") (:end . 127)\n  (:start . 116) (:id . 60))\n ((:tag . "VBN") (:stem . "impose") (:form . "imposed") (:end . 135)\n  (:start . 128) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 138) (:start . 136)\n  (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 143) (:start . 139)\n  (:id . 63))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 148) (:start . 144)\n  (:id . 64))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 155)\n  (:start . 149) (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 158) (:start . 156)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 167)\n  (:start . 159) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 170) (:start . 168)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 180)\n  (:start . 171) (:id . 69))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 185) (:start . 181)\n  (:id . 70))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 194)\n  (:start . 186) (:id . 71))\n ((:tag . "NNS") (:stem . "characteristic") (:form . "characteristics")\n  (:end . 210) (:start . 195) (:id . 72))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 213) (:start . 211)\n  (:id . 73))\n ((:tag . "NN") (:stem . "behaviour") (:form . "behaviour") (:end . 223)\n  (:start . 214) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 226) (:start . 224)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 230) (:start . 227)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "AGENT") (:form . "AGENT") (:end . 236)\n  (:start . 231) (:id . 77))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 239) (:start . 237)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "THEME") (:form . "THEME") (:end . 245)\n  (:start . 240) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x12.374.1) (:span 149 155)))\n (:hscopes ((:id . :x12.374.1) (:span 144 245)))\n (:identifiers (:sid . :s12.374) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504177@unknown@formal@none@1@S@This, together with the fact that they are not particularly commonly occurring, could have made them more difficult to assign accurately.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 14)\n  (:start . 6) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 59)\n  (:start . 47) (:id . 52))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . "VBG") (:stem . "occur") (:form . "occurring") (:end . 78)\n  (:start . 69) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 90) (:start . 86)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 105) (:start . 101)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 115)\n  (:start . 106) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 118) (:start . 116)\n  (:id . 62))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 125)\n  (:start . 119) (:id . 63))\n ((:tag . "RB") (:stem . "accurately") (:form . "accurately") (:end . 136)\n  (:start . 126) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x12.375.1) (:span 80 85)))\n (:hscopes ((:id . :x12.375.1) (:span 0 136)))\n (:identifiers (:sid . :s12.375) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504178@unknown@formal@none@1@S@As future work, we will consider tightening the definitions and possibly splitting them into different roles.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "future") (:form . "future") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 23) (:start . 19)\n  (:id . 47))\n ((:tag . "VB") (:stem . "consider") (:form . "consider") (:end . 32)\n  (:start . 24) (:id . 48))\n ((:tag . "VBG") (:stem . "tighten") (:form . "tightening") (:end . 43)\n  (:start . 33) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "definition") (:form . "definitions") (:end . 59)\n  (:start . 48) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "RB") (:stem . "possibly") (:form . "possibly") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . "VBG") (:stem . "split") (:form . "splitting") (:end . 82)\n  (:start . 73) (:id . 54))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 102)\n  (:start . 93) (:id . 57))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 108)\n  (:start . 103) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 59)))@@@1@18@((:hcues ((:id . :x12.376.1) (:span 64 72)))\n (:hscopes ((:id . :x12.376.1) (:span 64 108)))\n (:identifiers (:sid . :s12.376) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504179@unknown@formal@none@1@S@Although it is desirable to keep the set of roles used as small and as general as possible in order to ease the burden on the annotator, a slightly larger range of more tightly-defined roles may help to improve agreement rates.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "desirable") (:form . "desirable") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VB") (:stem . "keep") (:form . "keep") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 49) (:start . 44)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 54) (:start . 50)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 63) (:start . 58)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 70) (:start . 68)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 78)\n  (:start . 71) (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 90)\n  (:start . 82) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 99) (:start . 94)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 102) (:start . 100)\n  (:id . 62))\n ((:tag . "VB") (:stem . "ease") (:form . "ease") (:end . 107) (:start . 103)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 64))\n ((:tag . "NN") (:stem . "burden") (:form . "burden") (:end . 118)\n  (:start . 112) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 121) (:start . 119)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 67))\n ((:tag . "NN") (:stem . "annotator") (:form . "annotator") (:end . 135)\n  (:start . 126) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 138) (:start . 137)\n  (:id . 70))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 147)\n  (:start . 139) (:id . 71))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 154)\n  (:start . 148) (:id . 72))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 160)\n  (:start . 155) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 74))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 168) (:start . 164)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "tightly-defined") (:form . "tightly-defined")\n  (:end . 184) (:start . 169) (:id . 76))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 190)\n  (:start . 185) (:id . 77))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 194) (:start . 191)\n  (:id . 78))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 199) (:start . 195)\n  (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 202) (:start . 200)\n  (:id . 80))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 210)\n  (:start . 203) (:id . 81))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 220)\n  (:start . 211) (:id . 82))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 226)\n  (:start . 221) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x12.377.1) (:span 191 194)))\n (:hscopes ((:id . :x12.377.1) (:span 191 226)))\n (:identifiers (:sid . :s12.377) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504180@unknown@formal@none@1@S@Biological concept assignment@(((:tag . "JJ") (:stem . "biological") (:form . "Biological") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 18)\n  (:start . 11) (:id . 43))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 29)\n  (:start . 19) (:id . 44)))@@@1@3@((:identifiers (:sid . :s12.378) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504181@unknown@formal@none@1@S@As observed in Table 11, there is much more discrepancy between certain biological concept categories than others, especially those that constitute context-specific concepts.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 47))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 30) (:start . 25)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 38) (:start . 34)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 43) (:start . 39)\n  (:id . 51))\n ((:tag . "NN") (:stem . "discrepancy") (:form . "discrepancy") (:end . 55)\n  (:start . 44) (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 63)\n  (:start . 56) (:id . 53))\n ((:tag . "JJ") (:stem . "certain") (:form . "certain") (:end . 71)\n  (:start . 64) (:id . 54))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 82)\n  (:start . 72) (:id . 55))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 90)\n  (:start . 83) (:id . 56))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 101)\n  (:start . 91) (:id . 57))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 106) (:start . 102)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 113)\n  (:start . 107) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 60))\n ((:tag . "RB") (:stem . "especially") (:form . "especially") (:end . 125)\n  (:start . 115) (:id . 61))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 131)\n  (:start . 126) (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 136) (:start . 132)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "constitute") (:form . "constitute") (:end . 147)\n  (:start . 137) (:id . 64))\n ((:tag . "JJ") (:stem . "context-specific") (:form . "context-specific")\n  (:end . 164) (:start . 148) (:id . 65))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 173)\n  (:start . 165) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s12.379) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504182@unknown@formal@none@1@S@An exception to this is Protein, which is a more general concept category within the Proteins supercategory.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "exception") (:form . "exception") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 38) (:start . 33)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n  (:id . 51))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 48) (:start . 44)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 56)\n  (:start . 49) (:id . 53))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 64)\n  (:start . 57) (:id . 54))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 73)\n  (:start . 65) (:id . 55))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 80)\n  (:start . 74) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "NNPS") (:stem . "Protein") (:form . "Proteins") (:end . 93)\n  (:start . 85) (:id . 58))\n ((:tag . "NN") (:stem . "supercategory") (:form . "supercategory")\n  (:end . 107) (:start . 94) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.380) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504183@unknown@formal@none@1@S@We therefore examined the most common concept categories with which Protein was confused.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "examine") (:form . "examined") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 61) (:start . 57)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 67) (:start . 62)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 75)\n  (:start . 68) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 79) (:start . 76)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "confuse") (:form . "confused") (:end . 88)\n  (:start . 80) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s12.381) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504184@unknown@formal@none@1@S@These are shown in Table 12.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 28) (:start . 27)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s12.382) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504185@unknown@formal@none@1@S@Most common concept categories confused with Protein@(((:tag . "RBS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "VBN") (:stem . "confuse") (:form . "confused") (:end . 39)\n  (:start . 31) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 44) (:start . 40)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 52)\n  (:start . 45) (:id . 48)))@@@1@7@((:identifiers (:sid . :s12.383) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504186@unknown@formal@none@1@S@With the exception of Gene (which belongs to the Nucleic_Acids superclass), all other categories confused with Protein are also categories within the Proteins supercategory.@(((:tag . "IN") (:stem . "with") (:form . "With") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "exception") (:form . "exception") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 33) (:start . 28)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "belong") (:form . "belongs") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Nucleic_Acid") (:form . "Nucleic_Acids")\n  (:end . 62) (:start . 49) (:id . 52))\n ((:tag . "NN") (:stem . "superclass") (:form . "superclass") (:end . 73)\n  (:start . 63) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 85) (:start . 80)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 96)\n  (:start . 86) (:id . 58))\n ((:tag . "VBN") (:stem . "confuse") (:form . "confused") (:end . 105)\n  (:start . 97) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 110) (:start . 106)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 118)\n  (:start . 111) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 122) (:start . 119)\n  (:id . 62))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 127) (:start . 123)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 138)\n  (:start . 128) (:id . 64))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 145)\n  (:start . 139) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 149) (:start . 146)\n  (:id . 66))\n ((:tag . "NNPS") (:stem . "Protein") (:form . "Proteins") (:end . 158)\n  (:start . 150) (:id . 67))\n ((:tag . "NN") (:stem . "supercategory") (:form . "supercategory")\n  (:end . 172) (:start . 159) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.384) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504187@unknown@formal@none@1@S@This suggests that some annotators were using the Protein category to encompass all things related to proteins, rather than assigning more specific category labels.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 66)\n  (:start . 58) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "VB") (:stem . "encompass") (:form . "encompass") (:end . 79)\n  (:start . 70) (:id . 53))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "thing") (:form . "things") (:end . 90)\n  (:start . 84) (:id . 55))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 98)\n  (:start . 91) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 110)\n  (:start . 102) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 59))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 118)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 123) (:start . 119)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "assign") (:form . "assigning") (:end . 133)\n  (:start . 124) (:id . 62))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 138) (:start . 134)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 147)\n  (:start . 139) (:id . 64))\n ((:tag . "NN") (:stem . "category") (:form . "category") (:end . 156)\n  (:start . 148) (:id . 65))\n ((:tag . "NNS") (:stem . "label") (:form . "labels") (:end . 163)\n  (:start . 157) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x12.385.1) (:span 5 13)))\n (:hscopes ((:id . :x12.385.1) (:span 5 163)))\n (:identifiers (:sid . :s12.385) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504188@unknown@formal@none@1@S@This may be related to their differing levels of knowledge regarding gene regulation and expression.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 28)\n  (:start . 23) (:id . 47))\n ((:tag . "VBG") (:stem . "differ") (:form . "differing") (:end . 38)\n  (:start . 29) (:id . 48))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "VBG") (:stem . "regard") (:form . "regarding") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 84)\n  (:start . 74) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 99)\n  (:start . 89) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 100) (:start . 99)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x12.386.1) (:span 5 8)))\n (:hscopes ((:id . :x12.386.1) (:span 0 99)))\n (:identifiers (:sid . :s12.386) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504189@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s12.387) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504190@unknown@formal@none@1@S@We have designed an event annotation scheme for biomedical texts and produced an associated corpus, the GREC, consisting of 240 MEDLINE abstracts annotated with 3067 gene regulation event instances.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 36)\n  (:start . 26) (:id . 47))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 58)\n  (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 64) (:start . 59)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "produce") (:form . "produced") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 91)\n  (:start . 81) (:id . 55))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 98)\n  (:start . 92) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "consist") (:form . "consisting") (:end . 120)\n  (:start . 110) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "CD") (:stem . "240") (:form . "240") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "MEDLINE") (:form . "MEDLINE") (:end . 135)\n  (:start . 128) (:id . 64))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 145)\n  (:start . 136) (:id . 65))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 155)\n  (:start . 146) (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 160) (:start . 156)\n  (:id . 67))\n ((:tag . "CD") (:stem . "3067") (:form . "3067") (:end . 165) (:start . 161)\n  (:id . 68))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 170) (:start . 166)\n  (:id . 69))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 181)\n  (:start . 171) (:id . 70))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 187)\n  (:start . 182) (:id . 71))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 197)\n  (:start . 188) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s12.388) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504191@unknown@formal@none@1@S@The corpus is unique within the biomedical field in that it combines both linguistically-oriented features (i.e., event-independent semantic roles tuned to the domain) and biologically-oriented features (i.e., biological concepts linked to the Gene Regulation Ontology [43]).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "field") (:form . "field") (:end . 48) (:start . 43)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "combine") (:form . "combines") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "linguistically-oriented")\n  (:form . "linguistically-oriented") (:end . 97) (:start . 74) (:id . 55))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 106)\n  (:start . 98) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 57))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 112) (:start . 108)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "event-independent") (:form . "event-independent")\n  (:end . 131) (:start . 114) (:id . 60))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 140)\n  (:start . 132) (:id . 61))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 146)\n  (:start . 141) (:id . 62))\n ((:tag . "VBN") (:stem . "tune") (:form . "tuned") (:end . 152)\n  (:start . 147) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 155) (:start . 153)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 65))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 166)\n  (:start . 160) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "biologically-oriented")\n  (:form . "biologically-oriented") (:end . 193) (:start . 172) (:id . 69))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 202)\n  (:start . 194) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 204) (:start . 203)\n  (:id . 71))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 208) (:start . 204)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 209) (:start . 208)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 220)\n  (:start . 210) (:id . 74))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 229)\n  (:start . 221) (:id . 75))\n ((:tag . "VBN") (:stem . "link") (:form . "linked") (:end . 236)\n  (:start . 230) (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 239) (:start . 237)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 243) (:start . 240)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Gene") (:form . "Gene") (:end . 248) (:start . 244)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "Regulation") (:form . "Regulation") (:end . 259)\n  (:start . 249) (:id . 80))\n ((:tag . "NNP") (:stem . "Ontology") (:form . "Ontology") (:end . 268)\n  (:start . 260) (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 270) (:start . 269)\n  (:id . 82))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 272) (:start . 270)\n  (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 273) (:start . 272)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 274) (:start . 273)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 275) (:start . 274)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s12.389) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504192@unknown@formal@none@1@S@The corpus can act as a basis for creating domain-specific semantic frame resources, and has already been used in the production of semantic frames for inclusion within the BioLexicon [44], in which the semantic frames are linked with syntactic information.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 29) (:start . 24)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 33) (:start . 30)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "create") (:form . "creating") (:end . 42)\n  (:start . 34) (:id . 50))\n ((:tag . "JJ") (:stem . "domain-specific") (:form . "domain-specific")\n  (:end . 58) (:start . 43) (:id . 51))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 67)\n  (:start . 59) (:id . 52))\n ((:tag . "NN") (:stem . "frame") (:form . "frame") (:end . 73) (:start . 68)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 83)\n  (:start . 74) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 92) (:start . 89)\n  (:id . 57))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 110) (:start . 106)\n  (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 128)\n  (:start . 118) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 140)\n  (:start . 132) (:id . 65))\n ((:tag . "NNS") (:stem . "frame") (:form . "frames") (:end . 147)\n  (:start . 141) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 151) (:start . 148)\n  (:id . 67))\n ((:tag . "NN") (:stem . "inclusion") (:form . "inclusion") (:end . 161)\n  (:start . 152) (:id . 68))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 168)\n  (:start . 162) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 172) (:start . 169)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "BioLexicon") (:form . "BioLexicon") (:end . 183)\n  (:start . 173) (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 185) (:start . 184)\n  (:id . 72))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 187) (:start . 185)\n  (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 188) (:start . 187)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 192) (:start . 190)\n  (:id . 76))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 198)\n  (:start . 193) (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 202) (:start . 199)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 211)\n  (:start . 203) (:id . 79))\n ((:tag . "NNS") (:stem . "frame") (:form . "frames") (:end . 218)\n  (:start . 212) (:id . 80))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 222) (:start . 219)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "link") (:form . "linked") (:end . 229)\n  (:start . 223) (:id . 82))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 234) (:start . 230)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "syntactic") (:form . "syntactic") (:end . 244)\n  (:start . 235) (:id . 84))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 256)\n  (:start . 245) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s12.390) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504193@unknown@formal@none@1@S@It is also hoped that the corpus will boost research into other areas of bio-IE, such as the production of domain-specific SRLs, which have previously suffered due to the lack of a suitably annotated corpus.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "hop") (:form . "hoped") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 32)\n  (:start . 26) (:id . 48))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "VB") (:stem . "boost") (:form . "boost") (:end . 43) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 52)\n  (:start . 44) (:id . 51))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 63) (:start . 58)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 69) (:start . 64)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "bio-IE") (:form . "bio-IE") (:end . 79)\n  (:start . 73) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 85) (:start . 81)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 88) (:start . 86)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 60))\n ((:tag . "NN") (:stem . "production") (:form . "production") (:end . 103)\n  (:start . 93) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "domain-specific") (:form . "domain-specific")\n  (:end . 122) (:start . 107) (:id . 63))\n ((:tag . "NNS") (:stem . "srl") (:form . "SRLs") (:end . 127) (:start . 123)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 134)\n  (:start . 129) (:id . 66))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 139) (:start . 135)\n  (:id . 67))\n ((:tag . "RB") (:stem . "previously") (:form . "previously") (:end . 150)\n  (:start . 140) (:id . 68))\n ((:tag . "VBN") (:stem . "suffer") (:form . "suffered") (:end . 159)\n  (:start . 151) (:id . 69))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 163) (:start . 160)\n  (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 166) (:start . 164)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 72))\n ((:tag . "NN") (:stem . "lack") (:form . "lack") (:end . 175) (:start . 171)\n  (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 178) (:start . 176)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 180) (:start . 179)\n  (:id . 75))\n ((:tag . "RB") (:stem . "suitably") (:form . "suitably") (:end . 189)\n  (:start . 181) (:id . 76))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 199)\n  (:start . 190) (:id . 77))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 206)\n  (:start . 200) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x12.391.1) (:span 33 37)))\n (:hscopes ((:id . :x12.391.1) (:span 33 206)))\n (:identifiers (:sid . :s12.391) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504194@unknown@formal@none@1@S@Initial experiments have demonstrated the feasibility of training an SRL using the corpus and as such, we hope to exploit the corpus in future shared tasks with such an aim.@(((:tag . "JJ") (:stem . "initial") (:form . "Initial") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 19)\n  (:start . 8) (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 24) (:start . 20)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "demonstrate") (:form . "demonstrated") (:end . 37)\n  (:start . 25) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 46))\n ((:tag . "NN") (:stem . "feasibility") (:form . "feasibility") (:end . 53)\n  (:start . 42) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "train") (:form . "training") (:end . 65)\n  (:start . 57) (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 68) (:start . 66)\n  (:id . 50))\n ((:tag . "NN") (:stem . "srl") (:form . "SRL") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 78) (:start . 73)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 53))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 89)\n  (:start . 83) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 101) (:start . 97)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 105) (:start . 103)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "hope") (:form . "hope") (:end . 110) (:start . 106)\n  (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "VB") (:stem . "exploit") (:form . "exploit") (:end . 121)\n  (:start . 114) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 132)\n  (:start . 126) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "future") (:form . "future") (:end . 142)\n  (:start . 136) (:id . 66))\n ((:tag . "JJ") (:stem . "shared") (:form . "shared") (:end . 149)\n  (:start . 143) (:id . 67))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 155)\n  (:start . 150) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 160) (:start . 156)\n  (:id . 69))\n ((:tag . "PDT") (:stem . "such") (:form . "such") (:end . 165) (:start . 161)\n  (:id . 70))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 168) (:start . 166)\n  (:id . 71))\n ((:tag . "NN") (:stem . "aim") (:form . "aim") (:end . 172) (:start . 169)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s12.392) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504195@unknown@formal@none@1@S@There is also evidence to suggest that combining the GREC with other larger biomedical corpora may help to train more accurate IE systems.@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "VB") (:stem . "suggest") (:form . "suggest") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "combine") (:form . "combining") (:end . 48)\n  (:start . 39) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 75)\n  (:start . 69) (:id . 54))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 86)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 94)\n  (:start . 87) (:id . 56))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 103) (:start . 99)\n  (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "VB") (:stem . "train") (:form . "train") (:end . 112)\n  (:start . 107) (:id . 60))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 117) (:start . 113)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "accurate") (:form . "accurate") (:end . 126)\n  (:start . 118) (:id . 62))\n ((:tag . "JJ") (:stem . "ie") (:form . "IE") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 137)\n  (:start . 130) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x12.393.1) (:span 95 98)) ((:id . :x12.393.2) (:span 26 33)))\n (:hscopes ((:id . :x12.393.1) (:span 95 137))\n  ((:id . :x12.393.2) (:span 26 137)))\n (:identifiers (:sid . :s12.393) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504196@unknown@formal@none@1@S@Evaluation of the corpus quality was carried out using a newly-devised methodology, taking into account multiple aspects of the annotation task.@(((:tag . "NN") (:stem . "evaluation") (:form . "Evaluation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "newly-devised") (:form . "newly-devised")\n  (:end . 70) (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "methodology") (:form . "methodology") (:end . 82)\n  (:start . 71) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "take") (:form . "taking") (:end . 90) (:start . 84)\n  (:id . 55))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 95) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . "account") (:form . "account") (:end . 103)\n  (:start . 96) (:id . 57))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 112)\n  (:start . 104) (:id . 58))\n ((:tag . "NNS") (:stem . "aspect") (:form . "aspects") (:end . 120)\n  (:start . 113) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 61))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 138)\n  (:start . 128) (:id . 62))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 143) (:start . 139)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s12.394) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504197@unknown@formal@none@1@S@Average agreement rates for the various tasks fell within the range of 66% - 90% F-score.@(((:tag . "JJ") (:stem . "average") (:form . "Average") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "rate") (:form . "rates") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "fall") (:form . "fell") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 57)\n  (:start . 51) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 67) (:start . 62)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "CD") (:stem . "66") (:form . "66") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 76) (:start . 75)\n  (:id . 56))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . "NN") (:stem . "f-score") (:form . "F-score") (:end . 88)\n  (:start . 81) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 89) (:start . 88)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.395) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504198@unknown@formal@none@1@S@Through error analysis of the corpus, we identified the most problematic issues, which included difficulties in assigning particular semantic roles, particularly CONDITION and DESCRIPTIVE-THEME.@(((:tag . "IN") (:stem . "through") (:form . "Through") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 51)\n  (:start . 41) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "problematic") (:form . "problematic") (:end . 72)\n  (:start . 61) (:id . 53))\n ((:tag . "NNS") (:stem . "issue") (:form . "issues") (:end . 79)\n  (:start . 73) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 55))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 86) (:start . 81)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "include") (:form . "included") (:end . 95)\n  (:start . 87) (:id . 57))\n ((:tag . "NNS") (:stem . "difficulty") (:form . "difficulties") (:end . 108)\n  (:start . 96) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "assign") (:form . "assigning") (:end . 121)\n  (:start . 112) (:id . 60))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 132)\n  (:start . 122) (:id . 61))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 141)\n  (:start . 133) (:id . 62))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 147)\n  (:start . 142) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 64))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 161)\n  (:start . 149) (:id . 65))\n ((:tag . "NNP") (:stem . "CONDITION") (:form . "CONDITION") (:end . 171)\n  (:start . 162) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "DESCRIPTIVE-THEME") (:form . "DESCRIPTIVE-THEME")\n  (:end . 193) (:start . 176) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 194) (:start . 193)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.396) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504199@unknown@formal@none@1@S@A full examination of the problematic cases will allow us to further improve the guidelines and possibly impose further restrictions in the annotation software, to prevent common types of errors being made.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "examination") (:form . "examination") (:end . 18)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "problematic") (:form . "problematic") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 76)\n  (:start . 69) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "guideline") (:form . "guidelines") (:end . 91)\n  (:start . 81) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "RB") (:stem . "possibly") (:form . "possibly") (:end . 104)\n  (:start . 96) (:id . 58))\n ((:tag . "VB") (:stem . "impose") (:form . "impose") (:end . 111)\n  (:start . 105) (:id . 59))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 119)\n  (:start . 112) (:id . 60))\n ((:tag . "NNS") (:stem . "restriction") (:form . "restrictions") (:end . 132)\n  (:start . 120) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 63))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 150)\n  (:start . 140) (:id . 64))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 159)\n  (:start . 151) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 163) (:start . 161)\n  (:id . 67))\n ((:tag . "VB") (:stem . "prevent") (:form . "prevent") (:end . 171)\n  (:start . 164) (:id . 68))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 178)\n  (:start . 172) (:id . 69))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 184)\n  (:start . 179) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 194)\n  (:start . 188) (:id . 72))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 200) (:start . 195)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 205) (:start . 201)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x12.397.1) (:span 96 104)))\n (:hscopes ((:id . :x12.397.1) (:span 96 205)))\n (:identifiers (:sid . :s12.397) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504200@unknown@formal@none@1@S@As regards biological concepts, our results show that, although high levels of agreement can be achieved when considering a coarse-grained set of categories, the use of a fine-grained classification caused some difficulties.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "regard") (:form . "regards") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 75)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 88)\n  (:start . 79) (:id . 56))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 92) (:start . 89)\n  (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 104)\n  (:start . 96) (:id . 59))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 109) (:start . 105)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "consider") (:form . "considering") (:end . 121)\n  (:start . 110) (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 123) (:start . 122)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "coarse-grained") (:form . "coarse-grained")\n  (:end . 138) (:start . 124) (:id . 63))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 142) (:start . 139)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 145) (:start . 143)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 156)\n  (:start . 146) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 68))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 165) (:start . 162)\n  (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 170) (:start . 169)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "fine-grained") (:form . "fine-grained") (:end . 183)\n  (:start . 171) (:id . 72))\n ((:tag . "NN") (:stem . "classification") (:form . "classification")\n  (:end . 198) (:start . 184) (:id . 73))\n ((:tag . "VBD") (:stem . "cause") (:form . "caused") (:end . 205)\n  (:start . 199) (:id . 74))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 210) (:start . 206)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "difficulty") (:form . "difficulties") (:end . 223)\n  (:start . 211) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 224) (:start . 223)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x12.398.1) (:span 89 92)))\n (:hscopes ((:id . :x12.398.1) (:span 64 156)))\n (:identifiers (:sid . :s12.398) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504201@unknown@formal@none@1@S@This is possibly due to the differing levels of expertise of annotators within the gene regulation and expression domain, which may have resulted in varying levels of confidence in assigning more specific concepts.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "RB") (:stem . "possibly") (:form . "possibly") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "due") (:form . "due") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "differ") (:form . "differing") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "expertise") (:form . "expertise") (:end . 57)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 71)\n  (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 78)\n  (:start . 72) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gene") (:form . "gene") (:end . 87) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "regulation") (:form . "regulation") (:end . 98)\n  (:start . 88) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 113)\n  (:start . 103) (:id . 59))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 120)\n  (:start . 114) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 127)\n  (:start . 122) (:id . 62))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 131) (:start . 128)\n  (:id . 63))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 136) (:start . 132)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 145)\n  (:start . 137) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n  (:id . 66))\n ((:tag . "VBG") (:stem . "vary") (:form . "varying") (:end . 156)\n  (:start . 149) (:id . 67))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 163)\n  (:start . 157) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 166) (:start . 164)\n  (:id . 69))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 177)\n  (:start . 167) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 180) (:start . 178)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "assign") (:form . "assigning") (:end . 190)\n  (:start . 181) (:id . 72))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 195) (:start . 191)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 204)\n  (:start . 196) (:id . 74))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 213)\n  (:start . 205) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x12.399.1) (:span 128 131))\n  ((:id . :x12.399.2) (:span 8 16)))\n (:hscopes ((:id . :x12.399.1) (:span 128 213))\n  ((:id . :x12.399.2) (:span 8 213)))\n (:identifiers (:sid . :s12.399) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504202@unknown@formal@none@1@S@A solution for further phases of annotation would be to analyze the domain knowledge of annotators in greater detail and, where appropriate, provide extra training in the assignment of more specific categories.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "solution") (:form . "solution") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "phase") (:form . "phases") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "VB") (:stem . "analyze") (:form . "analyze") (:end . 63)\n  (:start . 56) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 74)\n  (:start . 68) (:id . 54))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 84)\n  (:start . 75) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "annotator") (:form . "annotators") (:end . 98)\n  (:start . 88) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 101) (:start . 99)\n  (:id . 58))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 109)\n  (:start . 102) (:id . 59))\n ((:tag . "NN") (:stem . "detail") (:form . "detail") (:end . 116)\n  (:start . 110) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 62))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 127)\n  (:start . 122) (:id . 63))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 139)\n  (:start . 128) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 148)\n  (:start . 141) (:id . 66))\n ((:tag . "JJ") (:stem . "extra") (:form . "extra") (:end . 154)\n  (:start . 149) (:id . 67))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 163)\n  (:start . 155) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 166) (:start . 164)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 70))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 181)\n  (:start . 171) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n  (:id . 72))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 189) (:start . 185)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 198)\n  (:start . 190) (:id . 74))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 209)\n  (:start . 199) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x12.400.1) (:span 44 49)))\n (:hscopes ((:id . :x12.400.1) (:span 44 209)))\n (:identifiers (:sid . :s12.400) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504203@unknown@formal@none@1@S@This may be combined with a re-evaluation and possible simplification of the concept hierarchies.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "re-evaluation") (:form . "re-evaluation")\n  (:end . 41) (:start . 28) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "simplification") (:form . "simplification")\n  (:end . 69) (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "concept") (:form . "concept") (:end . 84)\n  (:start . 77) (:id . 54))\n ((:tag . "NNS") (:stem . "hierarchy") (:form . "hierarchies") (:end . 96)\n  (:start . 85) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x12.401.1) (:span 46 54)) ((:id . :x12.401.2) (:span 5 8)))\n (:hscopes ((:id . :x12.401.1) (:span 46 96))\n  ((:id . :x12.401.2) (:span 0 96)))\n (:identifiers (:sid . :s12.401) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504204@unknown@formal@none@1@S@A further major direction of future work will be to apply our scheme to a greater range of biomedical texts that describe a wider range of event types.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "direction") (:form . "direction") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "future") (:form . "future") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "VB") (:stem . "apply") (:form . "apply") (:end . 57) (:start . 52)\n  (:id . 52))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 68)\n  (:start . 62) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 56))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 81)\n  (:start . 74) (:id . 57))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 87) (:start . 82)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 90) (:start . 88)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 101)\n  (:start . 91) (:id . 60))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 107)\n  (:start . 102) (:id . 61))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 112) (:start . 108)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 121)\n  (:start . 113) (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 123) (:start . 122)\n  (:id . 64))\n ((:tag . "JJR") (:stem . "wide") (:form . "wider") (:end . 129)\n  (:start . 124) (:id . 65))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 135)\n  (:start . 130) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 67))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 144)\n  (:start . 139) (:id . 68))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 150)\n  (:start . 145) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s12.402) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504205@unknown@formal@none@1@S@Whilst other event types may require the use of alternative biological concepts or ontologies, we would like to verify that our set of semantic roles is applicable to events in other areas of biomedicine.@(((:tag . "IN") (:stem . "whilst") (:form . "Whilst") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "event") (:form . "event") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "VB") (:stem . "require") (:form . "require") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 59)\n  (:start . 48) (:id . 51))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 70)\n  (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "concept") (:form . "concepts") (:end . 79)\n  (:start . 71) (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 82) (:start . 80)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "ontology") (:form . "ontologies") (:end . 93)\n  (:start . 83) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 103) (:start . 98)\n  (:id . 58))\n ((:tag . "VB") (:stem . "like") (:form . "like") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "VB") (:stem . "verify") (:form . "verify") (:end . 118)\n  (:start . 112) (:id . 61))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 123) (:start . 119)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 131) (:start . 128)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "semantic") (:form . "semantic") (:end . 143)\n  (:start . 135) (:id . 66))\n ((:tag . "NNS") (:stem . "role") (:form . "roles") (:end . 149)\n  (:start . 144) (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 152) (:start . 150)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "applicable") (:form . "applicable") (:end . 163)\n  (:start . 153) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 166) (:start . 164)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 173)\n  (:start . 167) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 176) (:start . 174)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 182)\n  (:start . 177) (:id . 73))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 188)\n  (:start . 183) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 191) (:start . 189)\n  (:id . 75))\n ((:tag . "NN") (:stem . "biomedicine") (:form . "biomedicine") (:end . 203)\n  (:start . 192) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 204) (:start . 203)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x12.403.1) (:span 25 28)))\n (:hscopes ((:id . :x12.403.1) (:span 25 93)))\n (:identifiers (:sid . :s12.403) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504206@unknown@formal@none@1@S@The texts we will consider will also include full texts, in which events may be expressed in different ways from abstracts, and may involve different (higher) numbers of arguments.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VB") (:stem . "consider") (:form . "consider") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "VB") (:stem . "include") (:form . "include") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "text") (:form . "texts") (:end . 55) (:start . 50)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 72)\n  (:start . 66) (:id . 55))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "express") (:form . "expressed") (:end . 89)\n  (:start . 80) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 102)\n  (:start . 93) (:id . 60))\n ((:tag . "NNS") (:stem . "way") (:form . "ways") (:end . 107) (:start . 103)\n  (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 112) (:start . 108)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "abstract") (:form . "abstracts") (:end . 122)\n  (:start . 113) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 127) (:start . 124)\n  (:id . 65))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 131) (:start . 128)\n  (:id . 66))\n ((:tag . "VB") (:stem . "involve") (:form . "involve") (:end . 139)\n  (:start . 132) (:id . 67))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 149)\n  (:start . 140) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 151) (:start . 150)\n  (:id . 69))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 157)\n  (:start . 151) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 166)\n  (:start . 159) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 169) (:start . 167)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "argument") (:form . "arguments") (:end . 179)\n  (:start . 170) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x12.404.1) (:span 128 131))\n  ((:id . :x12.404.2) (:span 73 76)))\n (:hscopes ((:id . :x12.404.1) (:span 128 179))\n  ((:id . :x12.404.2) (:span 66 122)))\n (:identifiers (:sid . :s12.404) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504207@unknown@formal@none@1@S@Finally, we wish to ensure that others can use and evaluate the GREC as simply as possible.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "wish") (:form . "wish") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 26)\n  (:start . 20) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 38)\n  (:start . 32) (:id . 49))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "VB") (:stem . "use") (:form . "use") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 52))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 59)\n  (:start . 51) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 71) (:start . 69)\n  (:id . 56))\n ((:tag . "RB") (:stem . "simply") (:form . "simply") (:end . 78)\n  (:start . 72) (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 90)\n  (:start . 82) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s12.405) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504208@unknown@formal@none@1@S@Our future plan includes facilitating this in two different ways:@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "future") (:form . "future") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "plan") (:form . "plan") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "VBG") (:stem . "facilitate") (:form . "facilitating") (:end . 37)\n  (:start . 25) (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 59)\n  (:start . 50) (:id . 50))\n ((:tag . "NNS") (:stem . "way") (:form . "ways") (:end . 64) (:start . 60)\n  (:id . 51))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 65) (:start . 64)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s12.406) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504209@unknown@formal@none@1@S@Firstly, in response to the current diversity of corpus annotation formats and the problems this causes in their comparative evaluation [63], a shared format has been created for resources for biomedical relation extraction [15], together with a standard for the evaluation of relation extraction methods using this data [64].@(((:tag . "RB") (:stem . "firstly") (:form . "Firstly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "response") (:form . "response") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 35)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "diversity") (:form . "diversity") (:end . 45)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 66)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "format") (:form . "formats") (:end . 74)\n  (:start . 67) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "problem") (:form . "problems") (:end . 91)\n  (:start . 83) (:id . 56))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "cause") (:form . "causes") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 112)\n  (:start . 107) (:id . 60))\n ((:tag . "JJ") (:stem . "comparative") (:form . "comparative") (:end . 124)\n  (:start . 113) (:id . 61))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 135)\n  (:start . 125) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 137) (:start . 136)\n  (:id . 63))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 139) (:start . 137)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 140) (:start . 139)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "shared") (:form . "shared") (:end . 150)\n  (:start . 144) (:id . 68))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 157)\n  (:start . 151) (:id . 69))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 161) (:start . 158)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 166) (:start . 162)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "create") (:form . "created") (:end . 174)\n  (:start . 167) (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 178) (:start . 175)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 188)\n  (:start . 179) (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 192) (:start . 189)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 203)\n  (:start . 193) (:id . 76))\n ((:tag . "NN") (:stem . "relation") (:form . "relation") (:end . 212)\n  (:start . 204) (:id . 77))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 223)\n  (:start . 213) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 225) (:start . 224)\n  (:id . 79))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 227) (:start . 225)\n  (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 228) (:start . 227)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 229) (:start . 228)\n  (:id . 82))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 238)\n  (:start . 230) (:id . 83))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 243) (:start . 239)\n  (:id . 84))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 245) (:start . 244)\n  (:id . 85))\n ((:tag . "NN") (:stem . "standard") (:form . "standard") (:end . 254)\n  (:start . 246) (:id . 86))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 258) (:start . 255)\n  (:id . 87))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 262) (:start . 259)\n  (:id . 88))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 273)\n  (:start . 263) (:id . 89))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 276) (:start . 274)\n  (:id . 90))\n ((:tag . "NN") (:stem . "relation") (:form . "relation") (:end . 285)\n  (:start . 277) (:id . 91))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 296)\n  (:start . 286) (:id . 92))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 304)\n  (:start . 297) (:id . 93))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 310) (:start . 305)\n  (:id . 94))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 315) (:start . 311)\n  (:id . 95))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 320)\n  (:start . 316) (:id . 96))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 322) (:start . 321)\n  (:id . 97))\n ((:tag . "CD") (:stem . "64") (:form . "64") (:end . 324) (:start . 322)\n  (:id . 98))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 325) (:start . 324)\n  (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 326) (:start . 325)\n  (:id . 100)))@@@1@59@((:identifiers (:sid . :s12.407) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504210@unknown@formal@none@1@S@We plan to convert our own corpus to this format, which has already been carried out for several biomedical corpora, e.g., [13,16,21,23].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "plan") (:form . "plan") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VB") (:stem . "convert") (:form . "convert") (:end . 18)\n  (:start . 11) (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "own") (:form . "own") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 33)\n  (:start . 27) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 41) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 48)\n  (:start . 42) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 55) (:start . 50)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 59) (:start . 56)\n  (:id . 54))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 67)\n  (:start . 60) (:id . 55))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 72) (:start . 68)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 80)\n  (:start . 73) (:id . 57))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 88) (:start . 85)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 96)\n  (:start . 89) (:id . 60))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 107)\n  (:start . 97) (:id . 61))\n ((:tag . "NN") (:stem . "corpora") (:form . "corpora") (:end . 115)\n  (:start . 108) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 63))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 121) (:start . 117)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 124) (:start . 123)\n  (:id . 66))\n ((:tag . "CD") (:stem . "13,16,21,23") (:form . "13,16,21,23") (:end . 135)\n  (:start . 124) (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 136) (:start . 135)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s12.408) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504211@unknown@formal@none@1@S@Secondly, we plan to develop a corpus reader which will allow the GREC to be made available within the U-Compare system [65](http://u-compare.org).@(((:tag . "RB") (:stem . "secondly") (:form . "Secondly") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "plan") (:form . "plan") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "VB") (:stem . "develop") (:form . "develop") (:end . 28)\n  (:start . 21) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "corpus") (:form . "corpus") (:end . 37)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "reader") (:form . "reader") (:end . 44)\n  (:start . 38) (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 50) (:start . 45)\n  (:id . 51))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 55) (:start . 51)\n  (:id . 52))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 61) (:start . 56)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "GREC") (:form . "GREC") (:end . 70) (:start . 66)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 76) (:start . 74)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 81) (:start . 77)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 91)\n  (:start . 82) (:id . 59))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 98)\n  (:start . 92) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 61))\n ((:tag . "NN") (:stem . "u-compare") (:form . "U-Compare") (:end . 112)\n  (:start . 103) (:id . 62))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 119)\n  (:start . 113) (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 121) (:start . 120)\n  (:id . 64))\n ((:tag . "NN") (:stem . "65](http://u-compare.org)")\n  (:form . "65](http://u-compare.org)") (:end . 146) (:start . 121)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s12.409) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504212@unknown@formal@none@1@S@This is an integrated text mining/natural language processing system based on the UIMA Framework [66], which provides access to a large collection of ready-to-use interoperable natural language processing components.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "integrate") (:form . "integrated") (:end . 21)\n  (:start . 11) (:id . 45))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mining/natural") (:form . "mining/natural")\n  (:end . 41) (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 61)\n  (:start . 51) (:id . 49))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 68)\n  (:start . 62) (:id . 50))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 74) (:start . 69)\n  (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 77) (:start . 75)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "UIMA") (:form . "UIMA") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Framework") (:form . "Framework") (:end . 96)\n  (:start . 87) (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 98) (:start . 97)\n  (:id . 56))\n ((:tag . "CD") (:stem . "66") (:form . "66") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 101) (:start . 100)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 108)\n  (:start . 103) (:id . 60))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 117)\n  (:start . 109) (:id . 61))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 124)\n  (:start . 118) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 129) (:start . 128)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 135)\n  (:start . 130) (:id . 65))\n ((:tag . "NN") (:stem . "collection") (:form . "collection") (:end . 146)\n  (:start . 136) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "ready-to-use") (:form . "ready-to-use") (:end . 162)\n  (:start . 150) (:id . 68))\n ((:tag . "JJ") (:stem . "interoperable") (:form . "interoperable")\n  (:end . 176) (:start . 163) (:id . 69))\n ((:tag . "JJ") (:stem . "natural") (:form . "natural") (:end . 184)\n  (:start . 177) (:id . 70))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 193)\n  (:start . 185) (:id . 71))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 204)\n  (:start . 194) (:id . 72))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 215)\n  (:start . 205) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s12.410) (:did . :pmc2774701) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504213@unknown@formal@none@1@S@A structure filter for the Eukaryotic Linear Motif Resource@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 11)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Eukaryotic") (:form . "Eukaryotic") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "NNP") (:stem . "Linear") (:form . "Linear") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "NNP") (:stem . "Motif") (:form . "Motif") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Resource") (:form . "Resource") (:end . 59)\n  (:start . 51) (:id . 50)))@@@1@9@((:identifiers (:sid . :s13.1) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5504214@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s13.2) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504215@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s13.3) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504216@unknown@formal@none@1@S@Many proteins are highly modular, being assembled from globular domains and segments of natively disordered polypeptides.@(((:tag . "JJ") (:stem . "many") (:form . "Many") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "JJ") (:stem . "modular") (:form . "modular") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "assemble") (:form . "assembled") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 84)\n  (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "RB") (:stem . "natively") (:form . "natively") (:end . 96)\n  (:start . 88) (:id . 56))\n ((:tag . "VBN") (:stem . "disorder") (:form . "disordered") (:end . 107)\n  (:start . 97) (:id . 57))\n ((:tag . "NNS") (:stem . "polypeptide") (:form . "polypeptides") (:end . 120)\n  (:start . 108) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s13.4) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504217@unknown@formal@none@1@S@Linear motifs, short sequence modules functioning independently of protein tertiary structure, are most abundant in natively disordered polypeptides but are also found in accessible parts of globular domains, such as exposed loops.@(((:tag . "JJ") (:stem . "linear") (:form . "Linear") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 13) (:start . 7)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "VBG") (:stem . "function") (:form . "functioning") (:end . 49)\n  (:start . 38) (:id . 48))\n ((:tag . "RB") (:stem . "independently") (:form . "independently")\n  (:end . 63) (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 74)\n  (:start . 67) (:id . 51))\n ((:tag . "NN") (:stem . "tertiary") (:form . "tertiary") (:end . 83)\n  (:start . 75) (:id . 52))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 93)\n  (:start . 84) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 98) (:start . 95)\n  (:id . 55))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 103) (:start . 99)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "abundant") (:form . "abundant") (:end . 112)\n  (:start . 104) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 58))\n ((:tag . "RB") (:stem . "natively") (:form . "natively") (:end . 124)\n  (:start . 116) (:id . 59))\n ((:tag . "VBN") (:stem . "disorder") (:form . "disordered") (:end . 135)\n  (:start . 125) (:id . 60))\n ((:tag . "NNS") (:stem . "polypeptide") (:form . "polypeptides") (:end . 148)\n  (:start . 136) (:id . 61))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 152) (:start . 149)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 156) (:start . 153)\n  (:id . 63))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 161) (:start . 157)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 167)\n  (:start . 162) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 170) (:start . 168)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "accessible") (:form . "accessible") (:end . 181)\n  (:start . 171) (:id . 67))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 187)\n  (:start . 182) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 190) (:start . 188)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 199)\n  (:start . 191) (:id . 70))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 207)\n  (:start . 200) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 208) (:start . 207)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 213) (:start . 209)\n  (:id . 73))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 216) (:start . 214)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 224)\n  (:start . 217) (:id . 75))\n ((:tag . "NNS") (:stem . "loop") (:form . "loops") (:end . 230)\n  (:start . 225) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s13.5) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504218@unknown@formal@none@1@S@The prediction of novel occurrences of known linear motifs attempts the difficult task of distinguishing functional matches from stochastically occurring non-functional matches.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "occurrence") (:form . "occurrences") (:end . 35)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "linear") (:form . "linear") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 58)\n  (:start . 52) (:id . 50))\n ((:tag . "VBZ") (:stem . "attempt") (:form . "attempts") (:end . 67)\n  (:start . 59) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "difficult") (:form . "difficult") (:end . 81)\n  (:start . 72) (:id . 53))\n ((:tag . "NN") (:stem . "task") (:form . "task") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "distinguish") (:form . "distinguishing")\n  (:end . 104) (:start . 90) (:id . 56))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 115)\n  (:start . 105) (:id . 57))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 123)\n  (:start . 116) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 128) (:start . 124)\n  (:id . 59))\n ((:tag . "RB") (:stem . "stochastically") (:form . "stochastically")\n  (:end . 143) (:start . 129) (:id . 60))\n ((:tag . "VBG") (:stem . "occur") (:form . "occurring") (:end . 153)\n  (:start . 144) (:id . 61))\n ((:tag . "JJ") (:stem . "non-functional") (:form . "non-functional")\n  (:end . 168) (:start . 154) (:id . 62))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 176)\n  (:start . 169) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s13.6) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504219@unknown@formal@none@1@S@Although functionality can only be confirmed experimentally, confidence in a putative motif is increased if a motif exhibits attributes associated with functional instances such as occurrence in the correct taxonomic range, cellular compartment, conservation in homologues and accessibility to interacting partners.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 22) (:start . 9) (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 26) (:start . 23)\n  (:id . 44))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 31) (:start . 27)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "confirm") (:form . "confirmed") (:end . 44)\n  (:start . 35) (:id . 47))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n  (:end . 59) (:start . 45) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 49))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 71)\n  (:start . 61) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 74) (:start . 72)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 76) (:start . 75)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 85)\n  (:start . 77) (:id . 53))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 91) (:start . 86)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 94) (:start . 92)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 104)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 107) (:start . 105)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 109) (:start . 108)\n  (:id . 58))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 115)\n  (:start . 110) (:id . 59))\n ((:tag . "VBZ") (:stem . "exhibit") (:form . "exhibits") (:end . 124)\n  (:start . 116) (:id . 60))\n ((:tag . "NNS") (:stem . "attribute") (:form . "attributes") (:end . 135)\n  (:start . 125) (:id . 61))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 146)\n  (:start . 136) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 151) (:start . 147)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 162)\n  (:start . 152) (:id . 64))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 172)\n  (:start . 163) (:id . 65))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 177) (:start . 173)\n  (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 180) (:start . 178)\n  (:id . 67))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 191)\n  (:start . 181) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 194) (:start . 192)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 198) (:start . 195)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "correct") (:form . "correct") (:end . 206)\n  (:start . 199) (:id . 71))\n ((:tag . "JJ") (:stem . "taxonomic") (:form . "taxonomic") (:end . 216)\n  (:start . 207) (:id . 72))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 222)\n  (:start . 217) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 223) (:start . 222)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 232)\n  (:start . 224) (:id . 75))\n ((:tag . "NN") (:stem . "compartment") (:form . "compartment") (:end . 244)\n  (:start . 233) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 245) (:start . 244)\n  (:id . 77))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 258)\n  (:start . 246) (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 261) (:start . 259)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "homologue") (:form . "homologues") (:end . 272)\n  (:start . 262) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 276) (:start . 273)\n  (:id . 81))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 290) (:start . 277) (:id . 82))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 293) (:start . 291)\n  (:id . 83))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 305)\n  (:start . 294) (:id . 84))\n ((:tag . "NNS") (:stem . "partner") (:form . "partners") (:end . 314)\n  (:start . 306) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 315) (:start . 314)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s13.7) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504220@unknown@formal@none@1@S@Several tools now use these attributes to classify putative motifs based on confidence of functionality.@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "use") (:form . "use") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "attribute") (:form . "attributes") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "VB") (:stem . "classify") (:form . "classify") (:end . 50)\n  (:start . 42) (:id . 49))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 66)\n  (:start . 60) (:id . 51))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 86)\n  (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 103) (:start . 90) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s13.8) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504221@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s13.9) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504222@unknown@formal@none@1@S@Current methods assessing motif accessibility do not consider much of the information available, either predicting accessibility from primary sequence or regarding any motif occurring in a globular region as low confidence.@(((:tag . "JJ") (:stem . "current") (:form . "Current") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBG") (:stem . "assess") (:form . "assessing") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 31) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 45) (:start . 32) (:id . 46))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 48) (:start . 46)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 52) (:start . 49)\n  (:id . 48))\n ((:tag . "VB") (:stem . "consider") (:form . "consider") (:end . 61)\n  (:start . 53) (:id . 49))\n ((:tag . "JJ") (:stem . "much") (:form . "much") (:end . 66) (:start . 62)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 85)\n  (:start . 74) (:id . 53))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 95)\n  (:start . 86) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 55))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 103)\n  (:start . 97) (:id . 56))\n ((:tag . "VBG") (:stem . "predict") (:form . "predicting") (:end . 114)\n  (:start . 104) (:id . 57))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 128) (:start . 115) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 133) (:start . 129)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 141)\n  (:start . 134) (:id . 60))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 150)\n  (:start . 142) (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 153) (:start . 151)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "regard") (:form . "regarding") (:end . 163)\n  (:start . 154) (:id . 63))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 167) (:start . 164)\n  (:id . 64))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 173)\n  (:start . 168) (:id . 65))\n ((:tag . "VBG") (:stem . "occur") (:form . "occurring") (:end . 183)\n  (:start . 174) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 186) (:start . 184)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 188) (:start . 187)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 197)\n  (:start . 189) (:id . 69))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 204)\n  (:start . 198) (:id . 70))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 207) (:start . 205)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 211) (:start . 208)\n  (:id . 72))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 222)\n  (:start . 212) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 223) (:start . 222)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s13.10) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504223@unknown@formal@none@1@S@We present a method considering accessibility and secondary structural context derived from experimentally solved protein structures to rectify this situation.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "present") (:form . "present") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "VBG") (:stem . "consider") (:form . "considering") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 45) (:start . 32) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 59)\n  (:start . 50) (:id . 49))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 70)\n  (:start . 60) (:id . 50))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 78)\n  (:start . 71) (:id . 51))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 86)\n  (:start . 79) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 91) (:start . 87)\n  (:id . 53))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n  (:end . 106) (:start . 92) (:id . 54))\n ((:tag . "VBN") (:stem . "solve") (:form . "solved") (:end . 113)\n  (:start . 107) (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 121)\n  (:start . 114) (:id . 56))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 132)\n  (:start . 122) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 58))\n ((:tag . "VB") (:stem . "rectify") (:form . "rectify") (:end . 143)\n  (:start . 136) (:id . 59))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 148) (:start . 144)\n  (:id . 60))\n ((:tag . "NN") (:stem . "situation") (:form . "situation") (:end . 158)\n  (:start . 149) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s13.11) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504224@unknown@formal@none@1@S@Putatively functional motif occurrences are mapped onto a representative domain, given that a high quality reference SCOP domain structure is available for the protein itself or a close relative.@(((:tag . "RB") (:stem . "putatively") (:form . "Putatively") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 27) (:start . 22)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "occurrence") (:form . "occurrences") (:end . 39)\n  (:start . 28) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 43) (:start . 40)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "map") (:form . "mapped") (:end . 50) (:start . 44)\n  (:id . 47))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 55) (:start . 51)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 72) (:start . 58) (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 79)\n  (:start . 73) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 86) (:start . 81)\n  (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 91) (:start . 87)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 93) (:start . 92)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 98) (:start . 94)\n  (:id . 56))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 106)\n  (:start . 99) (:id . 57))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 116)\n  (:start . 107) (:id . 58))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 121) (:start . 117)\n  (:id . 59))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 128)\n  (:start . 122) (:id . 60))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 138)\n  (:start . 129) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 141) (:start . 139)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 151)\n  (:start . 142) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 155) (:start . 152)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 65))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 167)\n  (:start . 160) (:id . 66))\n ((:tag . "PRP") (:stem . "itself") (:form . "itself") (:end . 174)\n  (:start . 168) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 177) (:start . 175)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 179) (:start . 178)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "close") (:form . "close") (:end . 185)\n  (:start . 180) (:id . 70))\n ((:tag . "NN") (:stem . "relative") (:form . "relative") (:end . 194)\n  (:start . 186) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 72)))@@@1@31@((:hcues ((:id . :x13.12.1) (:span 0 10)))\n (:hscopes ((:id . :x13.12.1) (:span 0 194)))\n (:identifiers (:sid . :s13.12) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504225@unknown@formal@none@1@S@Candidate motifs can then be scored for solvent-accessibility and secondary structure context.@(((:tag . "NN") (:stem . "candidate") (:form . "Candidate") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 16)\n  (:start . 10) (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "score") (:form . "scored") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "solvent-accessibility")\n  (:form . "solvent-accessibility") (:end . 61) (:start . 40) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 75)\n  (:start . 66) (:id . 51))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 85)\n  (:start . 76) (:id . 52))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 93)\n  (:start . 86) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s13.13) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504226@unknown@formal@none@1@S@The scores are calibrated on a benchmark set of experimentally verified motif instances compared with a set of random matches.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "calibrate") (:form . "calibrated") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "benchmark") (:form . "benchmark") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n  (:end . 62) (:start . 48) (:id . 51))\n ((:tag . "VBN") (:stem . "verify") (:form . "verified") (:end . 71)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 77) (:start . 72)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 87)\n  (:start . 78) (:id . 54))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 96)\n  (:start . 88) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 101) (:start . 97)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 103) (:start . 102)\n  (:id . 57))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 107) (:start . 104)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 117)\n  (:start . 111) (:id . 60))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 125)\n  (:start . 118) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s13.14) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504227@unknown@formal@none@1@S@A combined score yields 3-fold enrichment for functional motifs assigned to high confidence classifications and 2.5-fold enrichment for random motifs assigned to low confidence classifications.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "combined") (:form . "combined") (:end . 10)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "yield") (:form . "yields") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "JJ") (:stem . "3-fold") (:form . "3-fold") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 41)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 56)\n  (:start . 46) (:id . 49))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 63)\n  (:start . 57) (:id . 50))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 72)\n  (:start . 64) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 75) (:start . 73)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 80) (:start . 76)\n  (:id . 53))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 91)\n  (:start . 81) (:id . 54))\n ((:tag . "NNS") (:stem . "classification") (:form . "classifications")\n  (:end . 107) (:start . 92) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "2.5-fold") (:form . "2.5-fold") (:end . 120)\n  (:start . 112) (:id . 57))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 131)\n  (:start . 121) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 135) (:start . 132)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 142)\n  (:start . 136) (:id . 60))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 149)\n  (:start . 143) (:id . 61))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 158)\n  (:start . 150) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 161) (:start . 159)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 165) (:start . 162)\n  (:id . 64))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 176)\n  (:start . 166) (:id . 65))\n ((:tag . "NNS") (:stem . "classification") (:form . "classifications")\n  (:end . 192) (:start . 177) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s13.15) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504228@unknown@formal@none@1@S@The structure filter is implemented as a pipeline with both a graphical interface via the ELM resource http://elm.eu.org/ and through a Web Service protocol.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 35)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "pipeline") (:form . "pipeline") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "graphical") (:form . "graphical") (:end . 71)\n  (:start . 62) (:id . 53))\n ((:tag . "NN") (:stem . "interface") (:form . "interface") (:end . 81)\n  (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 102)\n  (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "http://elm.eu.org/") (:form . "http://elm.eu.org/")\n  (:end . 121) (:start . 103) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 60))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 133)\n  (:start . 126) (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 135) (:start . 134)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 139) (:start . 136)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "Service") (:form . "Service") (:end . 147)\n  (:start . 140) (:id . 64))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 156)\n  (:start . 148) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s13.16) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504229@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s13.17) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504230@unknown@formal@none@1@S@New occurrences of known linear motifs require experimental validation as the bioinformatics tools currently have limited reliability.@(((:tag . "JJ") (:stem . "new") (:form . "New") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "occurrence") (:form . "occurrences") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "linear") (:form . "linear") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 59)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 70)\n  (:start . 60) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 73) (:start . 71)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "bioinformatic") (:form . "bioinformatics")\n  (:end . 92) (:start . 78) (:id . 53))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 98) (:start . 93)\n  (:id . 54))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 108)\n  (:start . 99) (:id . 55))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 113) (:start . 109)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 121)\n  (:start . 114) (:id . 57))\n ((:tag . "NN") (:stem . "reliability") (:form . "reliability") (:end . 133)\n  (:start . 122) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s13.18) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504231@unknown@formal@none@1@S@The ELM structure filter will aid users assessing candidate motifs presenting in globular structural regions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VB") (:stem . "aid") (:form . "aid") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "assess") (:form . "assessing") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 59)\n  (:start . 50) (:id . 50))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 66)\n  (:start . 60) (:id . 51))\n ((:tag . "VBG") (:stem . "present") (:form . "presenting") (:end . 77)\n  (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 100)\n  (:start . 90) (:id . 55))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 108)\n  (:start . 101) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s13.19) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504232@unknown@formal@none@1@S@Most importantly, it will help users to decide whether to expend their valuable time and resources on experimental testing of interesting motif candidates.@(((:tag . "RBS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "importantly") (:form . "importantly") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "VB") (:stem . "decide") (:form . "decide") (:end . 46)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "VB") (:stem . "expend") (:form . "expend") (:end . 64)\n  (:start . 58) (:id . 53))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 70)\n  (:start . 65) (:id . 54))\n ((:tag . "JJ") (:stem . "valuable") (:form . "valuable") (:end . 79)\n  (:start . 71) (:id . 55))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 98)\n  (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 114)\n  (:start . 102) (:id . 60))\n ((:tag . "NN") (:stem . "testing") (:form . "testing") (:end . 122)\n  (:start . 115) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "interesting") (:form . "interesting") (:end . 137)\n  (:start . 126) (:id . 63))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 143)\n  (:start . 138) (:id . 64))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 154)\n  (:start . 144) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s13.20) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504233@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s13.21) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504234@unknown@formal@none@1@S@In recent years it has become clear that proteins with highly modular architectures possess numerous short peptide motifs that are essential to their function [1-5].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "year") (:form . "years") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "become") (:form . "become") (:end . 29)\n  (:start . 23) (:id . 47))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "JJ") (:stem . "modular") (:form . "modular") (:end . 69)\n  (:start . 62) (:id . 53))\n ((:tag . "NNS") (:stem . "architecture") (:form . "architectures")\n  (:end . 83) (:start . 70) (:id . 54))\n ((:tag . "VBP") (:stem . "possess") (:form . "possess") (:end . 91)\n  (:start . 84) (:id . 55))\n ((:tag . "JJ") (:stem . "numerous") (:form . "numerous") (:end . 100)\n  (:start . 92) (:id . 56))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 106)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 114)\n  (:start . 107) (:id . 58))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 121)\n  (:start . 115) (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 126) (:start . 122)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 130) (:start . 127)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 140)\n  (:start . 131) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n  (:id . 63))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 149)\n  (:start . 144) (:id . 64))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 158)\n  (:start . 150) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 160) (:start . 159)\n  (:id . 66))\n ((:tag . "CD") (:stem . "1-5") (:form . "1-5") (:end . 163) (:start . 160)\n  (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 164) (:start . 163)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s13.22) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504235@unknown@formal@none@1@S@Such peptides are termed Linear Motifs (LM) as, in contrast to the globular domains, their function is independent of tertiary structure and encoded solely by the amino acid sequence.@(((:tag . "JJ") (:stem . "such") (:form . "Such") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "term") (:form . "termed") (:end . 24) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "linear") (:form . "Linear") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "NNP") (:stem . "Motif") (:form . "Motifs") (:end . 38)\n  (:start . 32) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 46) (:start . 44)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 53))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 59)\n  (:start . 51) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 75)\n  (:start . 67) (:id . 57))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 83)\n  (:start . 76) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 59))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 90)\n  (:start . 85) (:id . 60))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 99)\n  (:start . 91) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 102) (:start . 100)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 114)\n  (:start . 103) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "tertiary") (:form . "tertiary") (:end . 126)\n  (:start . 118) (:id . 65))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 136)\n  (:start . 127) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "encode") (:form . "encoded") (:end . 148)\n  (:start . 141) (:id . 68))\n ((:tag . "RB") (:stem . "solely") (:form . "solely") (:end . 155)\n  (:start . 149) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 158) (:start . 156)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 162) (:start . 159)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 168)\n  (:start . 163) (:id . 72))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 173) (:start . 169)\n  (:id . 73))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 182)\n  (:start . 174) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s13.23) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504236@unknown@formal@none@1@S@They are found in a diverse range of proteins, such as membrane receptors, adaptors, scaffolds and transcription factors, and mediate numerous tasks, which can be as disparate as directing subcellular localization or acting as sites of cleavage.@(((:tag . "PRP") (:stem . "they") (:form . "They") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "diverse") (:form . "diverse") (:end . 27)\n  (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 33) (:start . 28)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 45)\n  (:start . 37) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 51) (:start . 47)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 54) (:start . 52)\n  (:id . 53))\n ((:tag . "NN") (:stem . "membrane") (:form . "membrane") (:end . 63)\n  (:start . 55) (:id . 54))\n ((:tag . "NNS") (:stem . "receptor") (:form . "receptors") (:end . 73)\n  (:start . 64) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "adaptor") (:form . "adaptors") (:end . 83)\n  (:start . 75) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "scaffold") (:form . "scaffolds") (:end . 94)\n  (:start . 85) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 60))\n ((:tag . "NN") (:stem . "transcription") (:form . "transcription")\n  (:end . 112) (:start . 99) (:id . 61))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 120)\n  (:start . 113) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 64))\n ((:tag . "VB") (:stem . "mediate") (:form . "mediate") (:end . 133)\n  (:start . 126) (:id . 65))\n ((:tag . "JJ") (:stem . "numerous") (:form . "numerous") (:end . 142)\n  (:start . 134) (:id . 66))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 148)\n  (:start . 143) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 68))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 155)\n  (:start . 150) (:id . 69))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 159) (:start . 156)\n  (:id . 70))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 162) (:start . 160)\n  (:id . 71))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 165) (:start . 163)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "disparate") (:form . "disparate") (:end . 175)\n  (:start . 166) (:id . 73))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 178) (:start . 176)\n  (:id . 74))\n ((:tag . "VBG") (:stem . "direct") (:form . "directing") (:end . 188)\n  (:start . 179) (:id . 75))\n ((:tag . "JJ") (:stem . "subcellular") (:form . "subcellular") (:end . 200)\n  (:start . 189) (:id . 76))\n ((:tag . "NN") (:stem . "localization") (:form . "localization") (:end . 213)\n  (:start . 201) (:id . 77))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 216) (:start . 214)\n  (:id . 78))\n ((:tag . "VBG") (:stem . "act") (:form . "acting") (:end . 223)\n  (:start . 217) (:id . 79))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 226) (:start . 224)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 232)\n  (:start . 227) (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 235) (:start . 233)\n  (:id . 82))\n ((:tag . "NN") (:stem . "cleavage") (:form . "cleavage") (:end . 244)\n  (:start . 236) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 245) (:start . 244)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x13.24.1) (:span 156 159)))\n (:hscopes ((:id . :x13.24.1) (:span 156 244)))\n (:identifiers (:sid . :s13.24) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504237@unknown@formal@none@1@S@Well-known LMs include peptides binding SH3, Cyclin, PDZ and WW domains [6-10] and phosphorylated peptides interacting with SH2, PTB, BRCT and FHA phosphopeptide-binding domains [11-17].@(((:tag . "JJ") (:stem . "well-known") (:form . "Well-known") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 39)\n  (:start . 32) (:id . 46))\n ((:tag . "NNP") (:stem . "SH3") (:form . "SH3") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Cyclin") (:form . "Cyclin") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PDZ") (:form . "PDZ") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "WW") (:form . "WW") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 71)\n  (:start . 64) (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "CD") (:stem . "6-10") (:form . "6-10") (:end . 77) (:start . 73)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 78) (:start . 77)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "phosphorylate") (:form . "phosphorylated")\n  (:end . 97) (:start . 83) (:id . 59))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 106)\n  (:start . 98) (:id . 60))\n ((:tag . "VBG") (:stem . "interact") (:form . "interacting") (:end . 118)\n  (:start . 107) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 123) (:start . 119)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "SH2") (:form . "SH2") (:end . 127) (:start . 124)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "PTB") (:form . "PTB") (:end . 132) (:start . 129)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "BRCT") (:form . "BRCT") (:end . 138) (:start . 134)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "FHA") (:form . "FHA") (:end . 146) (:start . 143)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "phosphopeptide-binding")\n  (:form . "phosphopeptide-binding") (:end . 169) (:start . 147) (:id . 70))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 177)\n  (:start . 170) (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 179) (:start . 178)\n  (:id . 72))\n ((:tag . "CD") (:stem . "11-17") (:form . "11-17") (:end . 184)\n  (:start . 179) (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 185) (:start . 184)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s13.25) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504238@unknown@formal@none@1@S@The biological properties and range of functions mediated by LMs are reviewed in detail elsewhere [4,18-20].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "review") (:form . "reviewed") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "NN") (:stem . "detail") (:form . "detail") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . "RB") (:stem . "elsewhere") (:form . "elsewhere") (:end . 97)\n  (:start . 88) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "CD") (:stem . "4,18-20") (:form . "4,18-20") (:end . 106)\n  (:start . 99) (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 107) (:start . 106)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s13.26) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504239@unknown@formal@none@1@S@In order to deconvolute the functional components of modular protein architectures, it is necessary to identify the set of LMs as well as the folded components.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "deconvolute") (:form . "deconvolute") (:end . 23)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 49)\n  (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "modular") (:form . "modular") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 68)\n  (:start . 61) (:id . 51))\n ((:tag . "NNS") (:stem . "architecture") (:form . "architectures")\n  (:end . 82) (:start . 69) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 86) (:start . 84)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 99)\n  (:start . 90) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 102) (:start . 100)\n  (:id . 57))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 111)\n  (:start . 103) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 59))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 126) (:start . 123)\n  (:id . 62))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 134) (:start . 130)\n  (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 137) (:start . 135)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "folded") (:form . "folded") (:end . 148)\n  (:start . 142) (:id . 67))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 159)\n  (:start . 149) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s13.27) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504240@unknown@formal@none@1@S@However, this is not straightforward because simple searches with short sequence patterns, known to act as functional modules, are uninformative - returning a flood of false positive matches.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "straightforward") (:form . "straightforward")\n  (:end . 36) (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "JJ") (:stem . "simple") (:form . "simple") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 60)\n  (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 65) (:start . 61)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 71) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 80)\n  (:start . 72) (:id . 53))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 96) (:start . 91)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "VB") (:stem . "act") (:form . "act") (:end . 103) (:start . 100)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 117)\n  (:start . 107) (:id . 60))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 125)\n  (:start . 118) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 126) (:start . 125)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "uninformative") (:form . "uninformative")\n  (:end . 144) (:start . 131) (:id . 64))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 146) (:start . 145)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "return") (:form . "returning") (:end . 156)\n  (:start . 147) (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 158) (:start . 157)\n  (:id . 67))\n ((:tag . "NN") (:stem . "flood") (:form . "flood") (:end . 164)\n  (:start . 159) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 167) (:start . 165)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 173)\n  (:start . 168) (:id . 70))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 182)\n  (:start . 174) (:id . 71))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 190)\n  (:start . 183) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s13.28) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504241@unknown@formal@none@1@S@Several tools have been developed to rank motifs based on confidence of functionality by classifying putative motifs based on the hypothesis that functional motifs will have attributes similar to experimentally discovered motifs.@(((:tag . "JJ") (:stem . "several") (:form . "Several") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 13) (:start . 8)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "develop") (:form . "developed") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "VB") (:stem . "rank") (:form . "rank") (:end . 41) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 48)\n  (:start . 42) (:id . 49))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 68)\n  (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 85) (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "classify") (:form . "classifying") (:end . 100)\n  (:start . 89) (:id . 56))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 109)\n  (:start . 101) (:id . 57))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 116)\n  (:start . 110) (:id . 58))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 122)\n  (:start . 117) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 125) (:start . 123)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 61))\n ((:tag . "NN") (:stem . "hypothesis") (:form . "hypothesis") (:end . 140)\n  (:start . 130) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 145) (:start . 141)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 156)\n  (:start . 146) (:id . 64))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 163)\n  (:start . 157) (:id . 65))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 168) (:start . 164)\n  (:id . 66))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 173) (:start . 169)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "attribute") (:form . "attributes") (:end . 184)\n  (:start . 174) (:id . 68))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 192)\n  (:start . 185) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 195) (:start . 193)\n  (:id . 70))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n  (:end . 210) (:start . 196) (:id . 71))\n ((:tag . "VBN") (:stem . "discover") (:form . "discovered") (:end . 221)\n  (:start . 211) (:id . 72))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 228)\n  (:start . 222) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s13.29) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504242@unknown@formal@none@1@S@Although classification tools cannot definitely confirm a motif as functional (only experimental analysis can achieve this) they can be used to attach a level of confidence to a motif.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "classification") (:form . "classification")\n  (:end . 23) (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 29) (:start . 24)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "cannot") (:form . "cannot") (:end . 36)\n  (:start . 30) (:id . 45))\n ((:tag . "RB") (:stem . "definitely") (:form . "definitely") (:end . 47)\n  (:start . 37) (:id . 46))\n ((:tag . "VB") (:stem . "confirm") (:form . "confirm") (:end . 55)\n  (:start . 48) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 48))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 63) (:start . 58)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 66) (:start . 64)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 77)\n  (:start . 67) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "only") (:form . "only") (:end . 83) (:start . 79)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 96)\n  (:start . 84) (:id . 54))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 105)\n  (:start . 97) (:id . 55))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 109) (:start . 106)\n  (:id . 56))\n ((:tag . "VB") (:stem . "achieve") (:form . "achieve") (:end . 117)\n  (:start . 110) (:id . 57))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 122) (:start . 118)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 123) (:start . 122)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 128) (:start . 124)\n  (:id . 60))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 132) (:start . 129)\n  (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 135) (:start . 133)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 140) (:start . 136)\n  (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n  (:id . 64))\n ((:tag . "VB") (:stem . "attach") (:form . "attach") (:end . 150)\n  (:start . 144) (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 152) (:start . 151)\n  (:id . 66))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 158)\n  (:start . 153) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 161) (:start . 159)\n  (:id . 68))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 172)\n  (:start . 162) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 175) (:start . 173)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 177) (:start . 176)\n  (:id . 71))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 183)\n  (:start . 178) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x13.30.1) (:span 106 109)) ((:id . :x13.30.2) (:span 30 55)))\n (:hscopes ((:id . :x13.30.1) (:span 106 122))\n  ((:id . :x13.30.2) (:span 30 77)))\n (:identifiers (:sid . :s13.30) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504243@unknown@formal@none@1@S@For example motifs which occur in an incorrect cellular compartment, or outside the known taxonomic range, are unlikely to be functional as are those which are not conserved in closely related proteins or buried in a globular domain inaccessible for interaction.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "incorrect") (:form . "incorrect") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "JJ") (:stem . "cellular") (:form . "cellular") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "compartment") (:form . "compartment") (:end . 67)\n  (:start . 56) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "IN") (:stem . "outside") (:form . "outside") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "known") (:form . "known") (:end . 89) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "taxonomic") (:form . "taxonomic") (:end . 99)\n  (:start . 90) (:id . 57))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 105)\n  (:start . 100) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 119)\n  (:start . 111) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 122) (:start . 120)\n  (:id . 62))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 125) (:start . 123)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 136)\n  (:start . 126) (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 139) (:start . 137)\n  (:id . 65))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 143) (:start . 140)\n  (:id . 66))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 149)\n  (:start . 144) (:id . 67))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 155)\n  (:start . 150) (:id . 68))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 159) (:start . 156)\n  (:id . 69))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 163) (:start . 160)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 173)\n  (:start . 164) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 176) (:start . 174)\n  (:id . 72))\n ((:tag . "RB") (:stem . "closely") (:form . "closely") (:end . 184)\n  (:start . 177) (:id . 73))\n ((:tag . "JJ") (:stem . "related") (:form . "related") (:end . 192)\n  (:start . 185) (:id . 74))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 201)\n  (:start . 193) (:id . 75))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 204) (:start . 202)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "bury") (:form . "buried") (:end . 211)\n  (:start . 205) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 214) (:start . 212)\n  (:id . 78))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 216) (:start . 215)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 225)\n  (:start . 217) (:id . 80))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 232)\n  (:start . 226) (:id . 81))\n ((:tag . "JJ") (:stem . "inaccessible") (:form . "inaccessible") (:end . 245)\n  (:start . 233) (:id . 82))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 249) (:start . 246)\n  (:id . 83))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 261)\n  (:start . 250) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 262) (:start . 261)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x13.31.1) (:span 111 119)))\n (:hscopes ((:id . :x13.31.1) (:span 12 261)))\n (:identifiers (:sid . :s13.31) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504244@unknown@formal@none@1@S@Available motif discovery tools vary in their implementation of confidence-related metrics.@(((:tag . "JJ") (:stem . "available") (:form . "Available") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "discovery") (:form . "discovery") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 31) (:start . 26)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "vary") (:form . "vary") (:end . 36) (:start . 32)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 45)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "implementation") (:form . "implementation")\n  (:end . 60) (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "confidence-related") (:form . "confidence-related")\n  (:end . 82) (:start . 64) (:id . 51))\n ((:tag . "NNS") (:stem . "metric") (:form . "metrics") (:end . 90)\n  (:start . 83) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s13.32) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504245@unknown@formal@none@1@S@ScanProsite [21], the web-based tool for detecting PROSITE [22] signature matches in protein sequences, recently integrated ProRules [23], a database containing additional information about PROSITE profiles, with the aim of increasing the discriminatory power of PROSITE profiles to facilitate function determination and provide biologically relevant information for the annotation of proteins.@(((:tag . "NNP") (:stem . "ScanProsite") (:form . "ScanProsite") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "web-based") (:form . "web-based") (:end . 31)\n  (:start . 22) (:id . 48))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 36) (:start . 32)\n  (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "detect") (:form . "detecting") (:end . 50)\n  (:start . 41) (:id . 51))\n ((:tag . "NN") (:stem . "prosite") (:form . "PROSITE") (:end . 58)\n  (:start . 51) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . "NN") (:stem . "signature") (:form . "signature") (:end . 73)\n  (:start . 64) (:id . 56))\n ((:tag . "VBZ") (:stem . "match") (:form . "matches") (:end . 81)\n  (:start . 74) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 92)\n  (:start . 85) (:id . 59))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 102)\n  (:start . 93) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 112)\n  (:start . 104) (:id . 62))\n ((:tag . "VBN") (:stem . "integrate") (:form . "integrated") (:end . 123)\n  (:start . 113) (:id . 63))\n ((:tag . "NNP") (:stem . "ProRule") (:form . "ProRules") (:end . 132)\n  (:start . 124) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 136) (:start . 134)\n  (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 137) (:start . 136)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 140) (:start . 139)\n  (:id . 69))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 149)\n  (:start . 141) (:id . 70))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 160)\n  (:start . 150) (:id . 71))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 171)\n  (:start . 161) (:id . 72))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 183)\n  (:start . 172) (:id . 73))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 189)\n  (:start . 184) (:id . 74))\n ((:tag . "NN") (:stem . "prosite") (:form . "PROSITE") (:end . 197)\n  (:start . 190) (:id . 75))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 206)\n  (:start . 198) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 207) (:start . 206)\n  (:id . 77))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 212) (:start . 208)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 216) (:start . 213)\n  (:id . 79))\n ((:tag . "NN") (:stem . "aim") (:form . "aim") (:end . 220) (:start . 217)\n  (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 223) (:start . 221)\n  (:id . 81))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 234)\n  (:start . 224) (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 238) (:start . 235)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "discriminatory") (:form . "discriminatory")\n  (:end . 253) (:start . 239) (:id . 84))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 259)\n  (:start . 254) (:id . 85))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 262) (:start . 260)\n  (:id . 86))\n ((:tag . "NN") (:stem . "prosite") (:form . "PROSITE") (:end . 270)\n  (:start . 263) (:id . 87))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 279)\n  (:start . 271) (:id . 88))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 282) (:start . 280)\n  (:id . 89))\n ((:tag . "VB") (:stem . "facilitate") (:form . "facilitate") (:end . 293)\n  (:start . 283) (:id . 90))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 302)\n  (:start . 294) (:id . 91))\n ((:tag . "NN") (:stem . "determination") (:form . "determination")\n  (:end . 316) (:start . 303) (:id . 92))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 320) (:start . 317)\n  (:id . 93))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 328)\n  (:start . 321) (:id . 94))\n ((:tag . "RB") (:stem . "biologically") (:form . "biologically") (:end . 341)\n  (:start . 329) (:id . 95))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 350)\n  (:start . 342) (:id . 96))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 362)\n  (:start . 351) (:id . 97))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 366) (:start . 363)\n  (:id . 98))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 370) (:start . 367)\n  (:id . 99))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 381)\n  (:start . 371) (:id . 100))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 384) (:start . 382)\n  (:id . 101))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 393)\n  (:start . 385) (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 394) (:start . 393)\n  (:id . 103)))@@@1@62@((:identifiers (:sid . :s13.33) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504246@unknown@formal@none@1@S@MnM [24,25], a motif database and a web-based tool for identifying candidate motif occurrences in proteins, addresses the issue of non-functional false positives by implementing evolutionary conservation, surface prediction and frequency scores to rank motif occurrences in a protein query.@(((:tag . "NNP") (:stem . "MnM") (:form . "MnM") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "CD") (:stem . "24,25") (:form . "24,25") (:end . 10) (:start . 5)\n  (:id . 44))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n  (:id . 47))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 20) (:start . 15)\n  (:id . 48))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 29)\n  (:start . 21) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 35) (:start . 34)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "web-based") (:form . "web-based") (:end . 45)\n  (:start . 36) (:id . 52))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 50) (:start . 46)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 54) (:start . 51)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 66)\n  (:start . 55) (:id . 55))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 76)\n  (:start . 67) (:id . 56))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 82) (:start . 77)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "occurrence") (:form . "occurrences") (:end . 94)\n  (:start . 83) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 106)\n  (:start . 98) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "address") (:form . "addresses") (:end . 117)\n  (:start . 108) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 63))\n ((:tag . "NN") (:stem . "issue") (:form . "issue") (:end . 127)\n  (:start . 122) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "non-functional") (:form . "non-functional")\n  (:end . 145) (:start . 131) (:id . 66))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 151)\n  (:start . 146) (:id . 67))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 161)\n  (:start . 152) (:id . 68))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 164) (:start . 162)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "implement") (:form . "implementing") (:end . 177)\n  (:start . 165) (:id . 70))\n ((:tag . "JJ") (:stem . "evolutionary") (:form . "evolutionary") (:end . 190)\n  (:start . 178) (:id . 71))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 203)\n  (:start . 191) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 204) (:start . 203)\n  (:id . 73))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 212)\n  (:start . 205) (:id . 74))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 223)\n  (:start . 213) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 227) (:start . 224)\n  (:id . 76))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 237)\n  (:start . 228) (:id . 77))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 244)\n  (:start . 238) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 247) (:start . 245)\n  (:id . 79))\n ((:tag . "VB") (:stem . "rank") (:form . "rank") (:end . 252) (:start . 248)\n  (:id . 80))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 258)\n  (:start . 253) (:id . 81))\n ((:tag . "NNS") (:stem . "occurrence") (:form . "occurrences") (:end . 270)\n  (:start . 259) (:id . 82))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 273) (:start . 271)\n  (:id . 83))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 275) (:start . 274)\n  (:id . 84))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 283)\n  (:start . 276) (:id . 85))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 289)\n  (:start . 284) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 290) (:start . 289)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s13.34) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504247@unknown@formal@none@1@S@The Eukaryotic Linear Motif (ELM) resource filters implausible motif occurrences according to cell compartment and taxonomic range [2].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Eukaryotic") (:form . "Eukaryotic") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Linear") (:form . "Linear") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "NNP") (:stem . "Motif") (:form . "Motif") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 42)\n  (:start . 34) (:id . 49))\n ((:tag . "VBZ") (:stem . "filter") (:form . "filters") (:end . 50)\n  (:start . 43) (:id . 50))\n ((:tag . "JJ") (:stem . "implausible") (:form . "implausible") (:end . 62)\n  (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 68) (:start . 63)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "occurrence") (:form . "occurrences") (:end . 80)\n  (:start . 69) (:id . 53))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 90)\n  (:start . 81) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 55))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 98) (:start . 94)\n  (:id . 56))\n ((:tag . "NN") (:stem . "compartment") (:form . "compartment") (:end . 110)\n  (:start . 99) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "taxonomic") (:form . "taxonomic") (:end . 124)\n  (:start . 115) (:id . 59))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 130)\n  (:start . 125) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 132) (:start . 131)\n  (:id . 61))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 133) (:start . 132)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 134) (:start . 133)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s13.35) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504248@unknown@formal@none@1@S@It also indicates less likely matches that lie within globular domains annotated in the SMART [26] and Pfam [27] resources and contrasts these with intrinsically unstructured polypeptide (IUP) regions predicted by GlobPlot [28] that are more likely to be motif-rich [5].@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "lie") (:form . "lie") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 53)\n  (:start . 47) (:id . 50))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 70)\n  (:start . 63) (:id . 52))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 80)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 83) (:start . 81)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "SMART") (:form . "SMART") (:end . 93) (:start . 88)\n  (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Pfam") (:form . "Pfam") (:end . 107) (:start . 103)\n  (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 111) (:start . 109)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "resource") (:form . "resources") (:end . 122)\n  (:start . 113) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "contrast") (:form . "contrasts") (:end . 136)\n  (:start . 127) (:id . 67))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 142)\n  (:start . 137) (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 147) (:start . 143)\n  (:id . 69))\n ((:tag . "RB") (:stem . "intrinsically") (:form . "intrinsically")\n  (:end . 161) (:start . 148) (:id . 70))\n ((:tag . "JJ") (:stem . "unstructured") (:form . "unstructured") (:end . 174)\n  (:start . 162) (:id . 71))\n ((:tag . "NN") (:stem . "polypeptide") (:form . "polypeptide") (:end . 186)\n  (:start . 175) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 188) (:start . 187)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "IUP") (:form . "IUP") (:end . 191) (:start . 188)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 192) (:start . 191)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 200)\n  (:start . 193) (:id . 76))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 210)\n  (:start . 201) (:id . 77))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 213) (:start . 211)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "GlobPlot") (:form . "GlobPlot") (:end . 222)\n  (:start . 214) (:id . 79))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 224) (:start . 223)\n  (:id . 80))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 226) (:start . 224)\n  (:id . 81))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 227) (:start . 226)\n  (:id . 82))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 232) (:start . 228)\n  (:id . 83))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 236) (:start . 233)\n  (:id . 84))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 241) (:start . 237)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 248)\n  (:start . 242) (:id . 86))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 251) (:start . 249)\n  (:id . 87))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 254) (:start . 252)\n  (:id . 88))\n ((:tag . "JJ") (:stem . "motif-rich") (:form . "motif-rich") (:end . 265)\n  (:start . 255) (:id . 89))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 267) (:start . 266)\n  (:id . 90))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 268) (:start . 267)\n  (:id . 91))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 269) (:start . 268)\n  (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n  (:id . 93)))@@@1@52@((:hcues ((:id . :x13.36.1) (:span 242 248)) ((:id . :x13.36.2) (:span 8 17)))\n (:hscopes ((:id . :x13.36.1) (:span 233 265))\n  ((:id . :x13.36.2) (:span 8 122)))\n (:identifiers (:sid . :s13.36) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504249@unknown@formal@none@1@S@DILIMOT and SLiMFinder - tools designed for discovery of candidate novel peptide patterns significantly enriched in protein interaction datasets - also use some of these techniques to improve confidence in returned motifs [29,30].@(((:tag . "NNP") (:stem . "DILIMOT") (:form . "DILIMOT") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "SLiMFinder") (:form . "SLiMFinder") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 39)\n  (:start . 31) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "discovery") (:form . "discovery") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 66)\n  (:start . 57) (:id . 51))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 80)\n  (:start . 73) (:id . 53))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 103) (:start . 90) (:id . 55))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 112)\n  (:start . 104) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 57))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 123)\n  (:start . 116) (:id . 58))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 135)\n  (:start . 124) (:id . 59))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 144)\n  (:start . 136) (:id . 60))\n ((:tag . ":") (:stem . "-") (:form . "-") (:end . 146) (:start . 145)\n  (:id . 61))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 151) (:start . 147)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "use") (:form . "use") (:end . 155) (:start . 152)\n  (:id . 63))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 160) (:start . 156)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 65))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 169)\n  (:start . 164) (:id . 66))\n ((:tag . "NNS") (:stem . "technique") (:form . "techniques") (:end . 180)\n  (:start . 170) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 183) (:start . 181)\n  (:id . 68))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 191)\n  (:start . 184) (:id . 69))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 202)\n  (:start . 192) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 205) (:start . 203)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "return") (:form . "returned") (:end . 214)\n  (:start . 206) (:id . 72))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 221)\n  (:start . 215) (:id . 73))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 223) (:start . 222)\n  (:id . 74))\n ((:tag . "CD") (:stem . "29,30") (:form . "29,30") (:end . 228)\n  (:start . 223) (:id . 75))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 229) (:start . 228)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 230) (:start . 229)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s13.37) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504250@unknown@formal@none@1@S@Sequence conservation has also been shown to be effective in up-weighting true motifs relative to false positive matches [31-33].@(((:tag . "NN") (:stem . "sequence") (:form . "Sequence") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 21)\n  (:start . 9) (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 25) (:start . 22)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "up-weighte") (:form . "up-weighting") (:end . 73)\n  (:start . 61) (:id . 52))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 78) (:start . 74)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 85)\n  (:start . 79) (:id . 54))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 94)\n  (:start . 86) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 56))\n ((:tag . "VB") (:stem . "false") (:form . "false") (:end . 103) (:start . 98)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 112)\n  (:start . 104) (:id . 58))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 120)\n  (:start . 113) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 122) (:start . 121)\n  (:id . 60))\n ((:tag . "CD") (:stem . "31-33") (:form . "31-33") (:end . 127)\n  (:start . 122) (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 128) (:start . 127)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s13.38) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504251@unknown@formal@none@1@S@In the intracellular milieu, LMs are found to be particularly abundant in segments of IUP where they are readily accessible [34].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "intracellular") (:form . "intracellular")\n  (:end . 20) (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "milieu") (:form . "milieu") (:end . 27)\n  (:start . 21) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 42) (:start . 37)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 61)\n  (:start . 49) (:id . 52))\n ((:tag . "JJ") (:stem . "abundant") (:form . "abundant") (:end . 70)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 82)\n  (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "IUP") (:form . "IUP") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 95) (:start . 90)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 112)\n  (:start . 105) (:id . 61))\n ((:tag . "JJ") (:stem . "accessible") (:form . "accessible") (:end . 123)\n  (:start . 113) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 125) (:start . 124)\n  (:id . 63))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 127) (:start . 125)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 128) (:start . 127)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s13.39) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504252@unknown@formal@none@1@S@Accessibility is a basic requirement of LM function which is almost always mediated by direct interaction with globular domain ligands.@(((:tag . "NN") (:stem . "accessibility") (:form . "Accessibility")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "basic") (:form . "basic") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "requirement") (:form . "requirement") (:end . 36)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 67)\n  (:start . 61) (:id . 52))\n ((:tag . "RB") (:stem . "always") (:form . "always") (:end . 74)\n  (:start . 68) (:id . 53))\n ((:tag . "VBN") (:stem . "mediate") (:form . "mediated") (:end . 83)\n  (:start . 75) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 93)\n  (:start . 87) (:id . 56))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 105)\n  (:start . 94) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 110) (:start . 106)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 119)\n  (:start . 111) (:id . 59))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 126)\n  (:start . 120) (:id . 60))\n ((:tag . "NNS") (:stem . "ligand") (:form . "ligands") (:end . 134)\n  (:start . 127) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s13.40) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504253@unknown@formal@none@1@S@Extracellular proteins tend to have much less natively disordered polypeptide and therefore the extracellular linear motifs such as N-glycosylation sites [35] and the integrin-binding RGD motif [36] usually occur within globular domains, most often residing in exposed loop regions.@(((:tag . "JJ") (:stem . "extracellular") (:form . "Extracellular")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 22)\n  (:start . 14) (:id . 43))\n ((:tag . "VBP") (:stem . "tend") (:form . "tend") (:end . 27) (:start . 23)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 35) (:start . 31)\n  (:id . 46))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "RB") (:stem . "natively") (:form . "natively") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "VBN") (:stem . "disorder") (:form . "disordered") (:end . 65)\n  (:start . 55) (:id . 50))\n ((:tag . "NN") (:stem . "polypeptide") (:form . "polypeptide") (:end . 77)\n  (:start . 66) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 52))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 91)\n  (:start . 82) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 109) (:start . 96) (:id . 55))\n ((:tag . "JJ") (:stem . "linear") (:form . "linear") (:end . 116)\n  (:start . 110) (:id . 56))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 123)\n  (:start . 117) (:id . 57))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 128) (:start . 124)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 131) (:start . 129)\n  (:id . 59))\n ((:tag . "NN") (:stem . "n-glycosylation") (:form . "N-glycosylation")\n  (:end . 147) (:start . 132) (:id . 60))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 153)\n  (:start . 148) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 155) (:start . 154)\n  (:id . 62))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 157) (:start . 155)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 158) (:start . 157)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "integrin-binding") (:form . "integrin-binding")\n  (:end . 183) (:start . 167) (:id . 67))\n ((:tag . "NNP") (:stem . "RGD") (:form . "RGD") (:end . 187) (:start . 184)\n  (:id . 68))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 193)\n  (:start . 188) (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 195) (:start . 194)\n  (:id . 70))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 197) (:start . 195)\n  (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 198) (:start . 197)\n  (:id . 72))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 206)\n  (:start . 199) (:id . 73))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 212)\n  (:start . 207) (:id . 74))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 219)\n  (:start . 213) (:id . 75))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 228)\n  (:start . 220) (:id . 76))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 236)\n  (:start . 229) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 237) (:start . 236)\n  (:id . 78))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 242) (:start . 238)\n  (:id . 79))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 248)\n  (:start . 243) (:id . 80))\n ((:tag . "VBG") (:stem . "reside") (:form . "residing") (:end . 257)\n  (:start . 249) (:id . 81))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 260) (:start . 258)\n  (:id . 82))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 268)\n  (:start . 261) (:id . 83))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 273) (:start . 269)\n  (:id . 84))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 281)\n  (:start . 274) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 282) (:start . 281)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s13.41) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504254@unknown@formal@none@1@S@LMs are also regularly found in globular regions of intracellular proteins - for example phosphorylation sites are common in flexible loops [37].@(((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "RB") (:stem . "regularly") (:form . "regularly") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "intracellular") (:form . "intracellular")\n  (:end . 65) (:start . 52) (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 74)\n  (:start . 66) (:id . 52))\n ((:tag . ":") (:stem . "-") (:form . "-") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 88)\n  (:start . 81) (:id . 55))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 104) (:start . 89) (:id . 56))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 110)\n  (:start . 105) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 114) (:start . 111)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 121)\n  (:start . 115) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 124) (:start . 122)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "flexible") (:form . "flexible") (:end . 133)\n  (:start . 125) (:id . 61))\n ((:tag . "NNS") (:stem . "loop") (:form . "loops") (:end . 139)\n  (:start . 134) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 141) (:start . 140)\n  (:id . 63))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 143) (:start . 141)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 144) (:start . 143)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 145) (:start . 144)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s13.42) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504255@unknown@formal@none@1@S@However, close inspection of the literature also reveals many instances of candidate motifs falsely reported as functional on the basis of loss of function mutagenesis and out-of-context peptide-binding experiments, despite the motif being well structured and sometimes deeply buried in a globular domain [38-41].@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "JJ") (:stem . "close") (:form . "close") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "inspection") (:form . "inspection") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "literature") (:form . "literature") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 48) (:start . 44)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 71)\n  (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 84)\n  (:start . 75) (:id . 54))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 91)\n  (:start . 85) (:id . 55))\n ((:tag . "RB") (:stem . "falsely") (:form . "falsely") (:end . 99)\n  (:start . 92) (:id . 56))\n ((:tag . "VBD") (:stem . "report") (:form . "reported") (:end . 108)\n  (:start . 100) (:id . 57))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 122)\n  (:start . 112) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 125) (:start . 123)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 61))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 135)\n  (:start . 130) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 63))\n ((:tag . "NN") (:stem . "loss") (:form . "loss") (:end . 143) (:start . 139)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 146) (:start . 144)\n  (:id . 65))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 155)\n  (:start . 147) (:id . 66))\n ((:tag . "NN") (:stem . "mutagenesis") (:form . "mutagenesis") (:end . 167)\n  (:start . 156) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 171) (:start . 168)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "out-of-context") (:form . "out-of-context")\n  (:end . 186) (:start . 172) (:id . 69))\n ((:tag . "JJ") (:stem . "peptide-binding") (:form . "peptide-binding")\n  (:end . 202) (:start . 187) (:id . 70))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 214)\n  (:start . 203) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 215) (:start . 214)\n  (:id . 72))\n ((:tag . "IN") (:stem . "despite") (:form . "despite") (:end . 223)\n  (:start . 216) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 227) (:start . 224)\n  (:id . 74))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 233)\n  (:start . 228) (:id . 75))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 239) (:start . 234)\n  (:id . 76))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 244) (:start . 240)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "structure") (:form . "structured") (:end . 255)\n  (:start . 245) (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 259) (:start . 256)\n  (:id . 79))\n ((:tag . "RB") (:stem . "sometimes") (:form . "sometimes") (:end . 269)\n  (:start . 260) (:id . 80))\n ((:tag . "RB") (:stem . "deeply") (:form . "deeply") (:end . 276)\n  (:start . 270) (:id . 81))\n ((:tag . "VBN") (:stem . "bury") (:form . "buried") (:end . 283)\n  (:start . 277) (:id . 82))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 286) (:start . 284)\n  (:id . 83))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 288) (:start . 287)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 297)\n  (:start . 289) (:id . 85))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 304)\n  (:start . 298) (:id . 86))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 306) (:start . 305)\n  (:id . 87))\n ((:tag . "CD") (:stem . "38-41") (:form . "38-41") (:end . 311)\n  (:start . 306) (:id . 88))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 312) (:start . 311)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 313) (:start . 312)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s13.43) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504256@unknown@formal@none@1@S@This observation suggests that stringent examination of motif structural context should be an essential processing step for experimental analysis.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "stringent") (:form . "stringent") (:end . 40)\n  (:start . 31) (:id . 46))\n ((:tag . "NN") (:stem . "examination") (:form . "examination") (:end . 52)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 48))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 61) (:start . 56)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 72)\n  (:start . 62) (:id . 50))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 80)\n  (:start . 73) (:id . 51))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 87)\n  (:start . 81) (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 90) (:start . 88)\n  (:id . 53))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 93) (:start . 91)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 103)\n  (:start . 94) (:id . 55))\n ((:tag . "NN") (:stem . "processing") (:form . "processing") (:end . 114)\n  (:start . 104) (:id . 56))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 119) (:start . 115)\n  (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 123) (:start . 120)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 136)\n  (:start . 124) (:id . 59))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 145)\n  (:start . 137) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x13.44.1) (:span 81 87)) ((:id . :x13.44.2) (:span 17 25)))\n (:hscopes ((:id . :x13.44.1) (:span 81 145))\n  ((:id . :x13.44.2) (:span 17 145)))\n (:identifiers (:sid . :s13.44) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504257@unknown@formal@none@1@S@It also advocates the importance of high quality tools to identify such cases, as the cost associated with failure is detrimental both in terms of effort and quality of the literature.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "advocate") (:form . "advocates") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "importance") (:form . "importance") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 54) (:start . 49)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 66)\n  (:start . 58) (:id . 52))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 71) (:start . 67)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 77) (:start . 72)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 57))\n ((:tag . "NN") (:stem . "cost") (:form . "cost") (:end . 90) (:start . 86)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 101)\n  (:start . 91) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "failure") (:form . "failure") (:end . 114)\n  (:start . 107) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 117) (:start . 115)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "detrimental") (:form . "detrimental") (:end . 129)\n  (:start . 118) (:id . 63))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 134) (:start . 130)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 137) (:start . 135)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 143)\n  (:start . 138) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 146) (:start . 144)\n  (:id . 67))\n ((:tag . "NN") (:stem . "effort") (:form . "effort") (:end . 153)\n  (:start . 147) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 157) (:start . 154)\n  (:id . 69))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 165)\n  (:start . 158) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 172) (:start . 169)\n  (:id . 72))\n ((:tag . "NN") (:stem . "literature") (:form . "literature") (:end . 183)\n  (:start . 173) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 74)))@@@1@33@((:hcues ((:id . :x13.45.1) (:span 8 17)))\n (:hscopes ((:id . :x13.45.1) (:span 8 77)))\n (:identifiers (:sid . :s13.45) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504258@unknown@formal@none@1@S@Despite this, neither the ELM globular domain classification nor the MnM surface prediction score take advantage of all the information available to them in the form of the plethora of experimentally solved protein structures.@(((:tag . "IN") (:stem . "despite") (:form . "Despite") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "CC") (:stem . "neither") (:form . "neither") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 38)\n  (:start . 30) (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "classification") (:form . "classification")\n  (:end . 60) (:start . 46) (:id . 50))\n ((:tag . "CC") (:stem . "nor") (:form . "nor") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "MnM") (:form . "MnM") (:end . 72) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 80)\n  (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 91)\n  (:start . 81) (:id . 55))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 97) (:start . 92)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "take") (:form . "take") (:end . 102) (:start . 98)\n  (:id . 57))\n ((:tag . "NN") (:stem . "advantage") (:form . "advantage") (:end . 112)\n  (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 59))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 61))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 135)\n  (:start . 124) (:id . 62))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 145)\n  (:start . 136) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 64))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 153) (:start . 149)\n  (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 156) (:start . 154)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 160) (:start . 157)\n  (:id . 67))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 165) (:start . 161)\n  (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 172) (:start . 169)\n  (:id . 70))\n ((:tag . "NN") (:stem . "plethora") (:form . "plethora") (:end . 181)\n  (:start . 173) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n  (:id . 72))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n  (:end . 199) (:start . 185) (:id . 73))\n ((:tag . "VBN") (:stem . "solve") (:form . "solved") (:end . 206)\n  (:start . 200) (:id . 74))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 214)\n  (:start . 207) (:id . 75))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 225)\n  (:start . 215) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s13.46) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504259@unknown@formal@none@1@S@ELM globular domain classification is overly strict, classifying motifs occurring in these regions as low confidence.@(((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "classification") (:form . "classification")\n  (:end . 34) (:start . 20) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "RB") (:stem . "overly") (:form . "overly") (:end . 44)\n  (:start . 38) (:id . 47))\n ((:tag . "JJ") (:stem . "strict") (:form . "strict") (:end . 51)\n  (:start . 45) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "classify") (:form . "classifying") (:end . 64)\n  (:start . 53) (:id . 50))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 71)\n  (:start . 65) (:id . 51))\n ((:tag . "VBG") (:stem . "occur") (:form . "occurring") (:end . 81)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 84) (:start . 82)\n  (:id . 53))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 90) (:start . 85)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 98)\n  (:start . 91) (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 101) (:start . 99)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 105) (:start . 102)\n  (:id . 57))\n ((:tag . "NN") (:stem . "confidence") (:form . "confidence") (:end . 116)\n  (:start . 106) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s13.47) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504260@unknown@formal@none@1@S@The MnM surface prediction score uses primary sequence based prediction both in those cases where a structure is available and in regions where a disorder predictor will render secondary structure prediction unnecessary.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "MnM") (:form . "MnM") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "use") (:form . "uses") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "JJ") (:stem . "based") (:form . "based") (:end . 60) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 76) (:start . 72)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 85) (:start . 80)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 91) (:start . 86)\n  (:id . 55))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 97) (:start . 92)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 109)\n  (:start . 100) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 112) (:start . 110)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 122)\n  (:start . 113) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 137)\n  (:start . 130) (:id . 63))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 143)\n  (:start . 138) (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 145) (:start . 144)\n  (:id . 65))\n ((:tag . "NN") (:stem . "disorder") (:form . "disorder") (:end . 154)\n  (:start . 146) (:id . 66))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 164)\n  (:start . 155) (:id . 67))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 169) (:start . 165)\n  (:id . 68))\n ((:tag . "VB") (:stem . "render") (:form . "render") (:end . 176)\n  (:start . 170) (:id . 69))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 186)\n  (:start . 177) (:id . 70))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 196)\n  (:start . 187) (:id . 71))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 207)\n  (:start . 197) (:id . 72))\n ((:tag . "JJ") (:stem . "unnecessary") (:form . "unnecessary") (:end . 219)\n  (:start . 208) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s13.48) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504261@unknown@formal@none@1@S@In the present manuscript, we address the issue of LM accessibility when the matches occur within globular domains for which a reference three-dimensional (3D) structure is available.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "manuscript") (:form . "manuscript") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "address") (:form . "address") (:end . 37)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "issue") (:form . "issue") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 67) (:start . 54) (:id . 53))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 84)\n  (:start . 77) (:id . 56))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 97)\n  (:start . 91) (:id . 58))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 106)\n  (:start . 98) (:id . 59))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 114)\n  (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 118) (:start . 115)\n  (:id . 61))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 124)\n  (:start . 119) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 126) (:start . 125)\n  (:id . 63))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 136)\n  (:start . 127) (:id . 64))\n ((:tag . "JJ") (:stem . "three-dimensional") (:form . "three-dimensional")\n  (:end . 154) (:start . 137) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 66))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 158) (:start . 156)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 68))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 169)\n  (:start . 160) (:id . 69))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 172) (:start . 170)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 182)\n  (:start . 173) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s13.49) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504262@unknown@formal@none@1@S@Development and calibration of a structure filter is currently not straightforward as there are relatively few available structures for most motif classes (an obvious exception being N-glycosylation sites), placing limitations on the training and benchmarking possibilities.@(((:tag . "NNP") (:stem . "Development") (:form . "Development") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 15) (:start . 12)\n  (:id . 43))\n ((:tag . "NN") (:stem . "calibration") (:form . "calibration") (:end . 27)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 49)\n  (:start . 43) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 62)\n  (:start . 53) (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "VB") (:stem . "straightforward") (:form . "straightforward")\n  (:end . 82) (:start . 67) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 85) (:start . 83)\n  (:id . 53))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 91) (:start . 86)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 95) (:start . 92)\n  (:id . 55))\n ((:tag . "RB") (:stem . "relatively") (:form . "relatively") (:end . 106)\n  (:start . 96) (:id . 56))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 110) (:start . 107)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 120)\n  (:start . 111) (:id . 58))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 131)\n  (:start . 121) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 135) (:start . 132)\n  (:id . 60))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 140) (:start . 136)\n  (:id . 61))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 146)\n  (:start . 141) (:id . 62))\n ((:tag . "NNS") (:stem . "class") (:form . "classes") (:end . 154)\n  (:start . 147) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 64))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 158) (:start . 156)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "obvious") (:form . "obvious") (:end . 166)\n  (:start . 159) (:id . 66))\n ((:tag . "NN") (:stem . "exception") (:form . "exception") (:end . 176)\n  (:start . 167) (:id . 67))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 182) (:start . 177)\n  (:id . 68))\n ((:tag . "NN") (:stem . "n-glycosylation") (:form . "N-glycosylation")\n  (:end . 198) (:start . 183) (:id . 69))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 204)\n  (:start . 199) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 205) (:start . 204)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 206) (:start . 205)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "place") (:form . "placing") (:end . 214)\n  (:start . 207) (:id . 73))\n ((:tag . "NNS") (:stem . "limitation") (:form . "limitations") (:end . 226)\n  (:start . 215) (:id . 74))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 229) (:start . 227)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 233) (:start . 230)\n  (:id . 76))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 242)\n  (:start . 234) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 246) (:start . 243)\n  (:id . 78))\n ((:tag . "VBG") (:stem . "benchmarke") (:form . "benchmarking") (:end . 259)\n  (:start . 247) (:id . 79))\n ((:tag . "NNS") (:stem . "possibility") (:form . "possibilities")\n  (:end . 273) (:start . 260) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 274) (:start . 273)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s13.50) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504263@unknown@formal@none@1@S@Nevertheless, we have been able to develop a protocol in which reference domain structures are selected and then the matched motifs evaluated using accessibility and secondary structure parameters.@(((:tag . "RB") (:stem . "nevertheless") (:form . "Nevertheless") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "VB") (:stem . "develop") (:form . "develop") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 53)\n  (:start . 45) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 62) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 72)\n  (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 79)\n  (:start . 73) (:id . 55))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 90)\n  (:start . 80) (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 94) (:start . 91)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 103)\n  (:start . 95) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 112) (:start . 108)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "matched") (:form . "matched") (:end . 124)\n  (:start . 117) (:id . 62))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 131)\n  (:start . 125) (:id . 63))\n ((:tag . "VBN") (:stem . "evaluate") (:form . "evaluated") (:end . 141)\n  (:start . 132) (:id . 64))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 147) (:start . 142)\n  (:id . 65))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 161) (:start . 148) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 175)\n  (:start . 166) (:id . 68))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 185)\n  (:start . 176) (:id . 69))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 196)\n  (:start . 186) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s13.51) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504264@unknown@formal@none@1@S@Benchmarking of the structure filter suggests that deeply buried LM candidates are unlikely to be functional, and that the likelihood of motif matches being valid functional sites improves with accessibility.@(((:tag . "VBG") (:stem . "benchmarke") (:form . "Benchmarking") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 29)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 36)\n  (:start . 30) (:id . 46))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 50) (:start . 46)\n  (:id . 48))\n ((:tag . "RB") (:stem . "deeply") (:form . "deeply") (:end . 57)\n  (:start . 51) (:id . 49))\n ((:tag . "VBN") (:stem . "bury") (:form . "buried") (:end . 64) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 78)\n  (:start . 68) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 82) (:start . 79)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 91)\n  (:start . 83) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 94) (:start . 92)\n  (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 97) (:start . 95)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 108)\n  (:start . 98) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 118) (:start . 114)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 61))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 133)\n  (:start . 123) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 63))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 142)\n  (:start . 137) (:id . 64))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 150)\n  (:start . 143) (:id . 65))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 156) (:start . 151)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "valid") (:form . "valid") (:end . 162)\n  (:start . 157) (:id . 67))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 173)\n  (:start . 163) (:id . 68))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 179)\n  (:start . 174) (:id . 69))\n ((:tag . "VBZ") (:stem . "improve") (:form . "improves") (:end . 188)\n  (:start . 180) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 193) (:start . 189)\n  (:id . 71))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 207) (:start . 194) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 208) (:start . 207)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x13.52.1) (:span 83 91)) ((:id . :x13.52.2) (:span 37 45)))\n (:hscopes ((:id . :x13.52.1) (:span 51 108))\n  ((:id . :x13.52.2) (:span 37 207)))\n (:identifiers (:sid . :s13.52) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504265@unknown@formal@none@1@S@In this way, the new filter can aid researchers to decide whether they wish to invest effort inexperimentaltesting of candidate motifs.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 20) (:start . 17)\n  (:id . 47))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 27)\n  (:start . 21) (:id . 48))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 31) (:start . 28)\n  (:id . 49))\n ((:tag . "VB") (:stem . "aid") (:form . "aid") (:end . 35) (:start . 32)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "researcher") (:form . "researchers") (:end . 47)\n  (:start . 36) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "VB") (:stem . "decide") (:form . "decide") (:end . 57)\n  (:start . 51) (:id . 53))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 65)\n  (:start . 58) (:id . 54))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 70) (:start . 66)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "wish") (:form . "wish") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 57))\n ((:tag . "VB") (:stem . "invest") (:form . "invest") (:end . 85)\n  (:start . 79) (:id . 58))\n ((:tag . "NN") (:stem . "effort") (:form . "effort") (:end . 92)\n  (:start . 86) (:id . 59))\n ((:tag . "NN") (:stem . "inexperimentaltesting")\n  (:form . "inexperimentaltesting") (:end . 114) (:start . 93) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 61))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 127)\n  (:start . 118) (:id . 62))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 134)\n  (:start . 128) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x13.53.1) (:span 28 31)))\n (:hscopes ((:id . :x13.53.1) (:span 28 134)))\n (:identifiers (:sid . :s13.53) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504266@unknown@formal@none@1@S@The structure filter pipeline is implemented in a publicly available Python program accessible via a web-service interface [42].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "pipeline") (:form . "pipeline") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 44)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "RB") (:stem . "publicly") (:form . "publicly") (:end . 58)\n  (:start . 50) (:id . 50))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 68)\n  (:start . 59) (:id . 51))\n ((:tag . "NNP") (:stem . "Python") (:form . "Python") (:end . 75)\n  (:start . 69) (:id . 52))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 83)\n  (:start . 76) (:id . 53))\n ((:tag . "JJ") (:stem . "accessible") (:form . "accessible") (:end . 94)\n  (:start . 84) (:id . 54))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 98) (:start . 95)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 100) (:start . 99)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "web-service") (:form . "web-service") (:end . 112)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "interface") (:form . "interface") (:end . 122)\n  (:start . 113) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 124) (:start . 123)\n  (:id . 59))\n ((:tag . "CD") (:stem . "42") (:form . "42") (:end . 126) (:start . 124)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 127) (:start . 126)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s13.54) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504267@unknown@formal@none@1@S@The structure filter is fully integrated into the ELM server [43], providing graphical representation of the results in the context of the other filters.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "RB") (:stem . "fully") (:form . "fully") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "integrate") (:form . "integrated") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 45) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 60)\n  (:start . 54) (:id . 51))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "CD") (:stem . "43") (:form . "43") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 65) (:start . 64)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "provide") (:form . "providing") (:end . 76)\n  (:start . 67) (:id . 56))\n ((:tag . "JJ") (:stem . "graphical") (:form . "graphical") (:end . 86)\n  (:start . 77) (:id . 57))\n ((:tag . "NN") (:stem . "representation") (:form . "representation")\n  (:end . 101) (:start . 87) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 116)\n  (:start . 109) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 119) (:start . 117)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 131)\n  (:start . 124) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 144)\n  (:start . 139) (:id . 67))\n ((:tag . "NNS") (:stem . "filter") (:form . "filters") (:end . 152)\n  (:start . 145) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s13.55) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504268@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s13.56) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504269@unknown@formal@none@1@S@The ELM structure filter scoring scheme@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 39)\n  (:start . 33) (:id . 47)))@@@1@6@((:identifiers (:sid . :s13.57) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504270@unknown@formal@none@1@S@Structural analysis of true motif instances annotated in ELM supported what is expected from LM biology [3], i.e. that they tend to lie on the surface of protein domains and prefer unstructured and loop regions (See below "Analysis of the ELM 3D benchmarking dataset").@(((:tag . "JJ") (:stem . "structural") (:form . "Structural") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 27) (:start . 23)\n  (:id . 45))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 53)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 70)\n  (:start . 61) (:id . 51))\n ((:tag . "WP") (:stem . "what") (:form . "what") (:end . 75) (:start . 71)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 92) (:start . 88)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 95) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "biology") (:form . "biology") (:end . 103)\n  (:start . 96) (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 113) (:start . 109)\n  (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 118) (:start . 114)\n  (:id . 63))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 123) (:start . 119)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "tend") (:form . "tend") (:end . 128) (:start . 124)\n  (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 131) (:start . 129)\n  (:id . 66))\n ((:tag . "VB") (:stem . "lie") (:form . "lie") (:end . 135) (:start . 132)\n  (:id . 67))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 138) (:start . 136)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n  (:id . 69))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 150)\n  (:start . 143) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 153) (:start . 151)\n  (:id . 71))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 161)\n  (:start . 154) (:id . 72))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 169)\n  (:start . 162) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 173) (:start . 170)\n  (:id . 74))\n ((:tag . "VBP") (:stem . "prefer") (:form . "prefer") (:end . 180)\n  (:start . 174) (:id . 75))\n ((:tag . "JJ") (:stem . "unstructured") (:form . "unstructured") (:end . 193)\n  (:start . 181) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 197) (:start . 194)\n  (:id . 77))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 202) (:start . 198)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 210)\n  (:start . 203) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 212) (:start . 211)\n  (:id . 80))\n ((:tag . "VB") (:stem . "see") (:form . "See") (:end . 215) (:start . 212)\n  (:id . 81))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 221)\n  (:start . 216) (:id . 82))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 223) (:start . 222)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "Analysis") (:form . "Analysis") (:end . 231)\n  (:start . 223) (:id . 84))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 234) (:start . 232)\n  (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 238) (:start . 235)\n  (:id . 86))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 242) (:start . 239)\n  (:id . 87))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 245) (:start . 243)\n  (:id . 88))\n ((:tag . "VBG") (:stem . "benchmarke") (:form . "benchmarking") (:end . 258)\n  (:start . 246) (:id . 89))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 266)\n  (:start . 259) (:id . 90))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 267) (:start . 266)\n  (:id . 91))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 268) (:start . 267)\n  (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 269) (:start . 268)\n  (:id . 93)))@@@1@52@((:identifiers (:sid . :s13.58) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504271@unknown@formal@none@1@S@Figure 1 shows two examples of motifs lying on domain interfaces whereas Figure 2 reports cases of motif instances whose functional residues protrude outwards from the domain surface and hence are accessible to the solvent.@(((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "VBG") (:stem . "lie") (:form . "lying") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 53)\n  (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "interface") (:form . "interfaces") (:end . 64)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 79)\n  (:start . 73) (:id . 54))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "report") (:form . "reports") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 95) (:start . 90)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 104) (:start . 99)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 114)\n  (:start . 105) (:id . 60))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 120)\n  (:start . 115) (:id . 61))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 131)\n  (:start . 121) (:id . 62))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 140)\n  (:start . 132) (:id . 63))\n ((:tag . "VBP") (:stem . "protrude") (:form . "protrude") (:end . 149)\n  (:start . 141) (:id . 64))\n ((:tag . "NNS") (:stem . "outward") (:form . "outwards") (:end . 158)\n  (:start . 150) (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 163) (:start . 159)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 67))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 174)\n  (:start . 168) (:id . 68))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 182)\n  (:start . 175) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 186) (:start . 183)\n  (:id . 70))\n ((:tag . "RB") (:stem . "hence") (:form . "hence") (:end . 192)\n  (:start . 187) (:id . 71))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 196) (:start . 193)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "accessible") (:form . "accessible") (:end . 207)\n  (:start . 197) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 210) (:start . 208)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 214) (:start . 211)\n  (:id . 75))\n ((:tag . "NN") (:stem . "solvent") (:form . "solvent") (:end . 222)\n  (:start . 215) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 223) (:start . 222)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s13.59) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504272@unknown@formal@none@1@S@This observation was further supported by the comparison between the accessibility and secondary structure distributions of true motifs vs random matches (determined as described in Methods) in our datasets (Figure 3), which highlights that true motifs are on average more accessible than random matches (p-value = 1.9e-55); moreover, loops are more represented (p-value = 1.13e-35) in true motifs than in random matches and both alpha-helices and strands are less represented in true motifs than in random matches (p-value = 3.69e-12 and 2.66e-16, respectively).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . 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"distribution") (:form . "distributions")\n  (:end . 120) (:start . 107) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 128) (:start . 124)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 135)\n  (:start . 129) (:id . 59))\n ((:tag . "IN") (:stem . "vs") (:form . "vs") (:end . 138) (:start . 136)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 145)\n  (:start . 139) (:id . 61))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 153)\n  (:start . 146) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 165)\n  (:start . 155) (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 168) (:start . 166)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "describe") (:form . 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"alpha-helices")\n  (:end . 443) (:start . 430) (:id . 117))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 447) (:start . 444)\n  (:id . 118))\n ((:tag . "NNS") (:stem . "strand") (:form . "strands") (:end . 455)\n  (:start . 448) (:id . 119))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 459) (:start . 456)\n  (:id . 120))\n ((:tag . "RBR") (:stem . "less") (:form . "less") (:end . 464) (:start . 460)\n  (:id . 121))\n ((:tag . "VBN") (:stem . "represent") (:form . "represented") (:end . 476)\n  (:start . 465) (:id . 122))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 479) (:start . 477)\n  (:id . 123))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 484) (:start . 480)\n  (:id . 124))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 491)\n  (:start . 485) (:id . 125))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 496) (:start . 492)\n  (:id . 126))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 499) (:start . 497)\n  (:id . 127))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 506)\n  (:start . 500) (:id . 128))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 514)\n  (:start . 507) (:id . 129))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 516) (:start . 515)\n  (:id . 130))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 523)\n  (:start . 516) (:id . 131))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 525) (:start . 524)\n  (:id . 132))\n ((:tag . "CD") (:stem . "3.69e-12") (:form . "3.69e-12") (:end . 534)\n  (:start . 526) (:id . 133))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 538) (:start . 535)\n  (:id . 134))\n ((:tag . "CD") (:stem . "2.66e-16") (:form . "2.66e-16") (:end . 547)\n  (:start . 539) (:id . 135))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 548) (:start . 547)\n  (:id . 136))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 561)\n  (:start . 549) (:id . 137))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 562) (:start . 561)\n  (:id . 138))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 563) (:start . 562)\n  (:id . 139)))@@@1@98@((:identifiers (:sid . :s13.60) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504273@unknown@formal@none@1@S@These results convinced us to base the structure filter scoring scheme on accessibility and secondary structure assignments.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "convince") (:form . "convinced") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "VB") (:stem . "base") (:form . "base") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 48)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 55)\n  (:start . 49) (:id . 50))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 63)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 70)\n  (:start . 64) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 87) (:start . 74) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 101)\n  (:start . 92) (:id . 56))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 111)\n  (:start . 102) (:id . 57))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 123)\n  (:start . 112) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 124) (:start . 123)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s13.61) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504274@unknown@formal@none@1@S@Two examples of linear motifs packed into structured domains. a) PDB 2D07: Sumo-interacting motif (orange) of TDG domain (green) bound to SUMO-3 protein (cyan); b) PDB 2PTK: closed conformation of the proto-oncogene tyrosine-protein kinase Src. Blue: SH2 domain; red: SH3 domain; green: protein kinase; orange: pTyr-527; yellow: linkers; yellow spheres: SH3 binding peptide.@(((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "linear") (:form . "linear") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "VBN") (:stem . "pack") (:form . "packed") (:end . 36) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . 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"VBN") (:stem . "close") (:form . "closed") (:end . 180)\n  (:start . 174) (:id . 80))\n ((:tag . "NN") (:stem . "conformation") (:form . "conformation") (:end . 193)\n  (:start . 181) (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 196) (:start . 194)\n  (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 200) (:start . 197)\n  (:id . 83))\n ((:tag . "NN") (:stem . "proto-oncogene") (:form . "proto-oncogene")\n  (:end . 215) (:start . 201) (:id . 84))\n ((:tag . "NN") (:stem . "tyrosine-protein") (:form . "tyrosine-protein")\n  (:end . 232) (:start . 216) (:id . 85))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 239)\n  (:start . 233) (:id . 86))\n ((:tag . "NNP") (:stem . "Src.") (:form . "Src.") (:end . 244) (:start . 240)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "Blue") (:form . "Blue") (:end . 249) (:start . 245)\n  (:id . 88))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 250) (:start . 249)\n  (:id . 89))\n ((:tag . 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";") (:end . 337) (:start . 336)\n  (:id . 110))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 344)\n  (:start . 338) (:id . 111))\n ((:tag . "NNS") (:stem . "sphere") (:form . "spheres") (:end . 352)\n  (:start . 345) (:id . 112))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 353) (:start . 352)\n  (:id . 113))\n ((:tag . "NN") (:stem . "sh3") (:form . "SH3") (:end . 357) (:start . 354)\n  (:id . 114))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 365)\n  (:start . 358) (:id . 115))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 373)\n  (:start . 366) (:id . 116))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 374) (:start . 373)\n  (:id . 117)))@@@1@76@((:identifiers (:sid . :s13.62) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504275@unknown@formal@none@1@S@All structure views were prepared with PyMOL http://www.pymol.org/.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "view") (:form . "views") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "prepare") (:form . "prepared") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PyMOL") (:form . "PyMOL") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "http://www.pymol.org/")\n  (:form . "http://www.pymol.org/") (:end . 66) (:start . 45) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s13.63) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504276@unknown@formal@none@1@S@Examples of linear motifs with functional residues protruding outwards from the structural domain surface. a) A very exposed instance (in white) of LIG_RGD in a loop of SCOP domain d1 mfn_2; b) An instance (in violet) of LIG_RGD in a region outside a domain (SCOP d1ssua_); c) An instance (in pink) of MOD_SUMO in an exposed loop of the d1kpsd_ SCOP domain; d) The MOD_CMANNOS C-Mannosylation site (in magenta) in the SCOP domain d1k2aa_; e) The two MOD_N-GLC_1 N-glycosylation sites (in yellow) in the SCOP domain d1qm3a_; f) The N-glycosylation site (in red) in the SCOP domain d1fl7b_; g), h) The N-glycosylation site (in green) in the SCOP domain d1o7ae2 and (in red) in the SCOP domain d1n26a1.@(((:tag . "NNS") (:stem . "example") (:form . "Examples") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "linear") (:form . 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"MOD_SUMO") (:form . "MOD_SUMO") (:end . 310)\n  (:start . 302) (:id . 107))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 313) (:start . 311)\n  (:id . 108))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 316) (:start . 314)\n  (:id . 109))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 324)\n  (:start . 317) (:id . 110))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 329) (:start . 325)\n  (:id . 111))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 332) (:start . 330)\n  (:id . 112))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 336) (:start . 333)\n  (:id . 113))\n ((:tag . "NNP") (:stem . "d1kpsd_") (:form . "d1kpsd_") (:end . 344)\n  (:start . 337) (:id . 114))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 349) (:start . 345)\n  (:id . 115))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 356)\n  (:start . 350) (:id . 116))\n ((:tag . ":") (:stem . ";") (:form . 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")") (:end . 410) (:start . 409)\n  (:id . 127))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 413) (:start . 411)\n  (:id . 128))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 417) (:start . 414)\n  (:id . 129))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 422) (:start . 418)\n  (:id . 130))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 429)\n  (:start . 423) (:id . 131))\n ((:tag . "NN") (:stem . "d1k2aa_") (:form . "d1k2aa_") (:end . 437)\n  (:start . 430) (:id . 132))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 438) (:start . 437)\n  (:id . 133))\n ((:tag . "LS") (:stem . "e") (:form . "e") (:end . 440) (:start . 439)\n  (:id . 134))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 441) (:start . 440)\n  (:id . 135))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 445) (:start . 442)\n  (:id . 136))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 449) (:start . 446)\n  (:id . 137))\n ((:tag . "NN") (:stem . "mod_n-glc_1") (:form . "MOD_N-GLC_1") (:end . 461)\n  (:start . 450) (:id . 138))\n ((:tag . "NN") (:stem . "n-glycosylation") (:form . "N-glycosylation")\n  (:end . 477) (:start . 462) (:id . 139))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 483)\n  (:start . 478) (:id . 140))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 485) (:start . 484)\n  (:id . 141))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 487) (:start . 485)\n  (:id . 142))\n ((:tag . "NN") (:stem . "yellow") (:form . "yellow") (:end . 494)\n  (:start . 488) (:id . 143))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 495) (:start . 494)\n  (:id . 144))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 498) (:start . 496)\n  (:id . 145))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 502) (:start . 499)\n  (:id . 146))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 507) (:start . 503)\n  (:id . 147))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 514)\n  (:start . 508) (:id . 148))\n ((:tag . "NN") (:stem . "d1qm3a_") (:form . "d1qm3a_") (:end . 522)\n  (:start . 515) (:id . 149))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 523) (:start . 522)\n  (:id . 150))\n ((:tag . "LS") (:stem . "f") (:form . "f") (:end . 525) (:start . 524)\n  (:id . 151))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 526) (:start . 525)\n  (:id . 152))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 530) (:start . 527)\n  (:id . 153))\n ((:tag . "NN") (:stem . "n-glycosylation") (:form . "N-glycosylation")\n  (:end . 546) (:start . 531) (:id . 154))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 551) (:start . 547)\n  (:id . 155))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 553) (:start . 552)\n  (:id . 156))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 555) (:start . 553)\n  (:id . 157))\n ((:tag . "VBN") (:stem . "red") (:form . "red") (:end . 559) (:start . 556)\n  (:id . 158))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 560) (:start . 559)\n  (:id . 159))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 563) (:start . 561)\n  (:id . 160))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 567) (:start . 564)\n  (:id . 161))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 572) (:start . 568)\n  (:id . 162))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 579)\n  (:start . 573) (:id . 163))\n ((:tag . "NN") (:stem . "d1fl7b_") (:form . "d1fl7b_") (:end . 587)\n  (:start . 580) (:id . 164))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 588) (:start . 587)\n  (:id . 165))\n ((:tag . "NN") (:stem . "g") (:form . "g") (:end . 590) (:start . 589)\n  (:id . 166))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 591) (:start . 590)\n  (:id . 167))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 592) (:start . 591)\n  (:id . 168))\n ((:tag . "NN") (:stem . "h") (:form . "h") (:end . 594) (:start . 593)\n  (:id . 169))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 595) (:start . 594)\n  (:id . 170))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 599) (:start . 596)\n  (:id . 171))\n ((:tag . "NN") (:stem . "n-glycosylation") (:form . "N-glycosylation")\n  (:end . 615) (:start . 600) (:id . 172))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 620) (:start . 616)\n  (:id . 173))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 622) (:start . 621)\n  (:id . 174))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 624) (:start . 622)\n  (:id . 175))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 630)\n  (:start . 625) (:id . 176))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 631) (:start . 630)\n  (:id . 177))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 634) (:start . 632)\n  (:id . 178))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 638) (:start . 635)\n  (:id . 179))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 643) (:start . 639)\n  (:id . 180))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 650)\n  (:start . 644) (:id . 181))\n ((:tag . "NN") (:stem . "d1o7ae2") (:form . "d1o7ae2") (:end . 658)\n  (:start . 651) (:id . 182))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 662) (:start . 659)\n  (:id . 183))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 664) (:start . 663)\n  (:id . 184))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 666) (:start . 664)\n  (:id . 185))\n ((:tag . "VBN") (:stem . "red") (:form . "red") (:end . 670) (:start . 667)\n  (:id . 186))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 671) (:start . 670)\n  (:id . 187))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 674) (:start . 672)\n  (:id . 188))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 678) (:start . 675)\n  (:id . 189))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 683) (:start . 679)\n  (:id . 190))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 690)\n  (:start . 684) (:id . 191))\n ((:tag . "NN") (:stem . "d1n26a1") (:form . "d1n26a1") (:end . 698)\n  (:start . 691) (:id . 192))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 699) (:start . 698)\n  (:id . 193)))@@@1@152@((:identifiers (:sid . :s13.64) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504277@unknown@formal@none@1@S@Secondary structure frequency and accessibility distribution for true motif instances and for random matches.@(((:tag . "JJ") (:stem . "secondary") (:form . "Secondary") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 19)\n  (:start . 10) (:id . 43))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 29)\n  (:start . 20) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 45))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 47) (:start . 34) (:id . 46))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 60)\n  (:start . 48) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 64) (:start . 61)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 69) (:start . 65)\n  (:id . 49))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 75) (:start . 70)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 85)\n  (:start . 76) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 93) (:start . 90)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 100)\n  (:start . 94) (:id . 54))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 108)\n  (:start . 101) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s13.65) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504278@unknown@formal@none@1@S@3a) Boxplots representing the accessibility distributions of true motif instances (orange) and of random matches (yellow), calculated for all motif positions (all positions), non-wildcard positions only (non-wildcard) and wildcard positions only (wildcard).@(((:tag . "LS") (:stem . "3a") (:form . "3a") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 43))\n ((:tag . "NNS") (:stem . "boxplot") (:form . "Boxplots") (:end . 12)\n  (:start . 4) (:id . 44))\n ((:tag . "VBG") (:stem . "represent") (:form . "representing") (:end . 25)\n  (:start . 13) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 43) (:start . 30) (:id . 47))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 57) (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 65) (:start . 61)\n  (:id . 50))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 71) (:start . 66)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 81)\n  (:start . 72) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 53))\n ((:tag . "NN") (:stem . "orange") (:form . "orange") (:end . 89)\n  (:start . 83) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 104)\n  (:start . 98) (:id . 58))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 112)\n  (:start . 105) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 120)\n  (:start . 114) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 121) (:start . 120)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 133)\n  (:start . 123) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 137) (:start . 134)\n  (:id . 65))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 141) (:start . 138)\n  (:id . 66))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 147)\n  (:start . 142) (:id . 67))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 157)\n  (:start . 148) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 69))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 162) (:start . 159)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 172)\n  (:start . 163) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 173) (:start . 172)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 187)\n  (:start . 175) (:id . 74))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 197)\n  (:start . 188) (:id . 75))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 202) (:start . 198)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 204) (:start . 203)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 216)\n  (:start . 204) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 217) (:start . 216)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 221) (:start . 218)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "wildcard") (:form . "wildcard") (:end . 230)\n  (:start . 222) (:id . 81))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 240)\n  (:start . 231) (:id . 82))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 245) (:start . 241)\n  (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 247) (:start . 246)\n  (:id . 84))\n ((:tag . "RB") (:stem . "wildcard") (:form . "wildcard") (:end . 255)\n  (:start . 247) (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 256) (:start . 255)\n  (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s13.66) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504279@unknown@formal@none@1@S@The solid box lower and upper bounds represent the 25th and 75th percentile, respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "solid") (:form . "solid") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "box") (:form . "box") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "upper") (:form . "upper") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "bound") (:form . "bounds") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 46)\n  (:start . 37) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "25th") (:form . "25th") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "75th") (:form . "75th") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "percentile") (:form . "percentile") (:end . 75)\n  (:start . 65) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 89)\n  (:start . 77) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s13.67) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504280@unknown@formal@none@1@S@Circles represent outliers; 3b) frequencies of each secondary structure element type in true motif instances and in random matches, calculated for all motif positions, for non-wildcard positions only and for wildcard positions only.@(((:tag . "NNS") (:stem . "circle") (:form . "Circles") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "outlier") (:form . "outliers") (:end . 26)\n  (:start . 18) (:id . 44))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "LS") (:stem . "3b") (:form . "3b") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "frequency") (:form . "frequencies") (:end . 43)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 71)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "element") (:form . "element") (:end . 79)\n  (:start . 72) (:id . 53))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 84) (:start . 80)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 92) (:start . 88)\n  (:id . 56))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 98) (:start . 93)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 108)\n  (:start . 99) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 122)\n  (:start . 116) (:id . 61))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 130)\n  (:start . 123) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 142)\n  (:start . 132) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 146) (:start . 143)\n  (:id . 65))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 150) (:start . 147)\n  (:id . 66))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 156)\n  (:start . 151) (:id . 67))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 166)\n  (:start . 157) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 171) (:start . 168)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 184)\n  (:start . 172) (:id . 71))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 194)\n  (:start . 185) (:id . 72))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 199) (:start . 195)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 203) (:start . 200)\n  (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 207) (:start . 204)\n  (:id . 75))\n ((:tag . "NN") (:stem . "wildcard") (:form . "wildcard") (:end . 216)\n  (:start . 208) (:id . 76))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 226)\n  (:start . 217) (:id . 77))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 231) (:start . 227)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s13.68) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504281@unknown@formal@none@1@S@The aim of the scoring procedure is to assign a score to LM candidates in the user query sequence given that a reference structure is available.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "aim") (:form . "aim") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 22)\n  (:start . 15) (:id . 46))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 32)\n  (:start . 23) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 45)\n  (:start . 39) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 53) (:start . 48)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 59) (:start . 57)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 70)\n  (:start . 60) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 82) (:start . 78)\n  (:id . 58))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 88) (:start . 83)\n  (:id . 59))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 97)\n  (:start . 89) (:id . 60))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 103) (:start . 98)\n  (:id . 61))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 110) (:start . 109)\n  (:id . 63))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 120)\n  (:start . 111) (:id . 64))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 130)\n  (:start . 121) (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 133) (:start . 131)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 143)\n  (:start . 134) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s13.69) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504282@unknown@formal@none@1@S@In order to do this, the structure filter scans the LM match 3D context position by position, evaluates the relative accessibility and the secondary structure of each single position i, and assigns an accessibility score (Qacc) and a secondary structure score (Qsse) to the motif match as the normalized sums of its single position scores.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "do") (:form . "do") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 48))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 34)\n  (:start . 25) (:id . 49))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 41)\n  (:start . 35) (:id . 50))\n ((:tag . "VBZ") (:stem . "scan") (:form . "scans") (:end . 47) (:start . 42)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 54) (:start . 52)\n  (:id . 53))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 60) (:start . 55)\n  (:id . 54))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 63) (:start . 61)\n  (:id . 55))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 71)\n  (:start . 64) (:id . 56))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 80)\n  (:start . 72) (:id . 57))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 83) (:start . 81)\n  (:id . 58))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 92)\n  (:start . 84) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "evaluate") (:form . "evaluates") (:end . 103)\n  (:start . 94) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 116)\n  (:start . 108) (:id . 63))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 130) (:start . 117) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 148)\n  (:start . 139) (:id . 67))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 158)\n  (:start . 149) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 161) (:start . 159)\n  (:id . 69))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 166) (:start . 162)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 173)\n  (:start . 167) (:id . 71))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 182)\n  (:start . 174) (:id . 72))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 184) (:start . 183)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 185) (:start . 184)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 189) (:start . 186)\n  (:id . 75))\n ((:tag . "VBZ") (:stem . "assign") (:form . "assigns") (:end . 197)\n  (:start . 190) (:id . 76))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 200) (:start . 198)\n  (:id . 77))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 214) (:start . 201) (:id . 78))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 220)\n  (:start . 215) (:id . 79))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 222) (:start . 221)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Qacc") (:form . "Qacc") (:end . 226) (:start . 222)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 227) (:start . 226)\n  (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 231) (:start . 228)\n  (:id . 83))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 233) (:start . 232)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 243)\n  (:start . 234) (:id . 85))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 253)\n  (:start . 244) (:id . 86))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 259)\n  (:start . 254) (:id . 87))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 261) (:start . 260)\n  (:id . 88))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 265) (:start . 261)\n  (:id . 89))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 266) (:start . 265)\n  (:id . 90))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 269) (:start . 267)\n  (:id . 91))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 273) (:start . 270)\n  (:id . 92))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 279)\n  (:start . 274) (:id . 93))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 285)\n  (:start . 280) (:id . 94))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 288) (:start . 286)\n  (:id . 95))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 292) (:start . 289)\n  (:id . 96))\n ((:tag . "JJ") (:stem . "normalized") (:form . "normalized") (:end . 303)\n  (:start . 293) (:id . 97))\n ((:tag . "NNS") (:stem . "sum") (:form . "sums") (:end . 308) (:start . 304)\n  (:id . 98))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 311) (:start . 309)\n  (:id . 99))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 315) (:start . 312)\n  (:id . 100))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 322)\n  (:start . 316) (:id . 101))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 331)\n  (:start . 323) (:id . 102))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 338)\n  (:start . 332) (:id . 103))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 339) (:start . 338)\n  (:id . 104)))@@@1@63@((:identifiers (:sid . :s13.70) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504283@unknown@formal@none@1@S@More specifically, the score of a motif match is calculated on the non-wildcard positions of the regular expression pattern for the motif as:@(((:tag . "RBR") (:stem . "more") (:form . "More") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 17)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 39) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 59)\n  (:start . 49) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 79)\n  (:start . 67) (:id . 55))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 89)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 104)\n  (:start . 97) (:id . 59))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 115)\n  (:start . 105) (:id . 60))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 123)\n  (:start . 116) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 127) (:start . 124)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 63))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 137)\n  (:start . 132) (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 141) (:start . 140)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s13.71) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504284@unknown@formal@none@1@S@where N is the number of non-wildcard positions of a match, i.e. the number of non-wildcard residues in a LM occurrence, i is the ith position along the match, i ∈ Ω means that the sum is limited to the set of non-wildcard positions, Ω, and q(i) is the positional score of position i.@(((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "N") (:form . "N") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 21)\n  (:start . 15) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 37)\n  (:start . 25) (:id . 48))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 64) (:start . 60)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 75)\n  (:start . 69) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 91)\n  (:start . 79) (:id . 58))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 100)\n  (:start . 92) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 103) (:start . 101)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 105) (:start . 104)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 108) (:start . 106)\n  (:id . 62))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 119)\n  (:start . 109) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 122) (:start . 121)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 125) (:start . 123)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "ith") (:form . "ith") (:end . 133) (:start . 130)\n  (:id . 68))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 142)\n  (:start . 134) (:id . 69))\n ((:tag . 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"Ω") (:end . 235) (:start . 234)\n  (:id . 90))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 236) (:start . 235)\n  (:id . 91))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 240) (:start . 237)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "q(i)") (:form . "q(i)") (:end . 245) (:start . 241)\n  (:id . 93))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 248) (:start . 246)\n  (:id . 94))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 252) (:start . 249)\n  (:id . 95))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 263)\n  (:start . 253) (:id . 96))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 269)\n  (:start . 264) (:id . 97))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 272) (:start . 270)\n  (:id . 98))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 281)\n  (:start . 273) (:id . 99))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 283) (:start . 282)\n  (:id . 100))\n ((:tag . 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5504285@unknown@formal@none@1@S@Note that Qacc and Qsse were also calculated for all LM positions (i.e. not limiting the sum to the set of non-wildcard positions) and found to be marginally less discriminating than those only based on non-wildcard positions.@(((:tag . "VB") (:stem . "note") (:form . "Note") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Qacc") (:form . "Qacc") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 44)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 65)\n  (:start . 56) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 71) (:start . 67)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "limit") (:form . "limiting") (:end . 84)\n  (:start . 76) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 58))\n ((:tag . "NN") (:stem . "sum") (:form . "sum") (:end . 92) (:start . 89)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 61))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 103) (:start . 100)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 106) (:start . 104)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 119)\n  (:start . 107) (:id . 64))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 129)\n  (:start . 120) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 134) (:start . 131)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 140)\n  (:start . 135) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 143) (:start . 141)\n  (:id . 69))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 146) (:start . 144)\n  (:id . 70))\n ((:tag . "RB") (:stem . "marginally") (:form . "marginally") (:end . 157)\n  (:start . 147) (:id . 71))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 162) (:start . 158)\n  (:id . 72))\n ((:tag . "VBG") (:stem . "discriminate") (:form . "discriminating")\n  (:end . 177) (:start . 163) (:id . 73))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 182) (:start . 178)\n  (:id . 74))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 188)\n  (:start . 183) (:id . 75))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 193) (:start . 189)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 199)\n  (:start . 194) (:id . 77))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 202) (:start . 200)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 215)\n  (:start . 203) (:id . 79))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 225)\n  (:start . 216) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 226) (:start . 225)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s13.73) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504286@unknown@formal@none@1@S@In this regard, Figure 3 shows that the accessibility differences between wildcard and non-wildcard positions are statistically significant in the case of true motifs (t-test's confidence level = 0.99, p-value = 3.058e-05) (Figure 3a) and that true motif non-wildcard positions have a more pronounced tendency to be in loops and a less marked disposition to be in helices and strands as opposed to the frequencies both of true motifs for all positions and for wildcard positions, even if none of these differences is statistically significant (Figure 3b).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "regard") (:form . "regard") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "figure") (:form . 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"if") (:end . 487) (:start . 485)\n  (:id . 127))\n ((:tag . "NN") (:stem . "none") (:form . "none") (:end . 492) (:start . 488)\n  (:id . 128))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 495) (:start . 493)\n  (:id . 129))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 501)\n  (:start . 496) (:id . 130))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 513)\n  (:start . 502) (:id . 131))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 516) (:start . 514)\n  (:id . 132))\n ((:tag . "RB") (:stem . "statistically") (:form . "statistically")\n  (:end . 530) (:start . 517) (:id . 133))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 542)\n  (:start . 531) (:id . 134))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 544) (:start . 543)\n  (:id . 135))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 550)\n  (:start . 544) (:id . 136))\n ((:tag . "NN") (:stem . "3b") (:form . "3b") (:end . 553) (:start . 551)\n  (:id . 137))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 554) (:start . 553)\n  (:id . 138))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 555) (:start . 554)\n  (:id . 139)))@@@1@98@((:identifiers (:sid . :s13.74) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504287@unknown@formal@none@1@S@For further details see additional file 1, additional file 2 (Figure S1) and additional file 3 (Figure S2).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 53)\n  (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 60) (:start . 59)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 68)\n  (:start . 62) (:id . 54))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 87)\n  (:start . 77) (:id . 58))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 92) (:start . 88)\n  (:id . 59))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 94) (:start . 93)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 102)\n  (:start . 96) (:id . 62))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 105) (:start . 103)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 106) (:start . 105)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s13.75) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504288@unknown@formal@none@1@S@We adopted as accessibility positional score, qacc(i), of position i, the normalized solvent exposure value of the residue in i, which ranges between 0 (non exposed) and 1.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "adopt") (:form . "adopted") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 27) (:start . 14) (:id . 45))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 44) (:start . 39)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "qacc(i)") (:form . "qacc(i)") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 66)\n  (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "normalized") (:form . "normalized") (:end . 84)\n  (:start . 74) (:id . 56))\n ((:tag . "NN") (:stem . "solvent") (:form . "solvent") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "exposure") (:form . "exposure") (:end . 101)\n  (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 107)\n  (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 61))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 122)\n  (:start . 115) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 125) (:start . 123)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 127) (:start . 126)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 134)\n  (:start . 129) (:id . 66))\n ((:tag . "VBZ") (:stem . "range") (:form . "ranges") (:end . 141)\n  (:start . 135) (:id . 67))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 149)\n  (:start . 142) (:id . 68))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 151) (:start . 150)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 70))\n ((:tag . "AFX") (:stem . "non") (:form . "non") (:end . 156) (:start . 153)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 164)\n  (:start . 157) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 169) (:start . 166)\n  (:id . 74))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 171) (:start . 170)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s13.76) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504289@unknown@formal@none@1@S@5. Thus, the higher the residue exposure, the more the corresponding position is rewarded.@(((:tag . "LS") (:stem . "5.") (:form . "5.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 45))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 19) (:start . 13)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 31)\n  (:start . 24) (:id . 48))\n ((:tag . "NN") (:stem . "exposure") (:form . "exposure") (:end . 40)\n  (:start . 32) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 51))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 50) (:start . 46)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "corresponding") (:form . "corresponding")\n  (:end . 68) (:start . 55) (:id . 54))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 77)\n  (:start . 69) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "reward") (:form . "rewarded") (:end . 89)\n  (:start . 81) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 90) (:start . 89)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s13.77) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504290@unknown@formal@none@1@S@The secondary structure positional score, qsse(i), was determined in a more complex manner.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "JJ") (:stem . "positional") (:form . "positional") (:end . 34)\n  (:start . 24) (:id . 45))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 40) (:start . 35)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "qsse(i)") (:form . "qsse(i)") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 65)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 83)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 90)\n  (:start . 84) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s13.78) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504291@unknown@formal@none@1@S@The analysis of LM instances on structural domains showed that they occur more frequently in loops and unstructured regions than expected by chance.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "VBD") (:stem . "show") (:form . "showed") (:end . 57) (:start . 51)\n  (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "occur") (:form . "occur") (:end . 73) (:start . 68)\n  (:id . 53))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 89)\n  (:start . 79) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "loop") (:form . "loops") (:end . 98) (:start . 93)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "unstructured") (:form . "unstructured") (:end . 115)\n  (:start . 103) (:id . 59))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 123)\n  (:start . 116) (:id . 60))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 128) (:start . 124)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 137)\n  (:start . 129) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 140) (:start . 138)\n  (:id . 63))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 147)\n  (:start . 141) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s13.79) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504292@unknown@formal@none@1@S@In order to quantify this observation, we calculated, for each secondary structure element (SSE) type (loop, helix, strand, 3/10 helix - see Methods), the ratio between the SSE type frequency (ν) among true motif instances and among random matches.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "quantify") (:form . "quantify") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "calculate") (:form . "calculated") (:end . 52)\n  (:start . 42) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 72)\n  (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 82)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "element") (:form . "element") (:end . 90)\n  (:start . 83) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "SSE") (:form . "SSE") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 101) (:start . 97)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 107) (:start . 103)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 63))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 114)\n  (:start . 109) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 65))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 122)\n  (:start . 116) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 67))\n ((:tag . "CD") (:stem . "3/10") (:form . "3/10") (:end . 128) (:start . 124)\n  (:id . 68))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 134)\n  (:start . 129) (:id . 69))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 136) (:start . 135)\n  (:id . 70))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 140) (:start . 137)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 148)\n  (:start . 141) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 149) (:start . 148)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 75))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 160)\n  (:start . 155) (:id . 76))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 168)\n  (:start . 161) (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 172) (:start . 169)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "SSE") (:form . "SSE") (:end . 176) (:start . 173)\n  (:id . 79))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 181) (:start . 177)\n  (:id . 80))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 191)\n  (:start . 182) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 193) (:start . 192)\n  (:id . 82))\n ((:tag . "NN") (:stem . "ν") (:form . "ν") (:end . 194) (:start . 193)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 84))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 201)\n  (:start . 196) (:id . 85))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 206) (:start . 202)\n  (:id . 86))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 212)\n  (:start . 207) (:id . 87))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 222)\n  (:start . 213) (:id . 88))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 226) (:start . 223)\n  (:id . 89))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 232)\n  (:start . 227) (:id . 90))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 239)\n  (:start . 233) (:id . 91))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 247)\n  (:start . 240) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 248) (:start . 247)\n  (:id . 93)))@@@1@52@((:identifiers (:sid . :s13.80) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504293@unknown@formal@none@1@S@The corresponding values are reported in Table 1.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 17)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 24)\n  (:start . 18) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 46) (:start . 41)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s13.81) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504294@unknown@formal@none@1@S@Frequency of secondary structure elements in true and in random motifs@(((:tag . "NN") (:stem . "frequency") (:form . "Frequency") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 32)\n  (:start . 23) (:id . 45))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 41)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 49) (:start . 45)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 63)\n  (:start . 57) (:id . 51))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 70)\n  (:start . 64) (:id . 52)))@@@1@11@((:identifiers (:sid . :s13.82) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504295@unknown@formal@none@1@S@Thus, the secondary structure score of a position i whose SSE assignment is loop (or 3/10 helix, helix, strand), is the ratio between the frequency of loops (or 3/10 helices, helices, strands) in the instance dataset and the frequency of loops (or 3/10 helices, helices, strands) in the random dataset.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 19)\n  (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 29)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 57) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "sse") (:form . "SSE") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 72)\n  (:start . 62) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "CD") (:stem . "3/10") (:form . "3/10") (:end . 89) (:start . 85)\n  (:id . 59))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 95) (:start . 90)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 61))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 102) (:start . 97)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 63))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 110)\n  (:start . 104) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 115) (:start . 113)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 68))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 125)\n  (:start . 120) (:id . 69))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 133)\n  (:start . 126) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 71))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 147)\n  (:start . 138) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "loop") (:form . "loops") (:end . 156)\n  (:start . 151) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 158) (:start . 157)\n  (:id . 75))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 160) (:start . 158)\n  (:id . 76))\n ((:tag . "CD") (:stem . "3/10") (:form . "3/10") (:end . 165) (:start . 161)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 173)\n  (:start . 166) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 182)\n  (:start . 175) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "strand") (:form . "strands") (:end . 191)\n  (:start . 184) (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 192) (:start . 191)\n  (:id . 83))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 195) (:start . 193)\n  (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 199) (:start . 196)\n  (:id . 85))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 208)\n  (:start . 200) (:id . 86))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 216)\n  (:start . 209) (:id . 87))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 220) (:start . 217)\n  (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 224) (:start . 221)\n  (:id . 89))\n ((:tag . "NN") (:stem . "frequency") (:form . "frequency") (:end . 234)\n  (:start . 225) (:id . 90))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 237) (:start . 235)\n  (:id . 91))\n ((:tag . "NNS") (:stem . "loop") (:form . "loops") (:end . 243)\n  (:start . 238) (:id . 92))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 245) (:start . 244)\n  (:id . 93))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 247) (:start . 245)\n  (:id . 94))\n ((:tag . "CD") (:stem . "3/10") (:form . "3/10") (:end . 252) (:start . 248)\n  (:id . 95))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 260)\n  (:start . 253) (:id . 96))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 261) (:start . 260)\n  (:id . 97))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 269)\n  (:start . 262) (:id . 98))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 270) (:start . 269)\n  (:id . 99))\n ((:tag . "NNS") (:stem . "strand") (:form . "strands") (:end . 278)\n  (:start . 271) (:id . 100))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 279) (:start . 278)\n  (:id . 101))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 282) (:start . 280)\n  (:id . 102))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 286) (:start . 283)\n  (:id . 103))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 293)\n  (:start . 287) (:id . 104))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 301)\n  (:start . 294) (:id . 105))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 302) (:start . 301)\n  (:id . 106)))@@@1@65@((:identifiers (:sid . :s13.83) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504296@unknown@formal@none@1@S@Assessing the predictive ability of the ELM structure filter@(((:tag . "VBG") (:stem . "assess") (:form . "Assessing") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "predictive") (:form . "predictive") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 60)\n  (:start . 54) (:id . 50)))@@@1@9@((:identifiers (:sid . :s13.84) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504297@unknown@formal@none@1@S@In order to assess the predictive ability of the ELM structure filter scoring scheme, we made use of five strategies, each introducing useful parameters for the evaluation of the discrimination power of our procedure: 1) we plotted ROC curves and calculated AUCs; 2) we assigned a p-value to predictions; 3) we built LM-specific background distributions; 4) we identified sparse/neutral/enriched score intervals; 5) we carried out a 5-fold cross validation in order to determine sensitivity, specificity and accuracy.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "predictive") (:form . "predictive") (:end . 33)\n  (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 77)\n  (:start . 70) (:id . 54))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 84)\n  (:start . 78) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "make") (:form . "made") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 60))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 105) (:start . 101)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 116)\n  (:start . 106) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 122) (:start . 118)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "introduce") (:form . "introducing") (:end . 134)\n  (:start . 123) (:id . 65))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 141)\n  (:start . 135) (:id . 66))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 152)\n  (:start . 142) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 156) (:start . 153)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 160) (:start . 157)\n  (:id . 69))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 171)\n  (:start . 161) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 174) (:start . 172)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 72))\n ((:tag . "NN") (:stem . "discrimination") (:form . "discrimination")\n  (:end . 193) (:start . 179) (:id . 73))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 199)\n  (:start . 194) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 202) (:start . 200)\n  (:id . 75))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 206) (:start . 203)\n  (:id . 76))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 216)\n  (:start . 207) (:id . 77))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 217) (:start . 216)\n  (:id . 78))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 219) (:start . 218)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 220) (:start . 219)\n  (:id . 80))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 223) (:start . 221)\n  (:id . 81))\n ((:tag . "VBD") (:stem . "plot") (:form . "plotted") (:end . 231)\n  (:start . 224) (:id . 82))\n ((:tag . "NNP") (:stem . "ROC") (:form . "ROC") (:end . 235) (:start . 232)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "curve") (:form . "curves") (:end . 242)\n  (:start . 236) (:id . 84))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 246) (:start . 243)\n  (:id . 85))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 257)\n  (:start . 247) (:id . 86))\n ((:tag . "NNS") (:stem . "auc") (:form . "AUCs") (:end . 262) (:start . 258)\n  (:id . 87))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 263) (:start . 262)\n  (:id . 88))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 265) (:start . 264)\n  (:id . 89))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 266) (:start . 265)\n  (:id . 90))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 269) (:start . 267)\n  (:id . 91))\n ((:tag . "VBD") (:stem . "assign") (:form . "assigned") (:end . 278)\n  (:start . 270) (:id . 92))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 280) (:start . 279)\n  (:id . 93))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 288)\n  (:start . 281) (:id . 94))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 291) (:start . 289)\n  (:id . 95))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 303)\n  (:start . 292) (:id . 96))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 304) (:start . 303)\n  (:id . 97))\n ((:tag . "LS") (:stem . "3") (:form . "3") (:end . 306) (:start . 305)\n  (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 307) (:start . 306)\n  (:id . 99))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 310) (:start . 308)\n  (:id . 100))\n ((:tag . "VBD") (:stem . "build") (:form . "built") (:end . 316)\n  (:start . 311) (:id . 101))\n ((:tag . "JJ") (:stem . "lm-specific") (:form . "LM-specific") (:end . 328)\n  (:start . 317) (:id . 102))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 339)\n  (:start . 329) (:id . 103))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 353) (:start . 340) (:id . 104))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 354) (:start . 353)\n  (:id . 105))\n ((:tag . "LS") (:stem . "4") (:form . "4") (:end . 356) (:start . 355)\n  (:id . 106))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 357) (:start . 356)\n  (:id . 107))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 360) (:start . 358)\n  (:id . 108))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 371)\n  (:start . 361) (:id . 109))\n ((:tag . "VBN") (:stem . "sparse/neutral/enriche")\n  (:form . "sparse/neutral/enriched") (:end . 395) (:start . 372) (:id . 110))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 401)\n  (:start . 396) (:id . 111))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 411)\n  (:start . 402) (:id . 112))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 412) (:start . 411)\n  (:id . 113))\n ((:tag . "LS") (:stem . "5") (:form . "5") (:end . 414) (:start . 413)\n  (:id . 114))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 415) (:start . 414)\n  (:id . 115))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 418) (:start . 416)\n  (:id . 116))\n ((:tag . "VBD") (:stem . "carry") (:form . "carried") (:end . 426)\n  (:start . 419) (:id . 117))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 430) (:start . 427)\n  (:id . 118))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 432) (:start . 431)\n  (:id . 119))\n ((:tag . "JJ") (:stem . "5-fold") (:form . "5-fold") (:end . 439)\n  (:start . 433) (:id . 120))\n ((:tag . "NN") (:stem . "cross") (:form . "cross") (:end . 445)\n  (:start . 440) (:id . 121))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 456)\n  (:start . 446) (:id . 122))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 459) (:start . 457)\n  (:id . 123))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 465)\n  (:start . 460) (:id . 124))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 468) (:start . 466)\n  (:id . 125))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 478)\n  (:start . 469) (:id . 126))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 490)\n  (:start . 479) (:id . 127))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 491) (:start . 490)\n  (:id . 128))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 503)\n  (:start . 492) (:id . 129))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 507) (:start . 504)\n  (:id . 130))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 516)\n  (:start . 508) (:id . 131))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 517) (:start . 516)\n  (:id . 132)))@@@1@91@((:identifiers (:sid . :s13.85) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504298@unknown@formal@none@1@S@In order that the structure filter may be a useful guide to the ELM resource user, we propose that the values of the above-mentioned parameters are used as decision-making tools in evaluating the score of LM predictions.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 50)\n  (:start . 44) (:id . 51))\n ((:tag . "NN") (:stem . "guide") (:form . "guide") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 76)\n  (:start . 68) (:id . 56))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 81) (:start . 77)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 85) (:start . 83)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "propose") (:form . "propose") (:end . 93)\n  (:start . 86) (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 98) (:start . 94)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 109)\n  (:start . 103) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 112) (:start . 110)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "above-mentioned") (:form . "above-mentioned")\n  (:end . 132) (:start . 117) (:id . 66))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 143)\n  (:start . 133) (:id . 67))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 147) (:start . 144)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 152) (:start . 148)\n  (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 155) (:start . 153)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "decision-making") (:form . "decision-making")\n  (:end . 171) (:start . 156) (:id . 71))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 177)\n  (:start . 172) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 180) (:start . 178)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "evaluate") (:form . "evaluating") (:end . 191)\n  (:start . 181) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 195) (:start . 192)\n  (:id . 75))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 201)\n  (:start . 196) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 204) (:start . 202)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 207) (:start . 205)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 219)\n  (:start . 208) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x13.86.1) (:span 86 93)) ((:id . :x13.86.2) (:span 35 38)))\n (:hscopes ((:id . :x13.86.1) (:span 86 219))\n  ((:id . :x13.86.2) (:span 35 81)))\n (:identifiers (:sid . :s13.86) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504299@unknown@formal@none@1@S@In particular, since having high accessibility and belonging to loop regions is not a prerogative of LMs alone and the random match dataset might in principle be "contaminated" by not yet annotated spurious true motifs, we suggest using as many indicators as possible in evaluating a prediction score and not relying on each single tool as a unique criterion for retaining/rejecting a prediction.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "have") (:form . "having") (:end . 27) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 46) (:start . 33) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "belong") (:form . "belonging") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "prerogative") (:form . "prerogative") (:end . 97)\n  (:start . 86) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "RB") (:stem . "alone") (:form . "alone") (:end . 110)\n  (:start . 105) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 125)\n  (:start . 119) (:id . 63))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 131)\n  (:start . 126) (:id . 64))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 139)\n  (:start . 132) (:id . 65))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 145)\n  (:start . 140) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n  (:id . 67))\n ((:tag . "NN") (:stem . "principle") (:form . "principle") (:end . 158)\n  (:start . 149) (:id . 68))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 161) (:start . 159)\n  (:id . 69))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 163) (:start . 162)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "contaminate") (:form . "contaminated") (:end . 175)\n  (:start . 163) (:id . 71))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 176) (:start . 175)\n  (:id . 72))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 179) (:start . 177)\n  (:id . 73))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 183) (:start . 180)\n  (:id . 74))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 187) (:start . 184)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 197)\n  (:start . 188) (:id . 76))\n ((:tag . "JJ") (:stem . "spurious") (:form . "spurious") (:end . 206)\n  (:start . 198) (:id . 77))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 211) (:start . 207)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 218)\n  (:start . 212) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 219) (:start . 218)\n  (:id . 80))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 222) (:start . 220)\n  (:id . 81))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 230)\n  (:start . 223) (:id . 82))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 236) (:start . 231)\n  (:id . 83))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 239) (:start . 237)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 244) (:start . 240)\n  (:id . 85))\n ((:tag . "NNS") (:stem . "indicator") (:form . "indicators") (:end . 255)\n  (:start . 245) (:id . 86))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 258) (:start . 256)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 267)\n  (:start . 259) (:id . 88))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 270) (:start . 268)\n  (:id . 89))\n ((:tag . "VBG") (:stem . "evaluate") (:form . "evaluating") (:end . 281)\n  (:start . 271) (:id . 90))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 283) (:start . 282)\n  (:id . 91))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 294)\n  (:start . 284) (:id . 92))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 300)\n  (:start . 295) (:id . 93))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 304) (:start . 301)\n  (:id . 94))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 308) (:start . 305)\n  (:id . 95))\n ((:tag . "VBG") (:stem . "rely") (:form . "relying") (:end . 316)\n  (:start . 309) (:id . 96))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 319) (:start . 317)\n  (:id . 97))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 324) (:start . 320)\n  (:id . 98))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 331)\n  (:start . 325) (:id . 99))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 336) (:start . 332)\n  (:id . 100))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 339) (:start . 337)\n  (:id . 101))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 341) (:start . 340)\n  (:id . 102))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 348)\n  (:start . 342) (:id . 103))\n ((:tag . "NN") (:stem . "criterion") (:form . "criterion") (:end . 358)\n  (:start . 349) (:id . 104))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 362) (:start . 359)\n  (:id . 105))\n ((:tag . "VBG") (:stem . "retaining/rejecte") (:form . "retaining/rejecting")\n  (:end . 382) (:start . 363) (:id . 106))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 384) (:start . 383)\n  (:id . 107))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 395)\n  (:start . 385) (:id . 108))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 396) (:start . 395)\n  (:id . 109)))@@@1@68@((:hcues ((:id . :x13.87.1) (:span 223 230))\n  ((:id . :x13.87.2) (:span 140 145)))\n (:hscopes ((:id . :x13.87.1) (:span 223 395))\n  ((:id . :x13.87.2) (:span 115 218)))\n (:identifiers (:sid . :s13.87) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504300@unknown@formal@none@1@S@In order to establish if one score is more discriminative than the others, we assigned an accessibility score (Qacc), a secondary structure score (Qsse) and a combined score (Qand = Qacc + Qsse) to the true positive instances of our dataset and to the random matches of the random dataset, plotted cumulative score distributions and ROC curves and calculated the area under the ROC curves (AUCs).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "establish") (:form . "establish") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 34) (:start . 29)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "discriminative") (:form . "discriminative")\n  (:end . 57) (:start . 43) (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "assign") (:form . "assigned") (:end . 86)\n  (:start . 78) (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 103) (:start . 90) (:id . 59))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 109)\n  (:start . 104) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Qacc") (:form . "Qacc") (:end . 115) (:start . 111)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 119) (:start . 118)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 129)\n  (:start . 120) (:id . 66))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 139)\n  (:start . 130) (:id . 67))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 145)\n  (:start . 140) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 151) (:start . 147)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 158) (:start . 157)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "combined") (:form . "combined") (:end . 167)\n  (:start . 159) (:id . 74))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 173)\n  (:start . 168) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 175) (:start . 174)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Qand") (:form . "Qand") (:end . 179) (:start . 175)\n  (:id . 77))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 181) (:start . 180)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Qacc") (:form . "Qacc") (:end . 186) (:start . 182)\n  (:id . 79))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 188) (:start . 187)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 193) (:start . 189)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n  (:id . 82))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 197) (:start . 195)\n  (:id . 83))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 201) (:start . 198)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 206) (:start . 202)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 215)\n  (:start . 207) (:id . 86))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 225)\n  (:start . 216) (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 228) (:start . 226)\n  (:id . 88))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 232) (:start . 229)\n  (:id . 89))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 240)\n  (:start . 233) (:id . 90))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 244) (:start . 241)\n  (:id . 91))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 247) (:start . 245)\n  (:id . 92))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 251) (:start . 248)\n  (:id . 93))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 258)\n  (:start . 252) (:id . 94))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 266)\n  (:start . 259) (:id . 95))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 269) (:start . 267)\n  (:id . 96))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 273) (:start . 270)\n  (:id . 97))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 280)\n  (:start . 274) (:id . 98))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 288)\n  (:start . 281) (:id . 99))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 289) (:start . 288)\n  (:id . 100))\n ((:tag . "VBD") (:stem . "plot") (:form . "plotted") (:end . 297)\n  (:start . 290) (:id . 101))\n ((:tag . "JJ") (:stem . "cumulative") (:form . "cumulative") (:end . 308)\n  (:start . 298) (:id . 102))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 314)\n  (:start . 309) (:id . 103))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 328) (:start . 315) (:id . 104))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 332) (:start . 329)\n  (:id . 105))\n ((:tag . "NNP") (:stem . "ROC") (:form . "ROC") (:end . 336) (:start . 333)\n  (:id . 106))\n ((:tag . "NNS") (:stem . "curve") (:form . "curves") (:end . 343)\n  (:start . 337) (:id . 107))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 347) (:start . 344)\n  (:id . 108))\n ((:tag . "VBD") (:stem . "calculate") (:form . "calculated") (:end . 358)\n  (:start . 348) (:id . 109))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 362) (:start . 359)\n  (:id . 110))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 367) (:start . 363)\n  (:id . 111))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 373)\n  (:start . 368) (:id . 112))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 377) (:start . 374)\n  (:id . 113))\n ((:tag . "NNP") (:stem . "ROC") (:form . "ROC") (:end . 381) (:start . 378)\n  (:id . 114))\n ((:tag . "NNS") (:stem . "curve") (:form . "curves") (:end . 388)\n  (:start . 382) (:id . 115))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 390) (:start . 389)\n  (:id . 116))\n ((:tag . "NNP") (:stem . "AUC") (:form . "AUCs") (:end . 394) (:start . 390)\n  (:id . 117))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 395) (:start . 394)\n  (:id . 118))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 396) (:start . 395)\n  (:id . 119)))@@@1@78@((:hcues ((:id . :x13.88.1) (:span 22 24)))\n (:hscopes ((:id . :x13.88.1) (:span 22 73)))\n (:identifiers (:sid . :s13.88) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504301@unknown@formal@none@1@S@In calculating the ROC curves, we assumed that random matches are all negative matches.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "calculate") (:form . "calculating") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "ROC") (:form . "ROC") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "curve") (:form . "curves") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "assume") (:form . "assumed") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 53)\n  (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 78)\n  (:start . 70) (:id . 55))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 86)\n  (:start . 79) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x13.89.1) (:span 34 41)))\n (:hscopes ((:id . :x13.89.1) (:span 34 86)))\n (:identifiers (:sid . :s13.89) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504302@unknown@formal@none@1@S@Figure 4 shows that the cumulative distribution of true motifs is clearly separated from that of random matches for each score type.@(((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "cumulative") (:form . "cumulative") (:end . 34)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 47)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "RB") (:stem . "clearly") (:form . "clearly") (:end . 73)\n  (:start . 66) (:id . 53))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 83)\n  (:start . 74) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 111)\n  (:start . 104) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 115) (:start . 112)\n  (:id . 60))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 120) (:start . 116)\n  (:id . 61))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 126)\n  (:start . 121) (:id . 62))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 131) (:start . 127)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s13.90) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504303@unknown@formal@none@1@S@Moreover, the ROC curves (Figure 5) show that all three score types are able to discriminate between the true motif and random match sets and that both Qacc and Qand perform better than Qsse; the AUC values for the three scores are 0.73 (Qacc), 0.66 (Qsse) and 0.72 (Qand); notice that, even though the AUC for Qand is slightly lower than that of Qacc, Qand performs similarly or better than Qacc in the range corresponding to the 20% of the ROC x-axis values.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "ROC") (:form . "ROC") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "curve") (:form . "curves") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . 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"(") (:stem . "(") (:form . "(") (:end . 238) (:start . 237)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "Qacc") (:form . "Qacc") (:end . 242) (:start . 238)\n  (:id . 90))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 243) (:start . 242)\n  (:id . 91))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 244) (:start . 243)\n  (:id . 92))\n ((:tag . "CD") (:stem . "0.66") (:form . "0.66") (:end . 249) (:start . 245)\n  (:id . 93))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 251) (:start . 250)\n  (:id . 94))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 255) (:start . 251)\n  (:id . 95))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 256) (:start . 255)\n  (:id . 96))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 260) (:start . 257)\n  (:id . 97))\n ((:tag . "CD") (:stem . "0.72") (:form . "0.72") (:end . 265) (:start . 261)\n  (:id . 98))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 267) (:start . 266)\n  (:id . 99))\n ((:tag . 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(:end . 460) (:start . 459)\n  (:id . 140)))@@@1@99@((:identifiers (:sid . :s13.91) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504304@unknown@formal@none@1@S@Cumulative score distributions. a) The cumulative distribution of (a) Qacc, (b) Qsse, and (c) Qand = Qacc + Qsse scores calculated for true motif matches (true motifs), and for random matches (random matches) in non-wildcard positions.@(((:tag . "JJ") (:stem . "cumulative") (:form . "Cumulative") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 16) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "distributions.") (:form . "distributions.")\n  (:end . 31) (:start . 17) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 34) (:start . 33)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "cumulative") (:form . "cumulative") (:end . 49)\n  (:start . 39) (:id . 48))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 62)\n  (:start . 50) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Qacc") (:form . "Qacc") (:end . 74) (:start . 70)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 78) (:start . 77)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 79) (:start . 78)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 84) (:start . 80)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 62))\n ((:tag . "LS") (:stem . "c") (:form . "c") (:end . 92) (:start . 91)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Qand") (:form . "Qand") (:end . 98) (:start . 94)\n  (:id . 65))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 100) (:start . 99)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Qacc") (:form . "Qacc") (:end . 105) (:start . 101)\n  (:id . 67))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 107) (:start . 106)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 112) (:start . 108)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 119)\n  (:start . 113) (:id . 70))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 130)\n  (:start . 120) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 134) (:start . 131)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 139) (:start . 135)\n  (:id . 73))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 145)\n  (:start . 140) (:id . 74))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 153)\n  (:start . 146) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 159) (:start . 155)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 166)\n  (:start . 160) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 167) (:start . 166)\n  (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 168) (:start . 167)\n  (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 172) (:start . 169)\n  (:id . 81))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 176) (:start . 173)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 183)\n  (:start . 177) (:id . 83))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 191)\n  (:start . 184) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 193) (:start . 192)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 199)\n  (:start . 193) (:id . 86))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 207)\n  (:start . 200) (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 208) (:start . 207)\n  (:id . 88))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 211) (:start . 209)\n  (:id . 89))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 224)\n  (:start . 212) (:id . 90))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 234)\n  (:start . 225) (:id . 91))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 235) (:start . 234)\n  (:id . 92)))@@@1@51@((:identifiers (:sid . :s13.92) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504305@unknown@formal@none@1@S@Red dashed lines indicate the percentile cut-off ensuring that the lower 40% random matches fall in the "sparse" bin.@(((:tag . "JJ") (:stem . "red") (:form . "Red") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "dashed") (:form . "dashed") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "percentile") (:form . "percentile") (:end . 40)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "cut-off") (:form . "cut-off") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "VBG") (:stem . "ensure") (:form . "ensuring") (:end . 57)\n  (:start . 49) (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 62) (:start . 58)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 72) (:start . 67)\n  (:id . 52))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 83)\n  (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 91)\n  (:start . 84) (:id . 56))\n ((:tag . "VBP") (:stem . "fall") (:form . "fall") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 59))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 111)\n  (:start . 105) (:id . 61))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 112) (:start . 111)\n  (:id . 62))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 116) (:start . 113)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s13.93) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504306@unknown@formal@none@1@S@The consequent percentage of true motifs falling in the "sparse" bin is about 15% (accessibility) and 20% (secondary structure).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "consequent") (:form . "consequent") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "VBG") (:stem . "fall") (:form . "falling") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 64) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "RB") (:stem . "about") (:form . "about") (:end . 77) (:start . 72)\n  (:id . 56))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 80) (:start . 78)\n  (:id . 57))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 81) (:start . 80)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 59))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 96) (:start . 83) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 62))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 104) (:start . 102)\n  (:id . 63))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 105) (:start . 104)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 116)\n  (:start . 107) (:id . 66))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 126)\n  (:start . 117) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 127) (:start . 126)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 128) (:start . 127)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s13.94) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504307@unknown@formal@none@1@S@This cut-off corresponds to Qacc~0.3 and Qsse~0.7.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cut-off") (:form . "cut-off") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Qacc~0.3") (:form . "Qacc~0.3") (:end . 36)\n  (:start . 28) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Qsse~0.7") (:form . "Qsse~0.7") (:end . 49)\n  (:start . 41) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 50) (:start . 49)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s13.95) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504308@unknown@formal@none@1@S@Black dotted lines indicate the percentile cut-off that guarantees that the enriched bin collects at least the top 30% true motifs.@(((:tag . "JJ") (:stem . "black") (:form . "Black") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "dot") (:form . "dotted") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "percentile") (:form . "percentile") (:end . 42)\n  (:start . 32) (:id . 47))\n ((:tag . "NN") (:stem . "cut-off") (:form . "cut-off") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 55) (:start . 51)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "guarantee") (:form . "guarantees") (:end . 66)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 71) (:start . 67)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 84)\n  (:start . 76) (:id . 53))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 88) (:start . 85)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "collect") (:form . "collects") (:end . 97)\n  (:start . 89) (:id . 55))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 106)\n  (:start . 101) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 114) (:start . 111)\n  (:id . 59))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 123) (:start . 119)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 130)\n  (:start . 124) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s13.96) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504309@unknown@formal@none@1@S@This cut-off corresponds to Qacc = 0.76, Qsse = 1.5, and Qand = 2.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "cut-off") (:form . "cut-off") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Qacc") (:form . "Qacc") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "CD") (:stem . "0.76") (:form . "0.76") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 47) (:start . 46)\n  (:id . 51))\n ((:tag . "CD") (:stem . "1.5") (:form . "1.5") (:end . 51) (:start . 48)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Qand") (:form . "Qand") (:end . 61) (:start . 57)\n  (:id . 55))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 63) (:start . 62)\n  (:id . 56))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 65) (:start . 64)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s13.97) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504310@unknown@formal@none@1@S@Qacc, Qsse and Qand = Qacc+ Qsse ROC curves.@(((:tag . "NNP") (:stem . "Qacc") (:form . "Qacc") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Qand") (:form . "Qand") (:end . 19) (:start . 15)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "=") (:form . "=") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Qacc+") (:form . "Qacc+") (:end . 27) (:start . 22)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 32) (:start . 28)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "ROC") (:form . "ROC") (:end . 36) (:start . 33)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "curve") (:form . "curves") (:end . 43)\n  (:start . 37) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 44) (:start . 43)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s13.98) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504311@unknown@formal@none@1@S@We determined the distribution of random matches and use it to assign a p-value to the score of each ELM prediction.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "determine") (:form . "determined") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 30)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "VB") (:stem . "use") (:form . "use") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 79)\n  (:start . 72) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 57))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 92) (:start . 87)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 100) (:start . 96)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 104) (:start . 101)\n  (:id . 61))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 115)\n  (:start . 105) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s13.99) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504312@unknown@formal@none@1@S@This p-value, which is implemented both in the Web Server and in the Web Service, is calculated using a Z-test and is a conservative estimate of the probability that a LM prediction with a given score is a true positive; more specifically it is the probability of obtaining a random match with a score at least as high as the one that was actually observed, and therefore we expect it to be very stringent.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 34)\n  (:start . 23) (:id . 47))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Server") (:form . "Server") (:end . 57)\n  (:start . 51) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Service") (:form . "Service") (:end . 80)\n  (:start . 73) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 84) (:start . 82)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 95)\n  (:start . 85) (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 101) (:start . 96)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 103) (:start . 102)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Z-test") (:form . "Z-test") (:end . 110)\n  (:start . 104) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 117) (:start . 115)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 119) (:start . 118)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "conservative") (:form . "conservative") (:end . 132)\n  (:start . 120) (:id . 67))\n ((:tag . "NN") (:stem . "estimate") (:form . "estimate") (:end . 141)\n  (:start . 133) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 70))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 160)\n  (:start . 149) (:id . 71))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 165) (:start . 161)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 167) (:start . 166)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 170) (:start . 168)\n  (:id . 74))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 181)\n  (:start . 171) (:id . 75))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 186) (:start . 182)\n  (:id . 76))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 188) (:start . 187)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 194)\n  (:start . 189) (:id . 78))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 200)\n  (:start . 195) (:id . 79))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 203) (:start . 201)\n  (:id . 80))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 205) (:start . 204)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 210) (:start . 206)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 219)\n  (:start . 211) (:id . 83))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 220) (:start . 219)\n  (:id . 84))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 225) (:start . 221)\n  (:id . 85))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 238)\n  (:start . 226) (:id . 86))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 241) (:start . 239)\n  (:id . 87))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 244) (:start . 242)\n  (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 248) (:start . 245)\n  (:id . 89))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 260)\n  (:start . 249) (:id . 90))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 263) (:start . 261)\n  (:id . 91))\n ((:tag . "VBG") (:stem . "obtain") (:form . "obtaining") (:end . 273)\n  (:start . 264) (:id . 92))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 275) (:start . 274)\n  (:id . 93))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 282)\n  (:start . 276) (:id . 94))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 288)\n  (:start . 283) (:id . 95))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 293) (:start . 289)\n  (:id . 96))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 295) (:start . 294)\n  (:id . 97))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 301)\n  (:start . 296) (:id . 98))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 304) (:start . 302)\n  (:id . 99))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 310)\n  (:start . 305) (:id . 100))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 313) (:start . 311)\n  (:id . 101))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 318) (:start . 314)\n  (:id . 102))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 321) (:start . 319)\n  (:id . 103))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 325) (:start . 322)\n  (:id . 104))\n ((:tag . "NN") (:stem . "one") (:form . "one") (:end . 329) (:start . 326)\n  (:id . 105))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 334) (:start . 330)\n  (:id . 106))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 338) (:start . 335)\n  (:id . 107))\n ((:tag . "RB") (:stem . "actually") (:form . "actually") (:end . 347)\n  (:start . 339) (:id . 108))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 356)\n  (:start . 348) (:id . 109))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 357) (:start . 356)\n  (:id . 110))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 361) (:start . 358)\n  (:id . 111))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 371)\n  (:start . 362) (:id . 112))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 374) (:start . 372)\n  (:id . 113))\n ((:tag . "VBP") (:stem . "expect") (:form . "expect") (:end . 381)\n  (:start . 375) (:id . 114))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 384) (:start . 382)\n  (:id . 115))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 387) (:start . 385)\n  (:id . 116))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 390) (:start . 388)\n  (:id . 117))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 395) (:start . 391)\n  (:id . 118))\n ((:tag . "JJ") (:stem . "stringent") (:form . "stringent") (:end . 405)\n  (:start . 396) (:id . 119))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 406) (:start . 405)\n  (:id . 120)))@@@1@79@((:hcues ((:id . :x13.100.1) (:span 375 381)))\n (:hscopes ((:id . :x13.100.1) (:span 375 405)))\n (:identifiers (:sid . :s13.100) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504313@unknown@formal@none@1@S@Due to the paucity of true motif instance data, we cannot build a true motif score distribution for each ELM motif (and therefore we cannot build a LM-specific structure filter yet) and compare it to the corresponding random motif score distribution.@(((:tag . "JJ") (:stem . "due") (:form . "Due") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "paucity") (:form . "paucity") (:end . 18)\n  (:start . 11) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "cannot") (:form . "cannot") (:end . 57)\n  (:start . 51) (:id . 53))\n ((:tag . "VB") (:stem . "build") (:form . "build") (:end . 63) (:start . 58)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 70) (:start . 66)\n  (:id . 56))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 76) (:start . 71)\n  (:id . 57))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 82) (:start . 77)\n  (:id . 58))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 95)\n  (:start . 83) (:id . 59))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 99) (:start . 96)\n  (:id . 60))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 104) (:start . 100)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 108) (:start . 105)\n  (:id . 62))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 114)\n  (:start . 109) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 116) (:start . 115)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n  (:id . 65))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 129)\n  (:start . 120) (:id . 66))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 132) (:start . 130)\n  (:id . 67))\n ((:tag . "VBP") (:stem . "cannot") (:form . "cannot") (:end . 139)\n  (:start . 133) (:id . 68))\n ((:tag . "VB") (:stem . "build") (:form . "build") (:end . 145)\n  (:start . 140) (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 147) (:start . 146)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "lm-specific") (:form . "LM-specific") (:end . 159)\n  (:start . 148) (:id . 71))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 169)\n  (:start . 160) (:id . 72))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 176)\n  (:start . 170) (:id . 73))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 180) (:start . 177)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 181) (:start . 180)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n  (:id . 76))\n ((:tag . "VBP") (:stem . "compare") (:form . "compare") (:end . 193)\n  (:start . 186) (:id . 77))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 196) (:start . 194)\n  (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 199) (:start . 197)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n  (:id . 80))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 217)\n  (:start . 204) (:id . 81))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 224)\n  (:start . 218) (:id . 82))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 230)\n  (:start . 225) (:id . 83))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 236)\n  (:start . 231) (:id . 84))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 249)\n  (:start . 237) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 250) (:start . 249)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s13.101) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504314@unknown@formal@none@1@S@However, we built, and displayed in the ELM web server output page, LM-specific random score distributions (as described in Methods) in order to use them as background score contexts, telling the users something about the average behavior (in terms of accessibility, secondary structure and combined scores), on a large dataset of structures, of each single LM.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "build") (:form . "built") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "display") (:form . "displayed") (:end . 32)\n  (:start . 23) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 54)\n  (:start . 48) (:id . 53))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 61)\n  (:start . 55) (:id . 54))\n ((:tag . "NN") (:stem . "page") (:form . "page") (:end . 66) (:start . 62)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "lm-specific") (:form . "LM-specific") (:end . 79)\n  (:start . 68) (:id . 57))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 86)\n  (:start . 80) (:id . 58))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 92) (:start . 87)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 106) (:start . 93) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 120)\n  (:start . 111) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 131)\n  (:start . 124) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 135) (:start . 133)\n  (:id . 67))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 141)\n  (:start . 136) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 144) (:start . 142)\n  (:id . 69))\n ((:tag . "VB") (:stem . "use") (:form . "use") (:end . 148) (:start . 145)\n  (:id . 70))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 153) (:start . 149)\n  (:id . 71))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 156) (:start . 154)\n  (:id . 72))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 167)\n  (:start . 157) (:id . 73))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 173)\n  (:start . 168) (:id . 74))\n ((:tag . "NNS") (:stem . "context") (:form . "contexts") (:end . 182)\n  (:start . 174) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 76))\n ((:tag . "VBG") (:stem . "tell") (:form . "telling") (:end . 191)\n  (:start . 184) (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 195) (:start . 192)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 201)\n  (:start . 196) (:id . 79))\n ((:tag . "NN") (:stem . "something") (:form . "something") (:end . 211)\n  (:start . 202) (:id . 80))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 217)\n  (:start . 212) (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 221) (:start . 218)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 229)\n  (:start . 222) (:id . 83))\n ((:tag . "NN") (:stem . "behavior") (:form . "behavior") (:end . 238)\n  (:start . 230) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 240) (:start . 239)\n  (:id . 85))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 242) (:start . 240)\n  (:id . 86))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 248)\n  (:start . 243) (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 251) (:start . 249)\n  (:id . 88))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 265) (:start . 252) (:id . 89))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 266) (:start . 265)\n  (:id . 90))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 276)\n  (:start . 267) (:id . 91))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 286)\n  (:start . 277) (:id . 92))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 290) (:start . 287)\n  (:id . 93))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 299)\n  (:start . 291) (:id . 94))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 306)\n  (:start . 300) (:id . 95))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 307) (:start . 306)\n  (:id . 96))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 308) (:start . 307)\n  (:id . 97))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 311) (:start . 309)\n  (:id . 98))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 313) (:start . 312)\n  (:id . 99))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 319)\n  (:start . 314) (:id . 100))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 327)\n  (:start . 320) (:id . 101))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 330) (:start . 328)\n  (:id . 102))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 341)\n  (:start . 331) (:id . 103))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 342) (:start . 341)\n  (:id . 104))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 345) (:start . 343)\n  (:id . 105))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 350) (:start . 346)\n  (:id . 106))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 357)\n  (:start . 351) (:id . 107))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 360) (:start . 358)\n  (:id . 108))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 361) (:start . 360)\n  (:id . 109)))@@@1@68@((:identifiers (:sid . :s13.102) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504315@unknown@formal@none@1@S@These background distributions are only intended as a supplementary guideline for the web users to evaluate whether or not the score assigned to a LM match is reasonably higher than the random match score average for that LM.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 30) (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 34) (:start . 31)\n  (:id . 45))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "intended") (:form . "intended") (:end . 48)\n  (:start . 40) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 51) (:start . 49)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 67) (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "guideline") (:form . "guideline") (:end . 77)\n  (:start . 68) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 81) (:start . 78)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 53))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 89) (:start . 86)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 95) (:start . 90)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n  (:id . 56))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 107)\n  (:start . 99) (:id . 57))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 115)\n  (:start . 108) (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 118) (:start . 116)\n  (:id . 59))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 122) (:start . 119)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 132)\n  (:start . 127) (:id . 62))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 141)\n  (:start . 133) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 146) (:start . 145)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 149) (:start . 147)\n  (:id . 66))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 155)\n  (:start . 150) (:id . 67))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 158) (:start . 156)\n  (:id . 68))\n ((:tag . "RB") (:stem . "reasonably") (:form . "reasonably") (:end . 169)\n  (:start . 159) (:id . 69))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 176)\n  (:start . 170) (:id . 70))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 181) (:start . 177)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 185) (:start . 182)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 192)\n  (:start . 186) (:id . 73))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 198)\n  (:start . 193) (:id . 74))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 204)\n  (:start . 199) (:id . 75))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 212)\n  (:start . 205) (:id . 76))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 216) (:start . 213)\n  (:id . 77))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 221) (:start . 217)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 224) (:start . 222)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 80)))@@@1@39@((:hcues ((:id . :x13.103.1) (:span 108 122)))\n (:hscopes ((:id . :x13.103.1) (:span 108 224)))\n (:identifiers (:sid . :s13.103) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504316@unknown@formal@none@1@S@The background score distributions for 103/112 motifs are shown in the additional file 4 (Figure S3).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 34) (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "CD") (:stem . "103/112") (:form . "103/112") (:end . 46)\n  (:start . 39) (:id . 47))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 53)\n  (:start . 47) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 57) (:start . 54)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 63) (:start . 58)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 81)\n  (:start . 71) (:id . 53))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 96)\n  (:start . 90) (:id . 57))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s13.104) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504317@unknown@formal@none@1@S@Correspondences between x-axis labels and ELM names are reported in the additional file 5@(((:tag . "NNS") (:stem . "correspondence") (:form . "Correspondences")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 23)\n  (:start . 16) (:id . 43))\n ((:tag . "JJ") (:stem . "x-axis") (:form . "x-axis") (:end . 30)\n  (:start . 24) (:id . 44))\n ((:tag . "NNS") (:stem . "label") (:form . "labels") (:end . 37)\n  (:start . 31) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 45) (:start . 42)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "name") (:form . "names") (:end . 51) (:start . 46)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 82)\n  (:start . 72) (:id . 53))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 87) (:start . 83)\n  (:id . 54))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 89) (:start . 88)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s13.105) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504318@unknown@formal@none@1@S@We chose two score thresholds for each score type aimed at defining three score intervals (or "bins"), one "sparse", lacking in true motifs and enriched in random matches, one identifying "neutral" matches, and one lacking in random matches and enriched in true motifs.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "aim") (:form . "aimed") (:end . 55) (:start . 50)\n  (:id . 51))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "define") (:form . "defining") (:end . 67)\n  (:start . 59) (:id . 53))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 79) (:start . 74)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 89)\n  (:start . 80) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 99) (:start . 95)\n  (:id . 60))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 100) (:start . 99)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 63))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 106) (:start . 103)\n  (:id . 64))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 108) (:start . 107)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 114)\n  (:start . 108) (:id . 66))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 115) (:start . 114)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "lack") (:form . "lacking") (:end . 124)\n  (:start . 117) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 127) (:start . 125)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 132) (:start . 128)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 139)\n  (:start . 133) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 152)\n  (:start . 144) (:id . 74))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 155) (:start . 153)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 162)\n  (:start . 156) (:id . 76))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 170)\n  (:start . 163) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 78))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 175) (:start . 172)\n  (:id . 79))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 187)\n  (:start . 176) (:id . 80))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 189) (:start . 188)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "neutral") (:form . "neutral") (:end . 196)\n  (:start . 189) (:id . 82))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 197) (:start . 196)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 205)\n  (:start . 198) (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 206) (:start . 205)\n  (:id . 85))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 210) (:start . 207)\n  (:id . 86))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 214) (:start . 211)\n  (:id . 87))\n ((:tag . "NN") (:stem . "lacking") (:form . "lacking") (:end . 222)\n  (:start . 215) (:id . 88))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 225) (:start . 223)\n  (:id . 89))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 232)\n  (:start . 226) (:id . 90))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 240)\n  (:start . 233) (:id . 91))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 244) (:start . 241)\n  (:id . 92))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 253)\n  (:start . 245) (:id . 93))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 256) (:start . 254)\n  (:id . 94))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 261) (:start . 257)\n  (:id . 95))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 268)\n  (:start . 262) (:id . 96))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 269) (:start . 268)\n  (:id . 97)))@@@1@56@((:identifiers (:sid . :s13.106) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504319@unknown@formal@none@1@S@We consider that such a three-interval scheme might effectively help the user in deciding whether to retain or reject a prediction.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "three-interval") (:form . "three-interval")\n  (:end . 38) (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 51) (:start . 46)\n  (:id . 49))\n ((:tag . "RB") (:stem . "effectively") (:form . "effectively") (:end . 63)\n  (:start . 52) (:id . 50))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 77) (:start . 73)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "decide") (:form . "deciding") (:end . 89)\n  (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 97)\n  (:start . 90) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 57))\n ((:tag . "VB") (:stem . "retain") (:form . "retain") (:end . 107)\n  (:start . 101) (:id . 58))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . "VB") (:stem . "reject") (:form . "reject") (:end . 117)\n  (:start . 111) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 119) (:start . 118)\n  (:id . 61))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 130)\n  (:start . 120) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 63)))@@@1@22@((:hcues ((:id . :x13.107.1) (:span 108 110))\n  ((:id . :x13.107.2) (:span 90 97)) ((:id . :x13.107.3) (:span 46 51)))\n (:hscopes ((:id . :x13.107.1) (:span 101 117))\n  ((:id . :x13.107.2) (:span 90 130)) ((:id . :x13.107.3) (:span 46 130)))\n (:identifiers (:sid . :s13.107) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504320@unknown@formal@none@1@S@In fact it is based on the idea that a predicted match that is assigned a score in the "enriched" interval will be indicated by our procedure as a good true motif candidate (i.e. likely to be a valid functional site), motif matches scoring in the bottom interval ("sparse" interval) as unlikely to be valid functional sites and those ranking in the middle one as "neutral".@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 19) (:start . 14)\n  (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 22) (:start . 20)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 48))\n ((:tag . "NN") (:stem . "idea") (:form . "idea") (:end . 31) (:start . 27)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 48)\n  (:start . 39) (:id . 52))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 54) (:start . 49)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 59) (:start . 55)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 62) (:start . 60)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 71)\n  (:start . 63) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 79) (:start . 74)\n  (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 60))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 88) (:start . 87)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "enriched") (:form . "enriched") (:end . 96)\n  (:start . 88) (:id . 62))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 97) (:start . 96)\n  (:id . 63))\n ((:tag . "NN") (:stem . "interval") (:form . "interval") (:end . 106)\n  (:start . 98) (:id . 64))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 111) (:start . 107)\n  (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 114) (:start . 112)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "indicate") (:form . "indicated") (:end . 124)\n  (:start . 115) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 127) (:start . 125)\n  (:id . 68))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 131) (:start . 128)\n  (:id . 69))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 141)\n  (:start . 132) (:id . 70))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 144) (:start . 142)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 146) (:start . 145)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "good") (:form . "good") (:end . 151) (:start . 147)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 156) (:start . 152)\n  (:id . 74))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 162)\n  (:start . 157) (:id . 75))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 172)\n  (:start . 163) (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 174) (:start . 173)\n  (:id . 77))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 178) (:start . 174)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 185)\n  (:start . 179) (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 188) (:start . 186)\n  (:id . 80))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 191) (:start . 189)\n  (:id . 81))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 193) (:start . 192)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "valid") (:form . "valid") (:end . 199)\n  (:start . 194) (:id . 83))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 210)\n  (:start . 200) (:id . 84))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 215) (:start . 211)\n  (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 216) (:start . 215)\n  (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 217) (:start . 216)\n  (:id . 87))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 223)\n  (:start . 218) (:id . 88))\n ((:tag . "VBZ") (:stem . "match") (:form . "matches") (:end . 231)\n  (:start . 224) (:id . 89))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 239)\n  (:start . 232) (:id . 90))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 242) (:start . 240)\n  (:id . 91))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 246) (:start . 243)\n  (:id . 92))\n ((:tag . "NN") (:stem . "bottom") (:form . "bottom") (:end . 253)\n  (:start . 247) (:id . 93))\n ((:tag . "NN") (:stem . "interval") (:form . "interval") (:end . 262)\n  (:start . 254) (:id . 94))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 264) (:start . 263)\n  (:id . 95))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 265) (:start . 264)\n  (:id . 96))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 271)\n  (:start . 265) (:id . 97))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 272) (:start . 271)\n  (:id . 98))\n ((:tag . "NN") (:stem . "interval") (:form . "interval") (:end . 281)\n  (:start . 273) (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 282) (:start . 281)\n  (:id . 100))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 285) (:start . 283)\n  (:id . 101))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 294)\n  (:start . 286) (:id . 102))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 297) (:start . 295)\n  (:id . 103))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 300) (:start . 298)\n  (:id . 104))\n ((:tag . "JJ") (:stem . "valid") (:form . "valid") (:end . 306)\n  (:start . 301) (:id . 105))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 317)\n  (:start . 307) (:id . 106))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 323)\n  (:start . 318) (:id . 107))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 327) (:start . 324)\n  (:id . 108))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 333)\n  (:start . 328) (:id . 109))\n ((:tag . "VBG") (:stem . "rank") (:form . "ranking") (:end . 341)\n  (:start . 334) (:id . 110))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 344) (:start . 342)\n  (:id . 111))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 348) (:start . 345)\n  (:id . 112))\n ((:tag . "JJ") (:stem . "middle") (:form . "middle") (:end . 355)\n  (:start . 349) (:id . 113))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 359) (:start . 356)\n  (:id . 114))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 362) (:start . 360)\n  (:id . 115))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 364) (:start . 363)\n  (:id . 116))\n ((:tag . "JJ") (:stem . "neutral") (:form . "neutral") (:end . 371)\n  (:start . 364) (:id . 117))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 372) (:start . 371)\n  (:id . 118))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 373) (:start . 372)\n  (:id . 119)))@@@1@78@((:hcues ((:id . :x13.108.1) (:span 286 294))\n  ((:id . :x13.108.2) (:span 179 185)))\n (:hscopes ((:id . :x13.108.1) (:span 286 323))\n  ((:id . :x13.108.2) (:span 179 215)))\n (:identifiers (:sid . :s13.108) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504321@unknown@formal@none@1@S@The score thresholds were chosen on the basis of the cumulative distributions of Figure 4 by selecting two cut-offs (one in the percentile range 0-50% and one in the percentile range 50%-100%), roughly corresponding to the inflection points of the random match cumulative distributions, and guaranteeing that at least the top 30% true motifs are retained in the enriched bin and at least the lower 40% random matches fall in the sparse bin.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 32)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "basis") (:form . "basis") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "cumulative") (:form . "cumulative") (:end . 63)\n  (:start . 53) (:id . 52))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 77) (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 89) (:start . 88)\n  (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "select") (:form . "selecting") (:end . 102)\n  (:start . 93) (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "cut-off") (:form . "cut-offs") (:end . 115)\n  (:start . 107) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 120) (:start . 117)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "NN") (:stem . "percentile") (:form . "percentile") (:end . 138)\n  (:start . 128) (:id . 65))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 144)\n  (:start . 139) (:id . 66))\n ((:tag . "CD") (:stem . "0-50") (:form . "0-50") (:end . 149) (:start . 145)\n  (:id . 67))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 150) (:start . 149)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 69))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 158) (:start . 155)\n  (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 161) (:start . 159)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 72))\n ((:tag . "NN") (:stem . "percentile") (:form . "percentile") (:end . 176)\n  (:start . 166) (:id . 73))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 182)\n  (:start . 177) (:id . 74))\n ((:tag . "CD") (:stem . "50%-100") (:form . "50%-100") (:end . 190)\n  (:start . 183) (:id . 75))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 191) (:start . 190)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 192) (:start . 191)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 193) (:start . 192)\n  (:id . 78))\n ((:tag . "RB") (:stem . "roughly") (:form . "roughly") (:end . 201)\n  (:start . 194) (:id . 79))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 215)\n  (:start . 202) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 218) (:start . 216)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 222) (:start . 219)\n  (:id . 82))\n ((:tag . "NN") (:stem . "inflection") (:form . "inflection") (:end . 233)\n  (:start . 223) (:id . 83))\n ((:tag . "NNS") (:stem . "point") (:form . "points") (:end . 240)\n  (:start . 234) (:id . 84))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 243) (:start . 241)\n  (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 247) (:start . 244)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 254)\n  (:start . 248) (:id . 87))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 260)\n  (:start . 255) (:id . 88))\n ((:tag . "JJ") (:stem . "cumulative") (:form . "cumulative") (:end . 271)\n  (:start . 261) (:id . 89))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 285) (:start . 272) (:id . 90))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 286) (:start . 285)\n  (:id . 91))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 290) (:start . 287)\n  (:id . 92))\n ((:tag . "VBG") (:stem . "guarantee") (:form . "guaranteeing") (:end . 303)\n  (:start . 291) (:id . 93))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 308) (:start . 304)\n  (:id . 94))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 311) (:start . 309)\n  (:id . 95))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 317)\n  (:start . 312) (:id . 96))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 321) (:start . 318)\n  (:id . 97))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 325) (:start . 322)\n  (:id . 98))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 328) (:start . 326)\n  (:id . 99))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 329) (:start . 328)\n  (:id . 100))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 334) (:start . 330)\n  (:id . 101))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 341)\n  (:start . 335) (:id . 102))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 345) (:start . 342)\n  (:id . 103))\n ((:tag . "VBN") (:stem . "retain") (:form . "retained") (:end . 354)\n  (:start . 346) (:id . 104))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 357) (:start . 355)\n  (:id . 105))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 361) (:start . 358)\n  (:id . 106))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 370)\n  (:start . 362) (:id . 107))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 374) (:start . 371)\n  (:id . 108))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 378) (:start . 375)\n  (:id . 109))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 381) (:start . 379)\n  (:id . 110))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 387)\n  (:start . 382) (:id . 111))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 391) (:start . 388)\n  (:id . 112))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 397) (:start . 392)\n  (:id . 113))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 400) (:start . 398)\n  (:id . 114))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 401) (:start . 400)\n  (:id . 115))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 408)\n  (:start . 402) (:id . 116))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 416)\n  (:start . 409) (:id . 117))\n ((:tag . "VBP") (:stem . "fall") (:form . "fall") (:end . 421) (:start . 417)\n  (:id . 118))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 424) (:start . 422)\n  (:id . 119))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 428) (:start . 425)\n  (:id . 120))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 435)\n  (:start . 429) (:id . 121))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 439) (:start . 436)\n  (:id . 122))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 440) (:start . 439)\n  (:id . 123)))@@@1@82@((:identifiers (:sid . :s13.109) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504322@unknown@formal@none@1@S@The "neutral" bin is delimited by the "sparse" and "enriched" cut-offs and contains the medium quality matches.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "neutral") (:form . "neutral") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 17) (:start . 14)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "delimit") (:form . "delimited") (:end . 30)\n  (:start . 21) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 50))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 39) (:start . 38)\n  (:id . 51))\n ((:tag . "NN") (:stem . "sparse") (:form . "sparse") (:end . 45)\n  (:start . 39) (:id . 52))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 46) (:start . 45)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 54))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 52) (:start . 51)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 60)\n  (:start . 52) (:id . 56))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 61) (:start . 60)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "cut-off") (:form . "cut-offs") (:end . 70)\n  (:start . 62) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 83)\n  (:start . 75) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 61))\n ((:tag . "NN") (:stem . "medium") (:form . "medium") (:end . 94)\n  (:start . 88) (:id . 62))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 102)\n  (:start . 95) (:id . 63))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 110)\n  (:start . 103) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s13.110) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504323@unknown@formal@none@1@S@Table 2 reports Qacc, Qsse and Qand thresholds defining the three bins.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "NNP") (:stem . "Qacc") (:form . "Qacc") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Qand") (:form . "Qand") (:end . 35) (:start . 31)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 46)\n  (:start . 36) (:id . 50))\n ((:tag . "VBG") (:stem . "define") (:form . "defining") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s13.111) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504324@unknown@formal@none@1@S@From Figure 4 and Table 3, it can be seen that, in the case of the accessibility score (Figure 4a), the cut-off on the top 30% of true motifs implies that only 10% of random matches are retained in the enriched bin and that the cut-off on the lower 40% random matches implies that only 15% true motifs incorrectly fall in the "sparse" bin.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 11)\n  (:start . 5) (:id . 43))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 29) (:start . 27)\n  (:id . 49))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 33) (:start . 30)\n  (:id . 50))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 36) (:start . 34)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 41) (:start . 37)\n  (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 46) (:start . 42)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 56))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 59) (:start . 55)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 59))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 80) (:start . 67) (:id . 60))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 86) (:start . 81)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 94)\n  (:start . 88) (:id . 63))\n ((:tag . "NN") (:stem . "4a") (:form . "4a") (:end . 97) (:start . 95)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 67))\n ((:tag . "NN") (:stem . "cut-off") (:form . "cut-off") (:end . 111)\n  (:start . 104) (:id . 68))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 114) (:start . 112)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 122) (:start . 119)\n  (:id . 71))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 125) (:start . 123)\n  (:id . 72))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 126) (:start . 125)\n  (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 134) (:start . 130)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 141)\n  (:start . 135) (:id . 76))\n ((:tag . "VBZ") (:stem . "imply") (:form . "implies") (:end . 149)\n  (:start . 142) (:id . 77))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 154) (:start . 150)\n  (:id . 78))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 159) (:start . 155)\n  (:id . 79))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 162) (:start . 160)\n  (:id . 80))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 163) (:start . 162)\n  (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 166) (:start . 164)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 173)\n  (:start . 167) (:id . 83))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 181)\n  (:start . 174) (:id . 84))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 185) (:start . 182)\n  (:id . 85))\n ((:tag . "VBN") (:stem . "retain") (:form . "retained") (:end . 194)\n  (:start . 186) (:id . 86))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 197) (:start . 195)\n  (:id . 87))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 201) (:start . 198)\n  (:id . 88))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 210)\n  (:start . 202) (:id . 89))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 214) (:start . 211)\n  (:id . 90))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 218) (:start . 215)\n  (:id . 91))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 223) (:start . 219)\n  (:id . 92))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 227) (:start . 224)\n  (:id . 93))\n ((:tag . "NN") (:stem . "cut-off") (:form . "cut-off") (:end . 235)\n  (:start . 228) (:id . 94))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 238) (:start . 236)\n  (:id . 95))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 242) (:start . 239)\n  (:id . 96))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 248) (:start . 243)\n  (:id . 97))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 251) (:start . 249)\n  (:id . 98))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 252) (:start . 251)\n  (:id . 99))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 259)\n  (:start . 253) (:id . 100))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 267)\n  (:start . 260) (:id . 101))\n ((:tag . "VBZ") (:stem . "imply") (:form . "implies") (:end . 275)\n  (:start . 268) (:id . 102))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 280) (:start . 276)\n  (:id . 103))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 285) (:start . 281)\n  (:id . 104))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 288) (:start . 286)\n  (:id . 105))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 289) (:start . 288)\n  (:id . 106))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 294) (:start . 290)\n  (:id . 107))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 301)\n  (:start . 295) (:id . 108))\n ((:tag . "RB") (:stem . "incorrectly") (:form . "incorrectly") (:end . 313)\n  (:start . 302) (:id . 109))\n ((:tag . "VBP") (:stem . "fall") (:form . "fall") (:end . 318) (:start . 314)\n  (:id . 110))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 321) (:start . 319)\n  (:id . 111))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 325) (:start . 322)\n  (:id . 112))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 327) (:start . 326)\n  (:id . 113))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 333)\n  (:start . 327) (:id . 114))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 334) (:start . 333)\n  (:id . 115))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 338) (:start . 335)\n  (:id . 116))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 339) (:start . 338)\n  (:id . 117)))@@@1@76@((:hcues ((:id . :x13.112.1) (:span 268 275))\n  ((:id . :x13.112.2) (:span 142 149)))\n (:hscopes ((:id . :x13.112.1) (:span 268 338))\n  ((:id . :x13.112.2) (:span 142 214)))\n (:identifiers (:sid . :s13.112) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504325@unknown@formal@none@1@S@In contrast, Qsse thresholds (Figure 4b) actually assign about the top 60% true motifs and 32% random matches to the enriched bin (see Table 3).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Qsse") (:form . "Qsse") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "NN") (:stem . "4b") (:form . "4b") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "RB") (:stem . "actually") (:form . "actually") (:end . 49)\n  (:start . 41) (:id . 51))\n ((:tag . "VBP") (:stem . "assign") (:form . "assign") (:end . 56)\n  (:start . 50) (:id . 52))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 62) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 74) (:start . 73)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 79) (:start . 75)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 86)\n  (:start . 80) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 60))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 93) (:start . 91)\n  (:id . 61))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 94) (:start . 93)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 101)\n  (:start . 95) (:id . 63))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 109)\n  (:start . 102) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 112) (:start . 110)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 125)\n  (:start . 117) (:id . 67))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 129) (:start . 126)\n  (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 69))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 134) (:start . 131)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 140)\n  (:start . 135) (:id . 71))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 142) (:start . 141)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s13.113) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504326@unknown@formal@none@1@S@This is due to the fact that the top 60% true motifs (and 32% random matches) uniformly get the highest score.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "IN") (:stem . "due") (:form . "due") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 23) (:start . 19)\n  (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 36) (:start . 33)\n  (:id . 50))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 39) (:start . 37)\n  (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 40) (:start . 39)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 45) (:start . 41)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 52)\n  (:start . 46) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 56))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 60) (:start . 58)\n  (:id . 57))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 61) (:start . 60)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 68)\n  (:start . 62) (:id . 59))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 76)\n  (:start . 69) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 77) (:start . 76)\n  (:id . 61))\n ((:tag . "RB") (:stem . "uniformly") (:form . "uniformly") (:end . 87)\n  (:start . 78) (:id . 62))\n ((:tag . "VB") (:stem . "get") (:form . "get") (:end . 91) (:start . 88)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 64))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 103)\n  (:start . 96) (:id . 65))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 109)\n  (:start . 104) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s13.114) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504327@unknown@formal@none@1@S@Finally, in the case of Qand (Figure 4c), only 9% random matches are retained in the enriched bin and only 16% of true motifs fall in the sparse bin (Table 3).@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Qand") (:form . "Qand") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 36)\n  (:start . 30) (:id . 50))\n ((:tag . "NN") (:stem . "4c") (:form . "4c") (:end . 39) (:start . 37)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 40) (:start . 39)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 53))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 46) (:start . 42)\n  (:id . 54))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 48) (:start . 47)\n  (:id . 55))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 49) (:start . 48)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 56)\n  (:start . 50) (:id . 57))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 64)\n  (:start . 57) (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 68) (:start . 65)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "retain") (:form . "retained") (:end . 77)\n  (:start . 69) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 93)\n  (:start . 85) (:id . 63))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 97) (:start . 94)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 65))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 106) (:start . 102)\n  (:id . 66))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 109) (:start . 107)\n  (:id . 67))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 110) (:start . 109)\n  (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 118) (:start . 114)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 125)\n  (:start . 119) (:id . 71))\n ((:tag . "VBP") (:stem . "fall") (:form . "fall") (:end . 130) (:start . 126)\n  (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 133) (:start . 131)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 144)\n  (:start . 138) (:id . 75))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 148) (:start . 145)\n  (:id . 76))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 155)\n  (:start . 150) (:id . 78))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 157) (:start . 156)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s13.115) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504328@unknown@formal@none@1@S@This gives to the users a measure of the percentage of false hits that they can expect in the enriched bin and of the percentage of true hits that they would miss if discarding all the predictions falling in the sparse interval.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "give") (:form . "gives") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "measure") (:form . "measure") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 51)\n  (:start . 41) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 60) (:start . 55)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 70) (:start . 66)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 79) (:start . 76)\n  (:id . 57))\n ((:tag . "VB") (:stem . "expect") (:form . "expect") (:end . 86)\n  (:start . 80) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 102)\n  (:start . 94) (:id . 61))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 106) (:start . 103)\n  (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 65))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 128)\n  (:start . 118) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 131) (:start . 129)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 136) (:start . 132)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 141) (:start . 137)\n  (:id . 69))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 146) (:start . 142)\n  (:id . 70))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 151) (:start . 147)\n  (:id . 71))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 157)\n  (:start . 152) (:id . 72))\n ((:tag . "VB") (:stem . "miss") (:form . "miss") (:end . 162) (:start . 158)\n  (:id . 73))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 165) (:start . 163)\n  (:id . 74))\n ((:tag . "VBG") (:stem . "discard") (:form . "discarding") (:end . 176)\n  (:start . 166) (:id . 75))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 180) (:start . 177)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 184) (:start . 181)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 196)\n  (:start . 185) (:id . 78))\n ((:tag . "VBG") (:stem . "fall") (:form . "falling") (:end . 204)\n  (:start . 197) (:id . 79))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 207) (:start . 205)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 211) (:start . 208)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 218)\n  (:start . 212) (:id . 82))\n ((:tag . "NN") (:stem . "interval") (:form . "interval") (:end . 227)\n  (:start . 219) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x13.116.1) (:span 152 157)))\n (:hscopes ((:id . :x13.116.1) (:span 152 227)))\n (:identifiers (:sid . :s13.116) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504329@unknown@formal@none@1@S@Score thresholds defining the "sparse", "neutral" and "enriched" bins@(((:tag . "NN") (:stem . "score") (:form . "Score") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "VBG") (:stem . "define") (:form . "defining") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 31) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sparse") (:form . "sparse") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "neutral") (:form . "neutral") (:end . 48)\n  (:start . 41) (:id . 51))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 53))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 55) (:start . 54)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 63)\n  (:start . 55) (:id . 55))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 64) (:start . 63)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 69) (:start . 65)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s13.117) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504330@unknown@formal@none@1@S@Number and percentage of true and random motifs assigned to each bin by the different score types@(((:tag . "NN") (:stem . "number") (:form . "Number") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 56)\n  (:start . 48) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 51))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 64) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 68) (:start . 65)\n  (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 85)\n  (:start . 76) (:id . 56))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 91) (:start . 86)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 97) (:start . 92)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s13.118) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504331@unknown@formal@none@1@S@In order to establish more rigorously the predictive ability of the structure filter in the enriched and sparse intervals, we carried out a 5-fold cross validation experiment.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "establish") (:form . "establish") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "RB") (:stem . "rigorously") (:form . "rigorously") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "predictive") (:form . "predictive") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 77)\n  (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 84)\n  (:start . 78) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 100)\n  (:start . 92) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 111)\n  (:start . 105) (:id . 59))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 121)\n  (:start . 112) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 61))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 125) (:start . 123)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "carry") (:form . "carried") (:end . 133)\n  (:start . 126) (:id . 63))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 137) (:start . 134)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 139) (:start . 138)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "5-fold") (:form . "5-fold") (:end . 146)\n  (:start . 140) (:id . 66))\n ((:tag . "NN") (:stem . "cross") (:form . "cross") (:end . 152)\n  (:start . 147) (:id . 67))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 163)\n  (:start . 153) (:id . 68))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 174)\n  (:start . 164) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s13.119) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504332@unknown@formal@none@1@S@Referring to score calibration and within the limits of the 5-fold cross validation experiment only, we defined two intervals instead of the three implemented in the ELM Web Server, by incorporating the neutral interval first into the enriched one and then into the sparse one.@(((:tag . "VBG") (:stem . "refer") (:form . "Referring") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "calibration") (:form . "calibration") (:end . 30)\n  (:start . 19) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 41)\n  (:start . 35) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "limit") (:form . "limits") (:end . 52)\n  (:start . 46) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "5-fold") (:form . "5-fold") (:end . 66)\n  (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "cross") (:form . "cross") (:end . 72) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 83)\n  (:start . 73) (:id . 54))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 94)\n  (:start . 84) (:id . 55))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 103) (:start . 101)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "define") (:form . "defined") (:end . 111)\n  (:start . 104) (:id . 59))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 115) (:start . 112)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 125)\n  (:start . 116) (:id . 61))\n ((:tag . "RB") (:stem . "instead") (:form . "instead") (:end . 133)\n  (:start . 126) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 64))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 146)\n  (:start . 141) (:id . 65))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 158)\n  (:start . 147) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 161) (:start . 159)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 169) (:start . 166)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 173) (:start . 170)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Server") (:form . "Server") (:end . 180)\n  (:start . 174) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 181) (:start . 180)\n  (:id . 72))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 184) (:start . 182)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "incorporate") (:form . "incorporating")\n  (:end . 198) (:start . 185) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 202) (:start . 199)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "neutral") (:form . "neutral") (:end . 210)\n  (:start . 203) (:id . 76))\n ((:tag . "NN") (:stem . "interval") (:form . "interval") (:end . 219)\n  (:start . 211) (:id . 77))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 225)\n  (:start . 220) (:id . 78))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 230) (:start . 226)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 234) (:start . 231)\n  (:id . 80))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 243)\n  (:start . 235) (:id . 81))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 247) (:start . 244)\n  (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 251) (:start . 248)\n  (:id . 83))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 256) (:start . 252)\n  (:id . 84))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 261) (:start . 257)\n  (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 265) (:start . 262)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 272)\n  (:start . 266) (:id . 87))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 276) (:start . 273)\n  (:id . 88))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 277) (:start . 276)\n  (:id . 89)))@@@1@48@((:identifiers (:sid . :s13.120) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504333@unknown@formal@none@1@S@This made it possible to properly determine sensitivity and specificity values in two different situations: the first accounting for an enrichment of sensitivity and the second for an enrichment of specificity.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "make") (:form . "made") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "RB") (:stem . "properly") (:form . "properly") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "VB") (:stem . "determine") (:form . "determine") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 55)\n  (:start . 44) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 71)\n  (:start . 60) (:id . 51))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 78)\n  (:start . 72) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 53))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 95)\n  (:start . 86) (:id . 55))\n ((:tag . "NNS") (:stem . "situation") (:form . "situations") (:end . 106)\n  (:start . 96) (:id . 56))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 107) (:start . 106)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 117)\n  (:start . 112) (:id . 59))\n ((:tag . "NN") (:stem . "accounting") (:form . "accounting") (:end . 128)\n  (:start . 118) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 132) (:start . 129)\n  (:id . 61))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 135) (:start . 133)\n  (:id . 62))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 146)\n  (:start . 136) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 64))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 161)\n  (:start . 150) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 169) (:start . 166)\n  (:id . 67))\n ((:tag . "NN") (:stem . "second") (:form . "second") (:end . 176)\n  (:start . 170) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 180) (:start . 177)\n  (:id . 69))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 183) (:start . 181)\n  (:id . 70))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 194)\n  (:start . 184) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 197) (:start . 195)\n  (:id . 72))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 209)\n  (:start . 198) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s13.121) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504334@unknown@formal@none@1@S@We defined the positive dataset as the one made up of the ELM true instances and the negative dataset as the set of all the un-annotated random matches.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "define") (:form . "defined") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "one") (:form . "one") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "make") (:form . "made") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 61) (:start . 58)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 66) (:start . 62)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 76)\n  (:start . 67) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 93)\n  (:start . 85) (:id . 59))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 101)\n  (:start . 94) (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 104) (:start . 102)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 62))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 112) (:start . 109)\n  (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 64))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 119) (:start . 116)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "un-annotated") (:form . "un-annotated") (:end . 136)\n  (:start . 124) (:id . 67))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 143)\n  (:start . 137) (:id . 68))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 151)\n  (:start . 144) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s13.122) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504335@unknown@formal@none@1@S@We split both the positive and the negative datasets into five subsets by random sampling the datasets without replacement, thus obtaining five non-overlapping positive and five non-overlapping negative training sets.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "split") (:form . "split") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 43)\n  (:start . 35) (:id . 49))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 52)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "subset") (:form . "subsets") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "random") (:form . "random") (:end . 80)\n  (:start . 74) (:id . 55))\n ((:tag . "VBG") (:stem . "sample") (:form . "sampling") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 102)\n  (:start . 94) (:id . 58))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 110)\n  (:start . 103) (:id . 59))\n ((:tag . "NN") (:stem . "replacement") (:form . "replacement") (:end . 122)\n  (:start . 111) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 61))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 128) (:start . 124)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "obtain") (:form . "obtaining") (:end . 138)\n  (:start . 129) (:id . 63))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 143) (:start . 139)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "non-overlapping") (:form . "non-overlapping")\n  (:end . 159) (:start . 144) (:id . 65))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 168)\n  (:start . 160) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 172) (:start . 169)\n  (:id . 67))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 177) (:start . 173)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "non-overlapping") (:form . "non-overlapping")\n  (:end . 193) (:start . 178) (:id . 69))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 202)\n  (:start . 194) (:id . 70))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 211)\n  (:start . 203) (:id . 71))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 216) (:start . 212)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s13.123) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504336@unknown@formal@none@1@S@Five positive (negative) test sets were determined by depriving cyclically the whole positive (negative) dataset of each of the five positive (negative) training sets.@(((:tag . "CD") (:stem . "five") (:form . "Five") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 39) (:start . 35)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "determine") (:form . "determined") (:end . 50)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 53) (:start . 51)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "deprive") (:form . "depriving") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "RB") (:stem . "cyclically") (:form . "cyclically") (:end . 74)\n  (:start . 64) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 84) (:start . 79)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 93)\n  (:start . 85) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 103)\n  (:start . 95) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 112)\n  (:start . 105) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 61))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 120) (:start . 116)\n  (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 132) (:start . 128)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 141)\n  (:start . 133) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 151)\n  (:start . 143) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 69))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 161)\n  (:start . 153) (:id . 70))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 166) (:start . 162)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s13.124) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504337@unknown@formal@none@1@S@We built the scoring schemes as described in the section "The ELM structure filter scoring scheme" and set up score acceptance/rejection thresholds on the training sets as explained above (subsection "Sparse/neutral/enriched score intervals").@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "build") (:form . "built") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "scheme") (:form . "schemes") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 41)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 75)\n  (:start . 66) (:id . 55))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 82)\n  (:start . 76) (:id . 56))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 90)\n  (:start . 83) (:id . 57))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 97)\n  (:start . 91) (:id . 58))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . "VB") (:stem . "set") (:form . "set") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 115)\n  (:start . 110) (:id . 63))\n ((:tag . "NN") (:stem . "acceptance/rejection")\n  (:form . "acceptance/rejection") (:end . 136) (:start . 116) (:id . 64))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 147)\n  (:start . 137) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 150) (:start . 148)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 67))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 163)\n  (:start . 155) (:id . 68))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 168) (:start . 164)\n  (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 171) (:start . 169)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "explain") (:form . "explained") (:end . 181)\n  (:start . 172) (:id . 71))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 187)\n  (:start . 182) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n  (:id . 73))\n ((:tag . "NN") (:stem . "subsection") (:form . "subsection") (:end . 199)\n  (:start . 189) (:id . 74))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 201) (:start . 200)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "sparse/neutral/enriched")\n  (:form . "Sparse/neutral/enriched") (:end . 224) (:start . 201) (:id . 76))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 230)\n  (:start . 225) (:id . 77))\n ((:tag . "NNS") (:stem . "interval") (:form . "intervals") (:end . 240)\n  (:start . 231) (:id . 78))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 241) (:start . 240)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 242) (:start . 241)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s13.125) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504338@unknown@formal@none@1@S@Then, we validated them on the corresponding test sets by calculating sensitivity (Sn), specificity (Sp), and accuracy defined as:@(((:tag . "RB") (:stem . "then") (:form . "Then") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "validate") (:form . "validated") (:end . 18)\n  (:start . 9) (:id . 45))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 44)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 54) (:start . 50)\n  (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "calculate") (:form . "calculating") (:end . 69)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 81)\n  (:start . 70) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Sn") (:form . "Sn") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 99)\n  (:start . 88) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Sp") (:form . "Sp") (:end . 103) (:start . 101)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 64))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 118)\n  (:start . 110) (:id . 65))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 126)\n  (:start . 119) (:id . 66))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 129) (:start . 127)\n  (:id . 67))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 130) (:start . 129)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s13.126) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504339@unknown@formal@none@1@S@In evaluating Sn, Sp and Accuracy, we assumed that a match belonging to the negative set and scoring above the "accept" threshold, is a FP and one scoring below, is a TN; a true instance scoring above the "accept" threshold is a TP and one scoring below is a FN.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "evaluate") (:form . "evaluating") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "NNP") (:stem . "Sn") (:form . "Sn") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Sp") (:form . "Sp") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Accuracy") (:form . "Accuracy") (:end . 33)\n  (:start . 25) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 37) (:start . 35)\n  (:id . 50))\n ((:tag . "VBD") (:stem . "assume") (:form . "assumed") (:end . 45)\n  (:start . 38) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 50) (:start . 46)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 58) (:start . 53)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "belong") (:form . "belonging") (:end . 68)\n  (:start . 59) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 84)\n  (:start . 76) (:id . 58))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 88) (:start . 85)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 100)\n  (:start . 93) (:id . 61))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 106)\n  (:start . 101) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . "NN") (:stem . "accept") (:form . "accept") (:end . 118)\n  (:start . 112) (:id . 65))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 119) (:start . 118)\n  (:id . 66))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 129)\n  (:start . 120) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 133) (:start . 131)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 135) (:start . 134)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "FP") (:form . "FP") (:end . 138) (:start . 136)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 72))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 146) (:start . 143)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 154)\n  (:start . 147) (:id . 74))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 160)\n  (:start . 155) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 76))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 164) (:start . 162)\n  (:id . 77))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 166) (:start . 165)\n  (:id . 78))\n ((:tag . "NN") (:stem . "tn") (:form . "TN") (:end . 169) (:start . 167)\n  (:id . 79))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 170) (:start . 169)\n  (:id . 80))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 172) (:start . 171)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 177) (:start . 173)\n  (:id . 82))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 186)\n  (:start . 178) (:id . 83))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 194)\n  (:start . 187) (:id . 84))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 200)\n  (:start . 195) (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 204) (:start . 201)\n  (:id . 86))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 206) (:start . 205)\n  (:id . 87))\n ((:tag . "NN") (:stem . "accept") (:form . "accept") (:end . 212)\n  (:start . 206) (:id . 88))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 213) (:start . 212)\n  (:id . 89))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 223)\n  (:start . 214) (:id . 90))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 226) (:start . 224)\n  (:id . 91))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 228) (:start . 227)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "TP") (:form . "TP") (:end . 231) (:start . 229)\n  (:id . 93))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 235) (:start . 232)\n  (:id . 94))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 239) (:start . 236)\n  (:id . 95))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 247)\n  (:start . 240) (:id . 96))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 253)\n  (:start . 248) (:id . 97))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 256) (:start . 254)\n  (:id . 98))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 258) (:start . 257)\n  (:id . 99))\n ((:tag . "NN") (:stem . "fn") (:form . "FN") (:end . 261) (:start . 259)\n  (:id . 100))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 262) (:start . 261)\n  (:id . 101)))@@@1@60@((:hcues ((:id . :x13.127.1) (:span 38 45)))\n (:hscopes ((:id . :x13.127.1) (:span 38 261)))\n (:identifiers (:sid . :s13.127) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504340@unknown@formal@none@1@S@Sensitivity (Sn) and specificity (Sp) and accuracy averaged over the five sets are reported in Table 4.@(((:tag . "NN") (:stem . "sensitivity") (:form . "Sensitivity") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Sn") (:form . "Sn") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 32)\n  (:start . 21) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Sp") (:form . "Sp") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 51))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 50)\n  (:start . 42) (:id . 52))\n ((:tag . "VBD") (:stem . "average") (:form . "averaged") (:end . 59)\n  (:start . 51) (:id . 53))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 64) (:start . 60)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 73) (:start . 69)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "set") (:form . "sets") (:end . 78) (:start . 74)\n  (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 91)\n  (:start . 83) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 100) (:start . 95)\n  (:id . 61))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s13.128) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504341@unknown@formal@none@1@S@Since the structure filter is designed as a guide to experimentation, we consider that sensitivity should be privileged over specificity - for not missing too many true motifs.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "guide") (:form . "guide") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "experimentation") (:form . "experimentation")\n  (:end . 68) (:start . 53) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 98)\n  (:start . 87) (:id . 57))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 105)\n  (:start . 99) (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "privilege") (:form . "privileged") (:end . 119)\n  (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 124) (:start . 120)\n  (:id . 61))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 136)\n  (:start . 125) (:id . 62))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 138) (:start . 137)\n  (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 142) (:start . 139)\n  (:id . 64))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 146) (:start . 143)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "miss") (:form . "missing") (:end . 154)\n  (:start . 147) (:id . 66))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 158) (:start . 155)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 163) (:start . 159)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 168) (:start . 164)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 175)\n  (:start . 169) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x13.129.1) (:span 99 105)))\n (:hscopes ((:id . :x13.129.1) (:span 87 136)))\n (:identifiers (:sid . :s13.129) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504342@unknown@formal@none@1@S@Based on this viewpoint, it can be observed in Tables 3 (last column) and 4 that the best performing scoring schemes - in terms of a trade-off between sensitivity, specificity, the percentage of true motifs erroneously discarded and the percentage of true motifs correctly retained - are Qacc and Qand.@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "viewpoint") (:form . "viewpoint") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 43)\n  (:start . 35) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Tables") (:form . "Tables") (:end . 53)\n  (:start . 47) (:id . 52))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "last") (:form . "last") (:end . 61) (:start . 57)\n  (:id . 55))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 68)\n  (:start . 62) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 58))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 75) (:start . 74)\n  (:id . 59))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 80) (:start . 76)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 61))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 89) (:start . 85)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "perform") (:form . "performing") (:end . 100)\n  (:start . 90) (:id . 63))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 108)\n  (:start . 101) (:id . 64))\n ((:tag . "NNS") (:stem . "scheme") (:form . "schemes") (:end . 116)\n  (:start . 109) (:id . 65))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 118) (:start . 117)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 121) (:start . 119)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "term") (:form . "terms") (:end . 127)\n  (:start . 122) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 132) (:start . 131)\n  (:id . 70))\n ((:tag . "NN") (:stem . "trade-off") (:form . "trade-off") (:end . 142)\n  (:start . 133) (:id . 71))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 150)\n  (:start . 143) (:id . 72))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 162)\n  (:start . 151) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 163) (:start . 162)\n  (:id . 74))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 175)\n  (:start . 164) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 176) (:start . 175)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 180) (:start . 177)\n  (:id . 77))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 191)\n  (:start . 181) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 194) (:start . 192)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 199) (:start . 195)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 206)\n  (:start . 200) (:id . 81))\n ((:tag . "RB") (:stem . "erroneously") (:form . "erroneously") (:end . 218)\n  (:start . 207) (:id . 82))\n ((:tag . "VBN") (:stem . "discard") (:form . "discarded") (:end . 228)\n  (:start . 219) (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 232) (:start . 229)\n  (:id . 84))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 236) (:start . 233)\n  (:id . 85))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 247)\n  (:start . 237) (:id . 86))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 250) (:start . 248)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 255) (:start . 251)\n  (:id . 88))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 262)\n  (:start . 256) (:id . 89))\n ((:tag . "RB") (:stem . "correctly") (:form . "correctly") (:end . 272)\n  (:start . 263) (:id . 90))\n ((:tag . "VBN") (:stem . "retain") (:form . "retained") (:end . 281)\n  (:start . 273) (:id . 91))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 283) (:start . 282)\n  (:id . 92))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 287) (:start . 284)\n  (:id . 93))\n ((:tag . "NNP") (:stem . "Qacc") (:form . "Qacc") (:end . 292) (:start . 288)\n  (:id . 94))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 296) (:start . 293)\n  (:id . 95))\n ((:tag . "NNP") (:stem . "Qand") (:form . "Qand") (:end . 301) (:start . 297)\n  (:id . 96))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 302) (:start . 301)\n  (:id . 97)))@@@1@56@((:identifiers (:sid . :s13.130) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504343@unknown@formal@none@1@S@Sensitivity, specificity and accuracy obtained with the 5-fold cross validation experiment.@(((:tag . "NN") (:stem . "sensitivity") (:form . "Sensitivity") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "specificity") (:form . "specificity") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 46)\n  (:start . 38) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "5-fold") (:form . "5-fold") (:end . 62)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "cross") (:form . "cross") (:end . 68) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 79)\n  (:start . 69) (:id . 52))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 90)\n  (:start . 80) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s13.131) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504344@unknown@formal@none@1@S@Notice that the Accuracy values reported in Table 4 might be affected by the fact that the positive and negative datasets are unbalanced.@(((:tag . "NNP") (:stem . "Notice") (:form . "Notice") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "accuracy") (:form . "Accuracy") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "affect") (:form . "affected") (:end . 69)\n  (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 99)\n  (:start . 91) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "negative") (:form . "negative") (:end . 112)\n  (:start . 104) (:id . 61))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 121)\n  (:start . 113) (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "unbalanced") (:form . "unbalanced") (:end . 136)\n  (:start . 126) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 65)))@@@1@24@((:hcues ((:id . :x13.132.1) (:span 52 57)))\n (:hscopes ((:id . :x13.132.1) (:span 12 136)))\n (:identifiers (:sid . :s13.132) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504345@unknown@formal@none@1@S@The analysis of the ROC curves, of the cumulative distributions and of the filter performance in the three score bins suggests a more relevant role of the accessibility in discriminating true from false motifs than the secondary structure assignment.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "ROC") (:form . "ROC") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "curve") (:form . "curves") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "cumulative") (:form . "cumulative") (:end . 49)\n  (:start . 39) (:id . 51))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 63) (:start . 50) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 81)\n  (:start . 75) (:id . 56))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 93)\n  (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 59))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 112)\n  (:start . 107) (:id . 61))\n ((:tag . "NNS") (:stem . "bin") (:form . "bins") (:end . 117) (:start . 113)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "suggest") (:form . "suggests") (:end . 126)\n  (:start . 118) (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 128) (:start . 127)\n  (:id . 64))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 133) (:start . 129)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 142)\n  (:start . 134) (:id . 66))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 147) (:start . 143)\n  (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 150) (:start . 148)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 69))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 168) (:start . 155) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 171) (:start . 169)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "discriminate") (:form . "discriminating")\n  (:end . 186) (:start . 172) (:id . 72))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 191) (:start . 187)\n  (:id . 73))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 196) (:start . 192)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 202)\n  (:start . 197) (:id . 75))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 209)\n  (:start . 203) (:id . 76))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 214) (:start . 210)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 218) (:start . 215)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 228)\n  (:start . 219) (:id . 79))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 238)\n  (:start . 229) (:id . 80))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 249)\n  (:start . 239) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 250) (:start . 249)\n  (:id . 82)))@@@1@41@((:hcues ((:id . :x13.133.1) (:span 118 126)))\n (:hscopes ((:id . :x13.133.1) (:span 118 249)))\n (:identifiers (:sid . :s13.133) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504346@unknown@formal@none@1@S@This observation is biologically sound since, while a buried motif is unlikely to be a genuine functional site, an exposed motif lying e.g. on a helix can in any case possess an interaction ability.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 16)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "RB") (:stem . "biologically") (:form . "biologically") (:end . 32)\n  (:start . 20) (:id . 45))\n ((:tag . "JJ") (:stem . "sound") (:form . "sound") (:end . 38) (:start . 33)\n  (:id . 46))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 44) (:start . 39)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 51) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "bury") (:form . "buried") (:end . 60) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 66) (:start . 61)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "genuine") (:form . "genuine") (:end . 94)\n  (:start . 87) (:id . 58))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 105)\n  (:start . 95) (:id . 59))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 110) (:start . 106)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 61))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 122)\n  (:start . 115) (:id . 63))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 128)\n  (:start . 123) (:id . 64))\n ((:tag . "VBG") (:stem . "lie") (:form . "lying") (:end . 134) (:start . 129)\n  (:id . 65))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 139) (:start . 135)\n  (:id . 66))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 142) (:start . 140)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 144) (:start . 143)\n  (:id . 68))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 150)\n  (:start . 145) (:id . 69))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 154) (:start . 151)\n  (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 157) (:start . 155)\n  (:id . 71))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 161) (:start . 158)\n  (:id . 72))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 166) (:start . 162)\n  (:id . 73))\n ((:tag . "VBP") (:stem . "possess") (:form . "possess") (:end . 174)\n  (:start . 167) (:id . 74))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 177) (:start . 175)\n  (:id . 75))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 189)\n  (:start . 178) (:id . 76))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 197)\n  (:start . 190) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x13.134.1) (:span 151 154))\n  ((:id . :x13.134.2) (:span 70 78)))\n (:hscopes ((:id . :x13.134.1) (:span 151 197))\n  ((:id . :x13.134.2) (:span 52 110)))\n (:identifiers (:sid . :s13.134) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504347@unknown@formal@none@1@S@Finally, our results show that the combined score is slightly more effective than the accessibility score and markedly better than the secondary structure score.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 43)\n  (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 61)\n  (:start . 53) (:id . 52))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 76)\n  (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 99) (:start . 86) (:id . 57))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 105)\n  (:start . 100) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "RB") (:stem . "markedly") (:form . "markedly") (:end . 118)\n  (:start . 110) (:id . 60))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 125)\n  (:start . 119) (:id . 61))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 130) (:start . 126)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 144)\n  (:start . 135) (:id . 64))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 154)\n  (:start . 145) (:id . 65))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 160)\n  (:start . 155) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s13.135) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504348@unknown@formal@none@1@S@The combined score Qand is implemented in both the Web Server and Web Service.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "combined") (:form . "combined") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Qand") (:form . "Qand") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 38)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Server") (:form . "Server") (:end . 61)\n  (:start . 55) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Service") (:form . "Service") (:end . 77)\n  (:start . 70) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s13.136) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504349@unknown@formal@none@1@S@Usage of the ELM structure filter@(((:tag . "NN") (:stem . "usage") (:form . "Usage") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 33)\n  (:start . 27) (:id . 47)))@@@1@6@((:identifiers (:sid . :s13.137) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504350@unknown@formal@none@1@S@For practical purposes, the filter exploits available information on protein structures to answer the question "Is it worth testing this motif candidate experimentally?" rather than to categorically tell the users whether they have a real motif or not.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "practical") (:form . "practical") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "purpose") (:form . "purposes") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "VBZ") (:stem . "exploit") (:form . "exploits") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 53)\n  (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 65)\n  (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 76)\n  (:start . 69) (:id . 52))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 87)\n  (:start . 77) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "VB") (:stem . "answer") (:form . "answer") (:end . 97)\n  (:start . 91) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 56))\n ((:tag . "NN") (:stem . "question") (:form . "question") (:end . 110)\n  (:start . 102) (:id . 57))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 112) (:start . 111)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 114) (:start . 112)\n  (:id . 59))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "worth") (:form . "worth") (:end . 123)\n  (:start . 118) (:id . 61))\n ((:tag . "VBG") (:stem . "test") (:form . "testing") (:end . 131)\n  (:start . 124) (:id . 62))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 136) (:start . 132)\n  (:id . 63))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 142)\n  (:start . 137) (:id . 64))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 152)\n  (:start . 143) (:id . 65))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n  (:end . 167) (:start . 153) (:id . 66))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 168) (:start . 167)\n  (:id . 67))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 169) (:start . 168)\n  (:id . 68))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 176)\n  (:start . 170) (:id . 69))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 181) (:start . 177)\n  (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 184) (:start . 182)\n  (:id . 71))\n ((:tag . "RB") (:stem . "categorically") (:form . "categorically")\n  (:end . 198) (:start . 185) (:id . 72))\n ((:tag . "VB") (:stem . "tell") (:form . "tell") (:end . 203) (:start . 199)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 207) (:start . 204)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 213)\n  (:start . 208) (:id . 75))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 221)\n  (:start . 214) (:id . 76))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 226) (:start . 222)\n  (:id . 77))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 231) (:start . 227)\n  (:id . 78))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 233) (:start . 232)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "real") (:form . "real") (:end . 238) (:start . 234)\n  (:id . 80))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 244)\n  (:start . 239) (:id . 81))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 247) (:start . 245)\n  (:id . 82))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 251) (:start . 248)\n  (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 84)))@@@1@43@((:hcues ((:id . :x13.138.1) (:span 245 247)))\n (:hscopes ((:id . :x13.138.1) (:span 232 251)))\n (:identifiers (:sid . :s13.138) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504351@unknown@formal@none@1@S@In deciding if a prediction is a good experimental candidate, the user should give more weight to accessibility score than to secondary structure score since a buried motif is unlikely to carry a function, whereas an exposed motif may function properly even if it is part of a beta strand or belongs to a helix (see examples in the benchmarking dataset, additional file 6 (Table S1).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "decide") (:form . "deciding") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 27)\n  (:start . 17) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "good") (:form . "good") (:end . 37) (:start . 33)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 50)\n  (:start . 38) (:id . 50))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 60)\n  (:start . 51) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 70) (:start . 66)\n  (:id . 54))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 77)\n  (:start . 71) (:id . 55))\n ((:tag . "VB") (:stem . "give") (:form . "give") (:end . 82) (:start . 78)\n  (:id . 56))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 87) (:start . 83)\n  (:id . 57))\n ((:tag . "NN") (:stem . "weight") (:form . "weight") (:end . 94)\n  (:start . 88) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 111) (:start . 98) (:id . 60))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 117)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 122) (:start . 118)\n  (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 125) (:start . 123)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 135)\n  (:start . 126) (:id . 64))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 145)\n  (:start . 136) (:id . 65))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 151)\n  (:start . 146) (:id . 66))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 157)\n  (:start . 152) (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 159) (:start . 158)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "bury") (:form . "buried") (:end . 166)\n  (:start . 160) (:id . 69))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 172)\n  (:start . 167) (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 175) (:start . 173)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 184)\n  (:start . 176) (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 187) (:start . 185)\n  (:id . 73))\n ((:tag . "VB") (:stem . "carry") (:form . "carry") (:end . 193)\n  (:start . 188) (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 195) (:start . 194)\n  (:id . 75))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 204)\n  (:start . 196) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 205) (:start . 204)\n  (:id . 77))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 213)\n  (:start . 206) (:id . 78))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 216) (:start . 214)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 224)\n  (:start . 217) (:id . 80))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 230)\n  (:start . 225) (:id . 81))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 234) (:start . 231)\n  (:id . 82))\n ((:tag . "VB") (:stem . "function") (:form . "function") (:end . 243)\n  (:start . 235) (:id . 83))\n ((:tag . "RB") (:stem . "properly") (:form . "properly") (:end . 252)\n  (:start . 244) (:id . 84))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 257) (:start . 253)\n  (:id . 85))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 260) (:start . 258)\n  (:id . 86))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 263) (:start . 261)\n  (:id . 87))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 266) (:start . 264)\n  (:id . 88))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 271) (:start . 267)\n  (:id . 89))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 274) (:start . 272)\n  (:id . 90))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 276) (:start . 275)\n  (:id . 91))\n ((:tag . "NN") (:stem . "beta") (:form . "beta") (:end . 281) (:start . 277)\n  (:id . 92))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 288)\n  (:start . 282) (:id . 93))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 291) (:start . 289)\n  (:id . 94))\n ((:tag . "VBZ") (:stem . "belong") (:form . "belongs") (:end . 299)\n  (:start . 292) (:id . 95))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 302) (:start . 300)\n  (:id . 96))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 304) (:start . 303)\n  (:id . 97))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 310)\n  (:start . 305) (:id . 98))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 312) (:start . 311)\n  (:id . 99))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 315) (:start . 312)\n  (:id . 100))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 324)\n  (:start . 316) (:id . 101))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 327) (:start . 325)\n  (:id . 102))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 331) (:start . 328)\n  (:id . 103))\n ((:tag . "VBG") (:stem . "benchmarke") (:form . "benchmarking") (:end . 344)\n  (:start . 332) (:id . 104))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 352)\n  (:start . 345) (:id . 105))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 353) (:start . 352)\n  (:id . 106))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 364)\n  (:start . 354) (:id . 107))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 369) (:start . 365)\n  (:id . 108))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 371) (:start . 370)\n  (:id . 109))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 373) (:start . 372)\n  (:id . 110))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 378)\n  (:start . 373) (:id . 111))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 381) (:start . 379)\n  (:id . 112))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 382) (:start . 381)\n  (:id . 113))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 383) (:start . 382)\n  (:id . 114)))@@@1@73@((:hcues ((:id . :x13.139.1) (:span 231 234))\n  ((:id . :x13.139.2) (:span 176 184)) ((:id . :x13.139.3) (:span 12 14)))\n (:hscopes ((:id . :x13.139.1) (:span 231 310))\n  ((:id . :x13.139.2) (:span 158 204)) ((:id . :x13.139.3) (:span 12 60)))\n (:identifiers (:sid . :s13.139) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504352@unknown@formal@none@1@S@The main exception to well buried candidates being nonfunctional concerns allosteric rearrangements [44].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "main") (:form . "main") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "exception") (:form . "exception") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "buried") (:form . "buried") (:end . 33)\n  (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 44)\n  (:start . 34) (:id . 48))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "nonfunctional") (:form . "nonfunctional")\n  (:end . 64) (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "concern") (:form . "concerns") (:end . 73)\n  (:start . 65) (:id . 51))\n ((:tag . "JJ") (:stem . "allosteric") (:form . "allosteric") (:end . 84)\n  (:start . 74) (:id . 52))\n ((:tag . "NNS") (:stem . "rearrangement") (:form . "rearrangements")\n  (:end . 99) (:start . 85) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 101) (:start . 100)\n  (:id . 54))\n ((:tag . "CD") (:stem . "44") (:form . "44") (:end . 103) (:start . 101)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 104) (:start . 103)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s13.140) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504353@unknown@formal@none@1@S@If the motif is in the core of a well-known domain like SH3 or a TIM barrel, a review of the accumulated structural knowledge will allow the user to conclude that the chance of valid function is negligible.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 27) (:start . 23)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "well-known") (:form . "well-known") (:end . 43)\n  (:start . 33) (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 50)\n  (:start . 44) (:id . 52))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "SH3") (:form . "SH3") (:end . 59) (:start . 56)\n  (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 62) (:start . 60)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "TIM") (:form . "TIM") (:end . 68) (:start . 65)\n  (:id . 57))\n ((:tag . "NN") (:stem . "barrel") (:form . "barrel") (:end . 75)\n  (:start . 69) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 78) (:start . 77)\n  (:id . 60))\n ((:tag . "NN") (:stem . "review") (:form . "review") (:end . 85)\n  (:start . 79) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "accumulate") (:form . "accumulated") (:end . 104)\n  (:start . 93) (:id . 64))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 115)\n  (:start . 105) (:id . 65))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 125)\n  (:start . 116) (:id . 66))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 130) (:start . 126)\n  (:id . 67))\n ((:tag . "VB") (:stem . "allow") (:form . "allow") (:end . 136)\n  (:start . 131) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 69))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 145) (:start . 141)\n  (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 71))\n ((:tag . "VB") (:stem . "conclude") (:form . "conclude") (:end . 157)\n  (:start . 149) (:id . 72))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 162) (:start . 158)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 74))\n ((:tag . "NN") (:stem . "chance") (:form . "chance") (:end . 173)\n  (:start . 167) (:id . 75))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "valid") (:form . "valid") (:end . 182)\n  (:start . 177) (:id . 77))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 191)\n  (:start . 183) (:id . 78))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 194) (:start . 192)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "negligible") (:form . "negligible") (:end . 205)\n  (:start . 195) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s13.141) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504354@unknown@formal@none@1@S@If there is evidence of allostery, however, depending on which parts of the structure are flexible, this might support or invalidate the motif.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "evidence") (:form . "evidence") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "allostery") (:form . "allostery") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 34) (:start . 33)\n  (:id . 48))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "depend") (:form . "depending") (:end . 53)\n  (:start . 44) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 62) (:start . 57)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 85)\n  (:start . 76) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "flexible") (:form . "flexible") (:end . 98)\n  (:start . 90) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 60))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 104) (:start . 100)\n  (:id . 61))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 110)\n  (:start . 105) (:id . 62))\n ((:tag . "VB") (:stem . "support") (:form . "support") (:end . 118)\n  (:start . 111) (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 121) (:start . 119)\n  (:id . 64))\n ((:tag . "VB") (:stem . "invalidate") (:form . "invalidate") (:end . 132)\n  (:start . 122) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 136) (:start . 133)\n  (:id . 66))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 142)\n  (:start . 137) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x13.142.1) (:span 119 121))\n  ((:id . :x13.142.2) (:span 105 110)))\n (:hscopes ((:id . :x13.142.1) (:span 111 132))\n  ((:id . :x13.142.2) (:span 105 142)))\n (:identifiers (:sid . :s13.142) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504355@unknown@formal@none@1@S@If nothing is known, then it should be kept in mind that most parts of most globular domains do not undergo major rearrangements, hence candidates from the sparse bin should not be eyed with hope.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "nothing") (:form . "nothing") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 35)\n  (:start . 29) (:id . 49))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "keep") (:form . "kept") (:end . 43) (:start . 39)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mind") (:form . "mind") (:end . 51) (:start . 47)\n  (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 56) (:start . 52)\n  (:id . 54))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 61) (:start . 57)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "part") (:form . "parts") (:end . 67) (:start . 62)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 57))\n ((:tag . "JJS") (:stem . "most") (:form . "most") (:end . 75) (:start . 71)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 84)\n  (:start . 76) (:id . 59))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 92)\n  (:start . 85) (:id . 60))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 95) (:start . 93)\n  (:id . 61))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 99) (:start . 96)\n  (:id . 62))\n ((:tag . "VB") (:stem . "undergo") (:form . "undergo") (:end . 107)\n  (:start . 100) (:id . 63))\n ((:tag . "JJ") (:stem . "major") (:form . "major") (:end . 113)\n  (:start . 108) (:id . 64))\n ((:tag . "NNS") (:stem . "rearrangement") (:form . "rearrangements")\n  (:end . 128) (:start . 114) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 66))\n ((:tag . "RB") (:stem . "hence") (:form . "hence") (:end . 135)\n  (:start . 130) (:id . 67))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 146)\n  (:start . 136) (:id . 68))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 151) (:start . 147)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 162)\n  (:start . 156) (:id . 71))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 166) (:start . 163)\n  (:id . 72))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 173)\n  (:start . 167) (:id . 73))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 177) (:start . 174)\n  (:id . 74))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 180) (:start . 178)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "eye") (:form . "eyed") (:end . 185) (:start . 181)\n  (:id . 76))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 190) (:start . 186)\n  (:id . 77))\n ((:tag . "NN") (:stem . "hope") (:form . "hope") (:end . 195) (:start . 191)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x13.143.1) (:span 167 173)))\n (:hscopes ((:id . :x13.143.1) (:span 136 195)))\n (:identifiers (:sid . :s13.143) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504356@unknown@formal@none@1@S@The user should also consider overall context in assessing the structure filter results.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "VB") (:stem . "consider") (:form . "consider") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "assess") (:form . "assessing") (:end . 58)\n  (:start . 49) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 79)\n  (:start . 73) (:id . 53))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 87)\n  (:start . 80) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s13.144) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504357@unknown@formal@none@1@S@Is the cell compartment correct: An exposed RGD motif with a significant p-value in an extracellular protein is a very good integrin-binding candidate: one in a nuclear protein is worthless.@(((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "compartment") (:form . "compartment") (:end . 23)\n  (:start . 12) (:id . 45))\n ((:tag . "VBP") (:stem . "correct") (:form . "correct") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "An") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "NN") (:stem . "rgd") (:form . "RGD") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 72)\n  (:start . 61) (:id . 54))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 80)\n  (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 86) (:start . 84)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 100) (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 108)\n  (:start . 101) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 113) (:start . 112)\n  (:id . 61))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 118) (:start . 114)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "good") (:form . "good") (:end . 123) (:start . 119)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "integrin-binding") (:form . "integrin-binding")\n  (:end . 140) (:start . 124) (:id . 64))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 150)\n  (:start . 141) (:id . 65))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 151) (:start . 150)\n  (:id . 66))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 155) (:start . 152)\n  (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 158) (:start . 156)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 160) (:start . 159)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "nuclear") (:form . "nuclear") (:end . 168)\n  (:start . 161) (:id . 70))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 176)\n  (:start . 169) (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 179) (:start . 177)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "worthless") (:form . "worthless") (:end . 189)\n  (:start . 180) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s13.145) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504358@unknown@formal@none@1@S@Is the motif conserved, at least within a phylogenetic lineage such as mammals, tetrapods or vertebrates: the motif should be conserved in such groups if it is functional in a regulatory system common to related organisms.@(((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 22)\n  (:start . 13) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 32) (:start . 27)\n  (:id . 48))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 39)\n  (:start . 33) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "phylogenetic") (:form . "phylogenetic") (:end . 54)\n  (:start . 42) (:id . 51))\n ((:tag . "NN") (:stem . "lineage") (:form . "lineage") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "mammal") (:form . "mammals") (:end . 78)\n  (:start . 71) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "tetrapod") (:form . "tetrapods") (:end . 89)\n  (:start . 80) (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "vertebrate") (:form . "vertebrates") (:end . 104)\n  (:start . 93) (:id . 59))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 61))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 115)\n  (:start . 110) (:id . 62))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 122)\n  (:start . 116) (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 125) (:start . 123)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 135)\n  (:start . 126) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 138) (:start . 136)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 143) (:start . 139)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "group") (:form . "groups") (:end . 150)\n  (:start . 144) (:id . 68))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 153) (:start . 151)\n  (:id . 69))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 156) (:start . 154)\n  (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 159) (:start . 157)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 170)\n  (:start . 160) (:id . 72))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 173) (:start . 171)\n  (:id . 73))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 175) (:start . 174)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 186)\n  (:start . 176) (:id . 75))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 193)\n  (:start . 187) (:id . 76))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 200)\n  (:start . 194) (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 203) (:start . 201)\n  (:id . 78))\n ((:tag . "VBN") (:stem . "relate") (:form . "related") (:end . 211)\n  (:start . 204) (:id . 79))\n ((:tag . "NNS") (:stem . "organism") (:form . "organisms") (:end . 221)\n  (:start . 212) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x13.146.1) (:span 116 122)))\n (:hscopes ((:id . :x13.146.1) (:span 106 221)))\n (:identifiers (:sid . :s13.146) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504359@unknown@formal@none@1@S@Is the biological context sensible: Is the query protein in some way functionally associated with the ligand protein; Are they in the same regulatory pathway; Are they in the same protein complex?@(((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "sensible") (:form . "sensible") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "Is") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "RB") (:stem . "functionally") (:form . "functionally") (:end . 81)\n  (:start . 69) (:id . 55))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 92)\n  (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 97) (:start . 93)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 58))\n ((:tag . "NN") (:stem . "ligand") (:form . "ligand") (:end . 108)\n  (:start . 102) (:id . 59))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 116)\n  (:start . 109) (:id . 60))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "Are") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 126) (:start . 122)\n  (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 138) (:start . 134)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 149)\n  (:start . 139) (:id . 67))\n ((:tag . "NN") (:stem . "pathway") (:form . "pathway") (:end . 157)\n  (:start . 150) (:id . 68))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 158) (:start . 157)\n  (:id . 69))\n ((:tag . "VBP") (:stem . "be") (:form . "Are") (:end . 162) (:start . 159)\n  (:id . 70))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 167) (:start . 163)\n  (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 170) (:start . 168)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 174) (:start . 171)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 179) (:start . 175)\n  (:id . 74))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 187)\n  (:start . 180) (:id . 75))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 195)\n  (:start . 188) (:id . 76))\n ((:tag . ".") (:stem . "?") (:form . "?") (:end . 196) (:start . 195)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s13.147) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504360@unknown@formal@none@1@S@Structural analysis of LMs: Classification and examples of motifs in protein structures@(((:tag . "JJ") (:stem . "structural") (:form . "Structural") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "LM") (:form . "LMs") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "classification") (:form . "Classification")\n  (:end . 42) (:start . 28) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 65)\n  (:start . 59) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 87)\n  (:start . 77) (:id . 54)))@@@1@13@((:identifiers (:sid . :s13.148) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504361@unknown@formal@none@1@S@Before the structural context of LMs can be evaluated, it is necessary to define and select the structural unit.@(((:tag . "IN") (:stem . "before") (:form . "Before") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "LM") (:form . "LMs") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "evaluate") (:form . "evaluated") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 70)\n  (:start . 61) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "VB") (:stem . "define") (:form . "define") (:end . 80)\n  (:start . 74) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "VB") (:stem . "select") (:form . "select") (:end . 91)\n  (:start . 85) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 106)\n  (:start . 96) (:id . 60))\n ((:tag . "NN") (:stem . "unit") (:form . "unit") (:end . 111) (:start . 107)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s13.149) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504362@unknown@formal@none@1@S@Structure files may contain large protein complexes, single proteins, single or multiple chains, single globular domains and many other types of molecule.@(((:tag . "NN") (:stem . "structure") (:form . "Structure") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 15) (:start . 10)\n  (:id . 43))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "VB") (:stem . "contain") (:form . "contain") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "NNS") (:stem . "complex") (:form . "complexes") (:end . 51)\n  (:start . 42) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 76)\n  (:start . 70) (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 88)\n  (:start . 80) (:id . 55))\n ((:tag . "NNS") (:stem . "chain") (:form . "chains") (:end . 95)\n  (:start . 89) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 112)\n  (:start . 104) (:id . 59))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 120)\n  (:start . 113) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 129) (:start . 125)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 135)\n  (:start . 130) (:id . 63))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 141)\n  (:start . 136) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "NN") (:stem . "molecule") (:form . "molecule") (:end . 153)\n  (:start . 145) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x13.150.1) (:span 16 19)))\n (:hscopes ((:id . :x13.150.1) (:span 16 153)))\n (:identifiers (:sid . :s13.150) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504363@unknown@formal@none@1@S@LMs may be bound to their ligands or in an unliganded state.@(((:tag . "NNP") (:stem . "LM") (:form . "LMs") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "bind") (:form . "bound") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 25)\n  (:start . 20) (:id . 47))\n ((:tag . "NNS") (:stem . "ligand") (:form . "ligands") (:end . 33)\n  (:start . 26) (:id . 48))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 36) (:start . 34)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 42) (:start . 40)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "unliganded") (:form . "unliganded") (:end . 53)\n  (:start . 43) (:id . 52))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 59) (:start . 54)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 54)))@@@1@13@((:hcues ((:id . :x13.151.1) (:span 34 36)) ((:id . :x13.151.2) (:span 4 7)))\n (:hscopes ((:id . :x13.151.1) (:span 11 59))\n  ((:id . :x13.151.2) (:span 0 59)))\n (:identifiers (:sid . :s13.151) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504364@unknown@formal@none@1@S@Figure 1a shows the Sumo-Interacting Motif (SIM) of TDG bound to SUMO-3 by beta augmentation but also well packed into the main TDG domain.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "1a") (:form . "1a") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "sumo-interacting") (:form . "Sumo-Interacting")\n  (:end . 36) (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "motif") (:form . "Motif") (:end . 42) (:start . 37)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "SIM") (:form . "SIM") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tdg") (:form . "TDG") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "bind") (:form . "bound") (:end . 61) (:start . 56)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sumo-3") (:form . "SUMO-3") (:end . 71)\n  (:start . 65) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . "SYM") (:stem . "beta") (:form . "beta") (:end . 79) (:start . 75)\n  (:id . 57))\n ((:tag . "NN") (:stem . "augmentation") (:form . "augmentation") (:end . 92)\n  (:start . 80) (:id . 58))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 101) (:start . 97)\n  (:id . 60))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 106) (:start . 102)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "pack") (:form . "packed") (:end . 113)\n  (:start . 107) (:id . 62))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 118) (:start . 114)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "main") (:form . "main") (:end . 127) (:start . 123)\n  (:id . 65))\n ((:tag . "NN") (:stem . "tdg") (:form . "TDG") (:end . 131) (:start . 128)\n  (:id . 66))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 138)\n  (:start . 132) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s13.152) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504365@unknown@formal@none@1@S@Clearly we need to measure accessibility of the SIM in the absence of the SUMO protein.@(((:tag . "RB") (:stem . "clearly") (:form . "Clearly") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "need") (:form . "need") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "VB") (:stem . "measure") (:form . "measure") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 40) (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "SIM") (:form . "SIM") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "absence") (:form . "absence") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "SUMO") (:form . "SUMO") (:end . 78) (:start . 74)\n  (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 86)\n  (:start . 79) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s13.153) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504366@unknown@formal@none@1@S@The open (active) and closed (inactive) conformations of the Src kinase are dependent on the phosphorylation states of several tyrosines.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "open") (:form . "open") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "active") (:form . "active") (:end . 16)\n  (:start . 10) (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "close") (:form . "closed") (:end . 28)\n  (:start . 22) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "inactive") (:form . "inactive") (:end . 38)\n  (:start . 30) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 39) (:start . 38)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "conformation") (:form . "conformations")\n  (:end . 53) (:start . 40) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Src") (:form . "Src") (:end . 64) (:start . 61)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 71)\n  (:start . 65) (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 75) (:start . 72)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "dependent") (:form . "dependent") (:end . 85)\n  (:start . 76) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 88) (:start . 86)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 60))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 108) (:start . 93) (:id . 61))\n ((:tag . "NNS") (:stem . "state") (:form . "states") (:end . 115)\n  (:start . 109) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "several") (:form . "several") (:end . 126)\n  (:start . 119) (:id . 64))\n ((:tag . "NNS") (:stem . "tyrosine") (:form . "tyrosines") (:end . 136)\n  (:start . 127) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s13.154) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504367@unknown@formal@none@1@S@In particular, the closed conformation is specified by an interaction between the Src SH2 domain and the C-terminal pTyr-527 and an interaction between the Src SH3 domain with a peptide linking the SH2 and kinase domains.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "closed") (:form . "closed") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "conformation") (:form . "conformation") (:end . 38)\n  (:start . 26) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 69)\n  (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Src") (:form . "Src") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "NN") (:stem . "sh2") (:form . "SH2") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 96)\n  (:start . 90) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 115)\n  (:start . 105) (:id . 60))\n ((:tag . "NN") (:stem . "ptyr-527") (:form . "pTyr-527") (:end . 124)\n  (:start . 116) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 62))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 131) (:start . 129)\n  (:id . 63))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 143)\n  (:start . 132) (:id . 64))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 151)\n  (:start . 144) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Src") (:form . "Src") (:end . 159) (:start . 156)\n  (:id . 67))\n ((:tag . "NN") (:stem . "sh3") (:form . "SH3") (:end . 163) (:start . 160)\n  (:id . 68))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 170)\n  (:start . 164) (:id . 69))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 175) (:start . 171)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 177) (:start . 176)\n  (:id . 71))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 185)\n  (:start . 178) (:id . 72))\n ((:tag . "VBG") (:stem . "link") (:form . "linking") (:end . 193)\n  (:start . 186) (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 197) (:start . 194)\n  (:id . 74))\n ((:tag . "NN") (:stem . "sh2") (:form . "SH2") (:end . 201) (:start . 198)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 205) (:start . 202)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 212)\n  (:start . 206) (:id . 77))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 220)\n  (:start . 213) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 221) (:start . 220)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s13.155) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504368@unknown@formal@none@1@S@Figure 1b shows the closed conformation with these elements highlighted.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "1b") (:form . "1b") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "closed") (:form . "closed") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "conformation") (:form . "conformation") (:end . 39)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . "VBD") (:stem . "highlight") (:form . "highlighted") (:end . 71)\n  (:start . 60) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s13.156) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504369@unknown@formal@none@1@S@In particular, the SH3 binding peptide is fully buried, even though it is not part of a globular domain.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sh3") (:form . "SH3") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 30)\n  (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "RB") (:stem . "fully") (:form . "fully") (:end . 47) (:start . 42)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "bury") (:form . "buried") (:end . 54) (:start . 48)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "RB") (:stem . "even") (:form . "even") (:end . 60) (:start . 56)\n  (:id . 53))\n ((:tag . "IN") (:stem . "though") (:form . "though") (:end . 67)\n  (:start . 61) (:id . 54))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 77) (:start . 74)\n  (:id . 57))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 82) (:start . 78)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 87) (:start . 86)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 96)\n  (:start . 88) (:id . 61))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 103)\n  (:start . 97) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s13.157) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504370@unknown@formal@none@1@S@In the open conformation this peptide is much more accessible, as is the C-terminal peptide which is released from the SH2 domain (e.g. 1Y57, [45]).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "open") (:form . "open") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "conformation") (:form . "conformation") (:end . 24)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "accessible") (:form . "accessible") (:end . 61)\n  (:start . 51) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 83)\n  (:start . 73) (:id . 56))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 91)\n  (:start . 84) (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 97) (:start . 92)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "release") (:form . "released") (:end . 109)\n  (:start . 101) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 114) (:start . 110)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 62))\n ((:tag . "NN") (:stem . "sh2") (:form . "SH2") (:end . 122) (:start . 119)\n  (:id . 63))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 129)\n  (:start . 123) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 65))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 135) (:start . 131)\n  (:id . 66))\n ((:tag . "NN") (:stem . "1y57") (:form . "1Y57") (:end . 140) (:start . 136)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 143) (:start . 142)\n  (:id . 69))\n ((:tag . "CD") (:stem . "45") (:form . "45") (:end . 145) (:start . 143)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 146) (:start . 145)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s13.158) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504371@unknown@formal@none@1@S@The dependency of LM accessibility on globular domain rearrangements implies that multi-domain structures are not a suitable structural unit for structure filtering.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "dependency") (:form . "dependency") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 34) (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "rearrangement") (:form . "rearrangements")\n  (:end . 68) (:start . 54) (:id . 50))\n ((:tag . "VBZ") (:stem . "imply") (:form . "implies") (:end . 76)\n  (:start . 69) (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 81) (:start . 77)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "multi-domain") (:form . "multi-domain") (:end . 94)\n  (:start . 82) (:id . 53))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 105)\n  (:start . 95) (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 109) (:start . 106)\n  (:id . 55))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 113) (:start . 110)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "suitable") (:form . "suitable") (:end . 124)\n  (:start . 116) (:id . 58))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 135)\n  (:start . 125) (:id . 59))\n ((:tag . "NN") (:stem . "unit") (:form . "unit") (:end . 140) (:start . 136)\n  (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 144) (:start . 141)\n  (:id . 61))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 154)\n  (:start . 145) (:id . 62))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 164)\n  (:start . 155) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x13.159.1) (:span 69 76)))\n (:hscopes ((:id . :x13.159.1) (:span 69 164)))\n (:identifiers (:sid . :s13.159) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504372@unknown@formal@none@1@S@The appropriate units therefore in the cases of LMs would be the individual globular domains themselves.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "unit") (:form . "units") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 44) (:start . 39)\n  (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 75)\n  (:start . 65) (:id . 54))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 84)\n  (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 92)\n  (:start . 85) (:id . 56))\n ((:tag . "PRP") (:stem . "themselves") (:form . "themselves") (:end . 103)\n  (:start . 93) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x13.160.1) (:span 52 57)))\n (:hscopes ((:id . :x13.160.1) (:span 52 103)))\n (:identifiers (:sid . :s13.160) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504373@unknown@formal@none@1@S@At least for domains that do not undergo allosteric rearrangement, a motif which is buried in the core of a structural domain unit is unlikely to be a true one.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "do") (:form . "do") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "VB") (:stem . "undergo") (:form . "undergo") (:end . 40)\n  (:start . 33) (:id . 49))\n ((:tag . "JJ") (:stem . "allosteric") (:form . "allosteric") (:end . 51)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "rearrangement") (:form . "rearrangement")\n  (:end . 65) (:start . 52) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 80) (:start . 75)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 83) (:start . 81)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "bury") (:form . "buried") (:end . 90) (:start . 84)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 102) (:start . 98)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 107) (:start . 106)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 118)\n  (:start . 108) (:id . 63))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 125)\n  (:start . 119) (:id . 64))\n ((:tag . "NN") (:stem . "unit") (:form . "unit") (:end . 130) (:start . 126)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 133) (:start . 131)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "unlikely") (:form . "unlikely") (:end . 142)\n  (:start . 134) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 145) (:start . 143)\n  (:id . 68))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 148) (:start . 146)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 150) (:start . 149)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 155) (:start . 151)\n  (:id . 71))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 159) (:start . 156)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 73)))@@@1@32@((:hcues ((:id . :x13.161.1) (:span 134 142)))\n (:hscopes ((:id . :x13.161.1) (:span 67 159)))\n (:identifiers (:sid . :s13.161) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504374@unknown@formal@none@1@S@Therefore we chose the SCOP [46] protein domain definition as provided by the ASTRAL resource [47] as the structure dataset to be used to implement the structure filter.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 18)\n  (:start . 13) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 31) (:start . 29)\n  (:id . 48))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 32) (:start . 31)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 40)\n  (:start . 33) (:id . 50))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 47)\n  (:start . 41) (:id . 51))\n ((:tag . "NN") (:stem . "definition") (:form . "definition") (:end . 58)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 70)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "astral") (:form . "ASTRAL") (:end . 84)\n  (:start . 78) (:id . 57))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 93)\n  (:start . 85) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 97) (:start . 95)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 98) (:start . 97)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 101) (:start . 99)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 63))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 115)\n  (:start . 106) (:id . 64))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 123)\n  (:start . 116) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 126) (:start . 124)\n  (:id . 66))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 129) (:start . 127)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 134) (:start . 130)\n  (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 137) (:start . 135)\n  (:id . 69))\n ((:tag . "VB") (:stem . "implement") (:form . "implement") (:end . 147)\n  (:start . 138) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 71))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 161)\n  (:start . 152) (:id . 72))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 168)\n  (:start . 162) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s13.162) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504375@unknown@formal@none@1@S@The inception of this work required the collection and analysis of the 3D occurrences of LM instances annotated in the ELM resource [1].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "inception") (:form . "inception") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "require") (:form . "required") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "collection") (:form . "collection") (:end . 50)\n  (:start . 40) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "occurrence") (:form . "occurrences") (:end . 85)\n  (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 101)\n  (:start . 92) (:id . 58))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 111)\n  (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 122) (:start . 119)\n  (:id . 62))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 131)\n  (:start . 123) (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 135) (:start . 134)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s13.163) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504376@unknown@formal@none@1@S@Here we present a discussion of our benchmark dataset.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "present") (:form . "present") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "discussion") (:form . "discussion") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 45)\n  (:start . 36) (:id . 49))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 54) (:start . 53)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s13.164) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504377@unknown@formal@none@1@S@Many details and specific examples are reported in the supplementary information (additional file 1).@(((:tag . "JJ") (:stem . "many") (:form . "Many") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 47)\n  (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "supplementary") (:form . "supplementary")\n  (:end . 68) (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 80)\n  (:start . 69) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 92)\n  (:start . 82) (:id . 54))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 97) (:start . 93)\n  (:id . 55))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 99) (:start . 98)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s13.165) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504378@unknown@formal@none@1@S@As described in Methods, we obtained a set of 158 3D non-redundant instances from 36 different LM entries (reported in additional file 6 (Table S1) from the ELM resource release June 2007.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "obtain") (:form . "obtained") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 51))\n ((:tag . "CD") (:stem . "158") (:form . "158") (:end . 49) (:start . 46)\n  (:id . 52))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 52) (:start . 50)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "non-redundant") (:form . "non-redundant")\n  (:end . 66) (:start . 53) (:id . 54))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 76)\n  (:start . 67) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 84) (:start . 82)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 94)\n  (:start . 85) (:id . 58))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 97) (:start . 95)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "entry") (:form . "entries") (:end . 105)\n  (:start . 98) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 115)\n  (:start . 107) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 118) (:start . 116)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 129)\n  (:start . 119) (:id . 64))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 134) (:start . 130)\n  (:id . 65))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 136) (:start . 135)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 143)\n  (:start . 138) (:id . 68))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 146) (:start . 144)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 70))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 152) (:start . 148)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 160) (:start . 157)\n  (:id . 73))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 169)\n  (:start . 161) (:id . 74))\n ((:tag . "NN") (:stem . "release") (:form . "release") (:end . 177)\n  (:start . 170) (:id . 75))\n ((:tag . "NNP") (:stem . "June") (:form . "June") (:end . 182) (:start . 178)\n  (:id . 76))\n ((:tag . "CD") (:stem . "2007") (:form . "2007") (:end . 187) (:start . 183)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s13.166) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504379@unknown@formal@none@1@S@Sixteen motifs match only one instance and twenty match two or more.@(((:tag . "CD") (:stem . "sixteen") (:form . "Sixteen") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "match") (:form . "match") (:end . 20) (:start . 15)\n  (:id . 44))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "CD") (:stem . "twenty") (:form . "twenty") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s13.167) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504380@unknown@formal@none@1@S@The majority (~60%) of LM instances are made up of residues whose relative accessibility to the solvent is at least 50% and are located entirely in loop, turn or unstructured regions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "CD") (:stem . "~60") (:form . "~60") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 19) (:start . 18)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 25) (:start . 23)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 35)\n  (:start . 26) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 44) (:start . 40)\n  (:id . 52))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 47) (:start . 45)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 59)\n  (:start . 51) (:id . 55))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 65) (:start . 60)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 74)\n  (:start . 66) (:id . 57))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 88) (:start . 75) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 91) (:start . 89)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 60))\n ((:tag . "NN") (:stem . "solvent") (:form . "solvent") (:end . 103)\n  (:start . 96) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 106) (:start . 104)\n  (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 109) (:start . 107)\n  (:id . 63))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 115)\n  (:start . 110) (:id . 64))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 118) (:start . 116)\n  (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 119) (:start . 118)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 67))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 127) (:start . 124)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "located") (:form . "located") (:end . 135)\n  (:start . 128) (:id . 69))\n ((:tag . "RB") (:stem . "entirely") (:form . "entirely") (:end . 144)\n  (:start . 136) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 147) (:start . 145)\n  (:id . 71))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 152) (:start . 148)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 73))\n ((:tag . "NN") (:stem . "turn") (:form . "turn") (:end . 158) (:start . 154)\n  (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 161) (:start . 159)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "unstructured") (:form . "unstructured") (:end . 174)\n  (:start . 162) (:id . 76))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 182)\n  (:start . 175) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s13.168) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504381@unknown@formal@none@1@S@Figure 2 shows two typical examples (LIG_RGD and MOD_SUMO) of a motif in a very exposed loop of a domain (2a and 2c) and a motif in a flexible region which is not in a domain (LIG_RGD, Figure 2b).@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "typical") (:form . "typical") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "LIG_RGD") (:form . "LIG_RGD") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "MOD_SUMO") (:form . "MOD_SUMO") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 58) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 69) (:start . 64)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 72) (:start . 70)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 74) (:start . 73)\n  (:id . 57))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 79) (:start . 75)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 87)\n  (:start . 80) (:id . 59))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 92) (:start . 88)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n  (:id . 62))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 104)\n  (:start . 98) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 64))\n ((:tag . "NN") (:stem . "2a") (:form . "2a") (:end . 108) (:start . 106)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 66))\n ((:tag . "NN") (:stem . "2c") (:form . "2c") (:end . 115) (:start . 113)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 120) (:start . 117)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 122) (:start . 121)\n  (:id . 70))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 128)\n  (:start . 123) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 131) (:start . 129)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 133) (:start . 132)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "flexible") (:form . "flexible") (:end . 142)\n  (:start . 134) (:id . 74))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 149)\n  (:start . 143) (:id . 75))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 155)\n  (:start . 150) (:id . 76))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 158) (:start . 156)\n  (:id . 77))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 162) (:start . 159)\n  (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 165) (:start . 163)\n  (:id . 79))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 167) (:start . 166)\n  (:id . 80))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 174)\n  (:start . 168) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 176) (:start . 175)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "LIG_RGD") (:form . "LIG_RGD") (:end . 183)\n  (:start . 176) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 191)\n  (:start . 185) (:id . 85))\n ((:tag . "NN") (:stem . "2b") (:form . "2b") (:end . 194) (:start . 192)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s13.169) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504382@unknown@formal@none@1@S@LIG_RGD is a short peptide ligand motif which interacts directly with extracellular domains of integrins whereas MOD_SUMO is a motif recognised for modification by SUMO-1.@(((:tag . "NNP") (:stem . "LIG_RGD") (:form . "LIG_RGD") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "ligand") (:form . "ligand") (:end . 33)\n  (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "interact") (:form . "interacts") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 64)\n  (:start . 56) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 69) (:start . 65)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "extracellular") (:form . "extracellular")\n  (:end . 83) (:start . 70) (:id . 53))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 91)\n  (:start . 84) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "integrin") (:form . "integrins") (:end . 104)\n  (:start . 95) (:id . 56))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 112)\n  (:start . 105) (:id . 57))\n ((:tag . "NNP") (:stem . "MOD_SUMO") (:form . "MOD_SUMO") (:end . 121)\n  (:start . 113) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 124) (:start . 122)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 126) (:start . 125)\n  (:id . 60))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 132)\n  (:start . 127) (:id . 61))\n ((:tag . "VBN") (:stem . "recognise") (:form . "recognised") (:end . 143)\n  (:start . 133) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 147) (:start . 144)\n  (:id . 63))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 160)\n  (:start . 148) (:id . 64))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 163) (:start . 161)\n  (:id . 65))\n ((:tag . "NN") (:stem . "sumo-1") (:form . "SUMO-1") (:end . 170)\n  (:start . 164) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s13.170) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504383@unknown@formal@none@1@S@The SUMO proteins are Small Ubiquitin-related MOdifiers that are covalently conjugated onto lysine residues within target sequences.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "SUMO") (:form . "SUMO") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "small") (:form . "Small") (:end . 27) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "ubiquitin-related") (:form . "Ubiquitin-related")\n  (:end . 45) (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "modifier") (:form . "MOdifiers") (:end . 55)\n  (:start . 46) (:id . 48))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 60) (:start . 56)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 64) (:start . 61)\n  (:id . 50))\n ((:tag . "RB") (:stem . "covalently") (:form . "covalently") (:end . 75)\n  (:start . 65) (:id . 51))\n ((:tag . "VBN") (:stem . "conjugate") (:form . "conjugated") (:end . 86)\n  (:start . 76) (:id . 52))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 91) (:start . 87)\n  (:id . 53))\n ((:tag . "NN") (:stem . "lysine") (:form . "lysine") (:end . 98)\n  (:start . 92) (:id . 54))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 107)\n  (:start . 99) (:id . 55))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 114)\n  (:start . 108) (:id . 56))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 121)\n  (:start . 115) (:id . 57))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 131)\n  (:start . 122) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s13.171) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504384@unknown@formal@none@1@S@Eight out of 36 LM entries have at least one instance which is entirely or almost entirely in helical conformation while two entries have at least one instance almost entirely in a strand conformation.@(((:tag . "CD") (:stem . "eight") (:form . "Eight") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "entry") (:form . "entries") (:end . 26)\n  (:start . 19) (:id . 47))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 31) (:start . 27)\n  (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 40) (:start . 35)\n  (:id . 50))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 44) (:start . 41)\n  (:id . 51))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 53)\n  (:start . 45) (:id . 52))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 59) (:start . 54)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . "RB") (:stem . "entirely") (:form . "entirely") (:end . 71)\n  (:start . 63) (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 74) (:start . 72)\n  (:id . 56))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 81)\n  (:start . 75) (:id . 57))\n ((:tag . "RB") (:stem . "entirely") (:form . "entirely") (:end . 90)\n  (:start . 82) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "helical") (:form . "helical") (:end . 101)\n  (:start . 94) (:id . 60))\n ((:tag . "NN") (:stem . "conformation") (:form . "conformation") (:end . 114)\n  (:start . 102) (:id . 61))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 120)\n  (:start . 115) (:id . 62))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 124) (:start . 121)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "entry") (:form . "entries") (:end . 132)\n  (:start . 125) (:id . 64))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 137) (:start . 133)\n  (:id . 65))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 140) (:start . 138)\n  (:id . 66))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 146)\n  (:start . 141) (:id . 67))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 150) (:start . 147)\n  (:id . 68))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 159)\n  (:start . 151) (:id . 69))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 166)\n  (:start . 160) (:id . 70))\n ((:tag . "RB") (:stem . "entirely") (:form . "entirely") (:end . 175)\n  (:start . 167) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 178) (:start . 176)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 180) (:start . 179)\n  (:id . 73))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 187)\n  (:start . 181) (:id . 74))\n ((:tag . "NN") (:stem . "conformation") (:form . "conformation") (:end . 200)\n  (:start . 188) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x13.172.1) (:span 72 74)))\n (:hscopes ((:id . :x13.172.1) (:span 63 90)))\n (:identifiers (:sid . :s13.172) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504385@unknown@formal@none@1@S@Notwithstanding the greater rigidity of helices as opposed to loops and unstructured regions, LMs found in helical conformation are not necessarily prevented from being exposed to the solvent and carrying out their functions.@(((:tag . "IN") (:stem . "notwithstanding") (:form . "Notwithstanding")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 43))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 27)\n  (:start . 20) (:id . 44))\n ((:tag . "NN") (:stem . "rigidity") (:form . "rigidity") (:end . 36)\n  (:start . 28) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 47)\n  (:start . 40) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "oppose") (:form . "opposed") (:end . 58)\n  (:start . 51) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "loop") (:form . "loops") (:end . 67) (:start . 62)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "unstructured") (:form . "unstructured") (:end . 84)\n  (:start . 72) (:id . 53))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 92)\n  (:start . 85) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 97) (:start . 94)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 103) (:start . 98)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "helical") (:form . "helical") (:end . 114)\n  (:start . 107) (:id . 59))\n ((:tag . "NN") (:stem . "conformation") (:form . "conformation") (:end . 127)\n  (:start . 115) (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 131) (:start . 128)\n  (:id . 61))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 135) (:start . 132)\n  (:id . 62))\n ((:tag . "RB") (:stem . "necessarily") (:form . "necessarily") (:end . 147)\n  (:start . 136) (:id . 63))\n ((:tag . "VBN") (:stem . "prevent") (:form . "prevented") (:end . 157)\n  (:start . 148) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 162) (:start . 158)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 168) (:start . 163)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 176)\n  (:start . 169) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 179) (:start . 177)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 183) (:start . 180)\n  (:id . 69))\n ((:tag . "NN") (:stem . "solvent") (:form . "solvent") (:end . 191)\n  (:start . 184) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 195) (:start . 192)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 204)\n  (:start . 196) (:id . 72))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 208) (:start . 205)\n  (:id . 73))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 214)\n  (:start . 209) (:id . 74))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 224)\n  (:start . 215) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s13.173) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504386@unknown@formal@none@1@S@Two clear examples are shown in Figure 2d and 2e.@(((:tag . "CD") (:stem . "two") (:form . "Two") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "2d") (:form . "2d") (:end . 41) (:start . 39)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "2e") (:form . "2e") (:end . 48) (:start . 46)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 49) (:start . 48)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s13.174) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504387@unknown@formal@none@1@S@Figure 2d shows an instance of the MOD_CMANNOS motif, which is part of a helix and is partly hidden by the C-term of the protein.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "2d") (:form . "2d") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "MOD_CMANNOS") (:form . "MOD_CMANNOS") (:end . 46)\n  (:start . 35) (:id . 49))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 78) (:start . 73)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 85) (:start . 83)\n  (:id . 59))\n ((:tag . "RB") (:stem . "partly") (:form . "partly") (:end . 92)\n  (:start . 86) (:id . 60))\n ((:tag . "VBN") (:stem . "hide") (:form . "hidden") (:end . 99) (:start . 93)\n  (:id . 61))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 102) (:start . 100)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 63))\n ((:tag . "NN") (:stem . "c-term") (:form . "C-term") (:end . 113)\n  (:start . 107) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 66))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 128)\n  (:start . 121) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s13.175) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504388@unknown@formal@none@1@S@C-Mannosylation is a type of protein glycosylation involving the attachment of a mannosyl residue to a tryptophan.@(((:tag . "NNP") (:stem . "C-Mannosylation") (:form . "C-Mannosylation")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "glycosylation") (:form . "glycosylation")\n  (:end . 50) (:start . 37) (:id . 48))\n ((:tag . "VBG") (:stem . "involve") (:form . "involving") (:end . 60)\n  (:start . 51) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 50))\n ((:tag . "NN") (:stem . "attachment") (:form . "attachment") (:end . 75)\n  (:start . 65) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 80) (:start . 79)\n  (:id . 53))\n ((:tag . "NN") (:stem . "mannosyl") (:form . "mannosyl") (:end . 89)\n  (:start . 81) (:id . 54))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 97)\n  (:start . 90) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 102) (:start . 101)\n  (:id . 57))\n ((:tag . "NN") (:stem . "tryptophan") (:form . "tryptophan") (:end . 113)\n  (:start . 103) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s13.176) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504389@unknown@formal@none@1@S@In this particular case, the most buried residues are those corresponding to wildcard positions in the MOD_MANNOS regular expression (W..W), whereas the conserved tryptophan needed for the mannose attachment is protruding outwards from the domain surface.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 18)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 33) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "buried") (:form . "buried") (:end . 40)\n  (:start . 34) (:id . 49))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 59) (:start . 54)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 73)\n  (:start . 60) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "VB") (:stem . "wildcard") (:form . "wildcard") (:end . 85)\n  (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 95)\n  (:start . 86) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 98) (:start . 96)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "MOD_MANNOS") (:form . "MOD_MANNOS") (:end . 113)\n  (:start . 103) (:id . 59))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 121)\n  (:start . 114) (:id . 60))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 132)\n  (:start . 122) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "W..W") (:form . "W..W") (:end . 138) (:start . 134)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 139) (:start . 138)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 65))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 148)\n  (:start . 141) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 162)\n  (:start . 153) (:id . 68))\n ((:tag . "NN") (:stem . "tryptophan") (:form . "tryptophan") (:end . 173)\n  (:start . 163) (:id . 69))\n ((:tag . "VBN") (:stem . "need") (:form . "needed") (:end . 180)\n  (:start . 174) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 184) (:start . 181)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 188) (:start . 185)\n  (:id . 72))\n ((:tag . "NN") (:stem . "mannose") (:form . "mannose") (:end . 196)\n  (:start . 189) (:id . 73))\n ((:tag . "NN") (:stem . "attachment") (:form . "attachment") (:end . 207)\n  (:start . 197) (:id . 74))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 210) (:start . 208)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "protrude") (:form . "protruding") (:end . 221)\n  (:start . 211) (:id . 76))\n ((:tag . "RB") (:stem . "outwards") (:form . "outwards") (:end . 230)\n  (:start . 222) (:id . 77))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 235) (:start . 231)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 239) (:start . 236)\n  (:id . 79))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 246)\n  (:start . 240) (:id . 80))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 254)\n  (:start . 247) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 255) (:start . 254)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s13.177) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504390@unknown@formal@none@1@S@Figure 2e reports two MOD_N-GLC_1 N-glycosylation sites on the same domain.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "2e") (:form . "2e") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "report") (:form . "reports") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mod_n-glc_1") (:form . "MOD_N-GLC_1") (:end . 33)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "n-glycosylation") (:form . "N-glycosylation")\n  (:end . 49) (:start . 34) (:id . 47))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 55) (:start . 50)\n  (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 58) (:start . 56)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 74)\n  (:start . 68) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s13.178) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504391@unknown@formal@none@1@S@N-linked glycosylation is a co-translational process involving the transfer of an oligosaccharide chain to an asparagine residue in the protein.@(((:tag . "VBN") (:stem . "n-linke") (:form . "N-linked") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "glycosylation") (:form . "glycosylation")\n  (:end . 22) (:start . 9) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 27) (:start . 26)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "co-translational") (:form . "co-translational")\n  (:end . 44) (:start . 28) (:id . 46))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 52)\n  (:start . 45) (:id . 47))\n ((:tag . "VBG") (:stem . "involve") (:form . "involving") (:end . 62)\n  (:start . 53) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 49))\n ((:tag . "NN") (:stem . "transfer") (:form . "transfer") (:end . 75)\n  (:start . 67) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 81) (:start . 79)\n  (:id . 52))\n ((:tag . "NN") (:stem . "oligosaccharide") (:form . "oligosaccharide")\n  (:end . 97) (:start . 82) (:id . 53))\n ((:tag . "NN") (:stem . "chain") (:form . "chain") (:end . 103) (:start . 98)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 106) (:start . 104)\n  (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 109) (:start . 107)\n  (:id . 56))\n ((:tag . "NN") (:stem . "asparagine") (:form . "asparagine") (:end . 120)\n  (:start . 110) (:id . 57))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 128)\n  (:start . 121) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 131) (:start . 129)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 135) (:start . 132)\n  (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 143)\n  (:start . 136) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s13.179) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504392@unknown@formal@none@1@S@In this case, one site is part of a well exposed helix whereas the other one consists of a loop with small helix overlap and it is very exposed.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 17) (:start . 14)\n  (:id . 46))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 22) (:start . 18)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 48))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 30) (:start . 26)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 35) (:start . 34)\n  (:id . 51))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 40) (:start . 36)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 48)\n  (:start . 41) (:id . 53))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 54) (:start . 49)\n  (:id . 54))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 62)\n  (:start . 55) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 72) (:start . 67)\n  (:id . 57))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 76) (:start . 73)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 85)\n  (:start . 77) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 90) (:start . 89)\n  (:id . 61))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 95) (:start . 91)\n  (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 100) (:start . 96)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 106)\n  (:start . 101) (:id . 64))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 112)\n  (:start . 107) (:id . 65))\n ((:tag . "NN") (:stem . "overlap") (:form . "overlap") (:end . 120)\n  (:start . 113) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 67))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 127) (:start . 125)\n  (:id . 68))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 130) (:start . 128)\n  (:id . 69))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 135) (:start . 131)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 143)\n  (:start . 136) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s13.180) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504393@unknown@formal@none@1@S@Figure 2f, g and 2h show cases of LMs in partly buried beta strands.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "2f") (:form . "2f") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "g") (:form . "g") (:end . 12) (:start . 11)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . "NN") (:stem . "2h") (:form . "2h") (:end . 19) (:start . 17)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 24) (:start . 20)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 30) (:start . 25)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 37) (:start . 34)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 52))\n ((:tag . "RB") (:stem . "partly") (:form . "partly") (:end . 47)\n  (:start . 41) (:id . 53))\n ((:tag . "VBN") (:stem . "bury") (:form . "buried") (:end . 54) (:start . 48)\n  (:id . 54))\n ((:tag . "NN") (:stem . "beta") (:form . "beta") (:end . 59) (:start . 55)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "strand") (:form . "strands") (:end . 67)\n  (:start . 60) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s13.181) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504394@unknown@formal@none@1@S@In figure 2f an instance of the MOD_N-GLC_1 motif is in a long edge beta strand, slightly disrupted, and quite exposed.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "figure") (:form . "figure") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "CD") (:stem . "2f") (:form . "2f") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "mod_n-glc_1") (:form . "MOD_N-GLC_1") (:end . 43)\n  (:start . 32) (:id . 49))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "long") (:form . "long") (:end . 62) (:start . 58)\n  (:id . 54))\n ((:tag . "NN") (:stem . "edge") (:form . "edge") (:end . 67) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "beta") (:form . "beta") (:end . 72) (:start . 68)\n  (:id . 56))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 79)\n  (:start . 73) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 58))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 89)\n  (:start . 81) (:id . 59))\n ((:tag . "VBN") (:stem . "disrupt") (:form . "disrupted") (:end . 99)\n  (:start . 90) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n  (:id . 62))\n ((:tag . "RB") (:stem . "quite") (:form . "quite") (:end . 110)\n  (:start . 105) (:id . 63))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 118)\n  (:start . 111) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s13.182) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504395@unknown@formal@none@1@S@The N-glycosylation sites of figures 2g and 2h are two examples of motifs lying on partially hidden beta strands but whose modified asparagine (involved in the functional activity) side chain is exposed to the solvent.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "n-glycosylation") (:form . "N-glycosylation")\n  (:end . 19) (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 25) (:start . 20)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "figure") (:form . "figures") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "NN") (:stem . "2g") (:form . "2g") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "2h") (:form . "2h") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "VBG") (:stem . "lie") (:form . "lying") (:end . 79) (:start . 74)\n  (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "RB") (:stem . "partially") (:form . "partially") (:end . 92)\n  (:start . 83) (:id . 57))\n ((:tag . "JJ") (:stem . "hidden") (:form . "hidden") (:end . 99)\n  (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "beta") (:form . "beta") (:end . 104) (:start . 100)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "strand") (:form . "strands") (:end . 112)\n  (:start . 105) (:id . 60))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "WP$") (:stem . "whose") (:form . "whose") (:end . 122)\n  (:start . 117) (:id . 62))\n ((:tag . "VBN") (:stem . "modify") (:form . "modified") (:end . 131)\n  (:start . 123) (:id . 63))\n ((:tag . "NN") (:stem . "asparagine") (:form . "asparagine") (:end . 142)\n  (:start . 132) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 144) (:start . 143)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 152)\n  (:start . 144) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 155) (:start . 153)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 159) (:start . 156)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 170)\n  (:start . 160) (:id . 69))\n ((:tag . "NN") (:stem . "activity") (:form . "activity") (:end . 179)\n  (:start . 171) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 71))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 185) (:start . 181)\n  (:id . 72))\n ((:tag . "NN") (:stem . "chain") (:form . "chain") (:end . 191)\n  (:start . 186) (:id . 73))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 194) (:start . 192)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 202)\n  (:start . 195) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 205) (:start . 203)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n  (:id . 77))\n ((:tag . "NN") (:stem . "solvent") (:form . "solvent") (:end . 217)\n  (:start . 210) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s13.183) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504396@unknown@formal@none@1@S@In our benchmarking dataset, 29/158 instances belonging to 11 different LMs [marked in dark orange in additional file 6 (Table S1)] have a very low average accessibility.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "benchmarke") (:form . "benchmarking") (:end . 19)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 27)\n  (:start . 20) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "CD") (:stem . "29/158") (:form . "29/158") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 45)\n  (:start . 36) (:id . 48))\n ((:tag . "VBG") (:stem . "belong") (:form . "belonging") (:end . 55)\n  (:start . 46) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 71)\n  (:start . 62) (:id . 52))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 75) (:start . 72)\n  (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 83) (:start . 77)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "dark") (:form . "dark") (:end . 91) (:start . 87)\n  (:id . 57))\n ((:tag . "NN") (:stem . "orange") (:form . "orange") (:end . 98)\n  (:start . 92) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 112)\n  (:start . 102) (:id . 60))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 117) (:start . 113)\n  (:id . 61))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 119) (:start . 118)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 126)\n  (:start . 121) (:id . 64))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 129) (:start . 127)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 131) (:start . 130)\n  (:id . 67))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 136) (:start . 132)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 138) (:start . 137)\n  (:id . 69))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 143) (:start . 139)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 147) (:start . 144)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 155)\n  (:start . 148) (:id . 72))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 169) (:start . 156) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s13.184) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504397@unknown@formal@none@1@S@In 15/29 of these instances, however, residues belonging to non-wildcard positions in the LM regular expression (e.g. the two tryptophans in the C-Mannosylation site regular expression W..W) display equal or higher accessibility values as opposed to wildcard positions (marked in bold in the acc_nwc column of Table S1, additional file 6).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "15/29") (:form . "15/29") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 47))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "VBG") (:stem . "belong") (:form . "belonging") (:end . 56)\n  (:start . 47) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 72)\n  (:start . 60) (:id . 53))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 82)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 111)\n  (:start . 101) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 117) (:start . 113)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "tryptophan") (:form . "tryptophans") (:end . 137)\n  (:start . 126) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 140) (:start . 138)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 66))\n ((:tag . "NN") (:stem . "c-mannosylation") (:form . "C-Mannosylation")\n  (:end . 160) (:start . 145) (:id . 67))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 165) (:start . 161)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 173)\n  (:start . 166) (:id . 69))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 184)\n  (:start . 174) (:id . 70))\n ((:tag . "NNP") (:stem . "W..W") (:form . "W..W") (:end . 189) (:start . 185)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 190) (:start . 189)\n  (:id . 72))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 198)\n  (:start . 191) (:id . 73))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 204)\n  (:start . 199) (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 207) (:start . 205)\n  (:id . 75))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 214)\n  (:start . 208) (:id . 76))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 228) (:start . 215) (:id . 77))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 235)\n  (:start . 229) (:id . 78))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 238) (:start . 236)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "oppose") (:form . "opposed") (:end . 246)\n  (:start . 239) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 249) (:start . 247)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "wildcard") (:form . "wildcard") (:end . 258)\n  (:start . 250) (:id . 82))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 268)\n  (:start . 259) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 270) (:start . 269)\n  (:id . 84))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 276)\n  (:start . 270) (:id . 85))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 279) (:start . 277)\n  (:id . 86))\n ((:tag . "NN") (:stem . "bold") (:form . "bold") (:end . 284) (:start . 280)\n  (:id . 87))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 287) (:start . 285)\n  (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 291) (:start . 288)\n  (:id . 89))\n ((:tag . "NN") (:stem . "acc_nwc") (:form . "acc_nwc") (:end . 299)\n  (:start . 292) (:id . 90))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 306)\n  (:start . 300) (:id . 91))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 309) (:start . 307)\n  (:id . 92))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 315)\n  (:start . 310) (:id . 93))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 318) (:start . 316)\n  (:id . 94))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 319) (:start . 318)\n  (:id . 95))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 330)\n  (:start . 320) (:id . 96))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 335) (:start . 331)\n  (:id . 97))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 337) (:start . 336)\n  (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 338) (:start . 337)\n  (:id . 99))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 339) (:start . 338)\n  (:id . 100)))@@@1@59@((:identifiers (:sid . :s13.185) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504398@unknown@formal@none@1@S@This seems reasonable since LMs are involved in protein interactions and the non-wildcard positions specify LM function.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "seem") (:form . "seems") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "reasonable") (:form . "reasonable") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "NNS") (:stem . "interaction") (:form . "interactions") (:end . 68)\n  (:start . 56) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 89)\n  (:start . 77) (:id . 54))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 99)\n  (:start . 90) (:id . 55))\n ((:tag . "VBP") (:stem . "specify") (:form . "specify") (:end . 107)\n  (:start . 100) (:id . 56))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 110) (:start . 108)\n  (:id . 57))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 119)\n  (:start . 111) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s13.186) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504399@unknown@formal@none@1@S@Importantly, this trend is not seen in the case of LM false positive matches, an observation which helped us to improve the benchmark set as it brought to light some poorly annotated instances.@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "trend") (:form . "trend") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "see") (:form . "seen") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 47) (:start . 43)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 53) (:start . 51)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 59) (:start . 54)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 68)\n  (:start . 60) (:id . 55))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 76)\n  (:start . 69) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 80) (:start . 78)\n  (:id . 58))\n ((:tag . "NN") (:stem . "observation") (:form . "observation") (:end . 92)\n  (:start . 81) (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 98) (:start . 93)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "help") (:form . "helped") (:end . 105)\n  (:start . 99) (:id . 61))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 108) (:start . 106)\n  (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n  (:id . 63))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 119)\n  (:start . 112) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "benchmark") (:form . "benchmark") (:end . 133)\n  (:start . 124) (:id . 66))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 137) (:start . 134)\n  (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 140) (:start . 138)\n  (:id . 68))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 143) (:start . 141)\n  (:id . 69))\n ((:tag . "VBD") (:stem . "bring") (:form . "brought") (:end . 151)\n  (:start . 144) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 154) (:start . 152)\n  (:id . 71))\n ((:tag . "VB") (:stem . "light") (:form . "light") (:end . 160)\n  (:start . 155) (:id . 72))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 165) (:start . 161)\n  (:id . 73))\n ((:tag . "RB") (:stem . "poorly") (:form . "poorly") (:end . 172)\n  (:start . 166) (:id . 74))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 182)\n  (:start . 173) (:id . 75))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 192)\n  (:start . 183) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s13.187) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504400@unknown@formal@none@1@S@See additional file 1 for details.@(((:tag . "VB") (:stem . "see") (:form . "See") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 19) (:start . 15)\n  (:id . 44))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 33)\n  (:start . 26) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 34) (:start . 33)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s13.188) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504401@unknown@formal@none@1@S@In the benchmark dataset there are a few cases (10/158) of almost completely buried true motif instances, i.e. displaying an average relative accessibility < 0.2 on the non-wildcard positions.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "benchmark") (:form . "benchmark") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "EX") (:stem . "there") (:form . "there") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "case") (:form . "cases") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "CD") (:stem . "10/158") (:form . "10/158") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 54))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 65)\n  (:start . 59) (:id . 55))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 76)\n  (:start . 66) (:id . 56))\n ((:tag . "VBN") (:stem . "bury") (:form . "buried") (:end . 83) (:start . 77)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 88) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 94) (:start . 89)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 104)\n  (:start . 95) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 61))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 110) (:start . 106)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "display") (:form . "displaying") (:end . 121)\n  (:start . 111) (:id . 63))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 124) (:start . 122)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 132)\n  (:start . 125) (:id . 65))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 141)\n  (:start . 133) (:id . 66))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 155) (:start . 142) (:id . 67))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 157) (:start . 156)\n  (:id . 68))\n ((:tag . "CD") (:stem . "0.2") (:form . "0.2") (:end . 161) (:start . 158)\n  (:id . 69))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 164) (:start . 162)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "non-wildcard") (:form . "non-wildcard") (:end . 181)\n  (:start . 169) (:id . 72))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 191)\n  (:start . 182) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s13.189) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504402@unknown@formal@none@1@S@We analysed them one by one by manual inspection and concluded that they fall in one of two situations: either their functional residue(s), or at least their side chains, are favourably oriented outwards from the domain surface (see additional file 1, additional file 6, and Figure 2g and 2h), or an allosteric effect is either known or reasonable to hypothesize.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "analyse") (:form . "analysed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "manual") (:form . "manual") (:end . 37)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "inspection") (:form . "inspection") (:end . 48)\n  (:start . 38) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "conclude") (:form . "concluded") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "fall") (:form . "fall") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "situation") (:form . "situations") (:end . 102)\n  (:start . 92) (:id . 60))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 110)\n  (:start . 104) (:id . 62))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 116)\n  (:start . 111) (:id . 63))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 127)\n  (:start . 117) (:id . 64))\n ((:tag . "NN") (:stem . "residue(s)") (:form . "residue(s)") (:end . 138)\n  (:start . 128) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 142) (:start . 140)\n  (:id . 67))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 145) (:start . 143)\n  (:id . 68))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 151)\n  (:start . 146) (:id . 69))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 157)\n  (:start . 152) (:id . 70))\n ((:tag . "NN") (:stem . "side") (:form . "side") (:end . 162) (:start . 158)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "chain") (:form . "chains") (:end . 169)\n  (:start . 163) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 170) (:start . 169)\n  (:id . 73))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 174) (:start . 171)\n  (:id . 74))\n ((:tag . "RB") (:stem . "favourably") (:form . "favourably") (:end . 185)\n  (:start . 175) (:id . 75))\n ((:tag . "VBN") (:stem . "orient") (:form . "oriented") (:end . 194)\n  (:start . 186) (:id . 76))\n ((:tag . "NNS") (:stem . "outward") (:form . "outwards") (:end . 203)\n  (:start . 195) (:id . 77))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 208) (:start . 204)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 212) (:start . 209)\n  (:id . 79))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 219)\n  (:start . 213) (:id . 80))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 227)\n  (:start . 220) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 229) (:start . 228)\n  (:id . 82))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 232) (:start . 229)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 243)\n  (:start . 233) (:id . 84))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 248) (:start . 244)\n  (:id . 85))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 250) (:start . 249)\n  (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 251) (:start . 250)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 262)\n  (:start . 252) (:id . 88))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 267) (:start . 263)\n  (:id . 89))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 269) (:start . 268)\n  (:id . 90))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 270) (:start . 269)\n  (:id . 91))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 274) (:start . 271)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 281)\n  (:start . 275) (:id . 93))\n ((:tag . "NN") (:stem . "2g") (:form . "2g") (:end . 284) (:start . 282)\n  (:id . 94))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 288) (:start . 285)\n  (:id . 95))\n ((:tag . "NN") (:stem . "2h") (:form . "2h") (:end . 291) (:start . 289)\n  (:id . 96))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 292) (:start . 291)\n  (:id . 97))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 293) (:start . 292)\n  (:id . 98))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 296) (:start . 294)\n  (:id . 99))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 299) (:start . 297)\n  (:id . 100))\n ((:tag . "JJ") (:stem . "allosteric") (:form . "allosteric") (:end . 310)\n  (:start . 300) (:id . 101))\n ((:tag . "NN") (:stem . "effect") (:form . "effect") (:end . 317)\n  (:start . 311) (:id . 102))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 320) (:start . 318)\n  (:id . 103))\n ((:tag . "RB") (:stem . "either") (:form . "either") (:end . 327)\n  (:start . 321) (:id . 104))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 333)\n  (:start . 328) (:id . 105))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 336) (:start . 334)\n  (:id . 106))\n ((:tag . "JJ") (:stem . "reasonable") (:form . "reasonable") (:end . 347)\n  (:start . 337) (:id . 107))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 350) (:start . 348)\n  (:id . 108))\n ((:tag . "VB") (:stem . "hypothesize") (:form . "hypothesize") (:end . 362)\n  (:start . 351) (:id . 109))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 363) (:start . 362)\n  (:id . 110)))@@@1@69@((:identifiers (:sid . :s13.190) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504403@unknown@formal@none@1@S@Additional file 1 reports details and specific examples.@(((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "report") (:form . "reports") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s13.191) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504404@unknown@formal@none@1@S@Discussion@(((:tag . "NN") (:stem . "discussion") (:form . "Discussion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s13.192) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504405@unknown@formal@none@1@S@We have set up a procedure to help in the discrimination of true from false positive LM matches, that is based on the information coming from two important features inherent to the 3D structure of proteins: accessibility to the solvent and secondary structure element.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 26)\n  (:start . 17) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 48))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 34) (:start . 30)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 37) (:start . 35)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 51))\n ((:tag . "NN") (:stem . "discrimination") (:form . "discrimination")\n  (:end . 56) (:start . 42) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 64) (:start . 60)\n  (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 69) (:start . 65)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 75) (:start . 70)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 84)\n  (:start . 76) (:id . 57))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 95)\n  (:start . 88) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 101) (:start . 97)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 104) (:start . 102)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 110)\n  (:start . 105) (:id . 63))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 113) (:start . 111)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 65))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 129)\n  (:start . 118) (:id . 66))\n ((:tag . "VBG") (:stem . "come") (:form . "coming") (:end . 136)\n  (:start . 130) (:id . 67))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 141) (:start . 137)\n  (:id . 68))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 145) (:start . 142)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 155)\n  (:start . 146) (:id . 70))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 164)\n  (:start . 156) (:id . 71))\n ((:tag . "JJ") (:stem . "inherent") (:form . "inherent") (:end . 173)\n  (:start . 165) (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 176) (:start . 174)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 180) (:start . 177)\n  (:id . 74))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 183) (:start . 181)\n  (:id . 75))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 193)\n  (:start . 184) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 196) (:start . 194)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 205)\n  (:start . 197) (:id . 78))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 206) (:start . 205)\n  (:id . 79))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 220) (:start . 207) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 223) (:start . 221)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 227) (:start . 224)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "solvent") (:form . "solvent") (:end . 235)\n  (:start . 228) (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 239) (:start . 236)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 249)\n  (:start . 240) (:id . 85))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 259)\n  (:start . 250) (:id . 86))\n ((:tag . "NN") (:stem . "element") (:form . "element") (:end . 267)\n  (:start . 260) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 268) (:start . 267)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s13.193) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504406@unknown@formal@none@1@S@The fact that functional LMs tend to be in flexible and accessible regions of proteins is biologically sound and is furthermore supported by the structural analysis of experimentally validated instances of LMs carried out in this work.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "tend") (:form . "tend") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "flexible") (:form . "flexible") (:end . 51)\n  (:start . 43) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "accessible") (:form . "accessible") (:end . 66)\n  (:start . 56) (:id . 53))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 74)\n  (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "RB") (:stem . "biologically") (:form . "biologically") (:end . 102)\n  (:start . 90) (:id . 58))\n ((:tag . "JJ") (:stem . "sound") (:form . "sound") (:end . 108)\n  (:start . 103) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 115) (:start . 113)\n  (:id . 61))\n ((:tag . "RB") (:stem . "furthermore") (:form . "furthermore") (:end . 127)\n  (:start . 116) (:id . 62))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 137)\n  (:start . 128) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 140) (:start . 138)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 155)\n  (:start . 145) (:id . 66))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 164)\n  (:start . 156) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 167) (:start . 165)\n  (:id . 68))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n  (:end . 182) (:start . 168) (:id . 69))\n ((:tag . "VBN") (:stem . "validate") (:form . "validated") (:end . 192)\n  (:start . 183) (:id . 70))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 202)\n  (:start . 193) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 209) (:start . 206)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 217)\n  (:start . 210) (:id . 74))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 221) (:start . 218)\n  (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 224) (:start . 222)\n  (:id . 76))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 229) (:start . 225)\n  (:id . 77))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 234) (:start . 230)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 235) (:start . 234)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s13.194) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504407@unknown@formal@none@1@S@As a consequence, our approach will advise a user against considering a match as a true motif if it resides in an unfavourable structural context.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "consequence") (:form . "consequence") (:end . 16)\n  (:start . 5) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 30)\n  (:start . 22) (:id . 47))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "VB") (:stem . "advise") (:form . "advise") (:end . 42)\n  (:start . 36) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 49) (:start . 45)\n  (:id . 51))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . "VBG") (:stem . "consider") (:form . "considering") (:end . 69)\n  (:start . 58) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 87) (:start . 83)\n  (:id . 58))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 93) (:start . 88)\n  (:id . 59))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 96) (:start . 94)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 99) (:start . 97)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "reside") (:form . "resides") (:end . 107)\n  (:start . 100) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n  (:id . 63))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 113) (:start . 111)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "unfavourable") (:form . "unfavourable") (:end . 126)\n  (:start . 114) (:id . 65))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 137)\n  (:start . 127) (:id . 66))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 145)\n  (:start . 138) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s13.195) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504408@unknown@formal@none@1@S@Nevertheless, the function of proteins can be regulated by an assortment of different mechanisms, and allosteric modifications or unusual LM position and/or conformation are infrequent but possible.@(((:tag . "RB") (:stem . "nevertheless") (:form . "Nevertheless") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "regulate") (:form . "regulated") (:end . 55)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "assortment") (:form . "assortment") (:end . 72)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 85)\n  (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "mechanism") (:form . "mechanisms") (:end . 96)\n  (:start . 86) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "allosteric") (:form . "allosteric") (:end . 112)\n  (:start . 102) (:id . 59))\n ((:tag . "NNS") (:stem . "modification") (:form . "modifications")\n  (:end . 126) (:start . 113) (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 129) (:start . 127)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "unusual") (:form . "unusual") (:end . 137)\n  (:start . 130) (:id . 62))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 140) (:start . 138)\n  (:id . 63))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 149)\n  (:start . 141) (:id . 64))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 156)\n  (:start . 150) (:id . 65))\n ((:tag . "NN") (:stem . "conformation") (:form . "conformation") (:end . 169)\n  (:start . 157) (:id . 66))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 173) (:start . 170)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "infrequent") (:form . "infrequent") (:end . 184)\n  (:start . 174) (:id . 68))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 188) (:start . 185)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 197)\n  (:start . 189) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x13.196.1) (:span 189 197)))\n (:hscopes ((:id . :x13.196.1) (:span 102 197)))\n (:identifiers (:sid . :s13.196) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504409@unknown@formal@none@1@S@In this sense, we encourage the user to carefully evaluate the possibility that a hidden motif can become exposed upon protein interaction and to use the ELM structure filter cum grano salis, i.e. not as a deterministic predictor but rather by exploiting the supplied 3D information on LM predictions as a supplement to a prior knowledge of the LM biological context.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "sense") (:form . "sense") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "encourage") (:form . "encourage") (:end . 27)\n  (:start . 18) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 36) (:start . 32)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "RB") (:stem . "carefully") (:form . "carefully") (:end . 49)\n  (:start . 40) (:id . 51))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 58)\n  (:start . 50) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "possibility") (:form . "possibility") (:end . 74)\n  (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 79) (:start . 75)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "hidden") (:form . "hidden") (:end . 88)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 94) (:start . 89)\n  (:id . 58))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "VB") (:stem . "become") (:form . "become") (:end . 105)\n  (:start . 99) (:id . 60))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 113)\n  (:start . 106) (:id . 61))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 118) (:start . 114)\n  (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 126)\n  (:start . 119) (:id . 63))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 138)\n  (:start . 127) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 145) (:start . 143)\n  (:id . 66))\n ((:tag . "VB") (:stem . "use") (:form . "use") (:end . 149) (:start . 146)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 157) (:start . 154)\n  (:id . 69))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 167)\n  (:start . 158) (:id . 70))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 174)\n  (:start . 168) (:id . 71))\n ((:tag . "NN") (:stem . "cum") (:form . "cum") (:end . 178) (:start . 175)\n  (:id . 72))\n ((:tag . "NN") (:stem . "grano") (:form . "grano") (:end . 184)\n  (:start . 179) (:id . 73))\n ((:tag . "NN") (:stem . "salis") (:form . "salis") (:end . 190)\n  (:start . 185) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n  (:id . 75))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 196) (:start . 192)\n  (:id . 76))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 200) (:start . 197)\n  (:id . 77))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 203) (:start . 201)\n  (:id . 78))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 205) (:start . 204)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "deterministic") (:form . "deterministic")\n  (:end . 219) (:start . 206) (:id . 80))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 229)\n  (:start . 220) (:id . 81))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 233) (:start . 230)\n  (:id . 82))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 240)\n  (:start . 234) (:id . 83))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 243) (:start . 241)\n  (:id . 84))\n ((:tag . "VBG") (:stem . "exploit") (:form . "exploiting") (:end . 254)\n  (:start . 244) (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 258) (:start . 255)\n  (:id . 86))\n ((:tag . "VBN") (:stem . "supply") (:form . "supplied") (:end . 267)\n  (:start . 259) (:id . 87))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 270) (:start . 268)\n  (:id . 88))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 282)\n  (:start . 271) (:id . 89))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 285) (:start . 283)\n  (:id . 90))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 288) (:start . 286)\n  (:id . 91))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 300)\n  (:start . 289) (:id . 92))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 303) (:start . 301)\n  (:id . 93))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 305) (:start . 304)\n  (:id . 94))\n ((:tag . "NN") (:stem . "supplement") (:form . "supplement") (:end . 316)\n  (:start . 306) (:id . 95))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 319) (:start . 317)\n  (:id . 96))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 321) (:start . 320)\n  (:id . 97))\n ((:tag . "JJ") (:stem . "prior") (:form . "prior") (:end . 327)\n  (:start . 322) (:id . 98))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 337)\n  (:start . 328) (:id . 99))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 340) (:start . 338)\n  (:id . 100))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 344) (:start . 341)\n  (:id . 101))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 347) (:start . 345)\n  (:id . 102))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 358)\n  (:start . 348) (:id . 103))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 366)\n  (:start . 359) (:id . 104))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 367) (:start . 366)\n  (:id . 105)))@@@1@64@((:hcues ((:id . :x13.197.1) (:span 95 98)) ((:id . :x13.197.2) (:span 50 74)))\n (:hscopes ((:id . :x13.197.1) (:span 95 138))\n  ((:id . :x13.197.2) (:span 50 366)))\n (:identifiers (:sid . :s13.197) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504410@unknown@formal@none@1@S@The ELM resource now provides three ways to aid the user about structural context for the query sequence.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "way") (:form . "ways") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n  (:id . 49))\n ((:tag . "VB") (:stem . "aid") (:form . "aid") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 62) (:start . 57)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 73)\n  (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 81)\n  (:start . 74) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 95) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 104)\n  (:start . 96) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s13.198) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504411@unknown@formal@none@1@S@The disorder predictor GlobPlot highlights potential motif-rich regions that are likely to be intrinsically unstructured.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "disorder") (:form . "disorder") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "globplot") (:form . "GlobPlot") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "VBZ") (:stem . "highlight") (:form . "highlights") (:end . 42)\n  (:start . 32) (:id . 46))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 52)\n  (:start . 43) (:id . 47))\n ((:tag . "JJ") (:stem . "motif-rich") (:form . "motif-rich") (:end . 63)\n  (:start . 53) (:id . 48))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 71)\n  (:start . 64) (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 76) (:start . 72)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 80) (:start . 77)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "likely") (:form . "likely") (:end . 87)\n  (:start . 81) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 90) (:start . 88)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 93) (:start . 91)\n  (:id . 54))\n ((:tag . "RB") (:stem . "intrinsically") (:form . "intrinsically")\n  (:end . 107) (:start . 94) (:id . 55))\n ((:tag . "JJ") (:stem . "unstructured") (:form . "unstructured") (:end . 120)\n  (:start . 108) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 57)))@@@1@16@((:hcues ((:id . :x13.199.1) (:span 81 87)) ((:id . :x13.199.2) (:span 43 52)))\n (:hscopes ((:id . :x13.199.1) (:span 77 120))\n  ((:id . :x13.199.2) (:span 43 71)))\n (:identifiers (:sid . :s13.199) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504412@unknown@formal@none@1@S@SMART and Pfam domains define regions of well-defined globular structure where LMs are expected to be rare.@(((:tag . "NN") (:stem . "smart") (:form . "SMART") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "pfam") (:form . "Pfam") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "VBP") (:stem . "define") (:form . "define") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "well-defined") (:form . "well-defined") (:end . 53)\n  (:start . 41) (:id . 49))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 72)\n  (:start . 63) (:id . 51))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 78) (:start . 73)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 82) (:start . 79)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 86) (:start . 83)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 95)\n  (:start . 87) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 101) (:start . 99)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "rare") (:form . "rare") (:end . 106) (:start . 102)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s13.200) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504413@unknown@formal@none@1@S@Where it can be applied, the new structure filter now provides a benchmarked estimate of LM likelihood.@(((:tag . "WRB") (:stem . "where") (:form . "Where") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 32) (:start . 29)\n  (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 42)\n  (:start . 33) (:id . 50))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 49)\n  (:start . 43) (:id . 51))\n ((:tag . "RB") (:stem . "now") (:form . "now") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 62)\n  (:start . 54) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "benchmarked") (:form . "benchmarked") (:end . 76)\n  (:start . 65) (:id . 55))\n ((:tag . "NN") (:stem . "estimate") (:form . "estimate") (:end . 85)\n  (:start . 77) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "likelihood") (:form . "likelihood") (:end . 102)\n  (:start . 92) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s13.201) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504414@unknown@formal@none@1@S@MnM has taken a different approach to structural context, a single score for each pattern match being provided by an accessibility prediction algorithm, SPS [24,48].@(((:tag . "NNP") (:stem . "MnM") (:form . "MnM") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 25)\n  (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 48)\n  (:start . 38) (:id . 49))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "single") (:form . "single") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 89)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 95) (:start . 90)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 110)\n  (:start . 102) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 116) (:start . 114)\n  (:id . 62))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 130) (:start . 117) (:id . 63))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 141)\n  (:start . 131) (:id . 64))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 151)\n  (:start . 142) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "SPS") (:form . "SPS") (:end . 156) (:start . 153)\n  (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 158) (:start . 157)\n  (:id . 68))\n ((:tag . "CD") (:stem . "24,48") (:form . "24,48") (:end . 163)\n  (:start . 158) (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 164) (:start . 163)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s13.202) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504415@unknown@formal@none@1@S@While MnM does not supply domain and tertiary structural information that is highly informative to the user, an accessibility predictor does have a unique value for a substantial fraction of protein sequence space that is predicted to be globular but is not known to be related to a solved domain structure.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "MnM") (:form . "MnM") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "VB") (:stem . "supply") (:form . "supply") (:end . 25)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 32)\n  (:start . 26) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "tertiary") (:form . "tertiary") (:end . 45)\n  (:start . 37) (:id . 49))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 68)\n  (:start . 57) (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 83)\n  (:start . 77) (:id . 54))\n ((:tag . "JJ") (:stem . "informative") (:form . "informative") (:end . 95)\n  (:start . 84) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 98) (:start . 96)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 107) (:start . 103)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 59))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 111) (:start . 109)\n  (:id . 60))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 125) (:start . 112) (:id . 61))\n ((:tag . "NN") (:stem . "predictor") (:form . "predictor") (:end . 135)\n  (:start . 126) (:id . 62))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 140) (:start . 136)\n  (:id . 63))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 145) (:start . 141)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 147) (:start . 146)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 154)\n  (:start . 148) (:id . 66))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 160)\n  (:start . 155) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 164) (:start . 161)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 166) (:start . 165)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "substantial") (:form . "substantial") (:end . 178)\n  (:start . 167) (:id . 70))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 187)\n  (:start . 179) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 190) (:start . 188)\n  (:id . 72))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 198)\n  (:start . 191) (:id . 73))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 207)\n  (:start . 199) (:id . 74))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 213)\n  (:start . 208) (:id . 75))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 218) (:start . 214)\n  (:id . 76))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 221) (:start . 219)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 231)\n  (:start . 222) (:id . 78))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 234) (:start . 232)\n  (:id . 79))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 237) (:start . 235)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 246)\n  (:start . 238) (:id . 81))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 250) (:start . 247)\n  (:id . 82))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 253) (:start . 251)\n  (:id . 83))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 257) (:start . 254)\n  (:id . 84))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 263)\n  (:start . 258) (:id . 85))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 266) (:start . 264)\n  (:id . 86))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 269) (:start . 267)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "related") (:form . "related") (:end . 277)\n  (:start . 270) (:id . 88))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 280) (:start . 278)\n  (:id . 89))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 282) (:start . 281)\n  (:id . 90))\n ((:tag . "VBN") (:stem . "solve") (:form . "solved") (:end . 289)\n  (:start . 283) (:id . 91))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 296)\n  (:start . 290) (:id . 92))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 306)\n  (:start . 297) (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 307) (:start . 306)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s13.203) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504416@unknown@formal@none@1@S@In future, we may also consider introducing a predictive accessibility filter into ELM for poorly characterised globular peptide segments.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "future") (:form . "future") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 17) (:start . 14)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 22) (:start . 18)\n  (:id . 47))\n ((:tag . "VB") (:stem . "consider") (:form . "consider") (:end . 31)\n  (:start . 23) (:id . 48))\n ((:tag . "VBG") (:stem . "introduce") (:form . "introducing") (:end . 43)\n  (:start . 32) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "predictive") (:form . "predictive") (:end . 56)\n  (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 70) (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 77)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 82) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "RB") (:stem . "poorly") (:form . "poorly") (:end . 97)\n  (:start . 91) (:id . 57))\n ((:tag . "VBN") (:stem . "characterise") (:form . "characterised")\n  (:end . 111) (:start . 98) (:id . 58))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 120)\n  (:start . 112) (:id . 59))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 128)\n  (:start . 121) (:id . 60))\n ((:tag . "NNS") (:stem . "segment") (:form . "segments") (:end . 137)\n  (:start . 129) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x13.204.1) (:span 14 17)))\n (:hscopes ((:id . :x13.204.1) (:span 14 137)))\n (:identifiers (:sid . :s13.204) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504417@unknown@formal@none@1@S@There are many algorithms in the literature, with the current best performing reported to be NetSurfP and Real_SPINE [49,50].@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "literature") (:form . "literature") (:end . 43)\n  (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 66) (:start . 62)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "perform") (:form . "performing") (:end . 77)\n  (:start . 67) (:id . 54))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 86)\n  (:start . 78) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "NetSurfP") (:form . "NetSurfP") (:end . 101)\n  (:start . 93) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Real_SPINE") (:form . "Real_SPINE") (:end . 116)\n  (:start . 106) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "CD") (:stem . "49,50") (:form . "49,50") (:end . 123)\n  (:start . 118) (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s13.205) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504418@unknown@formal@none@1@S@Besides the results on the structure filter discrimination power presented in this work, we want to point out that the process of developing the structure filter has already proven of value to the ELM resource.@(((:tag . "IN") (:stem . "besides") (:form . "Besides") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "discrimination") (:form . "discrimination")\n  (:end . 58) (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 64) (:start . 59)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "present") (:form . "presented") (:end . 74)\n  (:start . 65) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 52))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 82) (:start . 78)\n  (:id . 53))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 87) (:start . 83)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 91) (:start . 89)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "want") (:form . "want") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "VB") (:stem . "point") (:form . "point") (:end . 105)\n  (:start . 100) (:id . 59))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 109) (:start . 106)\n  (:id . 60))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 114) (:start . 110)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 62))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 126)\n  (:start . 119) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 140)\n  (:start . 130) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 66))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 154)\n  (:start . 145) (:id . 67))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 161)\n  (:start . 155) (:id . 68))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 165) (:start . 162)\n  (:id . 69))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 173)\n  (:start . 166) (:id . 70))\n ((:tag . "VBN") (:stem . "prove") (:form . "proven") (:end . 180)\n  (:start . 174) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 183) (:start . 181)\n  (:id . 72))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 189)\n  (:start . 184) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 192) (:start . 190)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 200) (:start . 197)\n  (:id . 76))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 209)\n  (:start . 201) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 210) (:start . 209)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s13.206) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504419@unknown@formal@none@1@S@The structural analysis of annotated motifs reported in section 2.1 highlighted a number of questionable motifs that turned out to be incorrectly annotated with weak or conflicting support in the literature.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 36)\n  (:start . 27) (:id . 46))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 43)\n  (:start . 37) (:id . 47))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 52)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "section") (:form . "section") (:end . 63)\n  (:start . 56) (:id . 50))\n ((:tag . "CD") (:stem . "2.1") (:form . "2.1") (:end . 67) (:start . 64)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "highlight") (:form . "highlighted") (:end . 79)\n  (:start . 68) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 81) (:start . 80)\n  (:id . 53))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 88)\n  (:start . 82) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "questionable") (:form . "questionable") (:end . 104)\n  (:start . 92) (:id . 56))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 111)\n  (:start . 105) (:id . 57))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 116) (:start . 112)\n  (:id . 58))\n ((:tag . "VBD") (:stem . "turn") (:form . "turned") (:end . 123)\n  (:start . 117) (:id . 59))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 127) (:start . 124)\n  (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 130) (:start . 128)\n  (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 133) (:start . 131)\n  (:id . 62))\n ((:tag . "RB") (:stem . "incorrectly") (:form . "incorrectly") (:end . 145)\n  (:start . 134) (:id . 63))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 155)\n  (:start . 146) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 160) (:start . 156)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "weak") (:form . "weak") (:end . 165) (:start . 161)\n  (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 168) (:start . 166)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "conflict") (:form . "conflicting") (:end . 180)\n  (:start . 169) (:id . 68))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 188)\n  (:start . 181) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 191) (:start . 189)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 195) (:start . 192)\n  (:id . 71))\n ((:tag . "NN") (:stem . "literature") (:form . "literature") (:end . 206)\n  (:start . 196) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s13.207) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504420@unknown@formal@none@1@S@In this regard, experimentalists should be aware that accurate annotation of LMs concurs with developing effective methodologies aimed at identifying new putative motifs and that inference of shortlists of candidate true motifs is especially useful to reduce the number of assays needed to experimentally validate a new LM.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "regard") (:form . "regard") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "experimentalist") (:form . "experimentalists")\n  (:end . 32) (:start . 16) (:id . 46))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "aware") (:form . "aware") (:end . 48) (:start . 43)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "accurate") (:form . "accurate") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 73)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "LM") (:form . "LMs") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "concur") (:form . "concurs") (:end . 88)\n  (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 93) (:start . 89)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "develop") (:form . "developing") (:end . 104)\n  (:start . 94) (:id . 57))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 114)\n  (:start . 105) (:id . 58))\n ((:tag . "NNS") (:stem . "methodology") (:form . "methodologies")\n  (:end . 128) (:start . 115) (:id . 59))\n ((:tag . "VBN") (:stem . "aim") (:form . "aimed") (:end . 134) (:start . 129)\n  (:id . 60))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 137) (:start . 135)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 149)\n  (:start . 138) (:id . 62))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 153) (:start . 150)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 162)\n  (:start . 154) (:id . 64))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 169)\n  (:start . 163) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 173) (:start . 170)\n  (:id . 66))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 178) (:start . 174)\n  (:id . 67))\n ((:tag . "NN") (:stem . "inference") (:form . "inference") (:end . 188)\n  (:start . 179) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 191) (:start . 189)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "shortlist") (:form . "shortlists") (:end . 202)\n  (:start . 192) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n  (:id . 71))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 215)\n  (:start . 206) (:id . 72))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 220) (:start . 216)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 227)\n  (:start . 221) (:id . 74))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 230) (:start . 228)\n  (:id . 75))\n ((:tag . "RB") (:stem . "especially") (:form . "especially") (:end . 241)\n  (:start . 231) (:id . 76))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 248)\n  (:start . 242) (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 251) (:start . 249)\n  (:id . 78))\n ((:tag . "VB") (:stem . "reduce") (:form . "reduce") (:end . 258)\n  (:start . 252) (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 262) (:start . 259)\n  (:id . 80))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 269)\n  (:start . 263) (:id . 81))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 272) (:start . 270)\n  (:id . 82))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 279)\n  (:start . 273) (:id . 83))\n ((:tag . "VBN") (:stem . "need") (:form . "needed") (:end . 286)\n  (:start . 280) (:id . 84))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 289) (:start . 287)\n  (:id . 85))\n ((:tag . "RB") (:stem . "experimentally") (:form . "experimentally")\n  (:end . 304) (:start . 290) (:id . 86))\n ((:tag . "VB") (:stem . "validate") (:form . "validate") (:end . 313)\n  (:start . 305) (:id . 87))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 315) (:start . 314)\n  (:id . 88))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 319) (:start . 316)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 322) (:start . 320)\n  (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 323) (:start . 322)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s13.208) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504421@unknown@formal@none@1@S@Thus, the experimental strategy adopted to detect functional motifs plays a fundamental role and incorporating some simple stratagems in experimental protocols might crucially help in reducing the number of false motifs in the literature.@(((:tag . "RB") (:stem . "thus") (:form . "Thus") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 22)\n  (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "VBN") (:stem . "adopt") (:form . "adopted") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 60)\n  (:start . 50) (:id . 50))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 67)\n  (:start . 61) (:id . 51))\n ((:tag . "VBZ") (:stem . "play") (:form . "plays") (:end . 73) (:start . 68)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "fundamental") (:form . "fundamental") (:end . 87)\n  (:start . 76) (:id . 54))\n ((:tag . "NN") (:stem . "role") (:form . "role") (:end . 92) (:start . 88)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "incorporate") (:form . "incorporating")\n  (:end . 110) (:start . 97) (:id . 57))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 115) (:start . 111)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "simple") (:form . "simple") (:end . 122)\n  (:start . 116) (:id . 59))\n ((:tag . "NNS") (:stem . "stratagem") (:form . "stratagems") (:end . 133)\n  (:start . 123) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 149)\n  (:start . 137) (:id . 62))\n ((:tag . "NNS") (:stem . "protocol") (:form . "protocols") (:end . 159)\n  (:start . 150) (:id . 63))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 165)\n  (:start . 160) (:id . 64))\n ((:tag . "RB") (:stem . "crucially") (:form . "crucially") (:end . 175)\n  (:start . 166) (:id . 65))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 180) (:start . 176)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 183) (:start . 181)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "reduce") (:form . "reducing") (:end . 192)\n  (:start . 184) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 196) (:start . 193)\n  (:id . 69))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 203)\n  (:start . 197) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 206) (:start . 204)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 212)\n  (:start . 207) (:id . 72))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 219)\n  (:start . 213) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 222) (:start . 220)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 226) (:start . 223)\n  (:id . 75))\n ((:tag . "NN") (:stem . "literature") (:form . "literature") (:end . 237)\n  (:start . 227) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x13.209.1) (:span 160 165)))\n (:hscopes ((:id . :x13.209.1) (:span 160 237)))\n (:identifiers (:sid . :s13.209) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504422@unknown@formal@none@1@S@We consider a pair of much too rarely undertaken controls to be especially important when candidate motifs are mutated [4]: (1)@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "consider") (:form . "consider") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "RB") (:stem . "too") (:form . "too") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "RB") (:stem . "rarely") (:form . "rarely") (:end . 37)\n  (:start . 31) (:id . 49))\n ((:tag . "VBN") (:stem . "undertake") (:form . "undertaken") (:end . 48)\n  (:start . 38) (:id . 50))\n ((:tag . "NNS") (:stem . "control") (:form . "controls") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "RB") (:stem . "especially") (:form . "especially") (:end . 74)\n  (:start . 64) (:id . 54))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 84)\n  (:start . 75) (:id . 55))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 99)\n  (:start . 90) (:id . 57))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 106)\n  (:start . 100) (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 110) (:start . 107)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 118)\n  (:start . 111) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 121) (:start . 120)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 123) (:start . 122)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 65))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 126) (:start . 125)\n  (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 127) (:start . 126)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s13.210) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504423@unknown@formal@none@1@S@Check if the motif mutation unfolds the protein by cloning in a tagged expression construct that allows fast and easy purification of the protein and examine folding status by e.g. circular dichroism (or NMR if available); (2)@(((:tag . "VB") (:stem . "check") (:form . "Check") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 27)\n  (:start . 19) (:id . 46))\n ((:tag . "VBZ") (:stem . "unfold") (:form . "unfolds") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "clone") (:form . "cloning") (:end . 58)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "tag") (:form . "tagged") (:end . 70) (:start . 64)\n  (:id . 54))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 81)\n  (:start . 71) (:id . 55))\n ((:tag . "NN") (:stem . "construct") (:form . "construct") (:end . 91)\n  (:start . 82) (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "JJ") (:stem . "fast") (:form . "fast") (:end . 108) (:start . 104)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "easy") (:form . "easy") (:end . 117) (:start . 113)\n  (:id . 61))\n ((:tag . "NN") (:stem . "purification") (:form . "purification") (:end . 130)\n  (:start . 118) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 64))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 145)\n  (:start . 138) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 149) (:start . 146)\n  (:id . 66))\n ((:tag . "NN") (:stem . "examine") (:form . "examine") (:end . 157)\n  (:start . 150) (:id . 67))\n ((:tag . "NN") (:stem . "folding") (:form . "folding") (:end . 165)\n  (:start . 158) (:id . 68))\n ((:tag . "NN") (:stem . "status") (:form . "status") (:end . 172)\n  (:start . 166) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 175) (:start . 173)\n  (:id . 70))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 180) (:start . 176)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "circular") (:form . "circular") (:end . 189)\n  (:start . 181) (:id . 72))\n ((:tag . "NN") (:stem . "dichroism") (:form . "dichroism") (:end . 199)\n  (:start . 190) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 201) (:start . 200)\n  (:id . 74))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 203) (:start . 201)\n  (:id . 75))\n ((:tag . "NN") (:stem . "nmr") (:form . "NMR") (:end . 207) (:start . 204)\n  (:id . 76))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 210) (:start . 208)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 220)\n  (:start . 211) (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 221) (:start . 220)\n  (:id . 79))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 222) (:start . 221)\n  (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 224) (:start . 223)\n  (:id . 81))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 225) (:start . 224)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 226) (:start . 225)\n  (:id . 83)))@@@1@42@((:hcues ((:id . :x13.211.1) (:span 6 8)))\n (:hscopes ((:id . :x13.211.1) (:span 6 145)))\n (:identifiers (:sid . :s13.211) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504424@unknown@formal@none@1@S@When transfecting with mutated proteins, examine the cells by microscopy for intracellular amyloid caused by massive overexpression of unfolded protein and, if it is present, then reason out why the assay is misleading (e.g. remember that amyloids are not subject to ubiquitin-mediated destruction processes so destruction box and degron motif mutation assays give misleading results).@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "transfecte") (:form . "transfecting") (:end . 17)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 22) (:start . 18)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "mutate") (:form . "mutated") (:end . 30)\n  (:start . 23) (:id . 45))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 39)\n  (:start . 31) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 47))\n ((:tag . "VB") (:stem . "examine") (:form . "examine") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 58) (:start . 53)\n  (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "NN") (:stem . "microscopy") (:form . "microscopy") (:end . 72)\n  (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 76) (:start . 73)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "intracellular") (:form . "intracellular")\n  (:end . 90) (:start . 77) (:id . 54))\n ((:tag . "NN") (:stem . "amyloid") (:form . "amyloid") (:end . 98)\n  (:start . 91) (:id . 55))\n ((:tag . "VBN") (:stem . "cause") (:form . "caused") (:end . 105)\n  (:start . 99) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 108) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "massive") (:form . "massive") (:end . 116)\n  (:start . 109) (:id . 58))\n ((:tag . "NN") (:stem . "overexpression") (:form . "overexpression")\n  (:end . 131) (:start . 117) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "unfolded") (:form . "unfolded") (:end . 143)\n  (:start . 135) (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 151)\n  (:start . 144) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 155) (:start . 152)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 64))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 159) (:start . 157)\n  (:id . 65))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 162) (:start . 160)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 165) (:start . 163)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 173)\n  (:start . 166) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 69))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 179) (:start . 175)\n  (:id . 70))\n ((:tag . "VB") (:stem . "reason") (:form . "reason") (:end . 186)\n  (:start . 180) (:id . 71))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 190) (:start . 187)\n  (:id . 72))\n ((:tag . "WRB") (:stem . "why") (:form . "why") (:end . 194) (:start . 191)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 198) (:start . 195)\n  (:id . 74))\n ((:tag . "NN") (:stem . "assay") (:form . "assay") (:end . 204)\n  (:start . 199) (:id . 75))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 207) (:start . 205)\n  (:id . 76))\n ((:tag . "VBG") (:stem . "mislead") (:form . "misleading") (:end . 218)\n  (:start . 208) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 220) (:start . 219)\n  (:id . 78))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 224) (:start . 220)\n  (:id . 79))\n ((:tag . "NN") (:stem . "remember") (:form . "remember") (:end . 233)\n  (:start . 225) (:id . 80))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 238) (:start . 234)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "amyloid") (:form . "amyloids") (:end . 247)\n  (:start . 239) (:id . 82))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 251) (:start . 248)\n  (:id . 83))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 255) (:start . 252)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "subject") (:form . "subject") (:end . 263)\n  (:start . 256) (:id . 85))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 266) (:start . 264)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "ubiquitin-mediated") (:form . "ubiquitin-mediated")\n  (:end . 285) (:start . 267) (:id . 87))\n ((:tag . "NN") (:stem . "destruction") (:form . "destruction") (:end . 297)\n  (:start . 286) (:id . 88))\n ((:tag . "NNS") (:stem . "process") (:form . "processes") (:end . 307)\n  (:start . 298) (:id . 89))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 310) (:start . 308)\n  (:id . 90))\n ((:tag . "NN") (:stem . "destruction") (:form . "destruction") (:end . 322)\n  (:start . 311) (:id . 91))\n ((:tag . "NN") (:stem . "box") (:form . "box") (:end . 326) (:start . 323)\n  (:id . 92))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 330) (:start . 327)\n  (:id . 93))\n ((:tag . "NN") (:stem . "degron") (:form . "degron") (:end . 337)\n  (:start . 331) (:id . 94))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 343)\n  (:start . 338) (:id . 95))\n ((:tag . "NN") (:stem . "mutation") (:form . "mutation") (:end . 352)\n  (:start . 344) (:id . 96))\n ((:tag . "NNS") (:stem . "assay") (:form . "assays") (:end . 359)\n  (:start . 353) (:id . 97))\n ((:tag . "VBP") (:stem . "give") (:form . "give") (:end . 364) (:start . 360)\n  (:id . 98))\n ((:tag . "VBG") (:stem . "mislead") (:form . "misleading") (:end . 375)\n  (:start . 365) (:id . 99))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 383)\n  (:start . 376) (:id . 100))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 384) (:start . 383)\n  (:id . 101))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 385) (:start . 384)\n  (:id . 102)))@@@1@61@((:identifiers (:sid . :s13.212) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504425@unknown@formal@none@1@S@We expect that the predictive power of the structure filter can be improved as more data becomes available.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "expect") (:form . "expect") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "predictive") (:form . "predictive") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "power") (:form . "power") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 59)\n  (:start . 53) (:id . 51))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "improve") (:form . "improved") (:end . 75)\n  (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "become") (:form . "becomes") (:end . 96)\n  (:start . 89) (:id . 58))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 106)\n  (:start . 97) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 60)))@@@1@19@((:hcues ((:id . :x13.213.1) (:span 60 63)) ((:id . :x13.213.2) (:span 3 9)))\n (:hscopes ((:id . :x13.213.1) (:span 15 106))\n  ((:id . :x13.213.2) (:span 3 106)))\n (:identifiers (:sid . :s13.213) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504426@unknown@formal@none@1@S@For example, one might devise a procedure trained on the structural data of specific motifs and qualified to make predictions only for those motifs.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "one") (:form . "one") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "MD") (:stem . "might") (:form . "might") (:end . 22) (:start . 17)\n  (:id . 46))\n ((:tag . "VB") (:stem . "devise") (:form . "devise") (:end . 29)\n  (:start . 23) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 41)\n  (:start . 32) (:id . 49))\n ((:tag . "VBN") (:stem . "train") (:form . "trained") (:end . 49)\n  (:start . 42) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 67)\n  (:start . 57) (:id . 53))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 72) (:start . 68)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 84)\n  (:start . 76) (:id . 56))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 91)\n  (:start . 85) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "qualify") (:form . "qualified") (:end . 105)\n  (:start . 96) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "VB") (:stem . "make") (:form . "make") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 125)\n  (:start . 114) (:id . 62))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 130) (:start . 126)\n  (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 134) (:start . 131)\n  (:id . 64))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 140)\n  (:start . 135) (:id . 65))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 147)\n  (:start . 141) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 148) (:start . 147)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x13.214.1) (:span 17 22)))\n (:hscopes ((:id . :x13.214.1) (:span 17 147)))\n (:identifiers (:sid . :s13.214) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504427@unknown@formal@none@1@S@We investigated this approach and concluded that it would currently be applicable only to the very few LMs that have enough instances in the database.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "investigate") (:form . "investigated") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "conclude") (:form . "concluded") (:end . 43)\n  (:start . 34) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 51) (:start . 49)\n  (:id . 49))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "RB") (:stem . "currently") (:form . "currently") (:end . 67)\n  (:start . 58) (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 70) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "applicable") (:form . "applicable") (:end . 81)\n  (:start . 71) (:id . 53))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 86) (:start . 82)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 56))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 98) (:start . 94)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 102) (:start . 99)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 111) (:start . 107)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 116) (:start . 112)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "enough") (:form . "enough") (:end . 123)\n  (:start . 117) (:id . 62))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 133)\n  (:start . 124) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 136) (:start . 134)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 65))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 149)\n  (:start . 141) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x13.215.1) (:span 52 57)))\n (:hscopes ((:id . :x13.215.1) (:span 52 149)))\n (:identifiers (:sid . :s13.215) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504428@unknown@formal@none@1@S@For the great majority of LMs, appropriate training and tests cannot be carried out and predictions turned out to be unacceptably stringent: An effective procedure should be based on many more instances per LM and these are not available at the moment.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "great") (:form . "great") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 22)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "LM") (:form . "LMs") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 42)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "training") (:form . "training") (:end . 51)\n  (:start . 43) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 61) (:start . 56)\n  (:id . 52))\n ((:tag . "NN") (:stem . "cannot") (:form . "cannot") (:end . 68)\n  (:start . 62) (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "carry") (:form . "carried") (:end . 79)\n  (:start . 72) (:id . 55))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 83) (:start . 80)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 99)\n  (:start . 88) (:id . 58))\n ((:tag . "VBD") (:stem . "turn") (:form . "turned") (:end . 106)\n  (:start . 100) (:id . 59))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 116) (:start . 114)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "unacceptably") (:form . "unacceptably") (:end . 129)\n  (:start . 117) (:id . 63))\n ((:tag . "NN") (:stem . "stringent") (:form . "stringent") (:end . 139)\n  (:start . 130) (:id . 64))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 140) (:start . 139)\n  (:id . 65))\n ((:tag . "DT") (:stem . "an") (:form . "An") (:end . 143) (:start . 141)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 153)\n  (:start . 144) (:id . 67))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 163)\n  (:start . 154) (:id . 68))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 170)\n  (:start . 164) (:id . 69))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 173) (:start . 171)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 179)\n  (:start . 174) (:id . 71))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 182) (:start . 180)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 187) (:start . 183)\n  (:id . 73))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 192) (:start . 188)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 202)\n  (:start . 193) (:id . 75))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 206) (:start . 203)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 209) (:start . 207)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 213) (:start . 210)\n  (:id . 78))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 219)\n  (:start . 214) (:id . 79))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 223) (:start . 220)\n  (:id . 80))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 227) (:start . 224)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 237)\n  (:start . 228) (:id . 82))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 240) (:start . 238)\n  (:id . 83))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 244) (:start . 241)\n  (:id . 84))\n ((:tag . "NN") (:stem . "moment") (:form . "moment") (:end . 251)\n  (:start . 245) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 86)))@@@1@45@((:hcues ((:id . :x13.216.1) (:span 164 170)))\n (:hscopes ((:id . :x13.216.1) (:span 141 251)))\n (:identifiers (:sid . :s13.216) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504429@unknown@formal@none@1@S@We believe that in the future, as an increasing number of protein structures become available and the quantity of ELM annotation data grows, it will be possible to appropriately train and test motif-specific structure filters for a significant number of LMs.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "believe") (:form . "believe") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "future") (:form . "future") (:end . 29)\n  (:start . 23) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 36) (:start . 34)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 47)\n  (:start . 37) (:id . 51))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 54)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 65)\n  (:start . 58) (:id . 54))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 76)\n  (:start . 66) (:id . 55))\n ((:tag . "VBP") (:stem . "become") (:form . "become") (:end . 83)\n  (:start . 77) (:id . 56))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 93)\n  (:start . 84) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "quantity") (:form . "quantity") (:end . 110)\n  (:start . 102) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 128)\n  (:start . 118) (:id . 63))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 133)\n  (:start . 129) (:id . 64))\n ((:tag . "VBZ") (:stem . "grow") (:form . "grows") (:end . 139)\n  (:start . 134) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 66))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 143) (:start . 141)\n  (:id . 67))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 148) (:start . 144)\n  (:id . 68))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 151) (:start . 149)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 160)\n  (:start . 152) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 163) (:start . 161)\n  (:id . 71))\n ((:tag . "RB") (:stem . "appropriately") (:form . "appropriately")\n  (:end . 177) (:start . 164) (:id . 72))\n ((:tag . "VB") (:stem . "train") (:form . "train") (:end . 183)\n  (:start . 178) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 187) (:start . 184)\n  (:id . 74))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 192) (:start . 188)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "motif-specific") (:form . "motif-specific")\n  (:end . 207) (:start . 193) (:id . 76))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 217)\n  (:start . 208) (:id . 77))\n ((:tag . "NNS") (:stem . "filter") (:form . "filters") (:end . 225)\n  (:start . 218) (:id . 78))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 229) (:start . 226)\n  (:id . 79))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 231) (:start . 230)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 243)\n  (:start . 232) (:id . 81))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 250)\n  (:start . 244) (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 253) (:start . 251)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "LM") (:form . "LMs") (:end . 257) (:start . 254)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 258) (:start . 257)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x13.217.1) (:span 152 160))\n  ((:id . :x13.217.2) (:span 3 10)))\n (:hscopes ((:id . :x13.217.1) (:span 152 257))\n  ((:id . :x13.217.2) (:span 3 257)))\n (:identifiers (:sid . :s13.217) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504430@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s13.218) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504431@unknown@formal@none@1@S@In conclusion, LMs are subject to enormous over-prediction, so that the few true motifs are lost amongst the many false positives.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "conclusion") (:form . "conclusion") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "subject") (:form . "subject") (:end . 30)\n  (:start . 23) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "enormous") (:form . "enormous") (:end . 42)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "over-prediction") (:form . "over-prediction")\n  (:end . 58) (:start . 43) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "few") (:form . "few") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 87)\n  (:start . 81) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "lose") (:form . "lost") (:end . 96) (:start . 92)\n  (:id . 59))\n ((:tag . "IN") (:stem . "amongst") (:form . "amongst") (:end . 104)\n  (:start . 97) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 113) (:start . 109)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 119)\n  (:start . 114) (:id . 63))\n ((:tag . "NNS") (:stem . "positive") (:form . "positives") (:end . 129)\n  (:start . 120) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s13.219) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504432@unknown@formal@none@1@S@Whenever a query can be modelled on a structure, the structure filter can help in discriminating true from false positive matches of LMs.@(((:tag . "WRB") (:stem . "whenever") (:form . "Whenever") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "model") (:form . "modelled") (:end . 32)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 47)\n  (:start . 38) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 62)\n  (:start . 53) (:id . 53))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 69)\n  (:start . 63) (:id . 54))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "VB") (:stem . "help") (:form . "help") (:end . 78) (:start . 74)\n  (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 81) (:start . 79)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "discriminate") (:form . "discriminating")\n  (:end . 96) (:start . 82) (:id . 58))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 101) (:start . 97)\n  (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 112)\n  (:start . 107) (:id . 61))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 121)\n  (:start . 113) (:id . 62))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 129)\n  (:start . 122) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "LM") (:form . "LMs") (:end . 136) (:start . 133)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x13.220.1) (:span 70 73)))\n (:hscopes ((:id . :x13.220.1) (:span 70 136)))\n (:identifiers (:sid . :s13.220) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504433@unknown@formal@none@1@S@Moreover, since the number of solved structures is rapidly increasing, a benchmark set of true positive structures is going to be available for an increasing number of motifs, thus allowing more reliable tests and consistent score threshold setups.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "solve") (:form . "solved") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 47)\n  (:start . 37) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "RB") (:stem . "rapidly") (:form . "rapidly") (:end . 58)\n  (:start . 51) (:id . 51))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 69)\n  (:start . 59) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "benchmark") (:form . "benchmark") (:end . 82)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 86) (:start . 83)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 94) (:start . 90)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 103)\n  (:start . 95) (:id . 59))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 114)\n  (:start . 104) (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 117) (:start . 115)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "go") (:form . "going") (:end . 123) (:start . 118)\n  (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 126) (:start . 124)\n  (:id . 63))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 129) (:start . 127)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 139)\n  (:start . 130) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 143) (:start . 140)\n  (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 146) (:start . 144)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "increase") (:form . "increasing") (:end . 157)\n  (:start . 147) (:id . 68))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 164)\n  (:start . 158) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 167) (:start . 165)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 174)\n  (:start . 168) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 72))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 180) (:start . 176)\n  (:id . 73))\n ((:tag . "VBG") (:stem . "allow") (:form . "allowing") (:end . 189)\n  (:start . 181) (:id . 74))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 194) (:start . 190)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "reliable") (:form . "reliable") (:end . 203)\n  (:start . 195) (:id . 76))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 209)\n  (:start . 204) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 213) (:start . 210)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 224)\n  (:start . 214) (:id . 79))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 230)\n  (:start . 225) (:id . 80))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 240)\n  (:start . 231) (:id . 81))\n ((:tag . "NNS") (:stem . "setup") (:form . "setups") (:end . 247)\n  (:start . 241) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 248) (:start . 247)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s13.221) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504434@unknown@formal@none@1@S@As a consequence, the structure filter, which can be considered to all intents and purposes as a precursor in the use of structural information for short LM false positive discrimination, is going to become increasingly indispensable for the ELM resource's filtering framework in the structural genomics era.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "consequence") (:form . "consequence") (:end . 16)\n  (:start . 5) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 31)\n  (:start . 22) (:id . 47))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 52) (:start . 50)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 63)\n  (:start . 53) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "intent") (:form . "intents") (:end . 78)\n  (:start . 71) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 82) (:start . 79)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "purpose") (:form . "purposes") (:end . 91)\n  (:start . 83) (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 94) (:start . 92)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 106)\n  (:start . 97) (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 63))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 117) (:start . 114)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 131)\n  (:start . 121) (:id . 66))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 143)\n  (:start . 132) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 147) (:start . 144)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 153)\n  (:start . 148) (:id . 69))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 156) (:start . 154)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 162)\n  (:start . 157) (:id . 71))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 171)\n  (:start . 163) (:id . 72))\n ((:tag . "NN") (:stem . "discrimination") (:form . "discrimination")\n  (:end . 186) (:start . 172) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 187) (:start . 186)\n  (:id . 74))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 190) (:start . 188)\n  (:id . 75))\n ((:tag . "VBG") (:stem . "go") (:form . "going") (:end . 196) (:start . 191)\n  (:id . 76))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 199) (:start . 197)\n  (:id . 77))\n ((:tag . "VB") (:stem . "become") (:form . "become") (:end . 206)\n  (:start . 200) (:id . 78))\n ((:tag . "RB") (:stem . "increasingly") (:form . "increasingly") (:end . 219)\n  (:start . 207) (:id . 79))\n ((:tag . "JJ") (:stem . "indispensable") (:form . "indispensable")\n  (:end . 233) (:start . 220) (:id . 80))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 237) (:start . 234)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 241) (:start . 238)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 245) (:start . 242)\n  (:id . 83))\n ((:tag . "NN") (:stem . "resource") (:form . "resource") (:end . 254)\n  (:start . 246) (:id . 84))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 256) (:start . 254)\n  (:id . 85))\n ((:tag . "VBG") (:stem . "filter") (:form . "filtering") (:end . 266)\n  (:start . 257) (:id . 86))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 276)\n  (:start . 267) (:id . 87))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 279) (:start . 277)\n  (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 283) (:start . 280)\n  (:id . 89))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 294)\n  (:start . 284) (:id . 90))\n ((:tag . "NNS") (:stem . "genomic") (:form . "genomics") (:end . 303)\n  (:start . 295) (:id . 91))\n ((:tag . "NN") (:stem . "era") (:form . "era") (:end . 307) (:start . 304)\n  (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 308) (:start . 307)\n  (:id . 93)))@@@1@52@((:hcues ((:id . :x13.222.1) (:span 46 49)))\n (:hscopes ((:id . :x13.222.1) (:span 40 186)))\n (:identifiers (:sid . :s13.222) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504435@unknown@formal@none@1@S@Methods@(((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s13.223) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504436@unknown@formal@none@1@S@Dataset of structural instances@(((:tag . "NNP") (:stem . "Dataset") (:form . "Dataset") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 31)\n  (:start . 22) (:id . 45)))@@@1@4@((:identifiers (:sid . :s13.224) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504437@unknown@formal@none@1@S@The ELM database ([1], release June 2007) collected 112 LM, 93 of which have annotated instances.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 21) (:start . 20)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 49))\n ((:tag . "NN") (:stem . "release") (:form . "release") (:end . 30)\n  (:start . 23) (:id . 50))\n ((:tag . "NNP") (:stem . "June") (:form . "June") (:end . 35) (:start . 31)\n  (:id . 51))\n ((:tag . "CD") (:stem . "2007") (:form . "2007") (:end . 40) (:start . 36)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 41) (:start . 40)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "collect") (:form . "collected") (:end . 51)\n  (:start . 42) (:id . 54))\n ((:tag . "CD") (:stem . "112") (:form . "112") (:end . 55) (:start . 52)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 58) (:start . 56)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 57))\n ((:tag . "CD") (:stem . "93") (:form . "93") (:end . 62) (:start . 60)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 71) (:start . 66)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 76) (:start . 72)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 86)\n  (:start . 77) (:id . 62))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 96)\n  (:start . 87) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s13.225) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504438@unknown@formal@none@1@S@The set of 1898 annotated instances in 1037 sequences from the 93 different LMs obtained from the ELM database represented our initial dataset.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "CD") (:stem . "1898") (:form . "1898") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 25)\n  (:start . 16) (:id . 46))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 35)\n  (:start . 26) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "CD") (:stem . "1037") (:form . "1037") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "CD") (:stem . "93") (:form . "93") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 75)\n  (:start . 66) (:id . 54))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 88)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 93) (:start . 89)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 101) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 110)\n  (:start . 102) (:id . 60))\n ((:tag . "VBD") (:stem . "represent") (:form . "represented") (:end . 122)\n  (:start . 111) (:id . 61))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 126) (:start . 123)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 134)\n  (:start . 127) (:id . 63))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 142)\n  (:start . 135) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s13.226) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504439@unknown@formal@none@1@S@In our vocabulary, "instance" means a true annotated LM occurrence, whereas "match" indicates any regular expression hit on a query sequence.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "vocabulary") (:form . "vocabulary") (:end . 17)\n  (:start . 7) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 28)\n  (:start . 20) (:id . 47))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "mean") (:form . "means") (:end . 35) (:start . 30)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 42) (:start . 38)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 52)\n  (:start . 43) (:id . 52))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 55) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 66)\n  (:start . 56) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . "IN") (:stem . "whereas") (:form . "whereas") (:end . 75)\n  (:start . 68) (:id . 56))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 77) (:start . 76)\n  (:id . 57))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 82) (:start . 77)\n  (:id . 58))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 83) (:start . 82)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 93)\n  (:start . 84) (:id . 60))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 97) (:start . 94)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 105)\n  (:start . 98) (:id . 62))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 116)\n  (:start . 106) (:id . 63))\n ((:tag . "VBN") (:stem . "hit") (:form . "hit") (:end . 120) (:start . 117)\n  (:id . 64))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 123) (:start . 121)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 125) (:start . 124)\n  (:id . 66))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 131)\n  (:start . 126) (:id . 67))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 140)\n  (:start . 132) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s13.227) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504440@unknown@formal@none@1@S@The instances were modeled onto SCOP domains [46] by BLAST alignment [51] of the sequence containing the instance to the reference domain sequence extracted from the PDB entry [52].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "model") (:form . "modeled") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 31) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 52) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "blast") (:form . "BLAST") (:end . 58) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 68)\n  (:start . 59) (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . "CD") (:stem . "51") (:form . "51") (:end . 72) (:start . 70)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 59))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 89)\n  (:start . 81) (:id . 60))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 100)\n  (:start . 90) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 62))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 113)\n  (:start . 105) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 116) (:start . 114)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 65))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 130)\n  (:start . 121) (:id . 66))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 137)\n  (:start . 131) (:id . 67))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 146)\n  (:start . 138) (:id . 68))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 156)\n  (:start . 147) (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 161) (:start . 157)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 169) (:start . 166)\n  (:id . 72))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 175)\n  (:start . 170) (:id . 73))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 177) (:start . 176)\n  (:id . 74))\n ((:tag . "CD") (:stem . "52") (:form . "52") (:end . 179) (:start . 177)\n  (:id . 75))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 180) (:start . 179)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s13.228) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504441@unknown@formal@none@1@S@In order to assign a "sequence instance" to a "structure instance", the aligned sequences must have at least 70% global identity (over the domain) and 100% local identity (i.e. along the instance positions).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 30)\n  (:start . 22) (:id . 48))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 39)\n  (:start . 31) (:id . 49))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 43) (:start . 41)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 47) (:start . 46)\n  (:id . 53))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 56)\n  (:start . 47) (:id . 54))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 65)\n  (:start . 57) (:id . 55))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 66) (:start . 65)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "aligned") (:form . "aligned") (:end . 79)\n  (:start . 72) (:id . 59))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 89)\n  (:start . 80) (:id . 60))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 94) (:start . 90)\n  (:id . 61))\n ((:tag . "VB") (:stem . "have") (:form . "have") (:end . 99) (:start . 95)\n  (:id . 62))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 102) (:start . 100)\n  (:id . 63))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 108)\n  (:start . 103) (:id . 64))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 111) (:start . 109)\n  (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 112) (:start . 111)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 119)\n  (:start . 113) (:id . 67))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 128)\n  (:start . 120) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 69))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 134) (:start . 130)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 71))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 145)\n  (:start . 139) (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 150) (:start . 147)\n  (:id . 74))\n ((:tag . "CD") (:stem . "100") (:form . "100") (:end . 154) (:start . 151)\n  (:id . 75))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 155) (:start . 154)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 161)\n  (:start . 156) (:id . 77))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 170)\n  (:start . 162) (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 172) (:start . 171)\n  (:id . 79))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 176) (:start . 172)\n  (:id . 80))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 182)\n  (:start . 177) (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 186) (:start . 183)\n  (:id . 82))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 195)\n  (:start . 187) (:id . 83))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 205)\n  (:start . 196) (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 206) (:start . 205)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s13.229) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504442@unknown@formal@none@1@S@The final dataset of structural instances comprised of 185 3D instances from 37 different LMs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 41)\n  (:start . 32) (:id . 47))\n ((:tag . "VBN") (:stem . "comprise") (:form . "comprised") (:end . 51)\n  (:start . 42) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "CD") (:stem . "185") (:form . "185") (:end . 58) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 61) (:start . 59)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 71)\n  (:start . 62) (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 89)\n  (:start . 80) (:id . 55))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 93) (:start . 90)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s13.230) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504443@unknown@formal@none@1@S@Redundancy was removed at the structure level: if two or more instances mapped on identical 3D sites, all but one were discarded, thus reducing the dataset to 158 3D instances from 36 different LMs.@(((:tag . "NNP") (:stem . "Redundancy") (:form . "Redundancy") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "remove") (:form . "removed") (:end . 22)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 45) (:start . 40)\n  (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 71)\n  (:start . 62) (:id . 54))\n ((:tag . "VBN") (:stem . "map") (:form . "mapped") (:end . 78) (:start . 72)\n  (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 91)\n  (:start . 82) (:id . 57))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 94) (:start . 92)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 100) (:start . 95)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 60))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 105) (:start . 102)\n  (:id . 61))\n ((:tag . "IN") (:stem . "but") (:form . "but") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 113) (:start . 110)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 118) (:start . 114)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "discard") (:form . "discarded") (:end . 128)\n  (:start . 119) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 66))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 134) (:start . 130)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "reduce") (:form . "reducing") (:end . 143)\n  (:start . 135) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n  (:id . 69))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 155)\n  (:start . 148) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 158) (:start . 156)\n  (:id . 71))\n ((:tag . "CD") (:stem . "158") (:form . "158") (:end . 162) (:start . 159)\n  (:id . 72))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 165) (:start . 163)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 175)\n  (:start . 166) (:id . 74))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 180) (:start . 176)\n  (:id . 75))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 183) (:start . 181)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 193)\n  (:start . 184) (:id . 77))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 197) (:start . 194)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 198) (:start . 197)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s13.231) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504444@unknown@formal@none@1@S@For each position of a 3D instance, the solvent accessibility and secondary structure values are collected from the DSSP [53] file of the target structure mapping the instance.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 34)\n  (:start . 26) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "solvent") (:form . "solvent") (:end . 47)\n  (:start . 40) (:id . 51))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 61) (:start . 48) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 75)\n  (:start . 66) (:id . 54))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 85)\n  (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 92)\n  (:start . 86) (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 96) (:start . 93)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 106)\n  (:start . 97) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 111) (:start . 107)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "DSSP") (:form . "DSSP") (:end . 120) (:start . 116)\n  (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . "CD") (:stem . "53") (:form . "53") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 130) (:start . 126)\n  (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 67))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 144)\n  (:start . 138) (:id . 68))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 154)\n  (:start . 145) (:id . 69))\n ((:tag . "VBG") (:stem . "map") (:form . "mapping") (:end . 162)\n  (:start . 155) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 166) (:start . 163)\n  (:id . 71))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 175)\n  (:start . 167) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s13.232) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504445@unknown@formal@none@1@S@For the solvent exposure of a residue, a relative (normalized) value is calculated as the ratio of the residue's DSSP accessibility value to the residue accessible surface area value as defined by Miller and co-workers [54] and which is calculated for the residue in a Gly-Xaa-Gly tripeptide in extended conformation.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "solvent") (:form . "solvent") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "exposure") (:form . "exposure") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 37)\n  (:start . 30) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 49)\n  (:start . 41) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "normalized") (:form . "normalized") (:end . 61)\n  (:start . 51) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 68) (:start . 63)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 82)\n  (:start . 72) (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 85) (:start . 83)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 59))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 95) (:start . 90)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 62))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 110)\n  (:start . 103) (:id . 63))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 112) (:start . 110)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "DSSP") (:form . "DSSP") (:end . 117) (:start . 113)\n  (:id . 65))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 131) (:start . 118) (:id . 66))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 137)\n  (:start . 132) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 140) (:start . 138)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 69))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 152)\n  (:start . 145) (:id . 70))\n ((:tag . "JJ") (:stem . "accessible") (:form . "accessible") (:end . 163)\n  (:start . 153) (:id . 71))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 171)\n  (:start . 164) (:id . 72))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 176) (:start . 172)\n  (:id . 73))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 182)\n  (:start . 177) (:id . 74))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 185) (:start . 183)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 193)\n  (:start . 186) (:id . 76))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 196) (:start . 194)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Miller") (:form . "Miller") (:end . 203)\n  (:start . 197) (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 207) (:start . 204)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "co-worker") (:form . "co-workers") (:end . 218)\n  (:start . 208) (:id . 80))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 220) (:start . 219)\n  (:id . 81))\n ((:tag . "CD") (:stem . "54") (:form . "54") (:end . 222) (:start . 220)\n  (:id . 82))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 223) (:start . 222)\n  (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 227) (:start . 224)\n  (:id . 84))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 233)\n  (:start . 228) (:id . 85))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 236) (:start . 234)\n  (:id . 86))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 247)\n  (:start . 237) (:id . 87))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 251) (:start . 248)\n  (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 255) (:start . 252)\n  (:id . 89))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 263)\n  (:start . 256) (:id . 90))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 266) (:start . 264)\n  (:id . 91))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 268) (:start . 267)\n  (:id . 92))\n ((:tag . "JJ") (:stem . "gly-xaa-gly") (:form . "Gly-Xaa-Gly") (:end . 280)\n  (:start . 269) (:id . 93))\n ((:tag . "NN") (:stem . "tripeptide") (:form . "tripeptide") (:end . 291)\n  (:start . 281) (:id . 94))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 294) (:start . 292)\n  (:id . 95))\n ((:tag . "VBN") (:stem . "extend") (:form . "extended") (:end . 303)\n  (:start . 295) (:id . 96))\n ((:tag . "NN") (:stem . "conformation") (:form . "conformation") (:end . 316)\n  (:start . 304) (:id . 97))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 317) (:start . 316)\n  (:id . 98)))@@@1@57@((:identifiers (:sid . :s13.233) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504446@unknown@formal@none@1@S@The DSSP secondary structure types are: H = alpha helix, B = residue in isolated beta-bridge, E = extended strand (participates in beta ladder), G = 3-helix (3/10 helix), I = 5 helix (pi helix), T = hydrogen bonded turn, and S = bend.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "DSSP") (:form . "DSSP") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "SYM") (:stem . "alpha") (:form . "alpha") (:end . 49) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 55) (:start . 50)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 58) (:start . 57)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "=") (:form . "=") (:end . 60) (:start . 59)\n  (:id . 55))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 68)\n  (:start . 61) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 71) (:start . 69)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "isolate") (:form . "isolated") (:end . 80)\n  (:start . 72) (:id . 58))\n ((:tag . "NN") (:stem . "beta-bridge") (:form . "beta-bridge") (:end . 92)\n  (:start . 81) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 95) (:start . 94)\n  (:id . 61))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 97) (:start . 96)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "extend") (:form . "extended") (:end . 106)\n  (:start . 98) (:id . 63))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 113)\n  (:start . 107) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "participate") (:form . "participates") (:end . 127)\n  (:start . 115) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 130) (:start . 128)\n  (:id . 67))\n ((:tag . "SYM") (:stem . "beta") (:form . "beta") (:end . 135) (:start . 131)\n  (:id . 68))\n ((:tag . "NN") (:stem . "ladder") (:form . "ladder") (:end . 142)\n  (:start . 136) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 143) (:start . 142)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 146) (:start . 145)\n  (:id . 72))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 148) (:start . 147)\n  (:id . 73))\n ((:tag . "CD") (:stem . "3-helix") (:form . "3-helix") (:end . 156)\n  (:start . 149) (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 158) (:start . 157)\n  (:id . 75))\n ((:tag . "CD") (:stem . "3/10") (:form . "3/10") (:end . 162) (:start . 158)\n  (:id . 76))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 168)\n  (:start . 163) (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 170) (:start . 169)\n  (:id . 79))\n ((:tag . "NN") (:stem . "i") (:form . "I") (:end . 172) (:start . 171)\n  (:id . 80))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 174) (:start . 173)\n  (:id . 81))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 176) (:start . 175)\n  (:id . 82))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 182)\n  (:start . 177) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 184) (:start . 183)\n  (:id . 84))\n ((:tag . "NN") (:stem . "pi") (:form . "pi") (:end . 186) (:start . 184)\n  (:id . 85))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 192)\n  (:start . 187) (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 193) (:start . 192)\n  (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 194) (:start . 193)\n  (:id . 88))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 196) (:start . 195)\n  (:id . 89))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 198) (:start . 197)\n  (:id . 90))\n ((:tag . "NN") (:stem . "hydrogen") (:form . "hydrogen") (:end . 207)\n  (:start . 199) (:id . 91))\n ((:tag . "VBD") (:stem . "bond") (:form . "bonded") (:end . 214)\n  (:start . 208) (:id . 92))\n ((:tag . "NN") (:stem . "turn") (:form . "turn") (:end . 219) (:start . 215)\n  (:id . 93))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 220) (:start . 219)\n  (:id . 94))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 224) (:start . 221)\n  (:id . 95))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 226) (:start . 225)\n  (:id . 96))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 228) (:start . 227)\n  (:id . 97))\n ((:tag . "NN") (:stem . "bend") (:form . "bend") (:end . 233) (:start . 229)\n  (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 99)))@@@1@58@((:identifiers (:sid . :s13.234) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504447@unknown@formal@none@1@S@Unstructured regions are marked as U.@(((:tag . "JJ") (:stem . "unstructured") (:form . "Unstructured") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 20)\n  (:start . 13) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 24) (:start . 21)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "mark") (:form . "marked") (:end . 31) (:start . 25)\n  (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 36) (:start . 35)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 37) (:start . 36)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s13.235) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504448@unknown@formal@none@1@S@In our study we grouped the SSE types in four categories: 1) helices (H, I); 2) 3/10 helices (G); 3) strand (E); 4) loops (B, T, S, U).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "group") (:form . "grouped") (:end . 23)\n  (:start . 16) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sse") (:form . "SSE") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 37) (:start . 32)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 45) (:start . 41)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "category") (:form . "categories") (:end . 56)\n  (:start . 46) (:id . 52))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 59) (:start . 58)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 68)\n  (:start . 61) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 71) (:start . 70)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 59))\n ((:tag . "NN") (:stem . "i") (:form . "I") (:end . 74) (:start . 73)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 76) (:start . 75)\n  (:id . 62))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 78) (:start . 77)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 79) (:start . 78)\n  (:id . 64))\n ((:tag . "CD") (:stem . "3/10") (:form . "3/10") (:end . 84) (:start . 80)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 92)\n  (:start . 85) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 95) (:start . 94)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 97) (:start . 96)\n  (:id . 70))\n ((:tag . "LS") (:stem . "3") (:form . "3") (:end . 99) (:start . 98)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 100) (:start . 99)\n  (:id . 72))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 107)\n  (:start . 101) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 110) (:start . 109)\n  (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 76))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 112) (:start . 111)\n  (:id . 77))\n ((:tag . "LS") (:stem . "4") (:form . "4") (:end . 114) (:start . 113)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 79))\n ((:tag . "VBZ") (:stem . "loop") (:form . "loops") (:end . 121)\n  (:start . 116) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 124) (:start . 123)\n  (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 83))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 127) (:start . 126)\n  (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 128) (:start . 127)\n  (:id . 85))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 130) (:start . 129)\n  (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 87))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 133) (:start . 132)\n  (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 134) (:start . 133)\n  (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s13.236) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504449@unknown@formal@none@1@S@Pi helices are usually attached to larger alpha helices; therefore we grouped them with helices.@(((:tag . "NNP") (:stem . "Pi") (:form . "Pi") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "attach") (:form . "attached") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "alpha") (:form . "alpha") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "RB") (:stem . "therefore") (:form . "therefore") (:end . 66)\n  (:start . 57) (:id . 52))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "VBD") (:stem . "group") (:form . "grouped") (:end . 77)\n  (:start . 70) (:id . 54))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 87) (:start . 83)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 95)\n  (:start . 88) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s13.237) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504450@unknown@formal@none@1@S@3/10 helices are often poorly conserved as part of a larger loop but sometimes they are continuously linked to a larger helix and so we decided to treat them separately.@(((:tag . "CD") (:stem . "3/10") (:form . "3/10") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "helix") (:form . "helices") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "RB") (:stem . "poorly") (:form . "poorly") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 39)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 64) (:start . 60)\n  (:id . 53))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "RB") (:stem . "sometimes") (:form . "sometimes") (:end . 78)\n  (:start . 69) (:id . 55))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "RB") (:stem . "continuously") (:form . "continuously") (:end . 100)\n  (:start . 88) (:id . 58))\n ((:tag . "VBN") (:stem . "link") (:form . "linked") (:end . 107)\n  (:start . 101) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "JJR") (:stem . "large") (:form . "larger") (:end . 119)\n  (:start . 113) (:id . 62))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 125)\n  (:start . 120) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 64))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 132) (:start . 130)\n  (:id . 65))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 135) (:start . 133)\n  (:id . 66))\n ((:tag . "VBD") (:stem . "decide") (:form . "decided") (:end . 143)\n  (:start . 136) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 146) (:start . 144)\n  (:id . 68))\n ((:tag . "VB") (:stem . "treat") (:form . "treat") (:end . 152)\n  (:start . 147) (:id . 69))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 157) (:start . 153)\n  (:id . 70))\n ((:tag . "RB") (:stem . "separately") (:form . "separately") (:end . 168)\n  (:start . 158) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s13.238) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504451@unknown@formal@none@1@S@B, T, S and U are grouped together because they usually belong to 3D flexible loop-like regions.@(((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 2) (:start . 1) (:id . 43))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 4) (:start . 3)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 45))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 7) (:start . 6)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "U") (:form . "U") (:end . 13) (:start . 12)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 17) (:start . 14)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "group") (:form . "grouped") (:end . 25)\n  (:start . 18) (:id . 50))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 34)\n  (:start . 26) (:id . 51))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 42)\n  (:start . 35) (:id . 52))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 47) (:start . 43)\n  (:id . 53))\n ((:tag . "RB") (:stem . "usually") (:form . "usually") (:end . 55)\n  (:start . 48) (:id . 54))\n ((:tag . "VBP") (:stem . "belong") (:form . "belong") (:end . 62)\n  (:start . 56) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 65) (:start . 63)\n  (:id . 56))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 68) (:start . 66)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "flexible") (:form . "flexible") (:end . 77)\n  (:start . 69) (:id . 58))\n ((:tag . "JJ") (:stem . "loop-like") (:form . "loop-like") (:end . 87)\n  (:start . 78) (:id . 59))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 95)\n  (:start . 88) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s13.239) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504452@unknown@formal@none@1@S@The non-redundant instance dataset is reported in Table S1 (additional file 6).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "non-redundant") (:form . "non-redundant")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 26)\n  (:start . 18) (:id . 44))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 34)\n  (:start . 27) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 37) (:start . 35)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 46)\n  (:start . 38) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 55) (:start . 50)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 70)\n  (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 79) (:start . 78)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s13.240) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504453@unknown@formal@none@1@S@Random structural matches@(((:tag . "NNP") (:stem . "Random") (:form . "Random") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 17)\n  (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 25)\n  (:start . 18) (:id . 44)))@@@1@3@((:identifiers (:sid . :s13.241) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504454@unknown@formal@none@1@S@Since the aim of our study was to set up a scoring scheme and to establish accessibility and secondary structure score thresholds for discriminating true motifs among random (mostly FP) matches, we performed a pattern search using all the LM regular expressions available in the ELM database (112) in the 1037 sequences known for having at least one true annotated instance.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "aim") (:form . "aim") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 26) (:start . 21)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 49))\n ((:tag . "VB") (:stem . "set") (:form . "set") (:end . 37) (:start . 34)\n  (:id . 50))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 40) (:start . 38)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 50)\n  (:start . 43) (:id . 53))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 57)\n  (:start . 51) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 56))\n ((:tag . "VB") (:stem . "establish") (:form . "establish") (:end . 74)\n  (:start . 65) (:id . 57))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 88) (:start . 75) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 102)\n  (:start . 93) (:id . 60))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 112)\n  (:start . 103) (:id . 61))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 118)\n  (:start . 113) (:id . 62))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 129)\n  (:start . 119) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 133) (:start . 130)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "discriminate") (:form . "discriminating")\n  (:end . 148) (:start . 134) (:id . 65))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 153) (:start . 149)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 160)\n  (:start . 154) (:id . 67))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 166)\n  (:start . 161) (:id . 68))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 173)\n  (:start . 167) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 175) (:start . 174)\n  (:id . 70))\n ((:tag . "RB") (:stem . "mostly") (:form . "mostly") (:end . 181)\n  (:start . 175) (:id . 71))\n ((:tag . "NNP") (:stem . "FP") (:form . "FP") (:end . 184) (:start . 182)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 185) (:start . 184)\n  (:id . 73))\n ((:tag . "VBZ") (:stem . "match") (:form . "matches") (:end . 193)\n  (:start . 186) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 194) (:start . 193)\n  (:id . 75))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 197) (:start . 195)\n  (:id . 76))\n ((:tag . "VBD") (:stem . "perform") (:form . "performed") (:end . 207)\n  (:start . 198) (:id . 77))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 209) (:start . 208)\n  (:id . 78))\n ((:tag . "NN") (:stem . "pattern") (:form . "pattern") (:end . 217)\n  (:start . 210) (:id . 79))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 224)\n  (:start . 218) (:id . 80))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 230) (:start . 225)\n  (:id . 81))\n ((:tag . "PDT") (:stem . "all") (:form . "all") (:end . 234) (:start . 231)\n  (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 238) (:start . 235)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 241) (:start . 239)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 249)\n  (:start . 242) (:id . 85))\n ((:tag . "NNS") (:stem . "expression") (:form . "expressions") (:end . 261)\n  (:start . 250) (:id . 86))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 271)\n  (:start . 262) (:id . 87))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 274) (:start . 272)\n  (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 278) (:start . 275)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 282) (:start . 279)\n  (:id . 90))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 291)\n  (:start . 283) (:id . 91))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 293) (:start . 292)\n  (:id . 92))\n ((:tag . "CD") (:stem . "112") (:form . "112") (:end . 296) (:start . 293)\n  (:id . 93))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 297) (:start . 296)\n  (:id . 94))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 300) (:start . 298)\n  (:id . 95))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 304) (:start . 301)\n  (:id . 96))\n ((:tag . "CD") (:stem . "1037") (:form . "1037") (:end . 309) (:start . 305)\n  (:id . 97))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 319)\n  (:start . 310) (:id . 98))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 325)\n  (:start . 320) (:id . 99))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 329) (:start . 326)\n  (:id . 100))\n ((:tag . "VBG") (:stem . "have") (:form . "having") (:end . 336)\n  (:start . 330) (:id . 101))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 339) (:start . 337)\n  (:id . 102))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 345)\n  (:start . 340) (:id . 103))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 349) (:start . 346)\n  (:id . 104))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 354) (:start . 350)\n  (:id . 105))\n ((:tag . "JJ") (:stem . "annotated") (:form . "annotated") (:end . 364)\n  (:start . 355) (:id . 106))\n ((:tag . "NN") (:stem . "instance") (:form . "instance") (:end . 373)\n  (:start . 365) (:id . 107))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 374) (:start . 373)\n  (:id . 108)))@@@1@67@((:identifiers (:sid . :s13.242) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504455@unknown@formal@none@1@S@True motif instances were filtered out from the resulting list of matches.@(((:tag . "JJ") (:stem . "true") (:form . "True") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 20)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "filter") (:form . "filtered") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 73)\n  (:start . 66) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s13.243) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504456@unknown@formal@none@1@S@Applying the same sequence-to-structure mapping procedure used for true motif instances, the sequences of random matches were modeled onto SCOP domains, resulting in 22,058 3D non-identical matches from 105 motifs.@(((:tag . "VBG") (:stem . "apply") (:form . "Applying") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sequence-to-structure")\n  (:form . "sequence-to-structure") (:end . 39) (:start . 18) (:id . 45))\n ((:tag . "VBG") (:stem . "map") (:form . "mapping") (:end . 47) (:start . 40)\n  (:id . 46))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 57)\n  (:start . 48) (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 62) (:start . 58)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 66) (:start . 63)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 71) (:start . 67)\n  (:id . 50))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 77) (:start . 72)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "instance") (:form . "instances") (:end . 87)\n  (:start . 78) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 102)\n  (:start . 93) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 112)\n  (:start . 106) (:id . 57))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 120)\n  (:start . 113) (:id . 58))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 125) (:start . 121)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "model") (:form . "modeled") (:end . 133)\n  (:start . 126) (:id . 60))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 138) (:start . 134)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 143) (:start . 139)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 151)\n  (:start . 144) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 162)\n  (:start . 153) (:id . 65))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 165) (:start . 163)\n  (:id . 66))\n ((:tag . "CD") (:stem . "22,058") (:form . "22,058") (:end . 172)\n  (:start . 166) (:id . 67))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 175) (:start . 173)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "non-identical") (:form . "non-identical")\n  (:end . 189) (:start . 176) (:id . 69))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 197)\n  (:start . 190) (:id . 70))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 202) (:start . 198)\n  (:id . 71))\n ((:tag . "CD") (:stem . "105") (:form . "105") (:end . 206) (:start . 203)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 213)\n  (:start . 207) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s13.244) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504457@unknown@formal@none@1@S@LM-specific background score distributions@(((:tag . "JJ") (:stem . "lm-specific") (:form . "LM-specific") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 22)\n  (:start . 12) (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 28) (:start . 23)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 42) (:start . 29) (:id . 45)))@@@1@4@((:identifiers (:sid . :s13.245) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504458@unknown@formal@none@1@S@Background score distributions have been obtained by scanning the 13,582 sequences of a non redundant PDB dataset (<50% sequence identity, downloaded from PDB clusters [55]) with the regular expressions of the 112 ELM motifs (total number of available motifs), mapping the 323,5412 matches onto SCOP domains and assigning them an accessibility score and a secondary structure score.@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 16) (:start . 11)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 30) (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 35) (:start . 31)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 40) (:start . 36)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 49)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 52) (:start . 50)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "scan") (:form . "scanning") (:end . 61)\n  (:start . 53) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 50))\n ((:tag . "CD") (:stem . "13,582") (:form . "13,582") (:end . 72)\n  (:start . 66) (:id . 51))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 82)\n  (:start . 73) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 87) (:start . 86)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "non") (:form . "non") (:end . 91) (:start . 88)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "redundant") (:form . "redundant") (:end . 101)\n  (:start . 92) (:id . 56))\n ((:tag . "NN") (:stem . "pdb") (:form . "PDB") (:end . 105) (:start . 102)\n  (:id . 57))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 113)\n  (:start . 106) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 59))\n ((:tag . "CD") (:stem . "<50") (:form . "<50") (:end . 118) (:start . 115)\n  (:id . 60))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 119) (:start . 118)\n  (:id . 61))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 128)\n  (:start . 120) (:id . 62))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 137)\n  (:start . 129) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "downloade") (:form . "downloaded") (:end . 149)\n  (:start . 139) (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 154) (:start . 150)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 158) (:start . 155)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "cluster") (:form . "clusters") (:end . 167)\n  (:start . 159) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 169) (:start . 168)\n  (:id . 69))\n ((:tag . "CD") (:stem . "55") (:form . "55") (:end . 171) (:start . 169)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 172) (:start . 171)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 173) (:start . 172)\n  (:id . 72))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 178) (:start . 174)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 182) (:start . 179)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 190)\n  (:start . 183) (:id . 75))\n ((:tag . "NNS") (:stem . "expression") (:form . "expressions") (:end . 202)\n  (:start . 191) (:id . 76))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 205) (:start . 203)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 209) (:start . 206)\n  (:id . 78))\n ((:tag . "CD") (:stem . "112") (:form . "112") (:end . 213) (:start . 210)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 217) (:start . 214)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 224)\n  (:start . 218) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 226) (:start . 225)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 231)\n  (:start . 226) (:id . 83))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 238)\n  (:start . 232) (:id . 84))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 241) (:start . 239)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 251)\n  (:start . 242) (:id . 86))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 258)\n  (:start . 252) (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 259) (:start . 258)\n  (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 260) (:start . 259)\n  (:id . 89))\n ((:tag . "VBG") (:stem . "map") (:form . "mapping") (:end . 268)\n  (:start . 261) (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 272) (:start . 269)\n  (:id . 91))\n ((:tag . "CD") (:stem . "323,5412") (:form . "323,5412") (:end . 281)\n  (:start . 273) (:id . 92))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 289)\n  (:start . 282) (:id . 93))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 294) (:start . 290)\n  (:id . 94))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 299) (:start . 295)\n  (:id . 95))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 307)\n  (:start . 300) (:id . 96))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 311) (:start . 308)\n  (:id . 97))\n ((:tag . "VBG") (:stem . "assign") (:form . "assigning") (:end . 321)\n  (:start . 312) (:id . 98))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 326) (:start . 322)\n  (:id . 99))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 329) (:start . 327)\n  (:id . 100))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 343) (:start . 330) (:id . 101))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 349)\n  (:start . 344) (:id . 102))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 353) (:start . 350)\n  (:id . 103))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 355) (:start . 354)\n  (:id . 104))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 365)\n  (:start . 356) (:id . 105))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 375)\n  (:start . 366) (:id . 106))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 381)\n  (:start . 376) (:id . 107))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 382) (:start . 381)\n  (:id . 108)))@@@1@67@((:identifiers (:sid . :s13.246) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504459@unknown@formal@none@1@S@Score distributions (for each feature) were then plotted for 103 LMs: score distributions for the 9 LMs with less than 10 matches are not reported.@(((:tag . "NN") (:stem . "score") (:form . "Score") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 19) (:start . 6) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 21) (:start . 20)\n  (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 37)\n  (:start . 30) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "plot") (:form . "plotted") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "CD") (:stem . "103") (:form . "103") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 69) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 75) (:start . 70)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 89) (:start . 76) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 99) (:start . 98)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 103) (:start . 100)\n  (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 108) (:start . 104)\n  (:id . 62))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 113) (:start . 109)\n  (:id . 63))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 118) (:start . 114)\n  (:id . 64))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 121) (:start . 119)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 129)\n  (:start . 122) (:id . 66))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 133) (:start . 130)\n  (:id . 67))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 137) (:start . 134)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 146)\n  (:start . 138) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s13.247) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504460@unknown@formal@none@1@S@LM-specific score distributions are shown in additional file 4 (Figure S3).@(((:tag . "JJ") (:stem . "lm-specific") (:form . "LM-specific") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 17) (:start . 12)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 31) (:start . 18) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 41) (:start . 36)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 55)\n  (:start . 45) (:id . 48))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 60) (:start . 56)\n  (:id . 49))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 62) (:start . 61)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 70)\n  (:start . 64) (:id . 52))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s13.248) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504461@unknown@formal@none@1@S@The ELM structure filter pipeline@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "pipeline") (:form . "pipeline") (:end . 33)\n  (:start . 25) (:id . 46)))@@@1@5@((:identifiers (:sid . :s13.249) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504462@unknown@formal@none@1@S@The user query sequence submitted through either the Web Interface or the Web Service is first scanned for LM matches and then aligned to the database of ASTRAL sequences [47] derived from SCOP domains [46].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "submit") (:form . "submitted") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 48)\n  (:start . 42) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Interface") (:form . "Interface") (:end . 66)\n  (:start . 57) (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 77) (:start . 74)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Service") (:form . "Service") (:end . 85)\n  (:start . 78) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 94) (:start . 89)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "scan") (:form . "scanned") (:end . 102)\n  (:start . 95) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 106) (:start . 103)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 109) (:start . 107)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 117)\n  (:start . 110) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 126) (:start . 122)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 134)\n  (:start . 127) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 137) (:start . 135)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 66))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 150)\n  (:start . 142) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 153) (:start . 151)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "astral") (:form . "ASTRAL") (:end . 160)\n  (:start . 154) (:id . 69))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 170)\n  (:start . 161) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 172) (:start . 171)\n  (:id . 71))\n ((:tag . "CD") (:stem . "47") (:form . "47") (:end . 174) (:start . 172)\n  (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 175) (:start . 174)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 183)\n  (:start . 176) (:id . 74))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 188) (:start . 184)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 193) (:start . 189)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 201)\n  (:start . 194) (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 203) (:start . 202)\n  (:id . 78))\n ((:tag . "CD") (:stem . "46") (:form . "46") (:end . 205) (:start . 203)\n  (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 206) (:start . 205)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 207) (:start . 206)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s13.250) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504463@unknown@formal@none@1@S@The hit with the highest sequence identity and coverage to the query sequence is selected as a reference structure.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "hit") (:form . "hit") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 68) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 77)\n  (:start . 69) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 80) (:start . 78)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 104)\n  (:start . 95) (:id . 59))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 114)\n  (:start . 105) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s13.251) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504464@unknown@formal@none@1@S@If more than one hit has the same sequence identity and coverage to the query sequence, the structure with the best experimental resolution is taken as reference and, for the same resolution, one hit is chosen randomly.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "hit") (:form . "hit") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 33) (:start . 29)\n  (:id . 49))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 42)\n  (:start . 34) (:id . 50))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 51)\n  (:start . 43) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "coverage") (:form . "coverage") (:end . 64)\n  (:start . 56) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 77) (:start . 72)\n  (:id . 56))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 86)\n  (:start . 78) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 101)\n  (:start . 92) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 106) (:start . 102)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 62))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 115) (:start . 111)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 128)\n  (:start . 116) (:id . 64))\n ((:tag . "NN") (:stem . "resolution") (:form . "resolution") (:end . 139)\n  (:start . 129) (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 142) (:start . 140)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 148)\n  (:start . 143) (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 151) (:start . 149)\n  (:id . 68))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 161)\n  (:start . 152) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 166) (:start . 165)\n  (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 170) (:start . 167)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 174) (:start . 171)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 179) (:start . 175)\n  (:id . 74))\n ((:tag . "NN") (:stem . "resolution") (:form . "resolution") (:end . 190)\n  (:start . 180) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 191) (:start . 190)\n  (:id . 76))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 195) (:start . 192)\n  (:id . 77))\n ((:tag . "NN") (:stem . "hit") (:form . "hit") (:end . 199) (:start . 196)\n  (:id . 78))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 202) (:start . 200)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 209)\n  (:start . 203) (:id . 80))\n ((:tag . "RB") (:stem . "randomly") (:form . "randomly") (:end . 218)\n  (:start . 210) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s13.252) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504465@unknown@formal@none@1@S@This approach may result, for example, in the organism of the reference structure being different from the source organism of the user query sequence.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VB") (:stem . "result") (:form . "result") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 37)\n  (:start . 30) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 54)\n  (:start . 46) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 54))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 71)\n  (:start . 62) (:id . 55))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 81)\n  (:start . 72) (:id . 56))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 87) (:start . 82)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 97)\n  (:start . 88) (:id . 58))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 113)\n  (:start . 107) (:id . 61))\n ((:tag . "NN") (:stem . "organism") (:form . "organism") (:end . 122)\n  (:start . 114) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 125) (:start . 123)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 64))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 134) (:start . 130)\n  (:id . 65))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 140)\n  (:start . 135) (:id . 66))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 149)\n  (:start . 141) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x13.253.1) (:span 14 17)))\n (:hscopes ((:id . :x13.253.1) (:span 14 149)))\n (:identifiers (:sid . :s13.253) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504466@unknown@formal@none@1@S@However, since proteins with identical sequences fold into identical structures, the procedure for the selection of the reference structure does not introduce any bias in the calculation of solvent accessibility and secondary structure values.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 48)\n  (:start . 39) (:id . 48))\n ((:tag . "RB") (:stem . "fold") (:form . "fold") (:end . 53) (:start . 49)\n  (:id . 49))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 58) (:start . 54)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 68)\n  (:start . 59) (:id . 51))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 79)\n  (:start . 69) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 54))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 94)\n  (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 98) (:start . 95)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 112)\n  (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 60))\n ((:tag . "NN") (:stem . "reference") (:form . "reference") (:end . 129)\n  (:start . 120) (:id . 61))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 139)\n  (:start . 130) (:id . 62))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 144) (:start . 140)\n  (:id . 63))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 148) (:start . 145)\n  (:id . 64))\n ((:tag . "VB") (:stem . "introduce") (:form . "introduce") (:end . 158)\n  (:start . 149) (:id . 65))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 162) (:start . 159)\n  (:id . 66))\n ((:tag . "NN") (:stem . "bias") (:form . "bias") (:end . 167) (:start . 163)\n  (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 170) (:start . 168)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 174) (:start . 171)\n  (:id . 69))\n ((:tag . "NN") (:stem . "calculation") (:form . "calculation") (:end . 186)\n  (:start . 175) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 189) (:start . 187)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "solvent") (:form . "solvent") (:end . 197)\n  (:start . 190) (:id . 72))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 211) (:start . 198) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 215) (:start . 212)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 225)\n  (:start . 216) (:id . 75))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 235)\n  (:start . 226) (:id . 76))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 242)\n  (:start . 236) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s13.254) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504467@unknown@formal@none@1@S@For the structure filter to be applicable, two conditions must hold: 1) the query sequence or a region of it can be aligned to one or more (non-overlapping) structural domains; 2) at least one LM match falls in an aligned region, i.e. can be mapped onto a 3D domain.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "applicable") (:form . "applicable") (:end . 41)\n  (:start . 31) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 57)\n  (:start . 47) (:id . 51))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "VB") (:stem . "hold") (:form . "hold") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 70) (:start . 69)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 57))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 81) (:start . 76)\n  (:id . 58))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 90)\n  (:start . 82) (:id . 59))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 95) (:start . 94)\n  (:id . 61))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 102)\n  (:start . 96) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 63))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 108) (:start . 106)\n  (:id . 64))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 112) (:start . 109)\n  (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 115) (:start . 113)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 123)\n  (:start . 116) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 126) (:start . 124)\n  (:id . 68))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 130) (:start . 127)\n  (:id . 69))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 133) (:start . 131)\n  (:id . 70))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 138) (:start . 134)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "non-overlapping") (:form . "non-overlapping")\n  (:end . 155) (:start . 140) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 167)\n  (:start . 157) (:id . 75))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 175)\n  (:start . 168) (:id . 76))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 176) (:start . 175)\n  (:id . 77))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 178) (:start . 177)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 79))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 182) (:start . 180)\n  (:id . 80))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 188)\n  (:start . 183) (:id . 81))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 192) (:start . 189)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 195) (:start . 193)\n  (:id . 83))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 201)\n  (:start . 196) (:id . 84))\n ((:tag . "VBZ") (:stem . "fall") (:form . "falls") (:end . 207)\n  (:start . 202) (:id . 85))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 210) (:start . 208)\n  (:id . 86))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 213) (:start . 211)\n  (:id . 87))\n ((:tag . "JJ") (:stem . "aligned") (:form . "aligned") (:end . 221)\n  (:start . 214) (:id . 88))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 228)\n  (:start . 222) (:id . 89))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 229) (:start . 228)\n  (:id . 90))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 234) (:start . 230)\n  (:id . 91))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 238) (:start . 235)\n  (:id . 92))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 241) (:start . 239)\n  (:id . 93))\n ((:tag . "VBN") (:stem . "map") (:form . "mapped") (:end . 248)\n  (:start . 242) (:id . 94))\n ((:tag . "IN") (:stem . "onto") (:form . "onto") (:end . 253) (:start . 249)\n  (:id . 95))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 255) (:start . 254)\n  (:id . 96))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 258) (:start . 256)\n  (:id . 97))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 265)\n  (:start . 259) (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 266) (:start . 265)\n  (:id . 99)))@@@1@58@((:identifiers (:sid . :s13.255) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504468@unknown@formal@none@1@S@The structural positions of the match are then analysed one by one and solvent accessibility and secondary structure values are collected and scored as described in Methods.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "analyse") (:form . "analysed") (:end . 55)\n  (:start . 47) (:id . 50))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "solvent") (:form . "solvent") (:end . 78)\n  (:start . 71) (:id . 55))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 92) (:start . 79) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 106)\n  (:start . 97) (:id . 58))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 116)\n  (:start . 107) (:id . 59))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 123)\n  (:start . 117) (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 127) (:start . 124)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "collect") (:form . "collected") (:end . 137)\n  (:start . 128) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "score") (:form . "scored") (:end . 148)\n  (:start . 142) (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 151) (:start . 149)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 161)\n  (:start . 152) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 164) (:start . 162)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 172)\n  (:start . 165) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s13.256) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504469@unknown@formal@none@1@S@The structure filter pipeline for a LM match is schematised in Figure 6 and a snapshot of the ELM server output page, displaying results of the structural filtering procedure, is reported and described in Figure 7.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "pipeline") (:form . "pipeline") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "LM") (:form . "LM") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "schematise") (:form . "schematised") (:end . 59)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . "NN") (:stem . "snapshot") (:form . "snapshot") (:end . 86)\n  (:start . 78) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 97) (:start . 94)\n  (:id . 60))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 104)\n  (:start . 98) (:id . 61))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 111)\n  (:start . 105) (:id . 62))\n ((:tag . "NN") (:stem . "page") (:form . "page") (:end . 116) (:start . 112)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "display") (:form . "displaying") (:end . 128)\n  (:start . 118) (:id . 65))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 136)\n  (:start . 129) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 139) (:start . 137)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 154)\n  (:start . 144) (:id . 69))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 164)\n  (:start . 155) (:id . 70))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 174)\n  (:start . 165) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 72))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 178) (:start . 176)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 187)\n  (:start . 179) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 191) (:start . 188)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 201)\n  (:start . 192) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 204) (:start . 202)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 211)\n  (:start . 205) (:id . 78))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 213) (:start . 212)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s13.257) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504470@unknown@formal@none@1@S@This latter, shows that a solved structure of the C-terminal domain of the RanGAP1 protein is available in SCOP entry d1kpsd_ that is used for structure filtering.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "solved") (:form . "solved") (:end . 32)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 42)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 60)\n  (:start . 50) (:id . 52))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 67)\n  (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "rangap1") (:form . "RanGAP1") (:end . 82)\n  (:start . 75) (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 90)\n  (:start . 83) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 103)\n  (:start . 94) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 111) (:start . 107)\n  (:id . 61))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 117)\n  (:start . 112) (:id . 62))\n ((:tag . "NN") (:stem . "d1kpsd_") (:form . "d1kpsd_") (:end . 125)\n  (:start . 118) (:id . 63))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 130) (:start . 126)\n  (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 133) (:start . 131)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 138) (:start . 134)\n  (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 142) (:start . 139)\n  (:id . 67))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 152)\n  (:start . 143) (:id . 68))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 162)\n  (:start . 153) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s13.258) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504471@unknown@formal@none@1@S@The remainder of the sequence is filtered by the cruder domain filter.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "remainder") (:form . "remainder") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 29)\n  (:start . 21) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "filter") (:form . "filtered") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "cruder") (:form . "cruder") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s13.259) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504472@unknown@formal@none@1@S@It can be observed that mouseover of the known sumoylation site reveals that it scores in the enriched bin and receives a significant p-value: if we did not already know it was a true motif, it would be an attractive candidate for experimental testing.@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 9) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 18)\n  (:start . 10) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mouseover") (:form . "mouseover") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "NN") (:stem . "sumoylation") (:form . "sumoylation") (:end . 58)\n  (:start . 47) (:id . 51))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 63) (:start . 59)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 71)\n  (:start . 64) (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "score") (:form . "scores") (:end . 86)\n  (:start . 80) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 102)\n  (:start . 94) (:id . 59))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "receive") (:form . "receives") (:end . 119)\n  (:start . 111) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 121) (:start . 120)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 133)\n  (:start . 122) (:id . 64))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 141)\n  (:start . 134) (:id . 65))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 142) (:start . 141)\n  (:id . 66))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 145) (:start . 143)\n  (:id . 67))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 148) (:start . 146)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 152) (:start . 149)\n  (:id . 69))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 156) (:start . 153)\n  (:id . 70))\n ((:tag . "RB") (:stem . "already") (:form . "already") (:end . 164)\n  (:start . 157) (:id . 71))\n ((:tag . "VB") (:stem . "know") (:form . "know") (:end . 169) (:start . 165)\n  (:id . 72))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 172) (:start . 170)\n  (:id . 73))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 176) (:start . 173)\n  (:id . 74))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 178) (:start . 177)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 183) (:start . 179)\n  (:id . 76))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 189)\n  (:start . 184) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n  (:id . 78))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 193) (:start . 191)\n  (:id . 79))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 199)\n  (:start . 194) (:id . 80))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 202) (:start . 200)\n  (:id . 81))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 205) (:start . 203)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "attractive") (:form . "attractive") (:end . 216)\n  (:start . 206) (:id . 83))\n ((:tag . "NN") (:stem . "candidate") (:form . "candidate") (:end . 226)\n  (:start . 217) (:id . 84))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 230) (:start . 227)\n  (:id . 85))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 243)\n  (:start . 231) (:id . 86))\n ((:tag . "NN") (:stem . "testing") (:form . "testing") (:end . 251)\n  (:start . 244) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 88)))@@@1@47@((:hcues ((:id . :x13.260.1) (:span 194 199)))\n (:hscopes ((:id . :x13.260.1) (:span 194 251)))\n (:identifiers (:sid . :s13.260) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504473@unknown@formal@none@1@S@Moreover, mouseover of a match to the NES motif reveals that it has poor accessibility and is assigned to the sparse bin.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "mouseover") (:form . "mouseover") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "NES") (:form . "NES") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 47) (:start . 42)\n  (:id . 51))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 55)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 60) (:start . 56)\n  (:id . 53))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 63) (:start . 61)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 67) (:start . 64)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "poor") (:form . "poor") (:end . 72) (:start . 68)\n  (:id . 56))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 86) (:start . 73) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 90) (:start . 87)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 102)\n  (:start . 94) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "sparse") (:form . "sparse") (:end . 116)\n  (:start . 110) (:id . 63))\n ((:tag . "NN") (:stem . "bin") (:form . "bin") (:end . 120) (:start . 117)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s13.261) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504474@unknown@formal@none@1@S@The NES motif is predominantly hydrophobic and this example, like many others falling in globular domains, is not a plausible functional site and experimental follow up would be a waste of valuable experimental effort.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "NES") (:form . "NES") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "motif") (:form . "motif") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "RB") (:stem . "predominantly") (:form . "predominantly")\n  (:end . 30) (:start . 17) (:id . 46))\n ((:tag . "JJ") (:stem . "hydrophobic") (:form . "hydrophobic") (:end . 42)\n  (:start . 31) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 51) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 51))\n ((:tag . "IN") (:stem . "like") (:form . "like") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 70) (:start . 66)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "VBG") (:stem . "fall") (:form . "falling") (:end . 85)\n  (:start . 78) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "globular") (:form . "globular") (:end . 97)\n  (:start . 89) (:id . 57))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 105)\n  (:start . 98) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 109) (:start . 107)\n  (:id . 60))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 113) (:start . 110)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "plausible") (:form . "plausible") (:end . 125)\n  (:start . 116) (:id . 63))\n ((:tag . "JJ") (:stem . "functional") (:form . "functional") (:end . 136)\n  (:start . 126) (:id . 64))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 141) (:start . 137)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 158)\n  (:start . 146) (:id . 67))\n ((:tag . "NN") (:stem . "follow") (:form . "follow") (:end . 165)\n  (:start . 159) (:id . 68))\n ((:tag . "RP") (:stem . "up") (:form . "up") (:end . 168) (:start . 166)\n  (:id . 69))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 174)\n  (:start . 169) (:id . 70))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 177) (:start . 175)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 179) (:start . 178)\n  (:id . 72))\n ((:tag . "NN") (:stem . "waste") (:form . "waste") (:end . 185)\n  (:start . 180) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 188) (:start . 186)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "valuable") (:form . "valuable") (:end . 197)\n  (:start . 189) (:id . 75))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 210)\n  (:start . 198) (:id . 76))\n ((:tag . "NN") (:stem . "effort") (:form . "effort") (:end . 217)\n  (:start . 211) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s13.262) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504475@unknown@formal@none@1@S@The Structure Filter (SF) pipeline.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Structure") (:form . "Structure") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "Filter") (:form . "Filter") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "SF") (:form . "SF") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "pipeline") (:form . "pipeline") (:end . 34)\n  (:start . 26) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 35) (:start . 34)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s13.263) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504476@unknown@formal@none@1@S@SA: Solvent Accessibility; SSE: Secondary Structure Element.@(((:tag . "NNP") (:stem . "SA") (:form . "SA") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 3) (:start . 2) (:id . 43))\n ((:tag . "JJ") (:stem . "solvent") (:form . "Solvent") (:end . 11)\n  (:start . 4) (:id . 44))\n ((:tag . "NN") (:stem . "accessibility") (:form . "Accessibility")\n  (:end . 25) (:start . 12) (:id . 45))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "SSE") (:form . "SSE") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "secondary") (:form . "Secondary") (:end . 41)\n  (:start . 32) (:id . 49))\n ((:tag . "NNP") (:stem . "Structure") (:form . "Structure") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "NNP") (:stem . "Element") (:form . "Element") (:end . 59)\n  (:start . 52) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s13.264) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504477@unknown@formal@none@1@S@The ELM server output page.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "page") (:form . "page") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 27) (:start . 26)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s13.265) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504478@unknown@formal@none@1@S@An example of the graphical output of the ELM structure filter for the RAGP1_MOUSE Swissprot [63] entry.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "graphical") (:form . "graphical") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 55)\n  (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "RAGP1_MOUSE") (:form . "RAGP1_MOUSE") (:end . 82)\n  (:start . 71) (:id . 55))\n ((:tag . "NNP") (:stem . "Swissprot") (:form . "Swissprot") (:end . 92)\n  (:start . 83) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 94) (:start . 93)\n  (:id . 57))\n ((:tag . "CD") (:stem . "63") (:form . "63") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 103) (:start . 98)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s13.266) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504479@unknown@formal@none@1@S@The key shows the elements of the graphic.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "key") (:form . "key") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 26)\n  (:start . 18) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "graphic") (:form . "graphic") (:end . 41)\n  (:start . 34) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s13.267) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504480@unknown@formal@none@1@S@Secondary structure elements (in this case helical) are shown as yellow boxes connected by black lines (unstructured loops that tend to be surface accessible).@(((:tag . "JJ") (:stem . "secondary") (:form . "Secondary") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 19)\n  (:start . 10) (:id . 43))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 28)\n  (:start . 20) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "helical") (:form . "helical") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 61) (:start . 56)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 64) (:start . 62)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 71)\n  (:start . 65) (:id . 54))\n ((:tag . "NNS") (:stem . "box") (:form . "boxes") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "connect") (:form . "connected") (:end . 87)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "black") (:form . "black") (:end . 96) (:start . 91)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 102) (:start . 97)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "unstructured") (:form . "unstructured") (:end . 116)\n  (:start . 104) (:id . 61))\n ((:tag . "NNS") (:stem . "loop") (:form . "loops") (:end . 122)\n  (:start . 117) (:id . 62))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 127) (:start . 123)\n  (:id . 63))\n ((:tag . "VBP") (:stem . "tend") (:form . "tend") (:end . 132) (:start . 128)\n  (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 135) (:start . 133)\n  (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 138) (:start . 136)\n  (:id . 66))\n ((:tag . "NN") (:stem . "surface") (:form . "surface") (:end . 146)\n  (:start . 139) (:id . 67))\n ((:tag . "JJ") (:stem . "accessible") (:form . "accessible") (:end . 157)\n  (:start . 147) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s13.268) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504481@unknown@formal@none@1@S@Mouseover of the site rectangles turns on a window reporting structural information; further details of the structure filter results are available by clicking on the site rectangle.@(((:tag . "NNP") (:stem . "Mouseover") (:form . "Mouseover") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "rectangle") (:form . "rectangles") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "NNS") (:stem . "turn") (:form . "turns") (:end . 38) (:start . 33)\n  (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "window") (:form . "window") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "VBG") (:stem . "report") (:form . "reporting") (:end . 60)\n  (:start . 51) (:id . 51))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 71)\n  (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 83)\n  (:start . 72) (:id . 53))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 84) (:start . 83)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 92)\n  (:start . 85) (:id . 55))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 100)\n  (:start . 93) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 58))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 117)\n  (:start . 108) (:id . 59))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 124)\n  (:start . 118) (:id . 60))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 132)\n  (:start . 125) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 136) (:start . 133)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 146)\n  (:start . 137) (:id . 63))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 149) (:start . 147)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "click") (:form . "clicking") (:end . 158)\n  (:start . 150) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 161) (:start . 159)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 67))\n ((:tag . "NN") (:stem . "site") (:form . "site") (:end . 170) (:start . 166)\n  (:id . 68))\n ((:tag . "NN") (:stem . "rectangle") (:form . "rectangle") (:end . 180)\n  (:start . 171) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s13.269) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504482@unknown@formal@none@1@S@The ELM structure filter Web interface and Web service@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "interface") (:form . "interface") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "service") (:form . "service") (:end . 54)\n  (:start . 47) (:id . 50)))@@@1@9@((:identifiers (:sid . :s13.270) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504483@unknown@formal@none@1@S@As an initial step for feedback in the development process of the structure filter pipeline methods, the ELM structure filter functionality was implemented directly into the ELM server.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "initial") (:form . "initial") (:end . 13)\n  (:start . 6) (:id . 44))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "feedback") (:form . "feedback") (:end . 31)\n  (:start . 23) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 50)\n  (:start . 39) (:id . 50))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 58)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 75)\n  (:start . 66) (:id . 54))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 82)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "pipeline") (:form . "pipeline") (:end . 91)\n  (:start . 83) (:id . 56))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 99)\n  (:start . 92) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 108) (:start . 105)\n  (:id . 60))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 118)\n  (:start . 109) (:id . 61))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 125)\n  (:start . 119) (:id . 62))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 139) (:start . 126) (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 143) (:start . 140)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 155)\n  (:start . 144) (:id . 65))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 164)\n  (:start . 156) (:id . 66))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 169) (:start . 165)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 173) (:start . 170)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 177) (:start . 174)\n  (:id . 69))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 184)\n  (:start . 178) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s13.271) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504484@unknown@formal@none@1@S@This involved integration work on both the display representation in the graphical output in addition to links to the more specific details of the results.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "display") (:form . "display") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "representation") (:form . "representation")\n  (:end . 65) (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "graphical") (:form . "graphical") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 89)\n  (:start . 83) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 92) (:start . 90)\n  (:id . 55))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 101)\n  (:start . 93) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "link") (:form . "links") (:end . 110)\n  (:start . 105) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 60))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 122) (:start . 118)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 131)\n  (:start . 123) (:id . 62))\n ((:tag . "NNS") (:stem . "detail") (:form . "details") (:end . 139)\n  (:start . 132) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 142) (:start . 140)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 154)\n  (:start . 147) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s13.272) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504485@unknown@formal@none@1@S@As a second step, in order to facilitate a clean encapsulation of the structure filter pipeline code functionality and to enable future remote tool integration, a SOAP Web Service to access the functionality programmatically has been implemented and is available at http://structurefilter.embl.de/webservice/structureFilter.wsdl.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 11) (:start . 5)\n  (:id . 44))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 20) (:start . 18)\n  (:id . 47))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 26) (:start . 21)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 49))\n ((:tag . "VB") (:stem . "facilitate") (:form . "facilitate") (:end . 40)\n  (:start . 30) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "clean") (:form . "clean") (:end . 48) (:start . 43)\n  (:id . 52))\n ((:tag . "NN") (:stem . "encapsulation") (:form . "encapsulation")\n  (:end . 62) (:start . 49) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 55))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 79)\n  (:start . 70) (:id . 56))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 86)\n  (:start . 80) (:id . 57))\n ((:tag . "NN") (:stem . "pipeline") (:form . "pipeline") (:end . 95)\n  (:start . 87) (:id . 58))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 100) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 114) (:start . 101) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "VB") (:stem . "enable") (:form . "enable") (:end . 128)\n  (:start . 122) (:id . 63))\n ((:tag . "JJ") (:stem . "future") (:form . "future") (:end . 135)\n  (:start . 129) (:id . 64))\n ((:tag . "JJ") (:stem . "remote") (:form . "remote") (:end . 142)\n  (:start . 136) (:id . 65))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 147) (:start . 143)\n  (:id . 66))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 159)\n  (:start . 148) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 162) (:start . 161)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "SOAP") (:form . "SOAP") (:end . 167) (:start . 163)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 171) (:start . 168)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Service") (:form . "Service") (:end . 179)\n  (:start . 172) (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 182) (:start . 180)\n  (:id . 73))\n ((:tag . "VB") (:stem . "access") (:form . "access") (:end . 189)\n  (:start . 183) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 193) (:start . 190)\n  (:id . 75))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 207) (:start . 194) (:id . 76))\n ((:tag . "RB") (:stem . "programmatically") (:form . "programmatically")\n  (:end . 224) (:start . 208) (:id . 77))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 228) (:start . 225)\n  (:id . 78))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 233) (:start . 229)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 245)\n  (:start . 234) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 249) (:start . 246)\n  (:id . 81))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 252) (:start . 250)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 262)\n  (:start . 253) (:id . 83))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 265) (:start . 263)\n  (:id . 84))\n ((:tag . "NN")\n  (:stem . "http://structurefilter.embl.de/webservice/structureFilter.wsdl")\n  (:form . "http://structurefilter.embl.de/webservice/structureFilter.wsdl")\n  (:end . 328) (:start . 266) (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 329) (:start . 328)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s13.273) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504486@unknown@formal@none@1@S@At this link the user can find a detailed description of the web service operations and an example client implementation.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "link") (:form . "link") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "VB") (:stem . "find") (:form . "find") (:end . 30) (:start . 26)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 32) (:start . 31)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 41)\n  (:start . 33) (:id . 50))\n ((:tag . "NN") (:stem . "description") (:form . "description") (:end . 53)\n  (:start . 42) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "service") (:form . "service") (:end . 72)\n  (:start . 65) (:id . 55))\n ((:tag . "NNS") (:stem . "operation") (:form . "operations") (:end . 83)\n  (:start . 73) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 90) (:start . 88)\n  (:id . 58))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 98)\n  (:start . 91) (:id . 59))\n ((:tag . "NN") (:stem . "client") (:form . "client") (:end . 105)\n  (:start . 99) (:id . 60))\n ((:tag . "NN") (:stem . "implementation") (:form . "implementation")\n  (:end . 120) (:start . 106) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s13.274) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504487@unknown@formal@none@1@S@The functionality provided by the web service encompasses the current ELM server interface functionality with some additional options.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 26)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 29) (:start . 27)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "service") (:form . "service") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "VBZ") (:stem . "encompass") (:form . "encompasses") (:end . 57)\n  (:start . 46) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 69)\n  (:start . 62) (:id . 51))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 73) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 80)\n  (:start . 74) (:id . 53))\n ((:tag . "NN") (:stem . "interface") (:form . "interface") (:end . 90)\n  (:start . 81) (:id . 54))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 104) (:start . 91) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 109) (:start . 105)\n  (:id . 56))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 114) (:start . 110)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 125)\n  (:start . 115) (:id . 58))\n ((:tag . "NNS") (:stem . "option") (:form . "options") (:end . 133)\n  (:start . 126) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s13.275) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504488@unknown@formal@none@1@S@For the ELM Server interface functionality, all LMs in the ELM database are matched against the query sequence and this is also the default functionality of the Web Service.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Server") (:form . "Server") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "interface") (:form . "interface") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 42) (:start . 29) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "lm") (:form . "LMs") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 71)\n  (:start . 63) (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "match") (:form . "matched") (:end . 83)\n  (:start . 76) (:id . 56))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 91)\n  (:start . 84) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 110)\n  (:start . 102) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 61))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 119) (:start . 115)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 127) (:start . 123)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 65))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 139)\n  (:start . 132) (:id . 66))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 153) (:start . 140) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 156) (:start . 154)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 160) (:start . 157)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 164) (:start . 161)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Service") (:form . "Service") (:end . 172)\n  (:start . 165) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s13.276) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504489@unknown@formal@none@1@S@The extra options implemented in the Web Service are to search the query sequence by one or more user-specified regular expressions, rather than the default ELM database regular expressions, and/or by one or more user-specified ELM identifiers from the ELM database.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "extra") (:form . "extra") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "option") (:form . "options") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 29)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Service") (:form . "Service") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "VB") (:stem . "search") (:form . "search") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 81)\n  (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 96) (:start . 92)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "user-specified") (:form . "user-specified")\n  (:end . 111) (:start . 97) (:id . 60))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 119)\n  (:start . 112) (:id . 61))\n ((:tag . "NNS") (:stem . "expression") (:form . "expressions") (:end . 131)\n  (:start . 120) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 63))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 139)\n  (:start . 133) (:id . 64))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 144) (:start . 140)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 66))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 156)\n  (:start . 149) (:id . 67))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 160) (:start . 157)\n  (:id . 68))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 169)\n  (:start . 161) (:id . 69))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 177)\n  (:start . 170) (:id . 70))\n ((:tag . "NNS") (:stem . "expression") (:form . "expressions") (:end . 189)\n  (:start . 178) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 190) (:start . 189)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 197)\n  (:start . 191) (:id . 73))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 200) (:start . 198)\n  (:id . 74))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 204) (:start . 201)\n  (:id . 75))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 207) (:start . 205)\n  (:id . 76))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 212) (:start . 208)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "user-specified") (:form . "user-specified")\n  (:end . 227) (:start . 213) (:id . 78))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 231) (:start . 228)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "identifier") (:form . "identifiers") (:end . 243)\n  (:start . 232) (:id . 80))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 248) (:start . 244)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 252) (:start . 249)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 256) (:start . 253)\n  (:id . 83))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 265)\n  (:start . 257) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 266) (:start . 265)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s13.277) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504490@unknown@formal@none@1@S@Where possible, to a limited extent, if the user-specified regular expression corresponds to an existing ELM this information is made known to the user.@(((:tag . "WRB") (:stem . "where") (:form . "Where") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 15) (:start . 14)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "limit") (:form . "limited") (:end . 28)\n  (:start . 21) (:id . 47))\n ((:tag . "NN") (:stem . "extent") (:form . "extent") (:end . 35)\n  (:start . 29) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 39) (:start . 37)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "user-specified") (:form . "user-specified")\n  (:end . 58) (:start . 44) (:id . 52))\n ((:tag . "JJ") (:stem . "regular") (:form . "regular") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "expression") (:form . "expression") (:end . 77)\n  (:start . 67) (:id . 54))\n ((:tag . "VBZ") (:stem . "correspond") (:form . "corresponds") (:end . 89)\n  (:start . 78) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n  (:id . 56))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 104)\n  (:start . 96) (:id . 58))\n ((:tag . "NNP") (:stem . "ELM") (:form . "ELM") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 113) (:start . 109)\n  (:id . 60))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 125)\n  (:start . 114) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 128) (:start . 126)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 133) (:start . 129)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "know") (:form . "known") (:end . 139)\n  (:start . 134) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 142) (:start . 140)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 66))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 151) (:start . 147)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s13.278) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504491@unknown@formal@none@1@S@The WSDL (Web Service Description Language) [56] file is WS-I compatible.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "WSDL") (:form . "WSDL") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Web") (:form . "Web") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Service") (:form . "Service") (:end . 21)\n  (:start . 14) (:id . 46))\n ((:tag . "NNP") (:stem . "Description") (:form . "Description") (:end . 33)\n  (:start . 22) (:id . 47))\n ((:tag . "NNP") (:stem . "Language") (:form . "Language") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "CD") (:stem . "56") (:form . "56") (:end . 47) (:start . 45)\n  (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 48) (:start . 47)\n  (:id . 52))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 53) (:start . 49)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 56) (:start . 54)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "WS-I") (:form . "WS-I") (:end . 61) (:start . 57)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "compatible") (:form . "compatible") (:end . 72)\n  (:start . 62) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s13.279) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504492@unknown@formal@none@1@S@The WS-Interoperability Basic Profile [57] proposes a set of rules to achieve interoperability of web services between different platforms.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "WS-Interoperability")\n  (:form . "WS-Interoperability") (:end . 23) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "basic") (:form . "Basic") (:end . 29) (:start . 24)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Profile") (:form . "Profile") (:end . 37)\n  (:start . 30) (:id . 45))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 39) (:start . 38)\n  (:id . 46))\n ((:tag . "CD") (:stem . "57") (:form . "57") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "propose") (:form . "proposes") (:end . 51)\n  (:start . 43) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "rule") (:form . "rules") (:end . 66) (:start . 61)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "VB") (:stem . "achieve") (:form . "achieve") (:end . 77)\n  (:start . 70) (:id . 55))\n ((:tag . "NN") (:stem . "interoperability") (:form . "interoperability")\n  (:end . 94) (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 101) (:start . 98)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "service") (:form . "services") (:end . 110)\n  (:start . 102) (:id . 59))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 118)\n  (:start . 111) (:id . 60))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 128)\n  (:start . 119) (:id . 61))\n ((:tag . "NNS") (:stem . "platform") (:form . "platforms") (:end . 138)\n  (:start . 129) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s13.280) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504493@unknown@formal@none@1@S@The WSDL file implements an XML document/literal style [58].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "WSDL") (:form . "WSDL") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "implement") (:form . "implements") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "XML") (:form . "XML") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "document/literal") (:form . "document/literal")\n  (:end . 48) (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "style") (:form . "style") (:end . 54) (:start . 49)\n  (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 56) (:start . 55)\n  (:id . 50))\n ((:tag . "CD") (:stem . "58") (:form . "58") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s13.281) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504494@unknown@formal@none@1@S@The back-end code is implemented in Java and runs on Axis2 [59] inside a Tomcat servlet container [60].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "back-end") (:form . "back-end") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "implement") (:form . "implemented") (:end . 32)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Java") (:form . "Java") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "run") (:form . "runs") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "axis2") (:form . "Axis2") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "CD") (:stem . "59") (:form . "59") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . "IN") (:stem . "inside") (:form . "inside") (:end . 70)\n  (:start . 64) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Tomcat") (:form . "Tomcat") (:end . 79)\n  (:start . 73) (:id . 58))\n ((:tag . "NN") (:stem . "servlet") (:form . "servlet") (:end . 87)\n  (:start . 80) (:id . 59))\n ((:tag . "NN") (:stem . "container") (:form . "container") (:end . 97)\n  (:start . 88) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 99) (:start . 98)\n  (:id . 61))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 101) (:start . 99)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 102) (:start . 101)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s13.282) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504495@unknown@formal@none@1@S@Statistical Details@(((:tag . "JJ") (:stem . "statistical") (:form . "Statistical") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Detail") (:form . "Details") (:end . 19)\n  (:start . 12) (:id . 43)))@@@1@2@((:identifiers (:sid . :s13.283) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504496@unknown@formal@none@1@S@Score distributions turned out to be normal after visual inspection and quantitative Shapiro-Wilk test [61] at the 0.01 significance level.@(((:tag . "NN") (:stem . "score") (:form . "Score") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 19) (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "turn") (:form . "turned") (:end . 26) (:start . 20)\n  (:id . 44))\n ((:tag . "RP") (:stem . "out") (:form . "out") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "normal") (:form . "normal") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 49) (:start . 44)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "visual") (:form . "visual") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "inspection") (:form . "inspection") (:end . 67)\n  (:start . 57) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 84)\n  (:start . 72) (:id . 53))\n ((:tag . "NN") (:stem . "shapiro-wilk") (:form . "Shapiro-Wilk") (:end . 97)\n  (:start . 85) (:id . 54))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 102) (:start . 98)\n  (:id . 55))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 104) (:start . 103)\n  (:id . 56))\n ((:tag . "CD") (:stem . "61") (:form . "61") (:end . 106) (:start . 104)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 110) (:start . 108)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 114) (:start . 111)\n  (:id . 60))\n ((:tag . "CD") (:stem . "0.01") (:form . "0.01") (:end . 119) (:start . 115)\n  (:id . 61))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 132)\n  (:start . 120) (:id . 62))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 138)\n  (:start . 133) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s13.284) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504497@unknown@formal@none@1@S@The average and standard deviation values from random match score distributions are used for the dynamical calculation of the Z-score and the corresponding one-sided p-value.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "deviation") (:form . "deviation") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 41)\n  (:start . 35) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 79) (:start . 66) (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 83) (:start . 80)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 88) (:start . 84)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "dynamical") (:form . "dynamical") (:end . 106)\n  (:start . 97) (:id . 57))\n ((:tag . "NN") (:stem . "calculation") (:form . "calculation") (:end . 118)\n  (:start . 107) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Z-score") (:form . "Z-score") (:end . 133)\n  (:start . 126) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 141) (:start . 138)\n  (:id . 63))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 155)\n  (:start . 142) (:id . 64))\n ((:tag . "JJ") (:stem . "one-sided") (:form . "one-sided") (:end . 165)\n  (:start . 156) (:id . 65))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 173)\n  (:start . 166) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s13.285) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504498@unknown@formal@none@1@S@The significance of the differences observed for accessibility and secondary structure frequencies in true motifs vs random matches was assessed through t-tests (for accessibility values) and chi-square tests (for secondary structure assignments).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 35)\n  (:start . 24) (:id . 46))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 44)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 62) (:start . 49) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 76)\n  (:start . 67) (:id . 51))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 86)\n  (:start . 77) (:id . 52))\n ((:tag . "NNS") (:stem . "frequency") (:form . "frequencies") (:end . 98)\n  (:start . 87) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 101) (:start . 99)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "true") (:form . "true") (:end . 106) (:start . 102)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "motif") (:form . "motifs") (:end . 113)\n  (:start . 107) (:id . 56))\n ((:tag . "IN") (:stem . "vs") (:form . "vs") (:end . 116) (:start . 114)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 123)\n  (:start . 117) (:id . 58))\n ((:tag . "NNS") (:stem . "match") (:form . "matches") (:end . 131)\n  (:start . 124) (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 135) (:start . 132)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 144)\n  (:start . 136) (:id . 61))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 152)\n  (:start . 145) (:id . 62))\n ((:tag . "NNS") (:stem . "t-test") (:form . "t-tests") (:end . 160)\n  (:start . 153) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 165) (:start . 162)\n  (:id . 65))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 179) (:start . 166) (:id . 66))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 186)\n  (:start . 180) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 187) (:start . 186)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 191) (:start . 188)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "chi-square") (:form . "chi-square") (:end . 202)\n  (:start . 192) (:id . 70))\n ((:tag . "NNS") (:stem . "test") (:form . "tests") (:end . 208)\n  (:start . 203) (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 210) (:start . 209)\n  (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 213) (:start . 210)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 223)\n  (:start . 214) (:id . 74))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 233)\n  (:start . 224) (:id . 75))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 245)\n  (:start . 234) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 246) (:start . 245)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 247) (:start . 246)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s13.286) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504499@unknown@formal@none@1@S@All the statistical calculations were performed with the R package [62].@(((:tag . "PDT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 19)\n  (:start . 8) (:id . 44))\n ((:tag . "NNS") (:stem . "calculation") (:form . "calculations") (:end . 32)\n  (:start . 20) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 37) (:start . 33)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 47)\n  (:start . 38) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 52) (:start . 48)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "NN") (:stem . "r") (:form . "R") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "CD") (:stem . "62") (:form . "62") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s13.287) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504500@unknown@formal@none@1@S@List of abbreviations@(((:tag . "NN") (:stem . "list") (:form . "List") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "abbreviation") (:form . "abbreviations")\n  (:end . 21) (:start . 8) (:id . 44)))@@@1@3@((:identifiers (:sid . :s13.288) (:did . :pmc2774702) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
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5504502@unknown@formal@none@1@S@multiplierz: an extensible API based desktop environment for proteomics data analysis@(((:tag . "LS") (:stem . "multiplierz") (:form . "multiplierz") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "extensible") (:form . "extensible") (:end . 26)\n  (:start . 16) (:id . 45))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "based") (:form . "based") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "desktop") (:form . "desktop") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 56)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 76) (:start . 72)\n  (:id . 52))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 85)\n  (:start . 77) (:id . 53)))@@@1@12@((:identifiers (:sid . :s14.1) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5504503@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s14.2) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
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5504505@unknown@formal@none@1@S@Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources.@(((:tag . "JJ") (:stem . "efficient") (:form . "Efficient") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 18)\n  (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 39) (:start . 35)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "spectrometry-based") (:form . "spectrometry-based")\n  (:end . 58) (:start . 40) (:id . 48))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 69)\n  (:start . 59) (:id . 49))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 81)\n  (:start . 70) (:id . 50))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 90)\n  (:start . 82) (:id . 51))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 97)\n  (:start . 91) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 53))\n ((:tag . "VB") (:stem . "disparate") (:form . "disparate") (:end . 110)\n  (:start . 101) (:id . 54))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 115)\n  (:start . 111) (:id . 55))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 121)\n  (:start . 116) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 132)\n  (:start . 123) (:id . 58))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 139)\n  (:start . 133) (:id . 59))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 144) (:start . 140)\n  (:id . 60))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 157)\n  (:start . 145) (:id . 61))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 163)\n  (:start . 158) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 63))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 171)\n  (:start . 165) (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 176) (:start . 172)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 187)\n  (:start . 177) (:id . 66))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 192) (:start . 188)\n  (:id . 67))\n ((:tag . "VBP") (:stem . "assign") (:form . "assign") (:end . 199)\n  (:start . 193) (:id . 68))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 207)\n  (:start . 200) (:id . 69))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 216)\n  (:start . 208) (:id . 70))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 219) (:start . 217)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 225)\n  (:start . 220) (:id . 72))\n ((:tag . "NNS") (:stem . "spectrum") (:form . "spectra") (:end . 233)\n  (:start . 226) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 234) (:start . 233)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 238) (:start . 235)\n  (:id . 75))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 249)\n  (:start . 239) (:id . 76))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 253) (:start . 250)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 262)\n  (:start . 254) (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 266) (:start . 263)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "pathway") (:form . "pathways") (:end . 275)\n  (:start . 267) (:id . 80))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 280) (:start . 276)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 288)\n  (:start . 281) (:id . 82))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 297)\n  (:start . 289) (:id . 83))\n ((:tag . "NNS") (:stem . "source") (:form . "sources") (:end . 305)\n  (:start . 298) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 306) (:start . 305)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s14.4) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504506@unknown@formal@none@1@S@Moreover, proteomics technologies and experimental methods are not yet standardized; hence a high degree of flexibility is necessary for efficient support of high- and low-throughput data analytic tasks.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "technology") (:form . "technologies") (:end . 33)\n  (:start . 21) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 50)\n  (:start . 38) (:id . 47))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 58)\n  (:start . 51) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 62) (:start . 59)\n  (:id . 49))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 70) (:start . 67)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "standardize") (:form . "standardized") (:end . 83)\n  (:start . 71) (:id . 52))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 84) (:start . 83)\n  (:id . 53))\n ((:tag . "RB") (:stem . "hence") (:form . "hence") (:end . 90) (:start . 85)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 92) (:start . 91)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 104)\n  (:start . 98) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "NN") (:stem . "flexibility") (:form . "flexibility") (:end . 119)\n  (:start . 108) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 122) (:start . 120)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "necessary") (:form . "necessary") (:end . 132)\n  (:start . 123) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 136) (:start . 133)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 146)\n  (:start . 137) (:id . 63))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 154)\n  (:start . 147) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 157) (:start . 155)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "high-") (:form . "high-") (:end . 163)\n  (:start . 158) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 167) (:start . 164)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "low-throughput") (:form . "low-throughput")\n  (:end . 182) (:start . 168) (:id . 68))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 187)\n  (:start . 183) (:id . 69))\n ((:tag . "JJ") (:stem . "analytic") (:form . "analytic") (:end . 196)\n  (:start . 188) (:id . 70))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 202)\n  (:start . 197) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s14.5) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504507@unknown@formal@none@1@S@Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge.@(((:tag . "NNP") (:stem . "Development") (:form . "Development") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "desktop") (:form . "desktop") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 36)\n  (:start . 25) (:id . 46))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "RB") (:stem . "sufficiently") (:form . "sufficiently") (:end . 57)\n  (:start . 45) (:id . 49))\n ((:tag . "JJ") (:stem . "robust") (:form . "robust") (:end . 64)\n  (:start . 58) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n  (:id . 51))\n ((:tag . "NN") (:stem . "deployment") (:form . "deployment") (:end . 79)\n  (:start . 69) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 82) (:start . 80)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 87) (:start . 83)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "analytic") (:form . "analytic") (:end . 96)\n  (:start . 88) (:id . 55))\n ((:tag . "NNS") (:stem . "pipeline") (:form . "pipelines") (:end . 106)\n  (:start . 97) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 58))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n  (:end . 126) (:start . 112) (:id . 59))\n ((:tag . "VBZ") (:stem . "support") (:form . "supports") (:end . 135)\n  (:start . 127) (:id . 60))\n ((:tag . "NN") (:stem . "customization") (:form . "customization")\n  (:end . 149) (:start . 136) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 153) (:start . 150)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "programmer") (:form . "programmers") (:end . 165)\n  (:start . 154) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 169) (:start . 166)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "non-programmer") (:form . "non-programmers")\n  (:end . 185) (:start . 170) (:id . 65))\n ((:tag . "RB") (:stem . "alike") (:form . "alike") (:end . 191)\n  (:start . 186) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 192) (:start . 191)\n  (:id . 67))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 196) (:start . 193)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "prove") (:form . "proven") (:end . 203)\n  (:start . 197) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 206) (:start . 204)\n  (:id . 70))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 209) (:start . 207)\n  (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 211) (:start . 210)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 223)\n  (:start . 212) (:id . 73))\n ((:tag . "NN") (:stem . "challenge") (:form . "challenge") (:end . 233)\n  (:start . 224) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s14.6) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504508@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s14.7) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504509@unknown@formal@none@1@S@We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "describe") (:form . "describe") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "flexible") (:form . "flexible") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "open-source") (:form . "open-source") (:end . 51)\n  (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "desktop") (:form . "desktop") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 71)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "comprehensive") (:form . "comprehensive")\n  (:end . 89) (:start . 76) (:id . 53))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 100)\n  (:start . 90) (:id . 54))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 105)\n  (:start . 101) (:id . 55))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 114)\n  (:start . 106) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s14.8) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504510@unknown@formal@none@1@S@We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "use") (:form . "use") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "VB") (:stem . "expose") (:form . "expose") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "prototype") (:form . "prototype") (:end . 43)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 51)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 67)\n  (:start . 59) (:id . 53))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 76)\n  (:start . 68) (:id . 54))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 83)\n  (:start . 77) (:id . 55))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "mzAPI") (:form . "mzAPI") (:end . 94) (:start . 89)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 104)\n  (:start . 96) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 115)\n  (:start . 109) (:id . 62))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 122)\n  (:start . 116) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 125) (:start . 123)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "proprietary") (:form . "proprietary") (:end . 137)\n  (:start . 126) (:id . 65))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 142) (:start . 138)\n  (:id . 66))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 155)\n  (:start . 143) (:id . 67))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 161)\n  (:start . 156) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s14.9) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504511@unknown@formal@none@1@S@In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "routine") (:form . "routine") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "analytic") (:form . "analytic") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 42) (:start . 37)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 55)\n  (:start . 44) (:id . 50))\n ((:tag . "VBZ") (:stem . "support") (:form . "supports") (:end . 64)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 75)\n  (:start . 65) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 53))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 90)\n  (:start . 79) (:id . 54))\n ((:tag . "JJ") (:stem . "rich") (:form . "rich") (:end . 95) (:start . 91)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "portable") (:form . "portable") (:end . 105)\n  (:start . 97) (:id . 57))\n ((:tag . "JJ") (:stem . "spreadsheet-based") (:form . "spreadsheet-based")\n  (:end . 123) (:start . 106) (:id . 58))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 131)\n  (:start . 124) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s14.10) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504512@unknown@formal@none@1@S@Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "around") (:form . "around") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 44) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "zero") (:form . "zero") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "infrastructure") (:form . "infrastructure")\n  (:end . 63) (:start . 49) (:id . 51))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 64) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "philosophy") (:form . "philosophy") (:end . 75)\n  (:start . 65) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "mean") (:form . "meaning") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 89) (:start . 85)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 99) (:start . 97)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "deploy") (:form . "deployed") (:end . 108)\n  (:start . 100) (:id . 60))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 111) (:start . 109)\n  (:id . 61))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 115) (:start . 112)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 121)\n  (:start . 116) (:id . 63))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 126) (:start . 122)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "little") (:form . "little") (:end . 133)\n  (:start . 127) (:id . 65))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 136) (:start . 134)\n  (:id . 66))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 139) (:start . 137)\n  (:id . 67))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 146)\n  (:start . 140) (:id . 68))\n ((:tag . "NN") (:stem . "administration") (:form . "administration")\n  (:end . 161) (:start . 147) (:id . 69))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 169)\n  (:start . 162) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s14.11) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504513@unknown@formal@none@1@S@Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 30)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 44) (:start . 31) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 47) (:start . 45)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 56)\n  (:start . 48) (:id . 49))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 60) (:start . 57)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "high-level") (:form . "high-level") (:end . 71)\n  (:start . 61) (:id . 51))\n ((:tag . "NNP") (:stem . "Python") (:form . "Python") (:end . 78)\n  (:start . 72) (:id . 52))\n ((:tag . "NNS") (:stem . "script") (:form . "scripts") (:end . 86)\n  (:start . 79) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 97)\n  (:start . 88) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 102) (:start . 101)\n  (:id . 57))\n ((:tag . "RB") (:stem . "fully") (:form . "fully") (:end . 108)\n  (:start . 103) (:id . 58))\n ((:tag . "JJ") (:stem . "extensible") (:form . "extensible") (:end . 119)\n  (:start . 109) (:id . 59))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 124)\n  (:start . 120) (:id . 60))\n ((:tag . "JJ") (:stem . "analytic") (:form . "analytic") (:end . 133)\n  (:start . 125) (:id . 61))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 145)\n  (:start . 134) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 149) (:start . 146)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 155)\n  (:start . 150) (:id . 64))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 167)\n  (:start . 156) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 170) (:start . 168)\n  (:id . 66))\n ((:tag . "NN") (:stem . "custom") (:form . "custom") (:end . 177)\n  (:start . 171) (:id . 67))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 188)\n  (:start . 178) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 192) (:start . 189)\n  (:id . 69))\n ((:tag . "NN") (:stem . "deployment") (:form . "deployment") (:end . 203)\n  (:start . 193) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 206) (:start . 204)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "high-throughput") (:form . "high-throughput")\n  (:end . 222) (:start . 207) (:id . 72))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 227)\n  (:start . 223) (:id . 73))\n ((:tag . "NNS") (:stem . "pipeline") (:form . "pipelines") (:end . 237)\n  (:start . 228) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 238) (:start . 237)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s14.12) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504514@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s14.13) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504515@unknown@formal@none@1@S@Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research.@(((:tag . "RB") (:stem . "collectively") (:form . "Collectively") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 35)\n  (:start . 24) (:id . 46))\n ((:tag . "VBP") (:stem . "facilitate") (:form . "facilitate") (:end . 46)\n  (:start . 36) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 53) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 76)\n  (:start . 68) (:id . 53))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 82) (:start . 77)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "span") (:form . "spanning") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . "NN") (:stem . "technology") (:form . "technology") (:end . 103)\n  (:start . 93) (:id . 57))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 115)\n  (:start . 104) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 118) (:start . 116)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 129)\n  (:start . 119) (:id . 60))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 140)\n  (:start . 130) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 145) (:start . 142)\n  (:id . 63))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 150) (:start . 146)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "spectrometry-based") (:form . "spectrometry-based")\n  (:end . 169) (:start . 151) (:id . 65))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 180)\n  (:start . 170) (:id . 66))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 189)\n  (:start . 181) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s14.14) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504516@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s14.15) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504517@unknown@formal@none@1@S@Mass spectrometry-based proteomics, particularly liquid chromatography coupled to electrospray ionization, has become the predominant technique for identification and quantification of proteins in biological systems [1].@(((:tag . "NNP") (:stem . "Mass") (:form . "Mass") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "spectrometry-based") (:form . "spectrometry-based")\n  (:end . 23) (:start . 5) (:id . 43))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 34)\n  (:start . 24) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 45))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 48)\n  (:start . 36) (:id . 46))\n ((:tag . "JJ") (:stem . "liquid") (:form . "liquid") (:end . 55)\n  (:start . 49) (:id . 47))\n ((:tag . "NN") (:stem . "chromatography") (:form . "chromatography")\n  (:end . 70) (:start . 56) (:id . 48))\n ((:tag . "VBN") (:stem . "couple") (:form . "coupled") (:end . 78)\n  (:start . 71) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 81) (:start . 79)\n  (:id . 50))\n ((:tag . "VB") (:stem . "electrospray") (:form . "electrospray") (:end . 94)\n  (:start . 82) (:id . 51))\n ((:tag . "NN") (:stem . "ionization") (:form . "ionization") (:end . 105)\n  (:start . 95) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 106) (:start . 105)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 110) (:start . 107)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "become") (:form . "become") (:end . 117)\n  (:start . 111) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "predominant") (:form . "predominant") (:end . 133)\n  (:start . 122) (:id . 57))\n ((:tag . "NN") (:stem . "technique") (:form . "technique") (:end . 143)\n  (:start . 134) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 147) (:start . 144)\n  (:id . 59))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 162) (:start . 148) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 166) (:start . 163)\n  (:id . 61))\n ((:tag . "NN") (:stem . "quantification") (:form . "quantification")\n  (:end . 181) (:start . 167) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 193)\n  (:start . 185) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 196) (:start . 194)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 207)\n  (:start . 197) (:id . 66))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 215)\n  (:start . 208) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 217) (:start . 216)\n  (:id . 68))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 218) (:start . 217)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 219) (:start . 218)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 220) (:start . 219)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s14.16) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504518@unknown@formal@none@1@S@Growing demand for improved annotation of primary proteomics data with biological information from various public databases has catalyzed interest in the development of software tools to support integration of these data types.@(((:tag . "VBG") (:stem . "grow") (:form . "Growing") (:end . 7) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "demand") (:form . "demand") (:end . 14) (:start . 8)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "improved") (:form . "improved") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 38)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 60)\n  (:start . 50) (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 65) (:start . 61)\n  (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 70) (:start . 66)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 81)\n  (:start . 71) (:id . 52))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 93)\n  (:start . 82) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 98) (:start . 94)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 106)\n  (:start . 99) (:id . 55))\n ((:tag . "JJ") (:stem . "public") (:form . "public") (:end . 113)\n  (:start . 107) (:id . 56))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 123)\n  (:start . 114) (:id . 57))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 127) (:start . 124)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "catalyze") (:form . "catalyzed") (:end . 137)\n  (:start . 128) (:id . 59))\n ((:tag . "NN") (:stem . "interest") (:form . "interest") (:end . 146)\n  (:start . 138) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 62))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 165)\n  (:start . 154) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n  (:id . 64))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 177)\n  (:start . 169) (:id . 65))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 183)\n  (:start . 178) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 186) (:start . 184)\n  (:id . 67))\n ((:tag . "VB") (:stem . "support") (:form . "support") (:end . 194)\n  (:start . 187) (:id . 68))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 206)\n  (:start . 195) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 209) (:start . 207)\n  (:id . 70))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 215)\n  (:start . 210) (:id . 71))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 220)\n  (:start . 216) (:id . 72))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 226)\n  (:start . 221) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s14.17) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504519@unknown@formal@none@1@S@Unfortunately, a number of factors, including lack of experimental standardization, rapid introduction of novel mass spectrometry technology, and the evolution of proprietary file formats associated with proteomics platforms represent a significant hurdle to the development of efficient and comprehensive software frameworks.@(((:tag . "RB") (:stem . "unfortunately") (:form . "Unfortunately")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . 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5504520@unknown@formal@none@1@S@To accommodate the emergent nature of proteomics-related technologies and the burgeoning number of databases that contain various biological annotations, data analytic systems must emphasize (i) intuitive and interactive interfaces, (ii) user-accessible coding frameworks to facilitate rapid prototyping of algorithms, and (iii) customizable sets of tools that can be readily integrated to provide pipelines that support a variety of proteomic workflows.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "accommodate") (:form . "accommodate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "emergent") (:form . "emergent") (:end . 27)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "nature") (:form . "nature") (:end . 34)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . 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5504521@unknown@formal@none@1@S@Task specific Windows desktop applications such as MSQuant [2] and InsilicosViewer [3] can access a subset of native mass spectrometry data files directly and provide flexibility through adjustable parameters, but are not readily extended across the full spectrum of data analytic activities required in modern proteomics research.@(((:tag . "NNP") (:stem . "Task") (:form . "Task") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "NNP") (:stem . "Window") (:form . "Windows") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "desktop") (:form . "desktop") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "NNS") (:stem . "application") (:form . "applications") (:end . 42)\n  (:start . 30) (:id . 46))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 47) (:start . 43)\n  (:id . 47))\n ((:tag . "IN") (:stem . "as") (:form . 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5504522@unknown@formal@none@1@S@To address the full spectrum of analyses, open source projects such as The OpenMS Proteomics Pipeline (TOPP) [4] and ProteoWizard [5] offer a set of modular tools for generation of pipelines.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "address") (:form . "address") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "spectrum") (:form . "spectrum") (:end . 28)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "open") (:form . "open") (:end . 46) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 53)\n  (:start . 47) (:id . 51))\n ((:tag . "NNS") (:stem . "project") (:form . "projects") (:end . 62)\n  (:start . 54) (:id . 52))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "OpenMS") (:form . "OpenMS") (:end . 81)\n  (:start . 75) (:id . 56))\n ((:tag . "NNP") (:stem . "Proteomic") (:form . "Proteomics") (:end . 92)\n  (:start . 82) (:id . 57))\n ((:tag . "NNP") (:stem . "Pipeline") (:form . "Pipeline") (:end . 101)\n  (:start . 93) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "TOPP") (:form . "TOPP") (:end . 107) (:start . 103)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 108) (:start . 107)\n  (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 110) (:start . 109)\n  (:id . 62))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 111) (:start . 110)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "ProteoWizard") (:form . "ProteoWizard")\n  (:end . 129) (:start . 117) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 131) (:start . 130)\n  (:id . 67))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 132) (:start . 131)\n  (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 133) (:start . 132)\n  (:id . 69))\n ((:tag . "VBP") (:stem . "offer") (:form . "offer") (:end . 139)\n  (:start . 134) (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 141) (:start . 140)\n  (:id . 71))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 145) (:start . 142)\n  (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "modular") (:form . "modular") (:end . 156)\n  (:start . 149) (:id . 74))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 162)\n  (:start . 157) (:id . 75))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 166) (:start . 163)\n  (:id . 76))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 177)\n  (:start . 167) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 180) (:start . 178)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "pipeline") (:form . "pipelines") (:end . 190)\n  (:start . 181) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s14.21) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504523@unknown@formal@none@1@S@The C++ coding environment of these tools is designed for performance and throughput, although researchers who lack programming experience often struggle to implement novel algorithms or other ad hoc tasks.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "c++") (:form . "C++") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "VBG") (:stem . "cod") (:form . "coding") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 35) (:start . 30)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 69)\n  (:start . 58) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "throughput") (:form . "throughput") (:end . 84)\n  (:start . 74) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 55))\n ((:tag . "IN") (:stem . "although") (:form . "although") (:end . 94)\n  (:start . 86) (:id . 56))\n ((:tag . "NNS") (:stem . "researcher") (:form . "researchers") (:end . 106)\n  (:start . 95) (:id . 57))\n ((:tag . "WP") (:stem . "who") (:form . "who") (:end . 110) (:start . 107)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "lack") (:form . "lack") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "program") (:form . "programming") (:end . 127)\n  (:start . 116) (:id . 60))\n ((:tag . "NN") (:stem . "experience") (:form . "experience") (:end . 138)\n  (:start . 128) (:id . 61))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 144)\n  (:start . 139) (:id . 62))\n ((:tag . "VBP") (:stem . "struggle") (:form . "struggle") (:end . 153)\n  (:start . 145) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 156) (:start . 154)\n  (:id . 64))\n ((:tag . "VB") (:stem . "implement") (:form . "implement") (:end . 166)\n  (:start . 157) (:id . 65))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 172)\n  (:start . 167) (:id . 66))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 183)\n  (:start . 173) (:id . 67))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 186) (:start . 184)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 192)\n  (:start . 187) (:id . 69))\n ((:tag . "NN") (:stem . "ad") (:form . "ad") (:end . 195) (:start . 193)\n  (:id . 70))\n ((:tag . "NN") (:stem . "hoc") (:form . "hoc") (:end . 199) (:start . 196)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 205)\n  (:start . 200) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 206) (:start . 205)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s14.22) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504524@unknown@formal@none@1@S@Therefore, software libraries such as InSilicoSpectro [6] and mspire [7] have been developed based on high-level languages such as Perl and Ruby respectively.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "NNS") (:stem . "library") (:form . "libraries") (:end . 29)\n  (:start . 20) (:id . 45))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "InSilicoSpectro") (:form . "InSilicoSpectro")\n  (:end . 53) (:start . 38) (:id . 48))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 55) (:start . 54)\n  (:id . 49))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 56) (:start . 55)\n  (:id . 50))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mspire") (:form . "mspire") (:end . 68)\n  (:start . 62) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 77) (:start . 73)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 82) (:start . 78)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "develop") (:form . "developed") (:end . 92)\n  (:start . 83) (:id . 59))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 98) (:start . 93)\n  (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 101) (:start . 99)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "high-level") (:form . "high-level") (:end . 112)\n  (:start . 102) (:id . 62))\n ((:tag . "NNS") (:stem . "language") (:form . "languages") (:end . 122)\n  (:start . 113) (:id . 63))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 127) (:start . 123)\n  (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 130) (:start . 128)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Perl") (:form . "Perl") (:end . 135) (:start . 131)\n  (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Ruby") (:form . "Ruby") (:end . 144) (:start . 140)\n  (:id . 68))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 157)\n  (:start . 145) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s14.23) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504525@unknown@formal@none@1@S@These libraries allow scripting of common data analysis tasks but cannot access raw binary data directly, and must rely instead on surrogate text files.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "library") (:form . "libraries") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "allow") (:form . "allow") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "scripte") (:form . "scripting") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 41)\n  (:start . 35) (:id . 47))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 61) (:start . 56)\n  (:id . 50))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "cannot") (:form . "cannot") (:end . 72)\n  (:start . 66) (:id . 52))\n ((:tag . "VB") (:stem . "access") (:form . "access") (:end . 79)\n  (:start . 73) (:id . 53))\n ((:tag . "JJ") (:stem . "raw") (:form . "raw") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "binary") (:form . "binary") (:end . 90)\n  (:start . 84) (:id . 55))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 95) (:start . 91)\n  (:id . 56))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 104)\n  (:start . 96) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 59))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 114) (:start . 110)\n  (:id . 60))\n ((:tag . "VB") (:stem . "rely") (:form . "rely") (:end . 119) (:start . 115)\n  (:id . 61))\n ((:tag . "RB") (:stem . "instead") (:form . "instead") (:end . 127)\n  (:start . 120) (:id . 62))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 130) (:start . 128)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "surrogate") (:form . "surrogate") (:end . 140)\n  (:start . 131) (:id . 64))\n ((:tag . "NN") (:stem . "text") (:form . "text") (:end . 145) (:start . 141)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 151)\n  (:start . 146) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s14.24) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504526@unknown@formal@none@1@S@Historically the proprietary nature of binary files associated with proteomics technologies represented a significant obstacle to efforts aimed at development of integrated, desktop environments.@(((:tag . "RB") (:stem . "historically") (:form . "Historically") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "proprietary") (:form . "proprietary") (:end . 28)\n  (:start . 17) (:id . 44))\n ((:tag . "NN") (:stem . "nature") (:form . "nature") (:end . 35)\n  (:start . 29) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "binary") (:form . "binary") (:end . 45)\n  (:start . 39) (:id . 47))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 51) (:start . 46)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 62)\n  (:start . 52) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 67) (:start . 63)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 78)\n  (:start . 68) (:id . 51))\n ((:tag . "NNS") (:stem . "technology") (:form . "technologies") (:end . 91)\n  (:start . 79) (:id . 52))\n ((:tag . "VBD") (:stem . "represent") (:form . "represented") (:end . 103)\n  (:start . 92) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 105) (:start . 104)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 117)\n  (:start . 106) (:id . 55))\n ((:tag . "NN") (:stem . "obstacle") (:form . "obstacle") (:end . 126)\n  (:start . 118) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 129) (:start . 127)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "effort") (:form . "efforts") (:end . 137)\n  (:start . 130) (:id . 58))\n ((:tag . "VBN") (:stem . "aim") (:form . "aimed") (:end . 143) (:start . 138)\n  (:id . 59))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 146) (:start . 144)\n  (:id . 60))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 158)\n  (:start . 147) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 161) (:start . 159)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "integrate") (:form . "integrated") (:end . 172)\n  (:start . 162) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 64))\n ((:tag . "NN") (:stem . "desktop") (:form . "desktop") (:end . 181)\n  (:start . 174) (:id . 65))\n ((:tag . "NNS") (:stem . "environment") (:form . "environments") (:end . 194)\n  (:start . 182) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 195) (:start . 194)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s14.25) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504527@unknown@formal@none@1@S@One solution proposed specifically for mass spectrometry is extraction of native data to a common file format, typically a dialect of XML [8,9].@(((:tag . "CD") (:stem . "one") (:form . "One") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "solution") (:form . "solution") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "RB") (:stem . "specifically") (:form . "specifically") (:end . 34)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 38) (:start . 35)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 43) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 56)\n  (:start . 44) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 59) (:start . 57)\n  (:id . 49))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 70)\n  (:start . 60) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 80)\n  (:start . 74) (:id . 52))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 85) (:start . 81)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 90) (:start . 89)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 97)\n  (:start . 91) (:id . 56))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 102) (:start . 98)\n  (:id . 57))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 109)\n  (:start . 103) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 59))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 120)\n  (:start . 111) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 122) (:start . 121)\n  (:id . 61))\n ((:tag . "NN") (:stem . "dialect") (:form . "dialect") (:end . 130)\n  (:start . 123) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 133) (:start . 131)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "XML") (:form . "XML") (:end . 137) (:start . 134)\n  (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 139) (:start . 138)\n  (:id . 65))\n ((:tag . "CD") (:stem . "8,9") (:form . "8,9") (:end . 142) (:start . 139)\n  (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s14.26) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504528@unknown@formal@none@1@S@We [10] and others [11] have challenged the technical merits of this approach.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 4) (:start . 3) (:id . 43))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 6) (:start . 4)\n  (:id . 44))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 7) (:start . 6) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "other") (:form . "others") (:end . 18)\n  (:start . 12) (:id . 47))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 20) (:start . 19)\n  (:id . 48))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 22) (:start . 20)\n  (:id . 49))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 23) (:start . 22)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 28) (:start . 24)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "challenge") (:form . "challenged") (:end . 39)\n  (:start . 29) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "technical") (:form . "technical") (:end . 53)\n  (:start . 44) (:id . 54))\n ((:tag . "NNS") (:stem . "merit") (:form . "merits") (:end . 60)\n  (:start . 54) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 56))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 68) (:start . 64)\n  (:id . 57))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 77)\n  (:start . 69) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s14.27) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504529@unknown@formal@none@1@S@Given that mass spectrometry manufacturers implicitly carry the burden of maintaining up-to-date libraries for access to their native data, we recently proposed that a common API [10] is a more rational solution for shared access to proprietary mass spectrometry files.@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 28)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "manufacturer") (:form . "manufacturers")\n  (:end . 42) (:start . 29) (:id . 46))\n ((:tag . "RB") (:stem . "implicitly") (:form . "implicitly") (:end . 53)\n  (:start . 43) (:id . 47))\n ((:tag . "VBP") (:stem . "carry") (:form . "carry") (:end . 59) (:start . 54)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 49))\n ((:tag . "NN") (:stem . "burden") (:form . "burden") (:end . 70)\n  (:start . 64) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 73) (:start . 71)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "maintain") (:form . "maintaining") (:end . 85)\n  (:start . 74) (:id . 52))\n ((:tag . "JJ") (:stem . "up-to-date") (:form . "up-to-date") (:end . 96)\n  (:start . 86) (:id . 53))\n ((:tag . "NNS") (:stem . "library") (:form . "libraries") (:end . 106)\n  (:start . 97) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 110) (:start . 107)\n  (:id . 55))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 117)\n  (:start . 111) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 120) (:start . 118)\n  (:id . 57))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 126)\n  (:start . 121) (:id . 58))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 133)\n  (:start . 127) (:id . 59))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 138)\n  (:start . 134) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 61))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 142) (:start . 140)\n  (:id . 62))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 151)\n  (:start . 143) (:id . 63))\n ((:tag . "VBD") (:stem . "propose") (:form . "proposed") (:end . 160)\n  (:start . 152) (:id . 64))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 165) (:start . 161)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 167) (:start . 166)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 174)\n  (:start . 168) (:id . 67))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 178) (:start . 175)\n  (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 180) (:start . 179)\n  (:id . 69))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 182) (:start . 180)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 183) (:start . 182)\n  (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 186) (:start . 184)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 188) (:start . 187)\n  (:id . 73))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 193) (:start . 189)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "rational") (:form . "rational") (:end . 202)\n  (:start . 194) (:id . 75))\n ((:tag . "NN") (:stem . "solution") (:form . "solution") (:end . 211)\n  (:start . 203) (:id . 76))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 215) (:start . 212)\n  (:id . 77))\n ((:tag . "JJ") (:stem . "shared") (:form . "shared") (:end . 222)\n  (:start . 216) (:id . 78))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 229)\n  (:start . 223) (:id . 79))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 232) (:start . 230)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "proprietary") (:form . "proprietary") (:end . 244)\n  (:start . 233) (:id . 81))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 249) (:start . 245)\n  (:id . 82))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 262)\n  (:start . 250) (:id . 83))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 268)\n  (:start . 263) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 269) (:start . 268)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s14.28) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504530@unknown@formal@none@1@S@Here we define and implement a minimal API (mzAPI) that provides direct, programmatic interaction with binary raw files and we demonstrate that performance for practical tasks is significantly faster as compared to equivalent operations for access to mzXML files.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "define") (:form . "define") (:end . 14)\n  (:start . 8) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "implement") (:form . "implement") (:end . 28)\n  (:start . 19) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "minimal") (:form . "minimal") (:end . 38)\n  (:start . 31) (:id . 48))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "mzAPI") (:form . "mzAPI") (:end . 49) (:start . 44)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 55) (:start . 51)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 64)\n  (:start . 56) (:id . 54))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 71)\n  (:start . 65) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "programmatic") (:form . "programmatic") (:end . 85)\n  (:start . 73) (:id . 57))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 97)\n  (:start . 86) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "binary") (:form . "binary") (:end . 109)\n  (:start . 103) (:id . 60))\n ((:tag . "JJ") (:stem . "raw") (:form . "raw") (:end . 113) (:start . 110)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 119)\n  (:start . 114) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 63))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 126) (:start . 124)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 138)\n  (:start . 127) (:id . 65))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 143) (:start . 139)\n  (:id . 66))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 155)\n  (:start . 144) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 159) (:start . 156)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "practical") (:form . "practical") (:end . 169)\n  (:start . 160) (:id . 69))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 175)\n  (:start . 170) (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 178) (:start . 176)\n  (:id . 71))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 192) (:start . 179) (:id . 72))\n ((:tag . "JJR") (:stem . "fast") (:form . "faster") (:end . 199)\n  (:start . 193) (:id . 73))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 202) (:start . 200)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 211)\n  (:start . 203) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 214) (:start . 212)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "equivalent") (:form . "equivalent") (:end . 225)\n  (:start . 215) (:id . 77))\n ((:tag . "NNS") (:stem . "operation") (:form . "operations") (:end . 236)\n  (:start . 226) (:id . 78))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 240) (:start . 237)\n  (:id . 79))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 247)\n  (:start . 241) (:id . 80))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 250) (:start . 248)\n  (:id . 81))\n ((:tag . "NN") (:stem . "mzxml") (:form . "mzXML") (:end . 256)\n  (:start . 251) (:id . 82))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 262)\n  (:start . 257) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 263) (:start . 262)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s14.29) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504531@unknown@formal@none@1@S@We implement mzAPI in Python to maximize accessibility; similarly, mzAPI is exposed to users through multiplierz, a Python-based desktop environment that combines an intuitive interface with a powerful and flexible high-level scripting platform.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "implement") (:form . "implement") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Python") (:form . "Python") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "VB") (:stem . "maximize") (:form . "maximize") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "accessibility") (:form . "accessibility")\n  (:end . 54) (:start . 41) (:id . 49))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "RB") (:stem . "similarly") (:form . "similarly") (:end . 65)\n  (:start . 56) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "mzAPI") (:form . "mzAPI") (:end . 72) (:start . 67)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "expose") (:form . "exposed") (:end . 83)\n  (:start . 76) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 100)\n  (:start . 93) (:id . 58))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 112)\n  (:start . 101) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "python-based") (:form . "Python-based") (:end . 128)\n  (:start . 116) (:id . 62))\n ((:tag . "NN") (:stem . "desktop") (:form . "desktop") (:end . 136)\n  (:start . 129) (:id . 63))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 148)\n  (:start . 137) (:id . 64))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 153) (:start . 149)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "combine") (:form . "combines") (:end . 162)\n  (:start . 154) (:id . 66))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 165) (:start . 163)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "intuitive") (:form . "intuitive") (:end . 175)\n  (:start . 166) (:id . 68))\n ((:tag . "NN") (:stem . "interface") (:form . "interface") (:end . 185)\n  (:start . 176) (:id . 69))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 190) (:start . 186)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 192) (:start . 191)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "powerful") (:form . "powerful") (:end . 201)\n  (:start . 193) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 205) (:start . 202)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "flexible") (:form . "flexible") (:end . 214)\n  (:start . 206) (:id . 74))\n ((:tag . "JJ") (:stem . "high-level") (:form . "high-level") (:end . 225)\n  (:start . 215) (:id . 75))\n ((:tag . "NN") (:stem . "scripting") (:form . "scripting") (:end . 235)\n  (:start . 226) (:id . 76))\n ((:tag . "NN") (:stem . "platform") (:form . "platform") (:end . 244)\n  (:start . 236) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 245) (:start . 244)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s14.30) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504532@unknown@formal@none@1@S@Together, mzAPI and multiplierz support a wide range of data analytic tasks and facilitate rapid prototyping of novel algorithms.@(((:tag . "RB") (:stem . "together") (:form . "Together") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "analytic") (:form . "analytic") (:end . 69)\n  (:start . 61) (:id . 53))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 75) (:start . 70)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "VB") (:stem . "facilitate") (:form . "facilitate") (:end . 90)\n  (:start . 80) (:id . 56))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "NN") (:stem . "prototyping") (:form . "prototyping") (:end . 108)\n  (:start . 97) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 117)\n  (:start . 112) (:id . 60))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 128)\n  (:start . 118) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s14.31) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504533@unknown@formal@none@1@S@In addition, the multiplierz environment is designed with a "zero-infrastructure" philosophy, meaning that it can be deployed by end users who lack system administration experience or support.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 28)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 40)\n  (:start . 29) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 59) (:start . 58)\n  (:id . 51))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 61) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "zero-infrastructure")\n  (:form . "zero-infrastructure") (:end . 80) (:start . 61) (:id . 53))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 81) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "philosophy") (:form . "philosophy") (:end . 92)\n  (:start . 82) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "mean") (:form . "meaning") (:end . 101)\n  (:start . 94) (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 106) (:start . 102)\n  (:id . 58))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 109) (:start . 107)\n  (:id . 59))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 113) (:start . 110)\n  (:id . 60))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 116) (:start . 114)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "deploy") (:form . "deployed") (:end . 125)\n  (:start . 117) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 128) (:start . 126)\n  (:id . 63))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 132) (:start . 129)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 138)\n  (:start . 133) (:id . 65))\n ((:tag . "WP") (:stem . "who") (:form . "who") (:end . 142) (:start . 139)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "lack") (:form . "lack") (:end . 147) (:start . 143)\n  (:id . 67))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 154)\n  (:start . 148) (:id . 68))\n ((:tag . "NN") (:stem . "administration") (:form . "administration")\n  (:end . 169) (:start . 155) (:id . 69))\n ((:tag . "NN") (:stem . "experience") (:form . "experience") (:end . 180)\n  (:start . 170) (:id . 70))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 183) (:start . 181)\n  (:id . 71))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 191)\n  (:start . 184) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s14.32) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504534@unknown@formal@none@1@S@We demonstrate the capabilities of multiplierz through a variety of proteomics case studies such as (i) label-free quantitative comparison and interactive validation of datasets from multi-acquisition experiments, (ii) automatic quality control of mass spectrometer performance, (iii) improved peptide sequence assignment via deisotoping of MS/MS spectra, and (iv) assessment of phosphopeptide enrichment efficiency through programmatic fragment ion extraction.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "capability") (:form . "capabilities") (:end . 31)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 46))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 46)\n  (:start . 35) (:id . 47))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 54)\n  (:start . 47) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 56) (:start . 55)\n  (:id . 49))\n ((:tag . "NN") (:stem . "variety") (:form . "variety") (:end . 64)\n  (:start . 57) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 78)\n  (:start . 68) (:id . 52))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 83) (:start . 79)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 91)\n  (:start . 84) (:id . 54))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 96) (:start . 92)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 99) (:start . 97)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 101) (:start . 100)\n  (:id . 57))\n ((:tag . "LS") (:stem . "i") (:form . "i") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "label-free") (:form . "label-free") (:end . 114)\n  (:start . 104) (:id . 60))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "quantitative") (:end . 127)\n  (:start . 115) (:id . 61))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 138)\n  (:start . 128) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "interactive") (:form . "interactive") (:end . 154)\n  (:start . 143) (:id . 64))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 165)\n  (:start . 155) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 168) (:start . 166)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "dataset") (:form . "datasets") (:end . 177)\n  (:start . 169) (:id . 67))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 182) (:start . 178)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "multi-acquisition") (:form . "multi-acquisition")\n  (:end . 200) (:start . 183) (:id . 69))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 212)\n  (:start . 201) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 213) (:start . 212)\n  (:id . 71))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 215) (:start . 214)\n  (:id . 72))\n ((:tag . "LS") (:stem . "ii") (:form . "ii") (:end . 217) (:start . 215)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 218) (:start . 217)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "automatic") (:form . "automatic") (:end . 228)\n  (:start . 219) (:id . 75))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 236)\n  (:start . 229) (:id . 76))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 244)\n  (:start . 237) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 247) (:start . 245)\n  (:id . 78))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 252) (:start . 248)\n  (:id . 79))\n ((:tag . "NN") (:stem . "spectrometer") (:form . "spectrometer") (:end . 265)\n  (:start . 253) (:id . 80))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 277)\n  (:start . 266) (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 278) (:start . 277)\n  (:id . 82))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 280) (:start . 279)\n  (:id . 83))\n ((:tag . "LS") (:stem . "iii") (:form . "iii") (:end . 283) (:start . 280)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 284) (:start . 283)\n  (:id . 85))\n ((:tag . "VBD") (:stem . "improve") (:form . "improved") (:end . 293)\n  (:start . 285) (:id . 86))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 301)\n  (:start . 294) (:id . 87))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 310)\n  (:start . 302) (:id . 88))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 321)\n  (:start . 311) (:id . 89))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 325) (:start . 322)\n  (:id . 90))\n ((:tag . "VBG") (:stem . "deisotope") (:form . "deisotoping") (:end . 337)\n  (:start . 326) (:id . 91))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 340) (:start . 338)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 346)\n  (:start . 341) (:id . 93))\n ((:tag . "NNS") (:stem . "spectrum") (:form . "spectra") (:end . 354)\n  (:start . 347) (:id . 94))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 355) (:start . 354)\n  (:id . 95))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 359) (:start . 356)\n  (:id . 96))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 361) (:start . 360)\n  (:id . 97))\n ((:tag . "LS") (:stem . "iv") (:form . "iv") (:end . 363) (:start . 361)\n  (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 364) (:start . 363)\n  (:id . 99))\n ((:tag . "NN") (:stem . "assessment") (:form . "assessment") (:end . 375)\n  (:start . 365) (:id . 100))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 378) (:start . 376)\n  (:id . 101))\n ((:tag . "NN") (:stem . "phosphopeptide") (:form . "phosphopeptide")\n  (:end . 393) (:start . 379) (:id . 102))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 404)\n  (:start . 394) (:id . 103))\n ((:tag . "NN") (:stem . "efficiency") (:form . "efficiency") (:end . 415)\n  (:start . 405) (:id . 104))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 423)\n  (:start . 416) (:id . 105))\n ((:tag . "JJ") (:stem . "programmatic") (:form . "programmatic") (:end . 436)\n  (:start . 424) (:id . 106))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 445)\n  (:start . 437) (:id . 107))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 449) (:start . 446)\n  (:id . 108))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 460)\n  (:start . 450) (:id . 109))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 461) (:start . 460)\n  (:id . 110)))@@@1@69@((:identifiers (:sid . :s14.33) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504535@unknown@formal@none@1@S@Implementation@(((:tag . "NN") (:stem . "implementation") (:form . "Implementation")\n  (:end . 14) (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s14.34) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504536@unknown@formal@none@1@S@mzAPI: A Common API for Direct Access to Proprietary File Formats@(((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 8) (:start . 7)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "common") (:form . "Common") (:end . 15) (:start . 9)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 19) (:start . 16)\n  (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "direct") (:form . "Direct") (:end . 30)\n  (:start . 24) (:id . 48))\n ((:tag . "NNP") (:stem . "Access") (:form . "Access") (:end . 37)\n  (:start . 31) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 40) (:start . 38)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Proprietary") (:form . "Proprietary") (:end . 52)\n  (:start . 41) (:id . 51))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Format") (:form . "Formats") (:end . 65)\n  (:start . 58) (:id . 53)))@@@1@12@((:identifiers (:sid . :s14.35) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504537@unknown@formal@none@1@S@As described above, direct access to native mass spectrometry data files is a key factor in the assembly of a powerful and flexible framework for proteomics data analysis.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 33)\n  (:start . 27) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 61)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "data") (:form . "data") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 72) (:start . 67)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 77) (:start . 76)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 81) (:start . 78)\n  (:id . 56))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 88)\n  (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 59))\n ((:tag . "NN") (:stem . "assembly") (:form . "assembly") (:end . 104)\n  (:start . 96) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "powerful") (:form . "powerful") (:end . 118)\n  (:start . 110) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "flexible") (:form . "flexible") (:end . 131)\n  (:start . 123) (:id . 65))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 141)\n  (:start . 132) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 145) (:start . 142)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 156)\n  (:start . 146) (:id . 68))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 161)\n  (:start . 157) (:id . 69))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 170)\n  (:start . 162) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s14.36) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504538@unknown@formal@none@1@S@Towards this end, we define a minimal mzAPI as consisting of the following key procedures:@(((:tag . "IN") (:stem . "towards") (:form . "Towards") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "define") (:form . "define") (:end . 27)\n  (:start . 21) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "minimal") (:form . "minimal") (:end . 37)\n  (:start . 30) (:id . 49))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 43) (:start . 38)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 46) (:start . 44)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "consist") (:form . "consisting") (:end . 57)\n  (:start . 47) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 74)\n  (:start . 65) (:id . 55))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 89)\n  (:start . 79) (:id . 57))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 90) (:start . 89)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s14.37) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504539@unknown@formal@none@1@S@1. scan(time) › [(mz, intensity)]@(((:tag . "LS") (:stem . "1.") (:form . "1.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "scan(time)") (:form . "scan(time)") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 13) (:start . 13)\n  (:id . 44))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mz") (:form . "mz") (:end . 20) (:start . 18)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 48))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 31)\n  (:start . 22) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 32) (:start . 31)\n  (:id . 50))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 33) (:start . 32)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s14.38) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504540@unknown@formal@none@1@S@2. scan_list(start_time, stop_time) › [(time, precursor)]@(((:tag . "LS") (:stem . "2.") (:form . "2.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "scan_list(start_time")\n  (:form . "scan_list(start_time") (:end . 23) (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 44))\n ((:tag . "NN") (:stem . "stop_time") (:form . "stop_time") (:end . 34)\n  (:start . 25) (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 35) (:start . 34)\n  (:id . 46))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 35) (:start . 35)\n  (:id . 47))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 44) (:start . 40)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 55)\n  (:start . 46) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 57) (:start . 56)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s14.39) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504541@unknown@formal@none@1@S@3. time_range() › (start_time, stop_time)@(((:tag . "LS") (:stem . "3.") (:form . "3.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "time_range()") (:form . "time_range()") (:end . 15)\n  (:start . 3) (:id . 43))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 15) (:start . 15)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "start_time") (:form . "start_time") (:end . 29)\n  (:start . 19) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "RB") (:stem . "stop_time") (:form . "stop_time") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 41) (:start . 40)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s14.40) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504542@unknown@formal@none@1@S@4. scan_time_from_scan_name (scan_name) › time@(((:tag . "LS") (:stem . "4.") (:form . "4.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "scan_time_from_scan_name")\n  (:form . "scan_time_from_scan_name") (:end . 27) (:start . 3) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 29) (:start . 28)\n  (:id . 44))\n ((:tag . "NN") (:stem . "scan_name") (:form . "scan_name") (:end . 38)\n  (:start . 29) (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 39) (:start . 38)\n  (:id . 46))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 39) (:start . 39)\n  (:id . 47))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 46) (:start . 42)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s14.41) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504543@unknown@formal@none@1@S@5. ric(start_time, stop_time, start_mz, stop_mz) › [(time, intensity)]@(((:tag . "LS") (:stem . "5.") (:form . "5.") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "ric(start_time") (:form . "ric(start_time")\n  (:end . 17) (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "NN") (:stem . "stop_time") (:form . "stop_time") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 29) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "start_mz") (:form . "start_mz") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "stop_mz") (:form . "stop_mz") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 48) (:start . 48)\n  (:id . 51))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 52) (:start . 51)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n  (:id . 53))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 57) (:start . 53)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 58) (:start . 57)\n  (:id . 55))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 68)\n  (:start . 59) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 57))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 70) (:start . 69)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s14.42) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504544@unknown@formal@none@1@S@The first two procedures in mzAPI return: 1) individual scans in the form of a list of (mz, intensity) pairs, and 2) a catalog of all scan descriptions in the form of a list of (time, precursor) pairs in the experiment.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 24)\n  (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "return") (:form . "return") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 41) (:start . 40)\n  (:id . 49))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 55)\n  (:start . 45) (:id . 52))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 61) (:start . 56)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 73) (:start . 69)\n  (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 78) (:start . 77)\n  (:id . 58))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 83) (:start . 79)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 61))\n ((:tag . "NN") (:stem . "mz") (:form . "mz") (:end . 90) (:start . 88)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 63))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 101)\n  (:start . 92) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 108)\n  (:start . 103) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 68))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 115) (:start . 114)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 118) (:start . 117)\n  (:id . 71))\n ((:tag . "NN") (:stem . "catalog") (:form . "catalog") (:end . 126)\n  (:start . 119) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 73))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 133) (:start . 130)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "scan") (:form . "scan") (:end . 138) (:start . 134)\n  (:id . 75))\n ((:tag . "NNS") (:stem . "description") (:form . "descriptions") (:end . 151)\n  (:start . 139) (:id . 76))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 154) (:start . 152)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n  (:id . 78))\n ((:tag . "NN") (:stem . "form") (:form . "form") (:end . 163) (:start . 159)\n  (:id . 79))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 166) (:start . 164)\n  (:id . 80))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 168) (:start . 167)\n  (:id . 81))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 173) (:start . 169)\n  (:id . 82))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 176) (:start . 174)\n  (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 178) (:start . 177)\n  (:id . 84))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 182) (:start . 178)\n  (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 183) (:start . 182)\n  (:id . 86))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 193)\n  (:start . 184) (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 194) (:start . 193)\n  (:id . 88))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 200)\n  (:start . 195) (:id . 89))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 203) (:start . 201)\n  (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 207) (:start . 204)\n  (:id . 91))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 218)\n  (:start . 208) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 93)))@@@1@52@((:identifiers (:sid . :s14.43) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504545@unknown@formal@none@1@S@In addition, the API provides: 3) 'time_range' that returns the earliest and latest acquisition times in the experiment, and 4) 'scan_time_from_scan_name' for translation of manufacturer-specific scan nomenclature to the mzAPI naming convention.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "LS") (:stem . "3") (:form . "3") (:end . 32) (:start . 31)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 33) (:start . 32)\n  (:id . 50))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 35) (:start . 34)\n  (:id . 51))\n ((:tag . "NN") (:stem . "time_range") (:form . "time_range") (:end . 45)\n  (:start . 35) (:id . 52))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 46) (:start . 45)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 51) (:start . 47)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "return") (:form . "returns") (:end . 59)\n  (:start . 52) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 56))\n ((:tag . "JJS") (:stem . "early") (:form . "earliest") (:end . 72)\n  (:start . 64) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 58))\n ((:tag . "JJS") (:stem . "late") (:form . "latest") (:end . 83) (:start . 77)\n  (:id . 59))\n ((:tag . "NN") (:stem . "acquisition") (:form . "acquisition") (:end . 95)\n  (:start . 84) (:id . 60))\n ((:tag . "NNS") (:stem . "time") (:form . "times") (:end . 101) (:start . 96)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 63))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 119)\n  (:start . 109) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 124) (:start . 121)\n  (:id . 66))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 126) (:start . 125)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 127) (:start . 126)\n  (:id . 68))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 129) (:start . 128)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "scan_time_from_scan_name")\n  (:form . "scan_time_from_scan_name") (:end . 153) (:start . 129) (:id . 70))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 154) (:start . 153)\n  (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 158) (:start . 155)\n  (:id . 72))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 170)\n  (:start . 159) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 173) (:start . 171)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "manufacturer-specific")\n  (:form . "manufacturer-specific") (:end . 195) (:start . 174) (:id . 75))\n ((:tag . "NN") (:stem . "scan") (:form . "scan") (:end . 200) (:start . 196)\n  (:id . 76))\n ((:tag . "NN") (:stem . "nomenclature") (:form . "nomenclature") (:end . 213)\n  (:start . 201) (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 216) (:start . 214)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 220) (:start . 217)\n  (:id . 79))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 226)\n  (:start . 221) (:id . 80))\n ((:tag . "NN") (:stem . "naming") (:form . "naming") (:end . 233)\n  (:start . 227) (:id . 81))\n ((:tag . "NN") (:stem . "convention") (:form . "convention") (:end . 244)\n  (:start . 234) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 245) (:start . 244)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s14.44) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504546@unknown@formal@none@1@S@We opted to rely on acquisition time as a common naming convention.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "opte") (:form . "opted") (:end . 8) (:start . 3)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "rely") (:form . "rely") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "acquisition") (:form . "acquisition") (:end . 31)\n  (:start . 20) (:id . 47))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 41) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 48)\n  (:start . 42) (:id . 51))\n ((:tag . "NN") (:stem . "naming") (:form . "naming") (:end . 55)\n  (:start . 49) (:id . 52))\n ((:tag . "NN") (:stem . "convention") (:form . "convention") (:end . 66)\n  (:start . 56) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s14.45) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504547@unknown@formal@none@1@S@In the case of LC-MS this is equivalent to chromatographic retention time.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "LC-MS") (:form . "LC-MS") (:end . 20) (:start . 15)\n  (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "equivalent") (:form . "equivalent") (:end . 39)\n  (:start . 29) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "chromatographic") (:form . "chromatographic")\n  (:end . 58) (:start . 43) (:id . 51))\n ((:tag . "NN") (:stem . "retention") (:form . "retention") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s14.46) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504548@unknown@formal@none@1@S@Finally, a fifth procedure generates a reconstructed ion chromatogram (RIC) for a given time and mass-to-charge range, returned as a set of (time, intensity) pairs.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "fifth") (:form . "fifth") (:end . 16) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "VBZ") (:stem . "generate") (:form . "generates") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "reconstruct") (:form . "reconstructed") (:end . 52)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "NN") (:stem . "chromatogram") (:form . "chromatogram") (:end . 69)\n  (:start . 57) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "RIC") (:form . "RIC") (:end . 74) (:start . 71)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 81) (:start . 80)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 87) (:start . 82)\n  (:id . 57))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "mass-to-charge") (:form . "mass-to-charge")\n  (:end . 111) (:start . 97) (:id . 60))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 117)\n  (:start . 112) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "return") (:form . "returned") (:end . 127)\n  (:start . 119) (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 130) (:start . 128)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 132) (:start . 131)\n  (:id . 65))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 136) (:start . 133)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 139) (:start . 137)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 141) (:start . 140)\n  (:id . 68))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 145) (:start . 141)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 146) (:start . 145)\n  (:id . 70))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 156)\n  (:start . 147) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 157) (:start . 156)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 163)\n  (:start . 158) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s14.47) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504549@unknown@formal@none@1@S@While in principle RICs can be generated using the first two calls, we believe that ubiquitous use of the RIC operation in proteomics data analysis justifies exposure of RIC extraction as a primitive in the API.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "principle") (:form . "principle") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "ric") (:form . "RICs") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "call") (:form . "calls") (:end . 66) (:start . 61)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "believe") (:form . "believe") (:end . 78)\n  (:start . 71) (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "ubiquitous") (:form . "ubiquitous") (:end . 94)\n  (:start . 84) (:id . 58))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 101) (:start . 99)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "RIC") (:form . "RIC") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "NN") (:stem . "operation") (:form . "operation") (:end . 119)\n  (:start . 110) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 122) (:start . 120)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 133)\n  (:start . 123) (:id . 65))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 138)\n  (:start . 134) (:id . 66))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 147)\n  (:start . 139) (:id . 67))\n ((:tag . "VBZ") (:stem . "justify") (:form . "justifies") (:end . 157)\n  (:start . 148) (:id . 68))\n ((:tag . "NN") (:stem . "exposure") (:form . "exposure") (:end . 166)\n  (:start . 158) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 169) (:start . 167)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "RIC") (:form . "RIC") (:end . 173) (:start . 170)\n  (:id . 71))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 184)\n  (:start . 174) (:id . 72))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 187) (:start . 185)\n  (:id . 73))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 189) (:start . 188)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "primitive") (:form . "primitive") (:end . 199)\n  (:start . 190) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 202) (:start . 200)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 206) (:start . 203)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 210) (:start . 207)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 211) (:start . 210)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x14.48.1) (:span 71 78)) ((:id . :x14.48.2) (:span 24 27)))\n (:hscopes ((:id . :x14.48.1) (:span 71 210))\n  ((:id . :x14.48.2) (:span 19 66)))\n (:identifiers (:sid . :s14.48) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504550@unknown@formal@none@1@S@Given that RIC extraction is provided by all manufacturer libraries, this procedure represents an excellent example of efficient re-use of native data system indexing and software.@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "RIC") (:form . "RIC") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 57)\n  (:start . 45) (:id . 50))\n ((:tag . "NNS") (:stem . "library") (:form . "libraries") (:end . 67)\n  (:start . 58) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 83)\n  (:start . 74) (:id . 54))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 94)\n  (:start . 84) (:id . 55))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 97) (:start . 95)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "excellent") (:form . "excellent") (:end . 107)\n  (:start . 98) (:id . 57))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 115)\n  (:start . 108) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 128)\n  (:start . 119) (:id . 60))\n ((:tag . "NN") (:stem . "re-use") (:form . "re-use") (:end . 135)\n  (:start . 129) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 145)\n  (:start . 139) (:id . 63))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 150)\n  (:start . 146) (:id . 64))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 157)\n  (:start . 151) (:id . 65))\n ((:tag . "NN") (:stem . "indexing") (:form . "indexing") (:end . 166)\n  (:start . 158) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 170) (:start . 167)\n  (:id . 67))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 179)\n  (:start . 171) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s14.49) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504551@unknown@formal@none@1@S@We propose that a proprietary file format is considered mzAPI compliant when the manufacturer provides a freely available, and preferably redistributable, implementation of the aforementioned 5 core procedures, or an extended version that may evolve from a community-driven standardization effort.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "propose") (:form . "propose") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "proprietary") (:form . "proprietary") (:end . 29)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 55)\n  (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "compliant") (:form . "compliant") (:end . 71)\n  (:start . 62) (:id . 52))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 80) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 93)\n  (:start . 81) (:id . 55))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 102)\n  (:start . 94) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 104) (:start . 103)\n  (:id . 57))\n ((:tag . "RB") (:stem . "freely") (:form . "freely") (:end . 111)\n  (:start . 105) (:id . 58))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 121)\n  (:start . 112) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 126) (:start . 123)\n  (:id . 61))\n ((:tag . "RB") (:stem . "preferably") (:form . "preferably") (:end . 137)\n  (:start . 127) (:id . 62))\n ((:tag . "JJ") (:stem . "redistributable") (:form . "redistributable")\n  (:end . 153) (:start . 138) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 64))\n ((:tag . "NN") (:stem . "implementation") (:form . "implementation")\n  (:end . 169) (:start . 155) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 172) (:start . 170)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 176) (:start . 173)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "aforementioned") (:form . "aforementioned")\n  (:end . 191) (:start . 177) (:id . 68))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 193) (:start . 192)\n  (:id . 69))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 198) (:start . 194)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 209)\n  (:start . 199) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 210) (:start . 209)\n  (:id . 72))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 213) (:start . 211)\n  (:id . 73))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 216) (:start . 214)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "extend") (:form . "extended") (:end . 225)\n  (:start . 217) (:id . 75))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 233)\n  (:start . 226) (:id . 76))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 238) (:start . 234)\n  (:id . 77))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 242) (:start . 239)\n  (:id . 78))\n ((:tag . "VB") (:stem . "evolve") (:form . "evolve") (:end . 249)\n  (:start . 243) (:id . 79))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 254) (:start . 250)\n  (:id . 80))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 256) (:start . 255)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "community-driven") (:form . "community-driven")\n  (:end . 273) (:start . 257) (:id . 82))\n ((:tag . "NN") (:stem . "standardization") (:form . "standardization")\n  (:end . 289) (:start . 274) (:id . 83))\n ((:tag . "NN") (:stem . "effort") (:form . "effort") (:end . 296)\n  (:start . 290) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 297) (:start . 296)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x14.50.1) (:span 239 242)) ((:id . :x14.50.2) (:span 3 10)))\n (:hscopes ((:id . :x14.50.1) (:span 239 296))\n  ((:id . :x14.50.2) (:span 3 296)))\n (:identifiers (:sid . :s14.50) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504552@unknown@formal@none@1@S@For example, ThermoFisher Scientific provides a data access library for .RAW files through the MSFileReader program, freely available for download at: http://sjsupport.thermofinnigan.com/public/detail.asp?id=586 or http://blais.dfci.harvard.edu/research/mass-informatics/mzAPI/vendor-libraries/.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "ThermoFisher") (:form . "ThermoFisher") (:end . 25)\n  (:start . 13) (:id . 45))\n ((:tag . "NNP") (:stem . "Scientific") (:form . "Scientific") (:end . 36)\n  (:start . 26) (:id . 46))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 67)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "NNP") (:stem . ".RAW") (:form . ".RAW") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 82) (:start . 77)\n  (:id . 54))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 90)\n  (:start . 83) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "MSFileReader") (:form . "MSFileReader")\n  (:end . 107) (:start . 95) (:id . 57))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 115)\n  (:start . 108) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 59))\n ((:tag . "RB") (:stem . "freely") (:form . "freely") (:end . 123)\n  (:start . 117) (:id . 60))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 133)\n  (:start . 124) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 137) (:start . 134)\n  (:id . 62))\n ((:tag . "NN") (:stem . "download") (:form . "download") (:end . 146)\n  (:start . 138) (:id . 63))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 149) (:start . 147)\n  (:id . 64))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 150) (:start . 149)\n  (:id . 65))\n ((:tag . "CD")\n  (:stem . "http://sjsupport.thermofinnigan.com/public/detail.asp?id=586")\n  (:form . "http://sjsupport.thermofinnigan.com/public/detail.asp?id=586")\n  (:end . 211) (:start . 151) (:id . 66))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 214) (:start . 212)\n  (:id . 67))\n ((:tag . "CD")\n  (:stem\n   . "http://blais.dfci.harvard.edu/research/mass-informatics/mzAPI/vendor-libraries/")\n  (:form\n   . "http://blais.dfci.harvard.edu/research/mass-informatics/mzAPI/vendor-libraries/")\n  (:end . 294) (:start . 215) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 295) (:start . 294)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s14.51) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504553@unknown@formal@none@1@S@Naturally, additional procedure calls, such as charge state or signal-to-noise values for each isotope cluster in MS or MS/MS scans, can be incorporated into the mzAPI framework by essentially subclassing the core mzFile class.@(((:tag . "RB") (:stem . "naturally") (:form . "Naturally") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 21)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 31)\n  (:start . 22) (:id . 45))\n ((:tag . "NNS") (:stem . "call") (:form . "calls") (:end . 37) (:start . 32)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 46) (:start . 44)\n  (:id . 49))\n ((:tag . "NN") (:stem . "charge") (:form . "charge") (:end . 53)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "signal-to-noise") (:form . "signal-to-noise")\n  (:end . 78) (:start . 63) (:id . 53))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 85)\n  (:start . 79) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 89) (:start . 86)\n  (:id . 55))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "NN") (:stem . "isotope") (:form . "isotope") (:end . 102)\n  (:start . 95) (:id . 57))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 110)\n  (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 113) (:start . 111)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "MS") (:form . "MS") (:end . 116) (:start . 114)\n  (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 119) (:start . 117)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 125)\n  (:start . 120) (:id . 62))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 131)\n  (:start . 126) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 132) (:start . 131)\n  (:id . 64))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 136) (:start . 133)\n  (:id . 65))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 139) (:start . 137)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "incorporate") (:form . "incorporated") (:end . 152)\n  (:start . 140) (:id . 67))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 157) (:start . 153)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 69))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 167)\n  (:start . 162) (:id . 70))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 177)\n  (:start . 168) (:id . 71))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 180) (:start . 178)\n  (:id . 72))\n ((:tag . "RB") (:stem . "essentially") (:form . "essentially") (:end . 192)\n  (:start . 181) (:id . 73))\n ((:tag . "VBG") (:stem . "subclasse") (:form . "subclassing") (:end . 204)\n  (:start . 193) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 208) (:start . 205)\n  (:id . 75))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 213) (:start . 209)\n  (:id . 76))\n ((:tag . "NN") (:stem . "mzfile") (:form . "mzFile") (:end . 220)\n  (:start . 214) (:id . 77))\n ((:tag . "NN") (:stem . "class") (:form . "class") (:end . 226)\n  (:start . 221) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 227) (:start . 226)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x14.52.1) (:span 133 136)))\n (:hscopes ((:id . :x14.52.1) (:span 11 226)))\n (:identifiers (:sid . :s14.52) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504554@unknown@formal@none@1@S@As a basic test of file access speed, we compared the time required for random access of scans in an LC-MS acquisition from a ThermoFisher .RAW file using mzAPI (through its Python implementation) versus libraries provided by the manufacturer and included in the native Xcalibur file browser (note that mzXML data was not considered for this comparison since it does not provide access by acquisition time as a primitive in the RAP or RAMP API).@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "basic") (:form . "basic") (:end . 10) (:start . 5)\n  (:id . 44))\n ((:tag . "NN") (:stem . "test") (:form . "test") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "file") (:form . 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"access") (:end . 385)\n  (:start . 379) (:id . 108))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 388) (:start . 386)\n  (:id . 109))\n ((:tag . "NN") (:stem . "acquisition") (:form . "acquisition") (:end . 400)\n  (:start . 389) (:id . 110))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 405) (:start . 401)\n  (:id . 111))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 408) (:start . 406)\n  (:id . 112))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 410) (:start . 409)\n  (:id . 113))\n ((:tag . "JJ") (:stem . "primitive") (:form . "primitive") (:end . 420)\n  (:start . 411) (:id . 114))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 423) (:start . 421)\n  (:id . 115))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 427) (:start . 424)\n  (:id . 116))\n ((:tag . "NNP") (:stem . "RAP") (:form . "RAP") (:end . 431) (:start . 428)\n  (:id . 117))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 434) (:start . 432)\n  (:id . 118))\n ((:tag . "NNP") (:stem . "RAMP") (:form . "RAMP") (:end . 439) (:start . 435)\n  (:id . 119))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 443) (:start . 440)\n  (:id . 120))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 444) (:start . 443)\n  (:id . 121))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 445) (:start . 444)\n  (:id . 122)))@@@1@81@((:identifiers (:sid . :s14.53) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504555@unknown@formal@none@1@S@Table 1 demonstrates that, as expected, random file access via mzAPI is slower than that obtained when working directly in the manufacturer's native environment.@(((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 7) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "demonstrate") (:form . "demonstrates") (:end . 20)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 38)\n  (:start . 30) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 46)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 58)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "mzAPI") (:form . "mzAPI") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "JJR") (:stem . "slow") (:form . "slower") (:end . 78) (:start . 72)\n  (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 88) (:start . 84)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 97)\n  (:start . 89) (:id . 59))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 102) (:start . 98)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "work") (:form . "working") (:end . 110)\n  (:start . 103) (:id . 61))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 119)\n  (:start . 111) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 122) (:start . 120)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 64))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 139)\n  (:start . 127) (:id . 65))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 141) (:start . 139)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 148)\n  (:start . 142) (:id . 67))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 160)\n  (:start . 149) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s14.54) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504556@unknown@formal@none@1@S@The performance of the common API could be further improved by implementation in C++ or C#, but we explicitly chose Python to maintain maximum flexibility through user defined scripts (see below).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "RBR") (:stem . "further") (:form . "further") (:end . 50)\n  (:start . 43) (:id . 50))\n ((:tag . "VBN") (:stem . "improve") (:form . "improved") (:end . 59)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "implementation") (:form . "implementation")\n  (:end . 77) (:start . 63) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "C++") (:form . "C++") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "#") (:stem . "#") (:form . "#") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 95) (:start . 92)\n  (:id . 60))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 98) (:start . 96)\n  (:id . 61))\n ((:tag . "RB") (:stem . "explicitly") (:form . "explicitly") (:end . 109)\n  (:start . 99) (:id . 62))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 115)\n  (:start . 110) (:id . 63))\n ((:tag . "NNP") (:stem . "Python") (:form . "Python") (:end . 122)\n  (:start . 116) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 125) (:start . 123)\n  (:id . 65))\n ((:tag . "VB") (:stem . "maintain") (:form . "maintain") (:end . 134)\n  (:start . 126) (:id . 66))\n ((:tag . "JJ") (:stem . "maximum") (:form . "maximum") (:end . 142)\n  (:start . 135) (:id . 67))\n ((:tag . "NN") (:stem . "flexibility") (:form . "flexibility") (:end . 154)\n  (:start . 143) (:id . 68))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 162)\n  (:start . 155) (:id . 69))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 167) (:start . 163)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 175)\n  (:start . 168) (:id . 71))\n ((:tag . "NNS") (:stem . "script") (:form . "scripts") (:end . 183)\n  (:start . 176) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 185) (:start . 184)\n  (:id . 73))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 188) (:start . 185)\n  (:id . 74))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 194)\n  (:start . 189) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 77)))@@@1@36@((:hcues ((:id . :x14.55.1) (:span 34 39)))\n (:hscopes ((:id . :x14.55.1) (:span 0 90)))\n (:identifiers (:sid . :s14.55) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504557@unknown@formal@none@1@S@Interestingly, one consequence of the common API strategy is that it provides a direct measure of manufacturer data system efficiency, as evidenced by the additional time required for random access to scans in .WIFF versus .RAW files.@(((:tag . "RB") (:stem . "interestingly") (:form . "Interestingly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 43))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "consequence") (:form . "consequence") (:end . 30)\n  (:start . 19) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 57)\n  (:start . 49) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 77)\n  (:start . 69) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 86)\n  (:start . 80) (:id . 56))\n ((:tag . "NN") (:stem . "measure") (:form . "measure") (:end . 94)\n  (:start . 87) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 110)\n  (:start . 98) (:id . 59))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 115)\n  (:start . 111) (:id . 60))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 122)\n  (:start . 116) (:id . 61))\n ((:tag . "NN") (:stem . "efficiency") (:form . "efficiency") (:end . 133)\n  (:start . 123) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 137) (:start . 135)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "evidence") (:form . "evidenced") (:end . 147)\n  (:start . 138) (:id . 65))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 150) (:start . 148)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 165)\n  (:start . 155) (:id . 68))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 170) (:start . 166)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 179)\n  (:start . 171) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 183) (:start . 180)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 190)\n  (:start . 184) (:id . 72))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 197)\n  (:start . 191) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 200) (:start . 198)\n  (:id . 74))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 206)\n  (:start . 201) (:id . 75))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 209) (:start . 207)\n  (:id . 76))\n ((:tag . "NNP") (:stem . ".WIFF") (:form . ".WIFF") (:end . 215)\n  (:start . 210) (:id . 77))\n ((:tag . "CC") (:stem . "versus") (:form . "versus") (:end . 222)\n  (:start . 216) (:id . 78))\n ((:tag . "NNP") (:stem . ".RAW") (:form . ".RAW") (:end . 227) (:start . 223)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 233)\n  (:start . 228) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 234) (:start . 233)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s14.56) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504558@unknown@formal@none@1@S@Regardless of native file type, the use of a common API eliminates the need for storage and tracking of surrogate files; based on previous reports, this can be particularly problematic for full profile data files, which can grow significantly in size upon conversion to XML [9].@(((:tag . "RB") (:stem . "regardless") (:form . "Regardless") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 48))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 42) (:start . 40)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 51)\n  (:start . 45) (:id . 52))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 55) (:start . 52)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "eliminate") (:form . "eliminates") (:end . 66)\n  (:start . 56) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "NN") (:stem . "need") (:form . "need") (:end . 75) (:start . 71)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n  (:id . 57))\n ((:tag . "NN") (:stem . "storage") (:form . "storage") (:end . 87)\n  (:start . 80) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "tracking") (:form . "tracking") (:end . 100)\n  (:start . 92) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "surrogate") (:form . "surrogate") (:end . 113)\n  (:start . 104) (:id . 62))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 119)\n  (:start . 114) (:id . 63))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 120) (:start . 119)\n  (:id . 64))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 126)\n  (:start . 121) (:id . 65))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 129) (:start . 127)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 138)\n  (:start . 130) (:id . 67))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 146)\n  (:start . 139) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 152) (:start . 148)\n  (:id . 70))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 156) (:start . 153)\n  (:id . 71))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 159) (:start . 157)\n  (:id . 72))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 172)\n  (:start . 160) (:id . 73))\n ((:tag . "JJ") (:stem . "problematic") (:form . "problematic") (:end . 184)\n  (:start . 173) (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 188) (:start . 185)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 193) (:start . 189)\n  (:id . 76))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 201)\n  (:start . 194) (:id . 77))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 206)\n  (:start . 202) (:id . 78))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 212)\n  (:start . 207) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 213) (:start . 212)\n  (:id . 80))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 219)\n  (:start . 214) (:id . 81))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 223) (:start . 220)\n  (:id . 82))\n ((:tag . "VB") (:stem . "grow") (:form . "grow") (:end . 228) (:start . 224)\n  (:id . 83))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 242) (:start . 229) (:id . 84))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 245) (:start . 243)\n  (:id . 85))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 250) (:start . 246)\n  (:id . 86))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 255) (:start . 251)\n  (:id . 87))\n ((:tag . "NN") (:stem . "conversion") (:form . "conversion") (:end . 266)\n  (:start . 256) (:id . 88))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 269) (:start . 267)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "XML") (:form . "XML") (:end . 273) (:start . 270)\n  (:id . 90))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 275) (:start . 274)\n  (:id . 91))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 276) (:start . 275)\n  (:id . 92))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 277) (:start . 276)\n  (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 278) (:start . 277)\n  (:id . 94)))@@@1@53@((:hcues ((:id . :x14.57.1) (:span 220 223))\n  ((:id . :x14.57.2) (:span 153 156)))\n (:hscopes ((:id . :x14.57.1) (:span 220 273))\n  ((:id . :x14.57.2) (:span 153 273)))\n (:identifiers (:sid . :s14.57) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504559@unknown@formal@none@1@S@Access Efficiency for Open and Proprietary Mass Spectrometry Data Files.@(((:tag . "NNP") (:stem . "Access") (:form . "Access") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Efficiency") (:form . "Efficiency") (:end . 17)\n  (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 21) (:start . 18)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Open") (:form . "Open") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Proprietary") (:form . "Proprietary") (:end . 42)\n  (:start . 31) (:id . 47))\n ((:tag . "NNP") (:stem . "Mass") (:form . "Mass") (:end . 47) (:start . 43)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Spectrometry") (:form . "Spectrometry") (:end . 60)\n  (:start . 48) (:id . 49))\n ((:tag . "NNP") (:stem . "Data") (:form . "Data") (:end . 65) (:start . 61)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Files") (:form . "Files") (:end . 71) (:start . 66)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 72) (:start . 71)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s14.58) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504560@unknown@formal@none@1@S@Given the multidimensional nature of mass-spectrometry data, extraction based on specific slices through the data space, rather than random file access, is a more relevant performance metric for mass spectrometry files.@(((:tag . "VBN") (:stem . "give") (:form . "Given") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "multidimensional") (:form . "multidimensional")\n  (:end . 26) (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "nature") (:form . "nature") (:end . 33)\n  (:start . 27) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mass-spectrometry") (:form . "mass-spectrometry")\n  (:end . 54) (:start . 37) (:id . 47))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 59) (:start . 55)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 49))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 71)\n  (:start . 61) (:id . 50))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 77) (:start . 72)\n  (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 80) (:start . 78)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 89)\n  (:start . 81) (:id . 53))\n ((:tag . "NNS") (:stem . "slice") (:form . "slices") (:end . 96)\n  (:start . 90) (:id . 54))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 104)\n  (:start . 97) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 113)\n  (:start . 109) (:id . 57))\n ((:tag . "NN") (:stem . "space") (:form . "space") (:end . 119)\n  (:start . 114) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 59))\n ((:tag . "RB") (:stem . "rather") (:form . "rather") (:end . 127)\n  (:start . 121) (:id . 60))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 132) (:start . 128)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 139)\n  (:start . 133) (:id . 62))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 144) (:start . 140)\n  (:id . 63))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 151)\n  (:start . 145) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 155) (:start . 153)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 162) (:start . 158)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 171)\n  (:start . 163) (:id . 69))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 183)\n  (:start . 172) (:id . 70))\n ((:tag . "JJ") (:stem . "metric") (:form . "metric") (:end . 190)\n  (:start . 184) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 194) (:start . 191)\n  (:id . 72))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 199) (:start . 195)\n  (:id . 73))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 212)\n  (:start . 200) (:id . 74))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 218)\n  (:start . 213) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s14.59) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504561@unknown@formal@none@1@S@Generation of RICs is perhaps the best example of a data slice procedure supported by all manufacturer data systems.@(((:tag . "NNP") (:stem . "Generation") (:form . "Generation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "RIC") (:form . "RICs") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "RB") (:stem . "perhaps") (:form . "perhaps") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "slice") (:form . "slice") (:end . 62) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "procedure") (:form . "procedure") (:end . 72)\n  (:start . 63) (:id . 54))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 82)\n  (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 85) (:start . 83)\n  (:id . 56))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 102)\n  (:start . 90) (:id . 58))\n ((:tag . "NN") (:stem . "data") (:form . "data") (:end . 107) (:start . 103)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 115)\n  (:start . 108) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 61)))@@@1@20@((:hcues ((:id . :x14.60.1) (:span 22 29)))\n (:hscopes ((:id . :x14.60.1) (:span 0 115)))\n (:identifiers (:sid . :s14.60) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504562@unknown@formal@none@1@S@Consequently we next sought to test the performance of mzAPI for creation of RICs directly from a .RAW file.@(((:tag . "RB") (:stem . "consequently") (:form . "Consequently") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "RB") (:stem . "next") (:form . "next") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "seek") (:form . "sought") (:end . 27) (:start . 21)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "VB") (:stem . "test") (:form . "test") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 51)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 60) (:start . 55)\n  (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "creation") (:form . "creation") (:end . 73)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "ric") (:form . "RICs") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 90)\n  (:start . 82) (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 95) (:start . 91)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 97) (:start . 96)\n  (:id . 58))\n ((:tag . "NNP") (:stem . ".RAW") (:form . ".RAW") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 107) (:start . 103)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s14.61) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504563@unknown@formal@none@1@S@As a point of comparison we generated the corresponding mzXML file (using TPP version 4.0) [12] and extracted RICs using both a graphical user interface (GUI) based browser tool (InsilicosViewer version 1.5.1) [3] as well as the Perl-based InSilicoSpectro environment (version 1.3.19) [6] and the R-based XCMS (version 1.12.1), [13] scriptable interface platforms.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 10) (:start . 5)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 24)\n  (:start . 14) (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 55)\n  (:start . 42) (:id . 50))\n ((:tag . "NN") (:stem . "mzxml") (:form . "mzXML") (:end . 61) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "TPP") (:form . "TPP") (:end . 77) (:start . 74)\n  (:id . 55))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 85)\n  (:start . 78) (:id . 56))\n ((:tag . "CD") (:stem . "4.0") (:form . "4.0") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 92) (:start . 91)\n  (:id . 59))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 94) (:start . 92)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 95) (:start . 94)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 109)\n  (:start . 100) (:id . 63))\n ((:tag . "NNS") (:stem . "ric") (:form . "RICs") (:end . 114) (:start . 110)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 120) (:start . 115)\n  (:id . 65))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 125) (:start . 121)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 127) (:start . 126)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "graphical") (:form . "graphical") (:end . 137)\n  (:start . 128) (:id . 68))\n ((:tag . "NN") (:stem . "user") (:form . 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"InSilicoSpectro") (:form . "InSilicoSpectro")\n  (:end . 255) (:start . 240) (:id . 90))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 267)\n  (:start . 256) (:id . 91))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 269) (:start . 268)\n  (:id . 92))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 276)\n  (:start . 269) (:id . 93))\n ((:tag . "CD") (:stem . "1.3.19") (:form . "1.3.19") (:end . 283)\n  (:start . 277) (:id . 94))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 284) (:start . 283)\n  (:id . 95))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 286) (:start . 285)\n  (:id . 96))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 287) (:start . 286)\n  (:id . 97))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 288) (:start . 287)\n  (:id . 98))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 292) (:start . 289)\n  (:id . 99))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 296) (:start . 293)\n  (:id . 100))\n ((:tag . "JJ") (:stem . "r-based") (:form . "R-based") (:end . 304)\n  (:start . 297) (:id . 101))\n ((:tag . "NN") (:stem . "xcms") (:form . "XCMS") (:end . 309) (:start . 305)\n  (:id . 102))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 311) (:start . 310)\n  (:id . 103))\n ((:tag . "NN") (:stem . "version") (:form . "version") (:end . 318)\n  (:start . 311) (:id . 104))\n ((:tag . "CD") (:stem . "1.12.1") (:form . "1.12.1") (:end . 325)\n  (:start . 319) (:id . 105))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 326) (:start . 325)\n  (:id . 106))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 327) (:start . 326)\n  (:id . 107))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 329) (:start . 328)\n  (:id . 108))\n ((:tag . "CD") (:stem . "13") (:form . "13") (:end . 331) (:start . 329)\n  (:id . 109))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 332) (:start . 331)\n  (:id . 110))\n ((:tag . "JJ") (:stem . "scriptable") (:form . "scriptable") (:end . 343)\n  (:start . 333) (:id . 111))\n ((:tag . "NN") (:stem . "interface") (:form . "interface") (:end . 353)\n  (:start . 344) (:id . 112))\n ((:tag . "NNS") (:stem . "platform") (:form . "platforms") (:end . 363)\n  (:start . 354) (:id . 113))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 364) (:start . 363)\n  (:id . 114)))@@@1@73@((:identifiers (:sid . :s14.62) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504564@unknown@formal@none@1@S@Although the latter two are designed to access a number of third-party file formats, none of the GUI- or command-line based tools supports access to specified subsets (in chromatographic time) of the underlying data.@(((:tag . "IN") (:stem . "although") (:form . "Although") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "latter") (:form . "latter") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "VB") (:stem . "access") (:form . "access") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 50))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "third-party") (:form . "third-party") (:end . 70)\n  (:start . 59) (:id . 53))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "format") (:form . "formats") (:end . 83)\n  (:start . 76) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "none") (:form . "none") (:end . 89) (:start . 85)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 59))\n ((:tag . "NN") (:stem . "gui-") (:form . "GUI-") (:end . 101) (:start . 97)\n  (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 104) (:start . 102)\n  (:id . 61))\n ((:tag . "NN") (:stem . "command-line") (:form . "command-line") (:end . 117)\n  (:start . 105) (:id . 62))\n ((:tag . "JJ") (:stem . "based") (:form . "based") (:end . 123)\n  (:start . 118) (:id . 63))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 129)\n  (:start . 124) (:id . 64))\n ((:tag . "VBZ") (:stem . "support") (:form . "supports") (:end . 138)\n  (:start . 130) (:id . 65))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 145)\n  (:start . 139) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 148) (:start . 146)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 158)\n  (:start . 149) (:id . 68))\n ((:tag . "NNS") (:stem . "subset") (:form . "subsets") (:end . 166)\n  (:start . 159) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 168) (:start . 167)\n  (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 170) (:start . 168)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "chromatographic") (:form . "chromatographic")\n  (:end . 186) (:start . 171) (:id . 72))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 191) (:start . 187)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 192) (:start . 191)\n  (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 195) (:start . 193)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 199) (:start . 196)\n  (:id . 76))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 210)\n  (:start . 200) (:id . 77))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 215)\n  (:start . 211) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s14.63) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504565@unknown@formal@none@1@S@As a result we generated RICs by extraction of a specific mass-to-charge range over the full data file, or in the case of InSilicoSpectro, which had no support for RIC generation, we simply timed the opening of mzXML files.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 24)\n  (:start . 15) (:id . 46))\n ((:tag . "NNS") (:stem . "ric") (:form . "RICs") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 43)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 57)\n  (:start . 49) (:id . 52))\n ((:tag . "JJ") (:stem . "mass-to-charge") (:form . "mass-to-charge")\n  (:end . 72) (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 78) (:start . 73)\n  (:id . 54))\n ((:tag . "IN") (:stem . "over") (:form . "over") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 92) (:start . 88)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 97) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 109) (:start . 107)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 63))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 118) (:start . 114)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "InSilicoSpectro") (:form . "InSilicoSpectro")\n  (:end . 137) (:start . 122) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 67))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 144)\n  (:start . 139) (:id . 68))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 148) (:start . 145)\n  (:id . 69))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 151) (:start . 149)\n  (:id . 70))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 159)\n  (:start . 152) (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 163) (:start . 160)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "RIC") (:form . "RIC") (:end . 167) (:start . 164)\n  (:id . 73))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 178)\n  (:start . 168) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 179) (:start . 178)\n  (:id . 75))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 182) (:start . 180)\n  (:id . 76))\n ((:tag . "RB") (:stem . "simply") (:form . "simply") (:end . 189)\n  (:start . 183) (:id . 77))\n ((:tag . "VBD") (:stem . "time") (:form . "timed") (:end . 195)\n  (:start . 190) (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 199) (:start . 196)\n  (:id . 79))\n ((:tag . "NN") (:stem . "opening") (:form . "opening") (:end . 207)\n  (:start . 200) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 210) (:start . 208)\n  (:id . 81))\n ((:tag . "NN") (:stem . "mzxml") (:form . "mzXML") (:end . 216)\n  (:start . 211) (:id . 82))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 222)\n  (:start . 217) (:id . 83))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 223) (:start . 222)\n  (:id . 84)))@@@1@43@((:identifiers (:sid . :s14.64) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504566@unknown@formal@none@1@S@While the mzXML schema includes a scan index that provides for random access to scans at speeds competitive with, or exceeding, proprietary data system (in this case ThermoFisher Xcalibur) [9], Table 1 shows that generation of specific data slices, or in this case RICs, is 5- to 10-fold faster when leveraging the underlying manufacturer's API compared to GUI or command line based access to mzXML (scripts used for all timings included in Additional File 1).@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mzxml") (:form . "mzXML") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "schema") (:form . "schema") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "scan") (:form . "scan") (:end . 38) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "index") (:form . "index") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 49) (:start . 45)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 58)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "random") (:form . "random") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 76)\n  (:start . 70) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "speed") (:form . "speeds") (:end . 95)\n  (:start . 89) (:id . 58))\n ((:tag . "JJ") (:stem . "competitive") (:form . "competitive") (:end . 107)\n  (:start . 96) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 112) (:start . 108)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 116) (:start . 114)\n  (:id . 62))\n ((:tag . "VBG") (:stem . "exceed") (:form . "exceeding") (:end . 126)\n  (:start . 117) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 127) (:start . 126)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "proprietary") (:form . "proprietary") (:end . 139)\n  (:start . 128) (:id . 65))\n ((:tag . "NN") (:stem . "data") (:form . "data") (:end . 144) (:start . 140)\n  (:id . 66))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 151)\n  (:start . 145) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 155) (:start . 153)\n  (:id . 69))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 160) (:start . 156)\n  (:id . 70))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 165) (:start . 161)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "ThermoFisher") (:form . "ThermoFisher")\n  (:end . 178) (:start . 166) (:id . 72))\n ((:tag . "NNP") (:stem . "Xcalibur") (:form . "Xcalibur") (:end . 187)\n  (:start . 179) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 74))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 190) (:start . 189)\n  (:id . 75))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 191) (:start . 190)\n  (:id . 76))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 192) (:start . 191)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 193) (:start . 192)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 199)\n  (:start . 194) (:id . 79))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 201) (:start . 200)\n  (:id . 80))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 207)\n  (:start . 202) (:id . 81))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 212) (:start . 208)\n  (:id . 82))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 223)\n  (:start . 213) (:id . 83))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 226) (:start . 224)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 235)\n  (:start . 227) (:id . 85))\n ((:tag . "NN") (:stem . "data") (:form . "data") (:end . 240) (:start . 236)\n  (:id . 86))\n ((:tag . "NNS") (:stem . "slice") (:form . "slices") (:end . 247)\n  (:start . 241) (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 248) (:start . 247)\n  (:id . 88))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 251) (:start . 249)\n  (:id . 89))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 254) (:start . 252)\n  (:id . 90))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 259) (:start . 255)\n  (:id . 91))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 264) (:start . 260)\n  (:id . 92))\n ((:tag . "NNS") (:stem . "ric") (:form . "RICs") (:end . 269) (:start . 265)\n  (:id . 93))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 270) (:start . 269)\n  (:id . 94))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 273) (:start . 271)\n  (:id . 95))\n ((:tag . "CD") (:stem . "5-") (:form . "5-") (:end . 276) (:start . 274)\n  (:id . 96))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 279) (:start . 277)\n  (:id . 97))\n ((:tag . "JJ") (:stem . "10-fold") (:form . "10-fold") (:end . 287)\n  (:start . 280) (:id . 98))\n ((:tag . "JJR") (:stem . "fast") (:form . "faster") (:end . 294)\n  (:start . 288) (:id . 99))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 299) (:start . 295)\n  (:id . 100))\n ((:tag . "VBG") (:stem . "leverage") (:form . "leveraging") (:end . 310)\n  (:start . 300) (:id . 101))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 314) (:start . 311)\n  (:id . 102))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 325)\n  (:start . 315) (:id . 103))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 338)\n  (:start . 326) (:id . 104))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 340) (:start . 338)\n  (:id . 105))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 344) (:start . 341)\n  (:id . 106))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 353)\n  (:start . 345) (:id . 107))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 356) (:start . 354)\n  (:id . 108))\n ((:tag . "NNP") (:stem . "GUI") (:form . "GUI") (:end . 360) (:start . 357)\n  (:id . 109))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 363) (:start . 361)\n  (:id . 110))\n ((:tag . "NN") (:stem . "command") (:form . "command") (:end . 371)\n  (:start . 364) (:id . 111))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 376) (:start . 372)\n  (:id . 112))\n ((:tag . "JJ") (:stem . "based") (:form . "based") (:end . 382)\n  (:start . 377) (:id . 113))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 389)\n  (:start . 383) (:id . 114))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 392) (:start . 390)\n  (:id . 115))\n ((:tag . "NN") (:stem . "mzxml") (:form . "mzXML") (:end . 398)\n  (:start . 393) (:id . 116))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 400) (:start . 399)\n  (:id . 117))\n ((:tag . "NNS") (:stem . "script") (:form . "scripts") (:end . 407)\n  (:start . 400) (:id . 118))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 412) (:start . 408)\n  (:id . 119))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 416) (:start . 413)\n  (:id . 120))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 420) (:start . 417)\n  (:id . 121))\n ((:tag . "NNS") (:stem . "timing") (:form . "timings") (:end . 428)\n  (:start . 421) (:id . 122))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 437)\n  (:start . 429) (:id . 123))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 440) (:start . 438)\n  (:id . 124))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 451)\n  (:start . 441) (:id . 125))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 456) (:start . 452)\n  (:id . 126))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 458) (:start . 457)\n  (:id . 127))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 459) (:start . 458)\n  (:id . 128))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 460) (:start . 459)\n  (:id . 129)))@@@1@88@((:identifiers (:sid . :s14.65) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504567@unknown@formal@none@1@S@This result supports the notion that pragmatic data access patterns are well supported by existing, albeit proprietary, manufacturer libraries, and more importantly, that these libraries can be efficiently utilized through a common and redistributable API.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "support") (:form . "supports") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "notion") (:form . "notion") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 36) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "pragmatic") (:form . "pragmatic") (:end . 46)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 51) (:start . 47)\n  (:id . 49))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 58)\n  (:start . 52) (:id . 50))\n ((:tag . "NNS") (:stem . "pattern") (:form . "patterns") (:end . 67)\n  (:start . 59) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 71) (:start . 68)\n  (:id . 52))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 86)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 89) (:start . 87)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 98)\n  (:start . 90) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "IN") (:stem . "albeit") (:form . "albeit") (:end . 106)\n  (:start . 100) (:id . 58))\n ((:tag . "JJ") (:stem . "proprietary") (:form . "proprietary") (:end . 118)\n  (:start . 107) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 132)\n  (:start . 120) (:id . 61))\n ((:tag . "NNS") (:stem . "library") (:form . "libraries") (:end . 142)\n  (:start . 133) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n  (:id . 64))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 152) (:start . 148)\n  (:id . 65))\n ((:tag . "RB") (:stem . "importantly") (:form . "importantly") (:end . 164)\n  (:start . 153) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 165) (:start . 164)\n  (:id . 67))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 170) (:start . 166)\n  (:id . 68))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 176)\n  (:start . 171) (:id . 69))\n ((:tag . "NNS") (:stem . "library") (:form . "libraries") (:end . 186)\n  (:start . 177) (:id . 70))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 190) (:start . 187)\n  (:id . 71))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 193) (:start . 191)\n  (:id . 72))\n ((:tag . "RB") (:stem . "efficiently") (:form . "efficiently") (:end . 205)\n  (:start . 194) (:id . 73))\n ((:tag . "VBN") (:stem . "utilize") (:form . "utilized") (:end . 214)\n  (:start . 206) (:id . 74))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 222)\n  (:start . 215) (:id . 75))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 224) (:start . 223)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 231)\n  (:start . 225) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 235) (:start . 232)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "redistributable") (:form . "redistributable")\n  (:end . 251) (:start . 236) (:id . 79))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 255) (:start . 252)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 256) (:start . 255)\n  (:id . 81)))@@@1@40@((:hcues ((:id . :x14.66.1) (:span 187 190)) ((:id . :x14.66.2) (:span 12 31)))\n (:hscopes ((:id . :x14.66.1) (:span 171 255))\n  ((:id . :x14.66.2) (:span 12 255)))\n (:identifiers (:sid . :s14.66) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504568@unknown@formal@none@1@S@multiplierz: An Open-Source and Interactive Environment for Proteomics Data Analysis@(((:tag . "LS") (:stem . "multiplierz") (:form . "multiplierz") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "an") (:form . "An") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Open-Source") (:form . "Open-Source") (:end . 27)\n  (:start . 16) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "interactive") (:form . "Interactive") (:end . 43)\n  (:start . 32) (:id . 47))\n ((:tag . "NNP") (:stem . "Environment") (:form . "Environment") (:end . 55)\n  (:start . 44) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Proteomics") (:form . "Proteomics") (:end . 70)\n  (:start . 60) (:id . 50))\n ((:tag . "NNP") (:stem . "Data") (:form . "Data") (:end . 75) (:start . 71)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Analysis") (:form . "Analysis") (:end . 84)\n  (:start . 76) (:id . 52)))@@@1@11@((:identifiers (:sid . :s14.67) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504569@unknown@formal@none@1@S@We extend the functionality of mzAPI by integration into multiplierz, an open-source Python-based environment that provides a flexible framework for comprehensive analysis of proteomics data.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "extend") (:form . "extend") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 27) (:start . 14) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 51)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 68)\n  (:start . 57) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "open-source") (:form . "open-source") (:end . 84)\n  (:start . 73) (:id . 54))\n ((:tag . "JJ") (:stem . "python-based") (:form . "Python-based") (:end . 97)\n  (:start . 85) (:id . 55))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 109)\n  (:start . 98) (:id . 56))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 114) (:start . 110)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 123)\n  (:start . 115) (:id . 58))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 125) (:start . 124)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "flexible") (:form . "flexible") (:end . 134)\n  (:start . 126) (:id . 60))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 144)\n  (:start . 135) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 148) (:start . 145)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "comprehensive") (:form . "comprehensive")\n  (:end . 162) (:start . 149) (:id . 63))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 171)\n  (:start . 163) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 174) (:start . 172)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 185)\n  (:start . 175) (:id . 66))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 190)\n  (:start . 186) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s14.68) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504570@unknown@formal@none@1@S@Figure 1 illustrates our proposed implementation; all associated code and scripts are available for download at: http://blais.dfci.harvard.edu/multiplierz.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "illustrate") (:form . "illustrates") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "implementation") (:form . "implementation")\n  (:end . 48) (:start . 34) (:id . 47))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 49) (:start . 48)\n  (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 64)\n  (:start . 54) (:id . 50))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 69) (:start . 65)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "script") (:form . "scripts") (:end . 81)\n  (:start . 74) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 85) (:start . 82)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 95)\n  (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 99) (:start . 96)\n  (:id . 56))\n ((:tag . "NN") (:stem . "download") (:form . "download") (:end . 108)\n  (:start . 100) (:id . 57))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . "NN") (:stem . "http://blais.dfci.harvard.edu/multiplierz")\n  (:form . "http://blais.dfci.harvard.edu/multiplierz") (:end . 154)\n  (:start . 113) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s14.69) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504571@unknown@formal@none@1@S@In the following sections, we provide a detailed description of core multiplierz capabilities.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "following") (:form . "following") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 37)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "detailed") (:form . "detailed") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "description") (:form . "description") (:end . 60)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 80)\n  (:start . 69) (:id . 54))\n ((:tag . "NNS") (:stem . "capability") (:form . "capabilities") (:end . 93)\n  (:start . 81) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s14.70) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504572@unknown@formal@none@1@S@A Common API and Desktop Environment for Mass Spectrometry Data Analysis.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Common") (:form . "Common") (:end . 8) (:start . 2)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "API") (:form . "API") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Desktop") (:form . "Desktop") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "NNP") (:stem . "Environment") (:form . "Environment") (:end . 36)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Mass") (:form . "Mass") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Spectrometry") (:form . "Spectrometry") (:end . 58)\n  (:start . 46) (:id . 50))\n ((:tag . "NNP") (:stem . "Data") (:form . "Data") (:end . 63) (:start . 59)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Analysis") (:form . "Analysis") (:end . 72)\n  (:start . 64) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 73) (:start . 72)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s14.71) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504573@unknown@formal@none@1@S@The multiplierz environment provides a central point for user interaction with proprietary data files (via mzAPI), protein/peptide identification algorithms, publicly available annotation databases, and commercial reporting and spreadsheet tools.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 27)\n  (:start . 16) (:id . 44))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 36)\n  (:start . 28) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 46)\n  (:start . 39) (:id . 47))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 52) (:start . 47)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 56) (:start . 53)\n  (:id . 49))\n ((:tag . "JJR") (:stem . "us") (:form . "user") (:end . 61) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 73)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 78) (:start . 74)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "proprietary") (:form . "proprietary") (:end . 90)\n  (:start . 79) (:id . 53))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 95) (:start . 91)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 101) (:start . 96)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 56))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 106) (:start . 103)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "mzAPI") (:form . "mzAPI") (:end . 112)\n  (:start . 107) (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 60))\n ((:tag . "NN") (:stem . "protein/peptide") (:form . "protein/peptide")\n  (:end . 130) (:start . 115) (:id . 61))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 145) (:start . 131) (:id . 62))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 156)\n  (:start . 146) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 157) (:start . 156)\n  (:id . 64))\n ((:tag . "RB") (:stem . "publicly") (:form . "publicly") (:end . 166)\n  (:start . 158) (:id . 65))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 176)\n  (:start . 167) (:id . 66))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 187)\n  (:start . 177) (:id . 67))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 197)\n  (:start . 188) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 198) (:start . 197)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 202) (:start . 199)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "commercial") (:form . "commercial") (:end . 213)\n  (:start . 203) (:id . 71))\n ((:tag . "NN") (:stem . "reporting") (:form . "reporting") (:end . 223)\n  (:start . 214) (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 227) (:start . 224)\n  (:id . 73))\n ((:tag . "NN") (:stem . "spreadsheet") (:form . "spreadsheet") (:end . 239)\n  (:start . 228) (:id . 74))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 245)\n  (:start . 240) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s14.72) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504574@unknown@formal@none@1@S@Our proposal calls for manufacturers to provide a minimal set of libraries for access to their native data files.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "proposal") (:form . "proposal") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "call") (:form . "calls") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "manufacturer") (:form . "manufacturers")\n  (:end . 36) (:start . 23) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 47)\n  (:start . 40) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "minimal") (:form . "minimal") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "library") (:form . "libraries") (:end . 74)\n  (:start . 65) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 85)\n  (:start . 79) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 94)\n  (:start . 89) (:id . 57))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 101)\n  (:start . 95) (:id . 58))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 106)\n  (:start . 102) (:id . 59))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 112)\n  (:start . 107) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s14.73) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504575@unknown@formal@none@1@S@Ad hoc data analysis tasks are supported through multiplierz scripting capability, including programmatic access for integration into data analytic pipelines.@(((:tag . "NNP") (:stem . "Ad") (:form . "Ad") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "hoc") (:form . "hoc") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "data") (:form . "data") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 20)\n  (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 40)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 48)\n  (:start . 41) (:id . 49))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 60)\n  (:start . 49) (:id . 50))\n ((:tag . "VBG") (:stem . "scripte") (:form . "scripting") (:end . 70)\n  (:start . 61) (:id . 51))\n ((:tag . "NN") (:stem . "capability") (:form . "capability") (:end . 81)\n  (:start . 71) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 92)\n  (:start . 83) (:id . 54))\n ((:tag . "JJ") (:stem . "programmatic") (:form . "programmatic") (:end . 105)\n  (:start . 93) (:id . 55))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 112)\n  (:start . 106) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 116) (:start . 113)\n  (:id . 57))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 128)\n  (:start . 117) (:id . 58))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 133) (:start . 129)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 138)\n  (:start . 134) (:id . 60))\n ((:tag . "JJ") (:stem . "analytic") (:form . "analytic") (:end . 147)\n  (:start . 139) (:id . 61))\n ((:tag . "NNS") (:stem . "pipeline") (:form . "pipelines") (:end . 157)\n  (:start . 148) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s14.74) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504576@unknown@formal@none@1@S@Regardless of final experimental goals, peptide identification is often the first or default operation performed subsequent to LC-MS data acquisition.@(((:tag . "RB") (:stem . "regardless") (:form . "Regardless") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 32)\n  (:start . 20) (:id . 45))\n ((:tag . "NNS") (:stem . "goal") (:form . "goals") (:end . 38) (:start . 33)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 47))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 47)\n  (:start . 40) (:id . 48))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 62) (:start . 48) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 65) (:start . 63)\n  (:id . 50))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 71) (:start . 66)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 81) (:start . 76)\n  (:id . 53))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 84) (:start . 82)\n  (:id . 54))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 92)\n  (:start . 85) (:id . 55))\n ((:tag . "NN") (:stem . "operation") (:form . "operation") (:end . 102)\n  (:start . 93) (:id . 56))\n ((:tag . "VBD") (:stem . "perform") (:form . "performed") (:end . 112)\n  (:start . 103) (:id . 57))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 123)\n  (:start . 113) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 126) (:start . 124)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "lc-ms") (:form . "LC-MS") (:end . 132)\n  (:start . 127) (:id . 60))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 137)\n  (:start . 133) (:id . 61))\n ((:tag . "NN") (:stem . "acquisition") (:form . "acquisition") (:end . 149)\n  (:start . 138) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s14.75) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504577@unknown@formal@none@1@S@We designed multiplierz to serve as a user-friendly, desktop tool for interaction with proteomics database search engines; consistent with our zero-infrastructure philosophy, X!Tandem [14] is fully integrated into the multiplierz installation package.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "design") (:form . "designed") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "VB") (:stem . "serve") (:form . "serve") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "user-friendly") (:form . "user-friendly")\n  (:end . 51) (:start . 38) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "desktop") (:form . "desktop") (:end . 60)\n  (:start . 53) (:id . 51))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 81)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 86) (:start . 82)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 97)\n  (:start . 87) (:id . 56))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 106)\n  (:start . 98) (:id . 57))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 113)\n  (:start . 107) (:id . 58))\n ((:tag . "NNS") (:stem . "engine") (:form . "engines") (:end . 121)\n  (:start . 114) (:id . 59))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 122) (:start . 121)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "consistent") (:form . "consistent") (:end . 133)\n  (:start . 123) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 138) (:start . 134)\n  (:id . 62))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 142) (:start . 139)\n  (:id . 63))\n ((:tag . "NN") (:stem . "zero-infrastructure")\n  (:form . "zero-infrastructure") (:end . 162) (:start . 143) (:id . 64))\n ((:tag . "NN") (:stem . "philosophy") (:form . "philosophy") (:end . 173)\n  (:start . 163) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 174) (:start . 173)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "X!Tandem") (:form . "X!Tandem") (:end . 183)\n  (:start . 175) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 185) (:start . 184)\n  (:id . 68))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 187) (:start . 185)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 188) (:start . 187)\n  (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 191) (:start . 189)\n  (:id . 71))\n ((:tag . "RB") (:stem . "fully") (:form . "fully") (:end . 197)\n  (:start . 192) (:id . 72))\n ((:tag . "VBN") (:stem . "integrate") (:form . "integrated") (:end . 208)\n  (:start . 198) (:id . 73))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 213) (:start . 209)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 217) (:start . 214)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 229)\n  (:start . 218) (:id . 76))\n ((:tag . "NN") (:stem . "installation") (:form . "installation") (:end . 242)\n  (:start . 230) (:id . 77))\n ((:tag . "NN") (:stem . "package") (:form . "package") (:end . 250)\n  (:start . 243) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 251) (:start . 250)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s14.76) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504578@unknown@formal@none@1@S@Similarly we include support for automated retrieval of Mascot search results.@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "automate") (:form . "automated") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "retrieval") (:form . "retrieval") (:end . 52)\n  (:start . 43) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 62)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 69)\n  (:start . 63) (:id . 51))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 77)\n  (:start . 70) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s14.77) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504579@unknown@formal@none@1@S@In this case, the URL for a particular search is easily and unambiguously accessed using the Mascot job ID (after completion of the search, the Mascot ID is both on the search submission page and in the Mascot Daemon).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 46))\n ((:tag . "NN") (:stem . "url") (:form . "URL") (:end . 21) (:start . 18)\n  (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 25) (:start . 22)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 27) (:start . 26)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 38)\n  (:start . 28) (:id . 50))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 45)\n  (:start . 39) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 48) (:start . 46)\n  (:id . 52))\n ((:tag . "RB") (:stem . "easily") (:form . "easily") (:end . 55)\n  (:start . 49) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 54))\n ((:tag . "RB") (:stem . "unambiguously") (:form . "unambiguously")\n  (:end . 73) (:start . 60) (:id . 55))\n ((:tag . "VBN") (:stem . "access") (:form . "accessed") (:end . 82)\n  (:start . 74) (:id . 56))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 88) (:start . 83)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 99)\n  (:start . 93) (:id . 59))\n ((:tag . "NN") (:stem . "job") (:form . "job") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "NN") (:stem . "id") (:form . "ID") (:end . 106) (:start . 104)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 62))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 113)\n  (:start . 108) (:id . 63))\n ((:tag . "NN") (:stem . "completion") (:form . "completion") (:end . 124)\n  (:start . 114) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 66))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 138)\n  (:start . 132) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 150)\n  (:start . 144) (:id . 70))\n ((:tag . "NNP") (:stem . "ID") (:form . "ID") (:end . 153) (:start . 151)\n  (:id . 71))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 156) (:start . 154)\n  (:id . 72))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 161) (:start . 157)\n  (:id . 73))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 164) (:start . 162)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 168) (:start . 165)\n  (:id . 75))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 175)\n  (:start . 169) (:id . 76))\n ((:tag . "NN") (:stem . "submission") (:form . "submission") (:end . 186)\n  (:start . 176) (:id . 77))\n ((:tag . "NN") (:stem . "page") (:form . "page") (:end . 191) (:start . 187)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 195) (:start . 192)\n  (:id . 79))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 198) (:start . 196)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 202) (:start . 199)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 209)\n  (:start . 203) (:id . 82))\n ((:tag . "NNP") (:stem . "Daemon") (:form . "Daemon") (:end . 216)\n  (:start . 210) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 217) (:start . 216)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s14.78) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504580@unknown@formal@none@1@S@The multiplierz module for downloading Mascot search results also allows input for Mascot-specific export options such as "Require Bold Red" and "Maximum Number of Protein hits."@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "module") (:form . "module") (:end . 22)\n  (:start . 16) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "downloade") (:form . "downloading") (:end . 38)\n  (:start . 27) (:id . 46))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 45)\n  (:start . 39) (:id . 47))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 52)\n  (:start . 46) (:id . 48))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 60)\n  (:start . 53) (:id . 49))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 65) (:start . 61)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 72)\n  (:start . 66) (:id . 51))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 78) (:start . 73)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 82) (:start . 79)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "mascot-specific") (:form . "Mascot-specific")\n  (:end . 98) (:start . 83) (:id . 54))\n ((:tag . "NN") (:stem . "export") (:form . "export") (:end . 105)\n  (:start . 99) (:id . 55))\n ((:tag . "NNS") (:stem . "option") (:form . "options") (:end . 113)\n  (:start . 106) (:id . 56))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 118) (:start . 114)\n  (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 121) (:start . 119)\n  (:id . 58))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 123) (:start . 122)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Require") (:form . "Require") (:end . 130)\n  (:start . 123) (:id . 60))\n ((:tag . "NNP") (:stem . "Bold") (:form . "Bold") (:end . 135) (:start . 131)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Red") (:form . "Red") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 140) (:start . 139)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n  (:id . 64))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 146) (:start . 145)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Maximum") (:form . "Maximum") (:end . 153)\n  (:start . 146) (:id . 66))\n ((:tag . "NNP") (:stem . "Number") (:form . "Number") (:end . 160)\n  (:start . 154) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 163) (:start . 161)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 171)\n  (:start . 164) (:id . 69))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 176) (:start . 172)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 71))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 178) (:start . 177)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s14.79) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504581@unknown@formal@none@1@S@Multiple search results are specified using either a comma- or dash-separated list of Mascot Job IDs (e.g., 6556, 5878, 5120-5125).@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "specify") (:form . "specified") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 43) (:start . 38)\n  (:id . 47))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 50)\n  (:start . 44) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "comma-") (:form . "comma-") (:end . 59)\n  (:start . 53) (:id . 50))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "dash-separated") (:form . "dash-separated")\n  (:end . 77) (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 82) (:start . 78)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 85) (:start . 83)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 92)\n  (:start . 86) (:id . 55))\n ((:tag . "NNP") (:stem . "Job") (:form . "Job") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "IDs") (:form . "IDs") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 106) (:start . 102)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . "CD") (:stem . "6556") (:form . "6556") (:end . 112) (:start . 108)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . "CD") (:stem . "5878") (:form . "5878") (:end . 118) (:start . 114)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 119) (:start . 118)\n  (:id . 64))\n ((:tag . "CD") (:stem . "5120-5125") (:form . "5120-5125") (:end . 129)\n  (:start . 120) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 130) (:start . 129)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s14.80) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504582@unknown@formal@none@1@S@Users can optionally include Mascot MS/MS fragment annotation images (that are displayed in multiple Mascot report web pages) and embed them within a singular multiplierz report; thus multiplierz provides users with comprehensive Mascot information, including images, in a convenient and portable report (described below).@(((:tag . "NNS") (:stem . "user") (:form . "Users") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "optionally") (:form . "optionally") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "VB") (:stem . "include") (:form . "include") (:end . 28)\n  (:start . 21) (:id . 45))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 35)\n  (:start . 29) (:id . 46))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 50)\n  (:start . 42) (:id . 48))\n ((:tag . "NN") (:stem . "annotation") (:form . "annotation") (:end . 61)\n  (:start . 51) (:id . 49))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 68)\n  (:start . 62) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "display") (:form . "displayed") (:end . 88)\n  (:start . 79) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 91) (:start . 89)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 100)\n  (:start . 92) (:id . 56))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 107)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 114)\n  (:start . 108) (:id . 58))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 118) (:start . 115)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "page") (:form . "pages") (:end . 124)\n  (:start . 119) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "embed") (:form . "embed") (:end . 135)\n  (:start . 130) (:id . 63))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 140) (:start . 136)\n  (:id . 64))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 147)\n  (:start . 141) (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 149) (:start . 148)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "singular") (:form . "singular") (:end . 158)\n  (:start . 150) (:id . 67))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 170)\n  (:start . 159) (:id . 68))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 177)\n  (:start . 171) (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 178) (:start . 177)\n  (:id . 70))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 183) (:start . 179)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 195)\n  (:start . 184) (:id . 72))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 204)\n  (:start . 196) (:id . 73))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 210)\n  (:start . 205) (:id . 74))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 215) (:start . 211)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "comprehensive") (:form . "comprehensive")\n  (:end . 229) (:start . 216) (:id . 76))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 236)\n  (:start . 230) (:id . 77))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 248)\n  (:start . 237) (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 249) (:start . 248)\n  (:id . 79))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 259)\n  (:start . 250) (:id . 80))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 266)\n  (:start . 260) (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 267) (:start . 266)\n  (:id . 82))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 270) (:start . 268)\n  (:id . 83))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 272) (:start . 271)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "convenient") (:form . "convenient") (:end . 283)\n  (:start . 273) (:id . 85))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 287) (:start . 284)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "portable") (:form . "portable") (:end . 296)\n  (:start . 288) (:id . 87))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 303)\n  (:start . 297) (:id . 88))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 305) (:start . 304)\n  (:id . 89))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 314)\n  (:start . 305) (:id . 90))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 320)\n  (:start . 315) (:id . 91))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 321) (:start . 320)\n  (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 322) (:start . 321)\n  (:id . 93)))@@@1@52@((:identifiers (:sid . :s14.81) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504583@unknown@formal@none@1@S@Importantly, none of the above tasks require server level administrative privileges.@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "none") (:form . "none") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "administrative") (:form . "administrative")\n  (:end . 72) (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "privilege") (:form . "privileges") (:end . 83)\n  (:start . 73) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s14.82) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504584@unknown@formal@none@1@S@For example, query of MS/MS peak annotations typically requires logon credentials within the web browser.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "peak") (:form . "peak") (:end . 32) (:start . 28)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "annotation") (:form . "annotations") (:end . 44)\n  (:start . 33) (:id . 49))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 54)\n  (:start . 45) (:id . 50))\n ((:tag . "VBZ") (:stem . "require") (:form . "requires") (:end . 63)\n  (:start . 55) (:id . 51))\n ((:tag . "NN") (:stem . "logon") (:form . "logon") (:end . 69) (:start . 64)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "credential") (:form . "credentials") (:end . 81)\n  (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 88)\n  (:start . 82) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "NN") (:stem . "browser") (:form . "browser") (:end . 104)\n  (:start . 97) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s14.83) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504585@unknown@formal@none@1@S@multiplierz interacts with the browser to "screen scrape" MS/MS images and store them within the default report format.@(((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "interact") (:form . "interacts") (:end . 21)\n  (:start . 12) (:id . 43))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 30) (:start . 27)\n  (:id . 45))\n ((:tag . "NN") (:stem . "browser") (:form . "browser") (:end . 38)\n  (:start . 31) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 47))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "VB") (:stem . "screen") (:form . "screen") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "NN") (:stem . "scrape") (:form . "scrape") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 70)\n  (:start . 64) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 54))\n ((:tag . "VB") (:stem . "store") (:form . "store") (:end . 80) (:start . 75)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 85) (:start . 81)\n  (:id . 56))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 92)\n  (:start . 86) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 104)\n  (:start . 97) (:id . 59))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 111)\n  (:start . 105) (:id . 60))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 118)\n  (:start . 112) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s14.84) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504586@unknown@formal@none@1@S@Users with full access to the Mascot server may parse results directly from the .DAT file using .mz scripts (multiplierz reports and .mz scripts and described below).@(((:tag . "NNS") (:stem . "user") (:form . "Users") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 10) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 25) (:start . 23)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "VB") (:stem . "parse") (:form . "parse") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 70)\n  (:start . 62) (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 55))\n ((:tag . "NNP") (:stem . ".DAT") (:form . ".DAT") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 89) (:start . 85)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 95) (:start . 90)\n  (:id . 58))\n ((:tag . "NN") (:stem . ".mz") (:form . ".mz") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "script") (:form . "scripts") (:end . 107)\n  (:start . 100) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 120)\n  (:start . 109) (:id . 62))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 128)\n  (:start . 121) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 64))\n ((:tag . "NN") (:stem . ".mz") (:form . ".mz") (:end . 136) (:start . 133)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "script") (:form . "scripts") (:end . 144)\n  (:start . 137) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 158)\n  (:start . 149) (:id . 68))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 164)\n  (:start . 159) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 166) (:start . 165)\n  (:id . 71)))@@@1@30@((:hcues ((:id . :x14.85.1) (:span 44 47)))\n (:hscopes ((:id . :x14.85.1) (:span 44 165)))\n (:identifiers (:sid . :s14.85) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504587@unknown@formal@none@1@S@Similar support is also provided for Protein Pilot [15] and OMSSA [16].@(((:tag . "JJ") (:stem . "similar") (:form . "Similar") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "provide") (:form . "provided") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "NN") (:stem . "pilot") (:form . "Pilot") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "OMSSA") (:form . "OMSSA") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 69) (:start . 67)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 70) (:start . 69)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s14.86) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504588@unknown@formal@none@1@S@For maximum flexibility in conversion of parsed data from other search engines we include modules for generation of multiplierz-compatible spreadsheets.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "maximum") (:form . "maximum") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "flexibility") (:form . "flexibility") (:end . 23)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "NN") (:stem . "conversion") (:form . "conversion") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "parse") (:form . "parsed") (:end . 47)\n  (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 52) (:start . 48)\n  (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 63) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 70)\n  (:start . 64) (:id . 52))\n ((:tag . "NNS") (:stem . "engine") (:form . "engines") (:end . 78)\n  (:start . 71) (:id . 53))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 89)\n  (:start . 82) (:id . 55))\n ((:tag . "NNS") (:stem . "module") (:form . "modules") (:end . 97)\n  (:start . 90) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 101) (:start . 98)\n  (:id . 57))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 112)\n  (:start . 102) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 115) (:start . 113)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "multiplierz-compatible")\n  (:form . "multiplierz-compatible") (:end . 138) (:start . 116) (:id . 60))\n ((:tag . "NNS") (:stem . "spreadsheet") (:form . "spreadsheets") (:end . 151)\n  (:start . 139) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 152) (:start . 151)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s14.87) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504589@unknown@formal@none@1@S@Calculation of a false discovery rate (FDR) for peptide sequence identifications is one mechanism to assess the overall quality of search results [17,18].@(((:tag . "NN") (:stem . "calculation") (:form . "Calculation") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "false") (:form . "false") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "discovery") (:form . "discovery") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "FDR") (:form . "FDR") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 43) (:start . 42)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 55)\n  (:start . 48) (:id . 52))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 64)\n  (:start . 56) (:id . 53))\n ((:tag . "NNS") (:stem . "identification") (:form . "identifications")\n  (:end . 80) (:start . 65) (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 83) (:start . 81)\n  (:id . 55))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 87) (:start . 84)\n  (:id . 56))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 97)\n  (:start . 88) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 107)\n  (:start . 101) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 119)\n  (:start . 112) (:id . 61))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 127)\n  (:start . 120) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 63))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 137)\n  (:start . 131) (:id . 64))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 145)\n  (:start . 138) (:id . 65))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 147) (:start . 146)\n  (:id . 66))\n ((:tag . "CD") (:stem . "17,18") (:form . "17,18") (:end . 152)\n  (:start . 147) (:id . 67))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 154) (:start . 153)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s14.88) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504590@unknown@formal@none@1@S@multiplierz supports calculation of a FDR upon retrieval of peptide identification data from both forward and reverse database searches.@(((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "support") (:form . "supports") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . "NN") (:stem . "calculation") (:form . "calculation") (:end . 32)\n  (:start . 21) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 37) (:start . 36)\n  (:id . 46))\n ((:tag . "NN") (:stem . "fdr") (:form . "FDR") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "retrieval") (:form . "retrieval") (:end . 56)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 67)\n  (:start . 60) (:id . 51))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 82) (:start . 68) (:id . 52))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 87) (:start . 83)\n  (:id . 53))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 92) (:start . 88)\n  (:id . 54))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 97) (:start . 93)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "forward") (:form . "forward") (:end . 105)\n  (:start . 98) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 117)\n  (:start . 110) (:id . 58))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 126)\n  (:start . 118) (:id . 59))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 135)\n  (:start . 127) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s14.89) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504591@unknown@formal@none@1@S@The FDR for a given score threshold is calculated as the ratio of reverse database search identifications to that from the forward plus reverse searches, each with a score greater than or equal to the chosen threshold.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fdr") (:form . "FDR") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 19) (:start . 14)\n  (:id . 46))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 25) (:start . 20)\n  (:id . 47))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 35)\n  (:start . 26) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "calculate") (:form . "calculated") (:end . 49)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 62) (:start . 57)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 73)\n  (:start . 66) (:id . 55))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 82)\n  (:start . 74) (:id . 56))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 89)\n  (:start . 83) (:id . 57))\n ((:tag . "NNS") (:stem . "identification") (:form . "identifications")\n  (:end . 105) (:start . 90) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 113) (:start . 109)\n  (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 118) (:start . 114)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "forward") (:form . "forward") (:end . 130)\n  (:start . 123) (:id . 63))\n ((:tag . "CC") (:stem . "plus") (:form . "plus") (:end . 135) (:start . 131)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 143)\n  (:start . 136) (:id . 65))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 152)\n  (:start . 144) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 67))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 158) (:start . 154)\n  (:id . 68))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 163) (:start . 159)\n  (:id . 69))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 165) (:start . 164)\n  (:id . 70))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 171)\n  (:start . 166) (:id . 71))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 179)\n  (:start . 172) (:id . 72))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 184) (:start . 180)\n  (:id . 73))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 187) (:start . 185)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 193)\n  (:start . 188) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 196) (:start . 194)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 200) (:start . 197)\n  (:id . 77))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 207)\n  (:start . 201) (:id . 78))\n ((:tag . "NN") (:stem . "threshold") (:form . "threshold") (:end . 217)\n  (:start . 208) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 218) (:start . 217)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s14.90) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504592@unknown@formal@none@1@S@The FDR thus represents the percentage of identified peptides in the forward search that would also be detected in the reverse database search.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fdr") (:form . "FDR") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 38)\n  (:start . 28) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 52)\n  (:start . 42) (:id . 49))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "forward") (:form . "forward") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 83)\n  (:start . 77) (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 94) (:start . 89)\n  (:id . 56))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 99) (:start . 95)\n  (:id . 57))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 102) (:start . 100)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 111)\n  (:start . 103) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "reverse") (:form . "reverse") (:end . 126)\n  (:start . 119) (:id . 62))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 135)\n  (:start . 127) (:id . 63))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 142)\n  (:start . 136) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s14.91) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504593@unknown@formal@none@1@S@multiplierz identifies score thresholds for commonly used FDR (1%, 2%, and 5%) as well as calculates the FDR for each forward peptide score via an .mz Script (see below; scripts for generating a reverse database and calculating the FDR are included in Additional File 2).@(((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "identify") (:form . "identifies") (:end . 22)\n  (:start . 12) (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 28) (:start . 23)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "threshold") (:form . "thresholds") (:end . 39)\n  (:start . 29) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 46))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 52)\n  (:start . 44) (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 57) (:start . 53)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "FDR") (:form . "FDR") (:end . 61) (:start . 58)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 50))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 64) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 69) (:start . 68)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 57))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 76) (:start . 75)\n  (:id . 58))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 77) (:start . 76)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 78) (:start . 77)\n  (:id . 60))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 61))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 86) (:start . 82)\n  (:id . 62))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 89) (:start . 87)\n  (:id . 63))\n ((:tag . "VBZ") (:stem . "calculate") (:form . "calculates") (:end . 100)\n  (:start . 90) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 65))\n ((:tag . "NN") (:stem . "fdr") (:form . "FDR") (:end . 108) (:start . 105)\n  (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 112) (:start . 109)\n  (:id . 67))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 117) (:start . 113)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "forward") (:form . "forward") (:end . 125)\n  (:start . 118) (:id . 69))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 133)\n  (:start . 126) (:id . 70))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 139)\n  (:start . 134) (:id . 71))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 143) (:start . 140)\n  (:id . 72))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 146) (:start . 144)\n  (:id . 73))\n ((:tag . "NN") (:stem . ".mz") (:form . ".mz") (:end . 150) (:start . 147)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Script") (:form . "Script") (:end . 157)\n  (:start . 151) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 159) (:start . 158)\n  (:id . 76))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 162) (:start . 159)\n  (:id . 77))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 168)\n  (:start . 163) (:id . 78))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 169) (:start . 168)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "script") (:form . "scripts") (:end . 177)\n  (:start . 170) (:id . 80))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 181) (:start . 178)\n  (:id . 81))\n ((:tag . "VBG") (:stem . "generate") (:form . "generating") (:end . 192)\n  (:start . 182) (:id . 82))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 194) (:start . 193)\n  (:id . 83))\n ((:tag . "NN") (:stem . "reverse") (:form . "reverse") (:end . 202)\n  (:start . 195) (:id . 84))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 211)\n  (:start . 203) (:id . 85))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 215) (:start . 212)\n  (:id . 86))\n ((:tag . "VBG") (:stem . "calculate") (:form . "calculating") (:end . 227)\n  (:start . 216) (:id . 87))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 231) (:start . 228)\n  (:id . 88))\n ((:tag . "NNP") (:stem . "FDR") (:form . "FDR") (:end . 235) (:start . 232)\n  (:id . 89))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 239) (:start . 236)\n  (:id . 90))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 248)\n  (:start . 240) (:id . 91))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 251) (:start . 249)\n  (:id . 92))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 262)\n  (:start . 252) (:id . 93))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 267) (:start . 263)\n  (:id . 94))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 269) (:start . 268)\n  (:id . 95))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 270) (:start . 269)\n  (:id . 96))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 271) (:start . 270)\n  (:id . 97)))@@@1@56@((:identifiers (:sid . :s14.92) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504594@unknown@formal@none@1@S@Correlation of identified peptide sequences with specific features in the source mass spectrometry data, such as chromatographic peak width or maximum precursor intensity, is often complicated by the requirement for users to move between disparate programs and interfaces.@(((:tag . "NN") (:stem . "correlation") (:form . "Correlation") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 33)\n  (:start . 26) (:id . 45))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 43)\n  (:start . 34) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 48) (:start . 44)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 57)\n  (:start . 49) (:id . 48))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 66)\n  (:start . 58) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 69) (:start . 67)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 51))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 80)\n  (:start . 74) (:id . 52))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 85) (:start . 81)\n  (:id . 53))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 98)\n  (:start . 86) (:id . 54))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 103) (:start . 99)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 109) (:start . 105)\n  (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 112) (:start . 110)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "chromatographic") (:form . "chromatographic")\n  (:end . 128) (:start . 113) (:id . 59))\n ((:tag . "JJ") (:stem . "peak") (:form . "peak") (:end . 133) (:start . 129)\n  (:id . 60))\n ((:tag . "NN") (:stem . "width") (:form . "width") (:end . 139)\n  (:start . 134) (:id . 61))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 142) (:start . 140)\n  (:id . 62))\n ((:tag . "NN") (:stem . "maximum") (:form . "maximum") (:end . 150)\n  (:start . 143) (:id . 63))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 160)\n  (:start . 151) (:id . 64))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 170)\n  (:start . 161) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 174) (:start . 172)\n  (:id . 67))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 180)\n  (:start . 175) (:id . 68))\n ((:tag . "VBN") (:stem . "complicate") (:form . "complicated") (:end . 192)\n  (:start . 181) (:id . 69))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 195) (:start . 193)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 199) (:start . 196)\n  (:id . 71))\n ((:tag . "NN") (:stem . "requirement") (:form . "requirement") (:end . 211)\n  (:start . 200) (:id . 72))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 215) (:start . 212)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 221)\n  (:start . 216) (:id . 74))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 224) (:start . 222)\n  (:id . 75))\n ((:tag . "VB") (:stem . "move") (:form . "move") (:end . 229) (:start . 225)\n  (:id . 76))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 237)\n  (:start . 230) (:id . 77))\n ((:tag . "JJ") (:stem . "disparate") (:form . "disparate") (:end . 247)\n  (:start . 238) (:id . 78))\n ((:tag . "NNS") (:stem . "program") (:form . "programs") (:end . 256)\n  (:start . 248) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 260) (:start . 257)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "interface") (:form . "interfaces") (:end . 271)\n  (:start . 261) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 272) (:start . 271)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s14.93) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504595@unknown@formal@none@1@S@The multiplierz desktop environment provides users with a centralized point of interaction with both search results and the underlying mass spectrometry files.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "desktop") (:form . "desktop") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 35)\n  (:start . 24) (:id . 45))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 44)\n  (:start . 36) (:id . 46))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 50) (:start . 45)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 55) (:start . 51)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "centralized") (:form . "centralized") (:end . 69)\n  (:start . 58) (:id . 50))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 75) (:start . 70)\n  (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 78) (:start . 76)\n  (:id . 52))\n ((:tag . "NN") (:stem . "interaction") (:form . "interaction") (:end . 90)\n  (:start . 79) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 95) (:start . 91)\n  (:id . 54))\n ((:tag . "DT") (:stem . "both") (:form . "both") (:end . 100) (:start . 96)\n  (:id . 55))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 107)\n  (:start . 101) (:id . 56))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 115)\n  (:start . 108) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 123) (:start . 120)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 134)\n  (:start . 124) (:id . 60))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 139) (:start . 135)\n  (:id . 61))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 152)\n  (:start . 140) (:id . 62))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 158)\n  (:start . 153) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s14.94) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504596@unknown@formal@none@1@S@For example, high-confidence peptide identifications may be used for direct generation of RICs across user-defined time and mass-to-charge ranges.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "high-confidence") (:form . "high-confidence")\n  (:end . 28) (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "NNS") (:stem . "identification") (:form . "identifications")\n  (:end . 52) (:start . 37) (:id . 47))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 56) (:start . 53)\n  (:id . 48))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 59) (:start . 57)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 64) (:start . 60)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 75)\n  (:start . 69) (:id . 52))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 86)\n  (:start . 76) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "ric") (:form . "RICs") (:end . 94) (:start . 90)\n  (:id . 55))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 101)\n  (:start . 95) (:id . 56))\n ((:tag . "JJ") (:stem . "user-defined") (:form . "user-defined") (:end . 114)\n  (:start . 102) (:id . 57))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 119) (:start . 115)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 123) (:start . 120)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "mass-to-charge") (:form . "mass-to-charge")\n  (:end . 138) (:start . 124) (:id . 60))\n ((:tag . "NNS") (:stem . "range") (:form . "ranges") (:end . 145)\n  (:start . 139) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 62)))@@@1@21@((:hcues ((:id . :x14.95.1) (:span 53 56)))\n (:hscopes ((:id . :x14.95.1) (:span 13 145)))\n (:identifiers (:sid . :s14.95) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504597@unknown@formal@none@1@S@Various metrics such as full peak width at half maximum (FWHM), peak area, and apex precursor intensity for peptide elution profiles are included in the output report.@(((:tag . "JJ") (:stem . "various") (:form . "Various") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "metric") (:form . "metrics") (:end . 15)\n  (:start . 8) (:id . 43))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 20) (:start . 16)\n  (:id . 44))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "peak") (:form . "peak") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "width") (:form . "width") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 42) (:start . 40)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "half") (:form . "half") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "maximum") (:form . "maximum") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "FWHM") (:form . "FWHM") (:end . 61) (:start . 57)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "peak") (:form . "peak") (:end . 68) (:start . 64)\n  (:id . 56))\n ((:tag . "NN") (:stem . "area") (:form . "area") (:end . 73) (:start . 69)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 59))\n ((:tag . "NN") (:stem . "apex") (:form . "apex") (:end . 83) (:start . 79)\n  (:id . 60))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 93)\n  (:start . 84) (:id . 61))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 103)\n  (:start . 94) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 107) (:start . 104)\n  (:id . 63))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 115)\n  (:start . 108) (:id . 64))\n ((:tag . "NN") (:stem . "elution") (:form . "elution") (:end . 123)\n  (:start . 116) (:id . 65))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 132)\n  (:start . 124) (:id . 66))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 136) (:start . 133)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 145)\n  (:start . 137) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 70))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 159)\n  (:start . 153) (:id . 71))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 166)\n  (:start . 160) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s14.96) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504598@unknown@formal@none@1@S@As described below these data are combined, annotated, and made available in portable, user-friendly reports.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "make") (:form . "made") (:end . 63) (:start . 59)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 73)\n  (:start . 64) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "portable") (:form . "portable") (:end . 85)\n  (:start . 77) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "user-friendly") (:form . "user-friendly")\n  (:end . 100) (:start . 87) (:id . 58))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 108)\n  (:start . 101) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s14.97) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504599@unknown@formal@none@1@S@Consistent with our underlying motivation to combine open-source and commercial software where appropriate, we opted to export multiplierz results into Microsoft Excel.@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 30)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "motivation") (:form . "motivation") (:end . 41)\n  (:start . 31) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 47))\n ((:tag . "VB") (:stem . "combine") (:form . "combine") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "JJ") (:stem . "open-source") (:form . "open-source") (:end . 64)\n  (:start . 53) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "commercial") (:form . "commercial") (:end . 79)\n  (:start . 69) (:id . 51))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 88)\n  (:start . 80) (:id . 52))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 94) (:start . 89)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 106)\n  (:start . 95) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 110) (:start . 108)\n  (:id . 56))\n ((:tag . "VBD") (:stem . "opte") (:form . "opted") (:end . 116)\n  (:start . 111) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 119) (:start . 117)\n  (:id . 58))\n ((:tag . "VB") (:stem . "export") (:form . "export") (:end . 126)\n  (:start . 120) (:id . 59))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 138)\n  (:start . 127) (:id . 60))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 146)\n  (:start . 139) (:id . 61))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 151) (:start . 147)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Microsoft") (:form . "Microsoft") (:end . 161)\n  (:start . 152) (:id . 63))\n ((:tag . "NNP") (:stem . "Excel") (:form . "Excel") (:end . 167)\n  (:start . 162) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s14.98) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504600@unknown@formal@none@1@S@We take advantage of Excel's ability to store images in the worksheet (as comments), thereby creating an information-rich, yet portable, report that may be readily formatted to meet specific scientific journal data submission requirements [19].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "take") (:form . "take") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "advantage") (:form . "advantage") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Excel") (:form . "Excel") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "VB") (:stem . "store") (:form . "store") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 52)\n  (:start . 46) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "NN") (:stem . "worksheet") (:form . "worksheet") (:end . 69)\n  (:start . 60) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 73) (:start . 71)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "comment") (:form . "comments") (:end . 82)\n  (:start . 74) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 59))\n ((:tag . "RB") (:stem . "thereby") (:form . "thereby") (:end . 92)\n  (:start . 85) (:id . 60))\n ((:tag . "VBG") (:stem . "create") (:form . "creating") (:end . 101)\n  (:start . 93) (:id . 61))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 104) (:start . 102)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "information-rich") (:form . "information-rich")\n  (:end . 121) (:start . 105) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 64))\n ((:tag . "RB") (:stem . "yet") (:form . "yet") (:end . 126) (:start . 123)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "portable") (:form . "portable") (:end . 135)\n  (:start . 127) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 67))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 143)\n  (:start . 137) (:id . 68))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 148) (:start . 144)\n  (:id . 69))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 152) (:start . 149)\n  (:id . 70))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 155) (:start . 153)\n  (:id . 71))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 163)\n  (:start . 156) (:id . 72))\n ((:tag . "VBN") (:stem . "format") (:form . "formatted") (:end . 173)\n  (:start . 164) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 176) (:start . 174)\n  (:id . 74))\n ((:tag . "VB") (:stem . "meet") (:form . "meet") (:end . 181) (:start . 177)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 190)\n  (:start . 182) (:id . 76))\n ((:tag . "JJ") (:stem . "scientific") (:form . "scientific") (:end . 201)\n  (:start . 191) (:id . 77))\n ((:tag . "NN") (:stem . "journal") (:form . "journal") (:end . 209)\n  (:start . 202) (:id . 78))\n ((:tag . "NN") (:stem . "data") (:form . "data") (:end . 214) (:start . 210)\n  (:id . 79))\n ((:tag . "NN") (:stem . "submission") (:form . "submission") (:end . 225)\n  (:start . 215) (:id . 80))\n ((:tag . "NNS") (:stem . "requirement") (:form . "requirements") (:end . 238)\n  (:start . 226) (:id . 81))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 240) (:start . 239)\n  (:id . 82))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 242) (:start . 240)\n  (:id . 83))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 243) (:start . 242)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x14.99.1) (:span 149 152)))\n (:hscopes ((:id . :x14.99.1) (:span 149 238)))\n (:identifiers (:sid . :s14.99) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504601@unknown@formal@none@1@S@Moreover, we note that the tendency towards analysis of increasingly complex mixtures along with continued efforts in relative protein quantification have placed increased emphasis on data reproducibility in proteomics experiments.@(((:tag . "RB") (:stem . "moreover") (:form . "Moreover") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "note") (:form . "note") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "tendency") (:form . "tendency") (:end . 35)\n  (:start . 27) (:id . 48))\n ((:tag . "IN") (:stem . "towards") (:form . "towards") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 52)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 51))\n ((:tag . "RB") (:stem . "increasingly") (:form . "increasingly") (:end . 68)\n  (:start . 56) (:id . 52))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "NNS") (:stem . "mixture") (:form . "mixtures") (:end . 85)\n  (:start . 77) (:id . 54))\n ((:tag . "IN") (:stem . "along") (:form . "along") (:end . 91) (:start . 86)\n  (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 96) (:start . 92)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "continue") (:form . "continued") (:end . 106)\n  (:start . 97) (:id . 57))\n ((:tag . "NNS") (:stem . "effort") (:form . "efforts") (:end . 114)\n  (:start . 107) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 126)\n  (:start . 118) (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 134)\n  (:start . 127) (:id . 61))\n ((:tag . "NN") (:stem . "quantification") (:form . "quantification")\n  (:end . 149) (:start . 135) (:id . 62))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 154) (:start . 150)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "place") (:form . "placed") (:end . 161)\n  (:start . 155) (:id . 64))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 171)\n  (:start . 162) (:id . 65))\n ((:tag . "NN") (:stem . "emphasis") (:form . "emphasis") (:end . 180)\n  (:start . 172) (:id . 66))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 183) (:start . 181)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 188)\n  (:start . 184) (:id . 68))\n ((:tag . "NN") (:stem . "reproducibility") (:form . "reproducibility")\n  (:end . 204) (:start . 189) (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 207) (:start . 205)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 218)\n  (:start . 208) (:id . 71))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 230)\n  (:start . 219) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 231) (:start . 230)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s14.100) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504602@unknown@formal@none@1@S@Hence it has become common practice to derive a "proteomics result" from comparison, or other manipulation, of multiple mass spectrometry acquisitions.@(((:tag . "RB") (:stem . "hence") (:form . "Hence") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "become") (:form . "become") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "practice") (:form . "practice") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "VB") (:stem . "derive") (:form . "derive") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 59)\n  (:start . 49) (:id . 52))\n ((:tag . "NN") (:stem . "result") (:form . "result") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 72) (:start . 68)\n  (:id . 55))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 83)\n  (:start . 73) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 93) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "manipulation") (:form . "manipulation") (:end . 106)\n  (:start . 94) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 119)\n  (:start . 111) (:id . 63))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 124) (:start . 120)\n  (:id . 64))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 137)\n  (:start . 125) (:id . 65))\n ((:tag . "NNS") (:stem . "acquisition") (:form . "acquisitions") (:end . 150)\n  (:start . 138) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s14.101) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504603@unknown@formal@none@1@S@In support of this experimental paradigm, multiplierz includes "multi-detect" and "multi-filter" tools that provide users tremendous flexibility in filtering and collating (e.g., by common or unique proteins, peptides, post-translational modifications, charge state, etc.) each data file obtained from a multiple acquisition study.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 31)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "paradigm") (:form . "paradigm") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . 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"(") (:end . 173) (:start . 172)\n  (:id . 68))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 177) (:start . 173)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 178) (:start . 177)\n  (:id . 70))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 181) (:start . 179)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 188)\n  (:start . 182) (:id . 72))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 191) (:start . 189)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 198)\n  (:start . 192) (:id . 74))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 207)\n  (:start . 199) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 208) (:start . 207)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 217)\n  (:start . 209) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 218) (:start . 217)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "post-translational") (:form . "post-translational")\n  (:end . 237) (:start . 219) (:id . 79))\n ((:tag . "NNS") (:stem . "modification") (:form . "modifications")\n  (:end . 251) (:start . 238) (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 252) (:start . 251)\n  (:id . 81))\n ((:tag . "NN") (:stem . "charge") (:form . "charge") (:end . 259)\n  (:start . 253) (:id . 82))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 265)\n  (:start . 260) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 266) (:start . 265)\n  (:id . 84))\n ((:tag . "FW") (:stem . "etc.") (:form . "etc.") (:end . 271) (:start . 267)\n  (:id . 85))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 272) (:start . 271)\n  (:id . 86))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 277) (:start . 273)\n  (:id . 87))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 282)\n  (:start . 278) (:id . 88))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 287) (:start . 283)\n  (:id . 89))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 296)\n  (:start . 288) (:id . 90))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 301) (:start . 297)\n  (:id . 91))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 303) (:start . 302)\n  (:id . 92))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 312)\n  (:start . 304) (:id . 93))\n ((:tag . "NN") (:stem . "acquisition") (:form . "acquisition") (:end . 324)\n  (:start . 313) (:id . 94))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 330)\n  (:start . 325) (:id . 95))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 331) (:start . 330)\n  (:id . 96)))@@@1@55@((:identifiers (:sid . :s14.102) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504604@unknown@formal@none@1@S@This feature provides database-like functionality without the need to install and maintain dedicated database servers.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 12)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "JJ") (:stem . "database-like") (:form . "database-like")\n  (:end . 35) (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 49) (:start . 36) (:id . 46))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 57)\n  (:start . 50) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 48))\n ((:tag . "NN") (:stem . "need") (:form . "need") (:end . 66) (:start . 62)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 69) (:start . 67)\n  (:id . 50))\n ((:tag . "VB") (:stem . "install") (:form . "install") (:end . 77)\n  (:start . 70) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 52))\n ((:tag . "VB") (:stem . "maintain") (:form . "maintain") (:end . 90)\n  (:start . 82) (:id . 53))\n ((:tag . "VBN") (:stem . "dedicate") (:form . "dedicated") (:end . 100)\n  (:start . 91) (:id . 54))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 109)\n  (:start . 101) (:id . 55))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 117)\n  (:start . 110) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s14.103) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504605@unknown@formal@none@1@S@Importantly, all multiplierz functions provide spreadsheet-based output with optional embedded images (see Figure 2 and discussion below).@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 28)\n  (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 38)\n  (:start . 29) (:id . 46))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 46)\n  (:start . 39) (:id . 47))\n ((:tag . "JJ") (:stem . "spreadsheet-based") (:form . "spreadsheet-based")\n  (:end . 64) (:start . 47) (:id . 48))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 71)\n  (:start . 65) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 76) (:start . 72)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "optional") (:form . "optional") (:end . 85)\n  (:start . 77) (:id . 51))\n ((:tag . "JJ") (:stem . "embedded") (:form . "embedded") (:end . 94)\n  (:start . 86) (:id . 52))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 101)\n  (:start . 95) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 54))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 106) (:start . 103)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 113)\n  (:start . 107) (:id . 56))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 115) (:start . 114)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n  (:id . 58))\n ((:tag . "NN") (:stem . "discussion") (:form . "discussion") (:end . 130)\n  (:start . 120) (:id . 59))\n ((:tag . "IN") (:stem . "below") (:form . "below") (:end . 136)\n  (:start . 131) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 138) (:start . 137)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s14.104) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504606@unknown@formal@none@1@S@Integration of Commercial Tools for multiplierz Reports.@(((:tag . "NN") (:stem . "integration") (:form . "Integration") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "commercial") (:form . "Commercial") (:end . 25)\n  (:start . 15) (:id . 44))\n ((:tag . "NNS") (:stem . "tool") (:form . "Tools") (:end . 31) (:start . 26)\n  (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 47)\n  (:start . 36) (:id . 47))\n ((:tag . "NNS") (:stem . "report") (:form . "Reports") (:end . 55)\n  (:start . 48) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 56) (:start . 55)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s14.105) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504607@unknown@formal@none@1@S@A spreadsheet-based report from multiplierz analysis of 11 LC-MS analyses, designed to interrogate performance of LC column geometry and flow rate (see also Figure 5 and Additional File 5).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "spreadsheet-based") (:form . "spreadsheet-based")\n  (:end . 19) (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 26)\n  (:start . 20) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 31) (:start . 27)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 43)\n  (:start . 32) (:id . 46))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 52)\n  (:start . 44) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 48))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 58) (:start . 56)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "LC-MS") (:form . "LC-MS") (:end . 64) (:start . 59)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 73)\n  (:start . 65) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 83)\n  (:start . 75) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 86) (:start . 84)\n  (:id . 54))\n ((:tag . "VB") (:stem . "interrogate") (:form . "interrogate") (:end . 98)\n  (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 110)\n  (:start . 99) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 113) (:start . 111)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "LC") (:form . "LC") (:end . 116) (:start . 114)\n  (:id . 58))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 123)\n  (:start . 117) (:id . 59))\n ((:tag . "NN") (:stem . "geometry") (:form . "geometry") (:end . 132)\n  (:start . 124) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 136) (:start . 133)\n  (:id . 61))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 141) (:start . 137)\n  (:id . 62))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 146) (:start . 142)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 148) (:start . 147)\n  (:id . 64))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 151) (:start . 148)\n  (:id . 65))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 156) (:start . 152)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 163)\n  (:start . 157) (:id . 67))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 165) (:start . 164)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 169) (:start . 166)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 180)\n  (:start . 170) (:id . 70))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 185) (:start . 181)\n  (:id . 71))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 187) (:start . 186)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 188) (:start . 187)\n  (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s14.106) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504608@unknown@formal@none@1@S@For clarity the spreadsheet shows peptide entries and characterization data from the two extremes in column size and flow rate.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "clarity") (:form . "clarity") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "spreadsheet") (:form . "spreadsheet") (:end . 27)\n  (:start . 16) (:id . 45))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "NNS") (:stem . "entry") (:form . "entries") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "characterization") (:form . "characterization")\n  (:end . 70) (:start . 54) (:id . 50))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 75) (:start . 71)\n  (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 80) (:start . 76)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 53))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 88) (:start . 85)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "extreme") (:form . "extremes") (:end . 97)\n  (:start . 89) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 107)\n  (:start . 101) (:id . 57))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 112) (:start . 108)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 59))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 121) (:start . 117)\n  (:id . 60))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 126) (:start . 122)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s14.107) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504609@unknown@formal@none@1@S@Informative images are embedded within spreadsheet cell comments and are accessed by mouse-over, thus facilitating rapid visual inspection.@(((:tag . "JJ") (:stem . "informative") (:form . "Informative") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 18)\n  (:start . 12) (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "embedded") (:form . "embedded") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 38)\n  (:start . 32) (:id . 46))\n ((:tag . "NN") (:stem . "spreadsheet") (:form . "spreadsheet") (:end . 50)\n  (:start . 39) (:id . 47))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 55) (:start . 51)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "comment") (:form . "comments") (:end . 64)\n  (:start . 56) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 68) (:start . 65)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "access") (:form . "accessed") (:end . 81)\n  (:start . 73) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 84) (:start . 82)\n  (:id . 53))\n ((:tag . "NN") (:stem . "mouse-over") (:form . "mouse-over") (:end . 95)\n  (:start . 85) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 55))\n ((:tag . "RB") (:stem . "thus") (:form . "thus") (:end . 101) (:start . 97)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "facilitate") (:form . "facilitating") (:end . 114)\n  (:start . 102) (:id . 57))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 120)\n  (:start . 115) (:id . 58))\n ((:tag . "JJ") (:stem . "visual") (:form . "visual") (:end . 127)\n  (:start . 121) (:id . 59))\n ((:tag . "NN") (:stem . "inspection") (:form . "inspection") (:end . 138)\n  (:start . 128) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s14.108) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504610@unknown@formal@none@1@S@Optional embedded images include: 1.)@(((:tag . "JJ") (:stem . "optional") (:form . "Optional") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "VBN") (:stem . "embed") (:form . "embedded") (:end . 17)\n  (:start . 9) (:id . 43))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 24)\n  (:start . 18) (:id . 44))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 32)\n  (:start . 25) (:id . 45))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 33) (:start . 32)\n  (:id . 46))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 37) (:start . 36)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s14.109) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504611@unknown@formal@none@1@S@MS/MS spectra that are annotated with b- and y-type fragment ion labels, peptide sequence, search engine score (in this case Mascot peptide score), and precursor charge state.@(((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "spectrum") (:form . "spectra") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 37) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "b-") (:form . "b-") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "y-type") (:form . "y-type") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 60)\n  (:start . 52) (:id . 51))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 64) (:start . 61)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "label") (:form . "labels") (:end . 71)\n  (:start . 65) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 80)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 97)\n  (:start . 91) (:id . 58))\n ((:tag . "NN") (:stem . "engine") (:form . "engine") (:end . 104)\n  (:start . 98) (:id . 59))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 110)\n  (:start . 105) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 114) (:start . 112)\n  (:id . 62))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 119) (:start . 115)\n  (:id . 63))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 124) (:start . 120)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 131)\n  (:start . 125) (:id . 65))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 139)\n  (:start . 132) (:id . 66))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 145)\n  (:start . 140) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 146) (:start . 145)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 151) (:start . 148)\n  (:id . 70))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 161)\n  (:start . 152) (:id . 71))\n ((:tag . "NN") (:stem . "charge") (:form . "charge") (:end . 168)\n  (:start . 162) (:id . 72))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 174)\n  (:start . 169) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s14.110) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504612@unknown@formal@none@1@S@A color scheme highlights modified amino acids (in this case oxidized methionine) and those residues inferred from b- and y-type fragment ion assignments (horizontal lines, red and blue denote singly- and doubly-charged ions, respectively). 2.)@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "color") (:form . "color") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "highlight") (:form . "highlights") (:end . 25)\n  (:start . 15) (:id . 45))\n ((:tag . "VBD") (:stem . "modify") (:form . "modified") (:end . 34)\n  (:start . 26) (:id . 46))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 40) (:start . 35)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 46) (:start . 41)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "oxidize") (:form . "oxidized") (:end . 69)\n  (:start . 61) (:id . 53))\n ((:tag . "NN") (:stem . "methionine") (:form . "methionine") (:end . 80)\n  (:start . 70) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 91) (:start . 86)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 100)\n  (:start . 92) (:id . 58))\n ((:tag . "VBN") (:stem . "infer") (:form . "inferred") (:end . 109)\n  (:start . 101) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 114) (:start . 110)\n  (:id . 60))\n ((:tag . "NN") (:stem . "b-") (:form . "b-") (:end . 117) (:start . 115)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "y-type") (:form . "y-type") (:end . 128)\n  (:start . 122) (:id . 63))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 137)\n  (:start . 129) (:id . 64))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 141) (:start . 138)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 153)\n  (:start . 142) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 155) (:start . 154)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "horizontal") (:form . "horizontal") (:end . 165)\n  (:start . 155) (:id . 68))\n ((:tag . "NNS") (:stem . "line") (:form . "lines") (:end . 171)\n  (:start . 166) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 176) (:start . 173)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 180) (:start . 177)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 185) (:start . 181)\n  (:id . 73))\n ((:tag . "NN") (:stem . "denote") (:form . "denote") (:end . 192)\n  (:start . 186) (:id . 74))\n ((:tag . "NN") (:stem . "singly-") (:form . "singly-") (:end . 200)\n  (:start . 193) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 204) (:start . 201)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "doubly-charged") (:form . "doubly-charged")\n  (:end . 219) (:start . 205) (:id . 77))\n ((:tag . "NNS") (:stem . "ion") (:form . "ions") (:end . 224) (:start . 220)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 225) (:start . 224)\n  (:id . 79))\n ((:tag . "CC") (:stem . "respectively).") (:form . "respectively).")\n  (:end . 240) (:start . 226) (:id . 80))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 242) (:start . 241)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 243) (:start . 242)\n  (:id . 82))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 244) (:start . 243)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s14.111) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504613@unknown@formal@none@1@S@RIC images in which MS scans are annotated with green squares, while yellow circles and blue triangles denote MS/MS scans for the precursor of interest, with the latter indicating the specific MS2 event described in the selected row of the spreadsheet. 3.) precursor region of the MS spectrum (not shown).@(((:tag . "NNP") (:stem . "RIC") (:form . "RIC") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "MS") (:form . "MS") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 32) (:start . 29)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 42)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "square") (:form . "squares") (:end . 61)\n  (:start . 54) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 68) (:start . 63)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . "NNS") (:stem . "circle") (:form . "circles") (:end . 83)\n  (:start . 76) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 92) (:start . 88)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "triangle") (:form . 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5504614@unknown@formal@none@1@S@The highly embedded, spreadsheet-based multiplierz reports provide a very flexible and user-friendly mechanism to query various metrics of the underlying native mass spectrometry data and quickly collate search results based on user-defined filter criteria.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "highly") (:form . "highly") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "embedded") (:form . "embedded") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "spreadsheet-based") (:form . "spreadsheet-based")\n  (:end . 38) (:start . 21) (:id . 46))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 50)\n  (:start . 39) (:id . 47))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 58)\n  (:start . 51) (:id . 48))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 66)\n  (:start . 59) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 68) (:start . 67)\n  (:id . 50))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 73) (:start . 69)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "flexible") (:form . "flexible") (:end . 82)\n  (:start . 74) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "user-friendly") (:form . "user-friendly")\n  (:end . 100) (:start . 87) (:id . 54))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 110)\n  (:start . 101) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 113) (:start . 111)\n  (:id . 56))\n ((:tag . "VB") (:stem . "query") (:form . "query") (:end . 119)\n  (:start . 114) (:id . 57))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 127)\n  (:start . 120) (:id . 58))\n ((:tag . "NNS") (:stem . "metric") (:form . "metrics") (:end . 135)\n  (:start . 128) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 153)\n  (:start . 143) (:id . 62))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 160)\n  (:start . 154) (:id . 63))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 165) (:start . 161)\n  (:id . 64))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 178)\n  (:start . 166) (:id . 65))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 183)\n  (:start . 179) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 187) (:start . 184)\n  (:id . 67))\n ((:tag . "RB") (:stem . "quickly") (:form . "quickly") (:end . 195)\n  (:start . 188) (:id . 68))\n ((:tag . "VBP") (:stem . "collate") (:form . "collate") (:end . 203)\n  (:start . 196) (:id . 69))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 210)\n  (:start . 204) (:id . 70))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 218)\n  (:start . 211) (:id . 71))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 224)\n  (:start . 219) (:id . 72))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 227) (:start . 225)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "user-defined") (:form . "user-defined") (:end . 240)\n  (:start . 228) (:id . 74))\n ((:tag . "NN") (:stem . "filter") (:form . "filter") (:end . 247)\n  (:start . 241) (:id . 75))\n ((:tag . "NNS") (:stem . "criterion") (:form . "criteria") (:end . 256)\n  (:start . 248) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 257) (:start . 256)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s14.113) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504615@unknown@formal@none@1@S@However, it is often the case that researchers must go beyond these general characterizations and focus on a small subset of their proteomics data in support of targeted biological questions.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 20) (:start . 15)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 29) (:start . 25)\n  (:id . 48))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "researcher") (:form . "researchers") (:end . 46)\n  (:start . 35) (:id . 50))\n ((:tag . "MD") (:stem . "must") (:form . "must") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "VB") (:stem . "go") (:form . "go") (:end . 54) (:start . 52)\n  (:id . 52))\n ((:tag . "IN") (:stem . "beyond") (:form . "beyond") (:end . 61)\n  (:start . 55) (:id . 53))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 67) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 75)\n  (:start . 68) (:id . 55))\n ((:tag . "NNS") (:stem . "characterization") (:form . "characterizations")\n  (:end . 93) (:start . 76) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 57))\n ((:tag . "VB") (:stem . "focus") (:form . "focus") (:end . 103) (:start . 98)\n  (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 114)\n  (:start . 109) (:id . 61))\n ((:tag . "NN") (:stem . "subset") (:form . "subset") (:end . 121)\n  (:start . 115) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 130)\n  (:start . 125) (:id . 64))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 141)\n  (:start . 131) (:id . 65))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 146)\n  (:start . 142) (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 149) (:start . 147)\n  (:id . 67))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 157)\n  (:start . 150) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 160) (:start . 158)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "target") (:form . "targeted") (:end . 169)\n  (:start . 161) (:id . 70))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 180)\n  (:start . 170) (:id . 71))\n ((:tag . "NNS") (:stem . "question") (:form . "questions") (:end . 190)\n  (:start . 181) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s14.114) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504616@unknown@formal@none@1@S@To enable this mode of data analysis, multiplierz includes a Peak Viewer tool (Figure 3) that provides dynamic and interactive plots for precursor RICs, and corresponding MS and MS/MS scans.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "enable") (:form . "enable") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "mode") (:form . "mode") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 36)\n  (:start . 28) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 49)\n  (:start . 38) (:id . 50))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 58)\n  (:start . 50) (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 60) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Peak") (:form . "Peak") (:end . 65) (:start . 61)\n  (:id . 53))\n ((:tag . "JJR") (:stem . "view") (:form . "Viewer") (:end . 72) (:start . 66)\n  (:id . 54))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 77) (:start . 73)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 85)\n  (:start . 79) (:id . 57))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 59))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 93) (:start . 89)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 102)\n  (:start . 94) (:id . 61))\n ((:tag . "JJ") (:stem . "dynamic") (:form . "dynamic") (:end . 110)\n  (:start . 103) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 114) (:start . 111)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "interactive") (:form . "interactive") (:end . 126)\n  (:start . 115) (:id . 64))\n ((:tag . "NNS") (:stem . "plot") (:form . "plots") (:end . 132)\n  (:start . 127) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 136) (:start . 133)\n  (:id . 66))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 146)\n  (:start . 137) (:id . 67))\n ((:tag . "NNS") (:stem . "ric") (:form . "RICs") (:end . 151) (:start . 147)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 70))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 170)\n  (:start . 157) (:id . 71))\n ((:tag . "NN") (:stem . "ms") (:form . "MS") (:end . 173) (:start . 171)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 177) (:start . 174)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 183)\n  (:start . 178) (:id . 74))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 189)\n  (:start . 184) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s14.115) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504617@unknown@formal@none@1@S@Additionally, users can edit and export publication quality images through a built-in Scrapbook tool (Figure 4).@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "VB") (:stem . "edit") (:form . "edit") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "VB") (:stem . "export") (:form . "export") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "publication") (:form . "publication") (:end . 51)\n  (:start . 40) (:id . 49))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 66)\n  (:start . 60) (:id . 51))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 74)\n  (:start . 67) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "built-in") (:form . "built-in") (:end . 85)\n  (:start . 77) (:id . 54))\n ((:tag . "NNP") (:stem . "Scrapbook") (:form . "Scrapbook") (:end . 95)\n  (:start . 86) (:id . 55))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 100) (:start . 96)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 108)\n  (:start . 102) (:id . 58))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 110) (:start . 109)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 112) (:start . 111)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s14.116) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504618@unknown@formal@none@1@S@Features of the Peak Viewer include (i) visualization of theoretical fragments superimposed on MS/MS spectra, (ii) automatic zoom-in display for iTRAQ and theoretical ions for rapid manual validation, and (iii) comparison of scans and RICs via mirror and overlay functions.@(((:tag . "NNPS") (:stem . "Feature") (:form . "Features") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Peak") (:form . "Peak") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Viewer") (:form . "Viewer") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "VBP") (:stem . "include") (:form . "include") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "LS") (:stem . "i") (:form . 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"NN") (:stem . "comparison") (:form . "comparison") (:end . 221)\n  (:start . 211) (:id . 80))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 224) (:start . 222)\n  (:id . 81))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 230)\n  (:start . 225) (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 234) (:start . 231)\n  (:id . 83))\n ((:tag . "NNS") (:stem . "ric") (:form . "RICs") (:end . 239) (:start . 235)\n  (:id . 84))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 243) (:start . 240)\n  (:id . 85))\n ((:tag . "NN") (:stem . "mirror") (:form . "mirror") (:end . 250)\n  (:start . 244) (:id . 86))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 254) (:start . 251)\n  (:id . 87))\n ((:tag . "NN") (:stem . "overlay") (:form . "overlay") (:end . 262)\n  (:start . 255) (:id . 88))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 272)\n  (:start . 263) (:id . 89))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 273) (:start . 272)\n  (:id . 90)))@@@1@49@((:identifiers (:sid . :s14.117) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504619@unknown@formal@none@1@S@For added convenience the Peak Viewer opens multiplierz spreadsheets and users can generate plots by a simple double-click on specific rows or peptide entries.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "add") (:form . "added") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "convenience") (:form . "convenience") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Peak") (:form . "Peak") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Viewer") (:form . "Viewer") (:end . 37)\n  (:start . 31) (:id . 47))\n ((:tag . "VBZ") (:stem . "open") (:form . "opens") (:end . 43) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 55)\n  (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "spreadsheet") (:form . "spreadsheets") (:end . 68)\n  (:start . 56) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 72) (:start . 69)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 78) (:start . 73)\n  (:id . 52))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 82) (:start . 79)\n  (:id . 53))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 91)\n  (:start . 83) (:id . 54))\n ((:tag . "NNS") (:stem . "plot") (:form . "plots") (:end . 97) (:start . 92)\n  (:id . 55))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 102) (:start . 101)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "simple") (:form . "simple") (:end . 109)\n  (:start . 103) (:id . 58))\n ((:tag . "NN") (:stem . "double-click") (:form . "double-click") (:end . 122)\n  (:start . 110) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 125) (:start . 123)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 134)\n  (:start . 126) (:id . 61))\n ((:tag . "NNS") (:stem . "row") (:form . "rows") (:end . 139) (:start . 135)\n  (:id . 62))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 142) (:start . 140)\n  (:id . 63))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 150)\n  (:start . 143) (:id . 64))\n ((:tag . "NNS") (:stem . "entry") (:form . "entries") (:end . 158)\n  (:start . 151) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s14.118) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504620@unknown@formal@none@1@S@Dynamic Visualization of Proprietary Mass Spectrometry Data Files.@(((:tag . "JJ") (:stem . "dynamic") (:form . "Dynamic") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Visualization") (:form . "Visualization")\n  (:end . 21) (:start . 8) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Proprietary") (:form . "Proprietary") (:end . 36)\n  (:start . 25) (:id . 45))\n ((:tag . "NNP") (:stem . "Mass") (:form . "Mass") (:end . 41) (:start . 37)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Spectrometry") (:form . "Spectrometry") (:end . 54)\n  (:start . 42) (:id . 47))\n ((:tag . "NNP") (:stem . "Data") (:form . "Data") (:end . 59) (:start . 55)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Files") (:form . "Files") (:end . 65) (:start . 60)\n  (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 66) (:start . 65)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s14.119) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504621@unknown@formal@none@1@S@The Peak Viewer tool in multiplierz provides interactive plots for precursor RICs, and corresponding MS and MS/MS scans, in centroid or profile modes.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Peak") (:form . "Peak") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJR") (:stem . "view") (:form . "Viewer") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 35)\n  (:start . 24) (:id . 47))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . "JJ") (:stem . "interactive") (:form . "interactive") (:end . 56)\n  (:start . 45) (:id . 49))\n ((:tag . "NNS") (:stem . "plot") (:form . "plots") (:end . 62) (:start . 57)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 76)\n  (:start . 67) (:id . 52))\n ((:tag . "NNS") (:stem . "ric") (:form . "RICs") (:end . 81) (:start . 77)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 100)\n  (:start . 87) (:id . 56))\n ((:tag . "NN") (:stem . "ms") (:form . "MS") (:end . 103) (:start . 101)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 113)\n  (:start . 108) (:id . 59))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 119)\n  (:start . 114) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "centroid") (:form . "centroid") (:end . 132)\n  (:start . 124) (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 135) (:start . 133)\n  (:id . 64))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 143)\n  (:start . 136) (:id . 65))\n ((:tag . "NNS") (:stem . "mode") (:form . "modes") (:end . 149)\n  (:start . 144) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s14.120) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504622@unknown@formal@none@1@S@Green squares in the RIC denote MS scans and red triangles indicate MS/MS events.@(((:tag . "JJ") (:stem . "green") (:form . "Green") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "square") (:form . "squares") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "RIC") (:form . "RIC") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "denote") (:form . "denote") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . "NNP") (:stem . "MS") (:form . "MS") (:end . 34) (:start . 32)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "triangle") (:form . "triangles") (:end . 58)\n  (:start . 49) (:id . 52))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 67)\n  (:start . 59) (:id . 53))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 80)\n  (:start . 74) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s14.121) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504623@unknown@formal@none@1@S@In addition, users may adjust the time or m/z range displayed in each data window.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "VB") (:stem . "adjust") (:form . "adjust") (:end . 29)\n  (:start . 23) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "NN") (:stem . "m/z") (:form . "m/z") (:end . 45) (:start . 42)\n  (:id . 51))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 51) (:start . 46)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "display") (:form . "displayed") (:end . 61)\n  (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 54))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 69) (:start . 65)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 74) (:start . 70)\n  (:id . 56))\n ((:tag . "NN") (:stem . "window") (:form . "window") (:end . 81)\n  (:start . 75) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x14.122.1) (:span 19 22)))\n (:hscopes ((:id . :x14.122.1) (:span 19 81)))\n (:identifiers (:sid . :s14.122) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504624@unknown@formal@none@1@S@Verification of peptide sequence is facilitated by overlay of theoretical fragment ions on the MS/MS spectra.@(((:tag . "NN") (:stem . "verification") (:form . "Verification") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 23)\n  (:start . 16) (:id . 44))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 35) (:start . 33)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "facilitate") (:form . "facilitated") (:end . 47)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "NN") (:stem . "overlay") (:form . "overlay") (:end . 58)\n  (:start . 51) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "theoretical") (:form . "theoretical") (:end . 73)\n  (:start . 62) (:id . 51))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 82)\n  (:start . 74) (:id . 52))\n ((:tag . "NNS") (:stem . "ion") (:form . "ions") (:end . 87) (:start . 83)\n  (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 90) (:start . 88)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 100)\n  (:start . 95) (:id . 56))\n ((:tag . "NNS") (:stem . "spectrum") (:form . "spectra") (:end . 108)\n  (:start . 101) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 109) (:start . 108)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s14.123) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504625@unknown@formal@none@1@S@Users may dynamically evaluate multiple peptide assignment options by changing the proposed sequence or post-translational modification state in the left-most pane.@(((:tag . "NNS") (:stem . "user") (:form . "Users") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "dynamically") (:form . "dynamically") (:end . 21)\n  (:start . 10) (:id . 44))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 39)\n  (:start . 31) (:id . 46))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 47)\n  (:start . 40) (:id . 47))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 58)\n  (:start . 48) (:id . 48))\n ((:tag . "NNS") (:stem . "option") (:form . "options") (:end . 66)\n  (:start . 59) (:id . 49))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 69) (:start . 67)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "change") (:form . "changing") (:end . 78)\n  (:start . 70) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 91)\n  (:start . 83) (:id . 53))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 100)\n  (:start . 92) (:id . 54))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 103) (:start . 101)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "post-translational") (:form . "post-translational")\n  (:end . 122) (:start . 104) (:id . 56))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 135)\n  (:start . 123) (:id . 57))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 141)\n  (:start . 136) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "left-most") (:form . "left-most") (:end . 158)\n  (:start . 149) (:id . 61))\n ((:tag . "NN") (:stem . "pane") (:form . "pane") (:end . 163) (:start . 159)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s14.124) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504626@unknown@formal@none@1@S@Generation of Publication Quality Images.@(((:tag . "NNP") (:stem . "Generation") (:form . "Generation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Publication") (:form . "Publication") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "NNP") (:stem . "Quality") (:form . "Quality") (:end . 33)\n  (:start . 26) (:id . 45))\n ((:tag . "NNP") (:stem . "Images") (:form . "Images") (:end . 40)\n  (:start . 34) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 41) (:start . 40)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s14.125) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504627@unknown@formal@none@1@S@A Scrapbook tool allows manipulation of Peak Viewer plot properties such as axes labels, titles, and size.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Scrapbook") (:form . "Scrapbook") (:end . 11)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "manipulation") (:form . "manipulation") (:end . 36)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Peak") (:form . "Peak") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "JJR") (:stem . "view") (:form . "Viewer") (:end . 51) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "plot") (:form . "plot") (:end . 56) (:start . 52)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 67)\n  (:start . 57) (:id . 51))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "ax") (:form . "axes") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "label") (:form . "labels") (:end . 87)\n  (:start . 81) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "title") (:form . "titles") (:end . 95)\n  (:start . 89) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 59))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 105) (:start . 101)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s14.126) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504628@unknown@formal@none@1@S@Multi-plot comparison via the mirror and overlay functions provide further modes for in-depth, manual data interrogation.@(((:tag . "JJ") (:stem . "multi-plot") (:form . "Multi-plot") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 21)\n  (:start . 11) (:id . 43))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 25) (:start . 22)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 45))\n ((:tag . "NN") (:stem . "mirror") (:form . "mirror") (:end . 36)\n  (:start . 30) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "overlay") (:form . "overlay") (:end . 48)\n  (:start . 41) (:id . 48))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 58)\n  (:start . 49) (:id . 49))\n ((:tag . "VBP") (:stem . "provide") (:form . "provide") (:end . 66)\n  (:start . 59) (:id . 50))\n ((:tag . "JJ") (:stem . "further") (:form . "further") (:end . 74)\n  (:start . 67) (:id . 51))\n ((:tag . "NNS") (:stem . "mode") (:form . "modes") (:end . 80) (:start . 75)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 84) (:start . 81)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "in-depth") (:form . "in-depth") (:end . 93)\n  (:start . 85) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 94) (:start . 93)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "manual") (:form . "manual") (:end . 101)\n  (:start . 95) (:id . 56))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 106)\n  (:start . 102) (:id . 57))\n ((:tag . "NN") (:stem . "interrogation") (:form . "interrogation")\n  (:end . 120) (:start . 107) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s14.127) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504629@unknown@formal@none@1@S@Users may export publication quality images from all Scrapbook plots.@(((:tag . "NNS") (:stem . "user") (:form . "Users") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VB") (:stem . "export") (:form . "export") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "publication") (:form . "publication") (:end . 28)\n  (:start . 17) (:id . 45))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 43)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Scrapbook") (:form . "Scrapbook") (:end . 62)\n  (:start . 53) (:id . 50))\n ((:tag . "NNS") (:stem . "plot") (:form . "plots") (:end . 68) (:start . 63)\n  (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 52)))@@@1@11@((:hcues ((:id . :x14.128.1) (:span 6 9)))\n (:hscopes ((:id . :x14.128.1) (:span 6 68)))\n (:identifiers (:sid . :s14.128) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504630@unknown@formal@none@1@S@Researchers are increasingly focused on integration of disparate data types in order to better understand biological phenomena at the so-called network or systems level.@(((:tag . "NNS") (:stem . "researcher") (:form . "Researchers") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 15) (:start . 12)\n  (:id . 43))\n ((:tag . "RB") (:stem . "increasingly") (:form . "increasingly") (:end . 28)\n  (:start . 16) (:id . 44))\n ((:tag . "VBN") (:stem . "focus") (:form . "focused") (:end . 36)\n  (:start . 29) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 39) (:start . 37)\n  (:id . 46))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 51)\n  (:start . 40) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "disparate") (:form . "disparate") (:end . 64)\n  (:start . 55) (:id . 49))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 69) (:start . 65)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 75) (:start . 70)\n  (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 52))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 84) (:start . 79)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n  (:id . 54))\n ((:tag . "RBR") (:stem . "well") (:form . "better") (:end . 94) (:start . 88)\n  (:id . 55))\n ((:tag . "VB") (:stem . "understand") (:form . "understand") (:end . 105)\n  (:start . 95) (:id . 56))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 116)\n  (:start . 106) (:id . 57))\n ((:tag . "NNS") (:stem . "phenomenon") (:form . "phenomena") (:end . 126)\n  (:start . 117) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 129) (:start . 127)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "so-called") (:form . "so-called") (:end . 143)\n  (:start . 134) (:id . 61))\n ((:tag . "NN") (:stem . "network") (:form . "network") (:end . 151)\n  (:start . 144) (:id . 62))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 154) (:start . 152)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 162)\n  (:start . 155) (:id . 64))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 168)\n  (:start . 163) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s14.129) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504631@unknown@formal@none@1@S@As a first step in support of these and similar activities, multiplierz automatically downloads GenBank data over the internet based on an identified protein list, parses information such as gene ontology and domain classification, along with the corresponding Entrez Gene, HPRD, HGNC, and OMIM entries, and then creates hyperlinks directly in the spreadsheet reports.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 10) (:start . 5)\n  (:id . 44))\n ((:tag . "NN") (:stem . "step") (:form . "step") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 46))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 26)\n  (:start . 19) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . 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"directly") (:end . 340)\n  (:start . 332) (:id . 98))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 343) (:start . 341)\n  (:id . 99))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 347) (:start . 344)\n  (:id . 100))\n ((:tag . "NN") (:stem . "spreadsheet") (:form . "spreadsheet") (:end . 359)\n  (:start . 348) (:id . 101))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 367)\n  (:start . 360) (:id . 102))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 368) (:start . 367)\n  (:id . 103)))@@@1@62@((:identifiers (:sid . :s14.130) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504632@unknown@formal@none@1@S@This and other tools including an in silico protein digestion tool and a peptide fragment calculator are described in Additional File 3.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "silico") (:form . "silico") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 51)\n  (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "digestion") (:form . "digestion") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 72) (:start . 71)\n  (:id . 54))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 80)\n  (:start . 73) (:id . 55))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . "NN") (:stem . "calculator") (:form . "calculator") (:end . 100)\n  (:start . 90) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 104) (:start . 101)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 114)\n  (:start . 105) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 117) (:start . 115)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 128)\n  (:start . 118) (:id . 61))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 133) (:start . 129)\n  (:id . 62))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 135) (:start . 134)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s14.131) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504633@unknown@formal@none@1@S@While multiplierz includes many built-in features and tools, we also recognize the difficulty of building a "one size fits all" application given the diversity of ideas and efforts pursued within individual research laboratories.@(((:tag . "IN") (:stem . "while") (:form . "While") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 17)\n  (:start . 6) (:id . 43))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 26)\n  (:start . 18) (:id . 44))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 31) (:start . 27)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "built-in") (:form . "built-in") (:end . 40)\n  (:start . 32) (:id . 46))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 49)\n  (:start . 41) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 59) (:start . 54)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . "VBP") (:stem . "recognize") (:form . "recognize") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 54))\n ((:tag . "NN") (:stem . "difficulty") (:form . "difficulty") (:end . 93)\n  (:start . 83) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "build") (:form . "building") (:end . 105)\n  (:start . 97) (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 107) (:start . 106)\n  (:id . 58))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 109) (:start . 108)\n  (:id . 59))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 112) (:start . 109)\n  (:id . 60))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 117) (:start . 113)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "fit") (:form . "fits") (:end . 122) (:start . 118)\n  (:id . 62))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 126) (:start . 123)\n  (:id . 63))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 127) (:start . 126)\n  (:id . 64))\n ((:tag . "NN") (:stem . "application") (:form . "application") (:end . 139)\n  (:start . 128) (:id . 65))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 145)\n  (:start . 140) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 149) (:start . 146)\n  (:id . 67))\n ((:tag . "NN") (:stem . "diversity") (:form . "diversity") (:end . 159)\n  (:start . 150) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 162) (:start . 160)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "idea") (:form . "ideas") (:end . 168)\n  (:start . 163) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 172) (:start . 169)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "effort") (:form . "efforts") (:end . 180)\n  (:start . 173) (:id . 72))\n ((:tag . "VBN") (:stem . "pursue") (:form . "pursued") (:end . 188)\n  (:start . 181) (:id . 73))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 195)\n  (:start . 189) (:id . 74))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 206)\n  (:start . 196) (:id . 75))\n ((:tag . "NN") (:stem . "research") (:form . "research") (:end . 215)\n  (:start . 207) (:id . 76))\n ((:tag . "NNS") (:stem . "laboratory") (:form . "laboratories") (:end . 228)\n  (:start . 216) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 229) (:start . 228)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s14.132) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504634@unknown@formal@none@1@S@Hence multiplierz includes a command line console as well as scripting capability (through ".mz" scripts) which together support ad hoc data analysis tasks.@(((:tag . "RB") (:stem . "hence") (:form . "Hence") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 17)\n  (:start . 6) (:id . 43))\n ((:tag . "VBZ") (:stem . "include") (:form . "includes") (:end . 26)\n  (:start . 18) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 45))\n ((:tag . "NN") (:stem . "command") (:form . "command") (:end . 36)\n  (:start . 29) (:id . 46))\n ((:tag . "NN") (:stem . "line") (:form . "line") (:end . 41) (:start . 37)\n  (:id . 47))\n ((:tag . "NN") (:stem . "console") (:form . "console") (:end . 49)\n  (:start . 42) (:id . 48))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 52) (:start . 50)\n  (:id . 49))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "scripte") (:form . "scripting") (:end . 70)\n  (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "capability") (:form . "capability") (:end . 81)\n  (:start . 71) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 54))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 90)\n  (:start . 83) (:id . 55))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 92) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . ".mz") (:form . ".mz") (:end . 95) (:start . 92)\n  (:id . 57))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 96) (:start . 95)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "script") (:form . "scripts") (:end . 104)\n  (:start . 97) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 111)\n  (:start . 106) (:id . 61))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 120)\n  (:start . 112) (:id . 62))\n ((:tag . "VBP") (:stem . "support") (:form . "support") (:end . 128)\n  (:start . 121) (:id . 63))\n ((:tag . "NN") (:stem . "ad") (:form . "ad") (:end . 131) (:start . 129)\n  (:id . 64))\n ((:tag . "NN") (:stem . "hoc") (:form . "hoc") (:end . 135) (:start . 132)\n  (:id . 65))\n ((:tag . "NN") (:stem . "data") (:form . "data") (:end . 140) (:start . 136)\n  (:id . 66))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 149)\n  (:start . 141) (:id . 67))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 155)\n  (:start . 150) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s14.133) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504635@unknown@formal@none@1@S@The scripting capability is particularly useful for niche experiments or proteomics workflows not otherwise supported by other open-source or proprietary data systems.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "scripte") (:form . "scripting") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "capability") (:form . "capability") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "RB") (:stem . "particularly") (:form . "particularly") (:end . 40)\n  (:start . 28) (:id . 46))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 47)\n  (:start . 41) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 51) (:start . 48)\n  (:id . 48))\n ((:tag . "NN") (:stem . "niche") (:form . "niche") (:end . 57) (:start . 52)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 69)\n  (:start . 58) (:id . 50))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 83)\n  (:start . 73) (:id . 52))\n ((:tag . "VBZ") (:stem . "workflow") (:form . "workflows") (:end . 93)\n  (:start . 84) (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 97) (:start . 94)\n  (:id . 54))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 107)\n  (:start . 98) (:id . 55))\n ((:tag . "VBN") (:stem . "support") (:form . "supported") (:end . 117)\n  (:start . 108) (:id . 56))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 120) (:start . 118)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 126)\n  (:start . 121) (:id . 58))\n ((:tag . "JJ") (:stem . "open-source") (:form . "open-source") (:end . 138)\n  (:start . 127) (:id . 59))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 141) (:start . 139)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "proprietary") (:form . "proprietary") (:end . 153)\n  (:start . 142) (:id . 61))\n ((:tag . "NN") (:stem . "data") (:form . "data") (:end . 158) (:start . 154)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 166)\n  (:start . 159) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s14.134) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504636@unknown@formal@none@1@S@All multiplierz tools are available through both the desktop GUI as well as scriptable procedures.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 21) (:start . 16)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NN") (:stem . "desktop") (:form . "desktop") (:end . 60)\n  (:start . 53) (:id . 50))\n ((:tag . "NNP") (:stem . "GUI") (:form . "GUI") (:end . 64) (:start . 61)\n  (:id . 51))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "scriptable") (:form . "scriptable") (:end . 86)\n  (:start . 76) (:id . 55))\n ((:tag . "NNS") (:stem . "procedure") (:form . "procedures") (:end . 97)\n  (:start . 87) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s14.135) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504637@unknown@formal@none@1@S@In addition, a pre-launch initialization ("rc.mz") script enables full customization of the application and its interfaces without recompiling the underlying code.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "pre-launch") (:form . "pre-launch") (:end . 25)\n  (:start . 15) (:id . 46))\n ((:tag . "NN") (:stem . "initialization") (:form . "initialization")\n  (:end . 40) (:start . 26) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "rc.mz") (:form . "rc.mz") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 50) (:start . 49)\n  (:id . 52))\n ((:tag . "NN") (:stem . "script") (:form . "script") (:end . 57)\n  (:start . 51) (:id . 53))\n ((:tag . "VBZ") (:stem . "enable") (:form . "enables") (:end . 65)\n  (:start . 58) (:id . 54))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 70) (:start . 66)\n  (:id . 55))\n ((:tag . "NN") (:stem . "customization") (:form . "customization")\n  (:end . 84) (:start . 71) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . "NN") (:stem . "application") (:form . "application") (:end . 103)\n  (:start . 92) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 60))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 111) (:start . 108)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "interface") (:form . "interfaces") (:end . 122)\n  (:start . 112) (:id . 62))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 130)\n  (:start . 123) (:id . 63))\n ((:tag . "VBG") (:stem . "recompile") (:form . "recompiling") (:end . 142)\n  (:start . 131) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "underlying") (:form . "underlying") (:end . 157)\n  (:start . 147) (:id . 66))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 162) (:start . 158)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s14.136) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504638@unknown@formal@none@1@S@Finally, we note that programmatic access to mzAPI allows incorporation of multiplierz into automated data-analytic pipelines.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "note") (:form . "note") (:end . 16) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "programmatic") (:form . "programmatic") (:end . 34)\n  (:start . 22) (:id . 47))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "mzAPI") (:form . "mzAPI") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 57)\n  (:start . 51) (:id . 51))\n ((:tag . "NN") (:stem . "incorporation") (:form . "incorporation")\n  (:end . 71) (:start . 58) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 53))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 86)\n  (:start . 75) (:id . 54))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 91) (:start . 87)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "automated") (:form . "automated") (:end . 101)\n  (:start . 92) (:id . 56))\n ((:tag . "JJ") (:stem . "data-analytic") (:form . "data-analytic")\n  (:end . 115) (:start . 102) (:id . 57))\n ((:tag . "NNS") (:stem . "pipeline") (:form . "pipelines") (:end . 125)\n  (:start . 116) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s14.137) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504639@unknown@formal@none@1@S@For example, users can submit jobs through a laboratory information management system (LIMS).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "VB") (:stem . "submit") (:form . "submit") (:end . 29)\n  (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "job") (:form . "jobs") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 42)\n  (:start . 35) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "laboratory") (:form . "laboratory") (:end . 55)\n  (:start . 45) (:id . 51))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 67)\n  (:start . 56) (:id . 52))\n ((:tag . "NN") (:stem . "management") (:form . "management") (:end . 78)\n  (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 85)\n  (:start . 79) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "LIMS") (:form . "LIMS") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 93) (:start . 92)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s14.138) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504640@unknown@formal@none@1@S@Upon completion of LC-MS acquisition(s) and database search(es), multiplierz executes .mz scripts to access both the search results and underlying .RAW or .WIFF file(s), in order to create a spreadsheet-based report.@(((:tag . "IN") (:stem . "upon") (:form . "Upon") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "completion") (:form . "completion") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "LC-MS") (:form . "LC-MS") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "acquisition(s)") (:form . "acquisition(s)")\n  (:end . 39) (:start . 25) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 52)\n  (:start . 44) (:id . 48))\n ((:tag . "NNS") (:stem . "search(es)") (:form . "search(es)") (:end . 63)\n  (:start . 53) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 76)\n  (:start . 65) (:id . 51))\n ((:tag . "NNS") (:stem . "execute") (:form . "executes") (:end . 85)\n  (:start . 77) (:id . 52))\n ((:tag . "VBP") (:stem . ".mz") (:form . ".mz") (:end . 89) (:start . 86)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "script") (:form . "scripts") (:end . 97)\n  (:start . 90) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 100) (:start . 98)\n  (:id . 55))\n ((:tag . "VB") (:stem . "access") (:form . "access") (:end . 107)\n  (:start . 101) (:id . 56))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 112) (:start . 108)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 58))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 123)\n  (:start . 117) (:id . 59))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 131)\n  (:start . 124) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "underlie") (:form . "underlying") (:end . 146)\n  (:start . 136) (:id . 62))\n ((:tag . "NNP") (:stem . ".RAW") (:form . ".RAW") (:end . 151) (:start . 147)\n  (:id . 63))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 154) (:start . 152)\n  (:id . 64))\n ((:tag . "NNP") (:stem . ".WIFF") (:form . ".WIFF") (:end . 160)\n  (:start . 155) (:id . 65))\n ((:tag . "NNP") (:stem . "file(s)") (:form . "file(s)") (:end . 168)\n  (:start . 161) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 172) (:start . 170)\n  (:id . 68))\n ((:tag . "NN") (:stem . "order") (:form . "order") (:end . 178)\n  (:start . 173) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 181) (:start . 179)\n  (:id . 70))\n ((:tag . "VB") (:stem . "create") (:form . "create") (:end . 188)\n  (:start . 182) (:id . 71))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 190) (:start . 189)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "spreadsheet-based") (:form . "spreadsheet-based")\n  (:end . 208) (:start . 191) (:id . 73))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 215)\n  (:start . 209) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s14.139) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504641@unknown@formal@none@1@S@Users can be notified by email and access their results via the multiplierz desktop environment.@(((:tag . "NNS") (:stem . "user") (:form . "Users") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "notify") (:form . "notified") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 24) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "email") (:form . "email") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 48))\n ((:tag . "VB") (:stem . "access") (:form . "access") (:end . 41)\n  (:start . 35) (:id . 49))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 47)\n  (:start . 42) (:id . 50))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 55)\n  (:start . 48) (:id . 51))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 75)\n  (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "desktop") (:form . "desktop") (:end . 83)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "environment") (:form . "environment") (:end . 95)\n  (:start . 84) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s14.140) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504642@unknown@formal@none@1@S@Importantly, multiplierz spreadsheet reports, whether generated in low- or high-throughput mode, are portable and readily formatted in accordance with journal-specific requirements for proteomics data.@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "spreadsheet") (:form . "spreadsheet") (:end . 36)\n  (:start . 25) (:id . 45))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 44)\n  (:start . 37) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 45) (:start . 44)\n  (:id . 47))\n ((:tag . "IN") (:stem . "whether") (:form . "whether") (:end . 53)\n  (:start . 46) (:id . 48))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 63)\n  (:start . 54) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 66) (:start . 64)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "low-") (:form . "low-") (:end . 71) (:start . 67)\n  (:id . 51))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "high-throughput") (:form . "high-throughput")\n  (:end . 90) (:start . 75) (:id . 53))\n ((:tag . "NN") (:stem . "mode") (:form . "mode") (:end . 95) (:start . 91)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 100) (:start . 97)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "portable") (:form . "portable") (:end . 109)\n  (:start . 101) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 58))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 121)\n  (:start . 114) (:id . 59))\n ((:tag . "VBN") (:stem . "format") (:form . "formatted") (:end . 131)\n  (:start . 122) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n  (:id . 61))\n ((:tag . "NN") (:stem . "accordance") (:form . "accordance") (:end . 145)\n  (:start . 135) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 150) (:start . 146)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "journal-specific") (:form . "journal-specific")\n  (:end . 167) (:start . 151) (:id . 64))\n ((:tag . "NNS") (:stem . "requirement") (:form . "requirements") (:end . 180)\n  (:start . 168) (:id . 65))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 184) (:start . 181)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 195)\n  (:start . 185) (:id . 67))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 200)\n  (:start . 196) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s14.141) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504643@unknown@formal@none@1@S@Collectively the features described above facilitate a wide range of data analysis tasks for mass spectrometry-based proteomics activities from technology development and evaluation to prioritization of protein identifications for subsequent biochemical validation.@(((:tag . "RB") (:stem . "collectively") (:form . "Collectively") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 35)\n  (:start . 26) (:id . 45))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 41) (:start . 36)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "facilitate") (:form . "facilitate") (:end . 52)\n  (:start . 42) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 59) (:start . 55)\n  (:id . 49))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 65) (:start . 60)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 73) (:start . 69)\n  (:id . 52))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 82)\n  (:start . 74) (:id . 53))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 88) (:start . 83)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 97) (:start . 93)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "spectrometry-based") (:form . "spectrometry-based")\n  (:end . 116) (:start . 98) (:id . 57))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 127)\n  (:start . 117) (:id . 58))\n ((:tag . "NNS") (:stem . "activity") (:form . "activities") (:end . 138)\n  (:start . 128) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 143) (:start . 139)\n  (:id . 60))\n ((:tag . "NN") (:stem . "technology") (:form . "technology") (:end . 154)\n  (:start . 144) (:id . 61))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 166)\n  (:start . 155) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 170) (:start . 167)\n  (:id . 63))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 181)\n  (:start . 171) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 184) (:start . 182)\n  (:id . 65))\n ((:tag . "NN") (:stem . "prioritization") (:form . "prioritization")\n  (:end . 199) (:start . 185) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 202) (:start . 200)\n  (:id . 67))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 210)\n  (:start . 203) (:id . 68))\n ((:tag . "NNS") (:stem . "identification") (:form . "identifications")\n  (:end . 226) (:start . 211) (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 230) (:start . 227)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 241)\n  (:start . 231) (:id . 71))\n ((:tag . "JJ") (:stem . "biochemical") (:form . "biochemical") (:end . 253)\n  (:start . 242) (:id . 72))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 264)\n  (:start . 254) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s14.142) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504644@unknown@formal@none@1@S@Importantly, multiplierz provides these capabilities to individual users at the desktop level.@(((:tag . "RB") (:stem . "importantly") (:form . "Importantly") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 33)\n  (:start . 25) (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 39) (:start . 34)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "capability") (:form . "capabilities") (:end . 52)\n  (:start . 40) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "individual") (:form . "individual") (:end . 66)\n  (:start . 56) (:id . 49))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 72) (:start . 67)\n  (:id . 50))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 75) (:start . 73)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 52))\n ((:tag . "NN") (:stem . "desktop") (:form . "desktop") (:end . 87)\n  (:start . 80) (:id . 53))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 93) (:start . 88)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s14.143) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504645@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s14.144) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504646@unknown@formal@none@1@S@In the following sections, we demonstrate the functionality of multiplierz through relevant examples based on data and results from work in our laboratory.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "following") (:form . "following") (:end . 16)\n  (:start . 7) (:id . 44))\n ((:tag . "NNS") (:stem . "section") (:form . "sections") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 41)\n  (:start . 30) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "functionality") (:form . "functionality")\n  (:end . 59) (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 74)\n  (:start . 63) (:id . 52))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 82)\n  (:start . 75) (:id . 53))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 91)\n  (:start . 83) (:id . 54))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 100)\n  (:start . 92) (:id . 55))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 106)\n  (:start . 101) (:id . 56))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 109) (:start . 107)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 114)\n  (:start . 110) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "result") (:form . "results") (:end . 126)\n  (:start . 119) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 131) (:start . 127)\n  (:id . 61))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 136) (:start . 132)\n  (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 139) (:start . 137)\n  (:id . 63))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 143) (:start . 140)\n  (:id . 64))\n ((:tag . "NN") (:stem . "laboratory") (:form . "laboratory") (:end . 154)\n  (:start . 144) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s14.145) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504647@unknown@formal@none@1@S@Significantly we note that these examples encompass data generated on mass spectrometers manufactured by ThermoFisher Scientific and AB-SCIEX.@(((:tag . "RB") (:stem . "significantly") (:form . "Significantly")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 16) (:start . 14)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "note") (:form . "note") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "VBP") (:stem . "encompass") (:form . "encompass") (:end . 51)\n  (:start . 42) (:id . 48))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 56) (:start . 52)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 66)\n  (:start . 57) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 69) (:start . 67)\n  (:id . 51))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "spectrometer") (:form . "spectrometers")\n  (:end . 88) (:start . 75) (:id . 53))\n ((:tag . "VBN") (:stem . "manufacture") (:form . "manufactured") (:end . 101)\n  (:start . 89) (:id . 54))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 104) (:start . 102)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "ThermoFisher") (:form . "ThermoFisher")\n  (:end . 117) (:start . 105) (:id . 56))\n ((:tag . "NNP") (:stem . "Scientific") (:form . "Scientific") (:end . 128)\n  (:start . 118) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "AB-SCIEX") (:form . "AB-SCIEX") (:end . 141)\n  (:start . 133) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s14.146) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504648@unknown@formal@none@1@S@Optimization of LC Assemblies and Methods@(((:tag . "NNP") (:stem . "Optimization") (:form . "Optimization") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "LC") (:form . "LC") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "NNPS") (:stem . "Assembly") (:form . "Assemblies") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 46))\n ((:tag . "NNPS") (:stem . "Method") (:form . "Methods") (:end . 41)\n  (:start . 34) (:id . 47)))@@@1@6@((:identifiers (:sid . :s14.147) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504649@unknown@formal@none@1@S@We recently described a novel protocol for fabrication of miniaturized LC-electrospray assemblies that provided significantly improved LC-MS performance [20].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "VBD") (:stem . "describe") (:form . "described") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 29) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protocol") (:form . "protocol") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "fabrication") (:form . "fabrication") (:end . 54)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "miniaturize") (:form . "miniaturized") (:end . 70)\n  (:start . 58) (:id . 51))\n ((:tag . "NN") (:stem . "lc-electrospray") (:form . "LC-electrospray")\n  (:end . 86) (:start . 71) (:id . 52))\n ((:tag . "NNS") (:stem . "assembly") (:form . "assemblies") (:end . 97)\n  (:start . 87) (:id . 53))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 102) (:start . 98)\n  (:id . 54))\n ((:tag . "VBD") (:stem . "provide") (:form . "provided") (:end . 111)\n  (:start . 103) (:id . 55))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 125) (:start . 112) (:id . 56))\n ((:tag . "VBN") (:stem . "improve") (:form . "improved") (:end . 134)\n  (:start . 126) (:id . 57))\n ((:tag . "NNP") (:stem . "LC-MS") (:form . "LC-MS") (:end . 140)\n  (:start . 135) (:id . 58))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 152)\n  (:start . 141) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 154) (:start . 153)\n  (:id . 60))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 156) (:start . 154)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 157) (:start . 156)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s14.148) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504650@unknown@formal@none@1@S@Not surprisingly, elucidation of relevant analytical figures of merit required in-depth and large scale data analysis.@(((:tag . "RB") (:stem . "not") (:form . "Not") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "surprisingly") (:form . "surprisingly") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "elucidation") (:form . "elucidation") (:end . 29)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 41)\n  (:start . 33) (:id . 47))\n ((:tag . "JJ") (:stem . "analytical") (:form . "analytical") (:end . 52)\n  (:start . 42) (:id . 48))\n ((:tag . "NNS") (:stem . "figure") (:form . "figures") (:end . 60)\n  (:start . 53) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 50))\n ((:tag . "NN") (:stem . "merit") (:form . "merit") (:end . 69) (:start . 64)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "require") (:form . "required") (:end . 78)\n  (:start . 70) (:id . 52))\n ((:tag . "JJ") (:stem . "in-depth") (:form . "in-depth") (:end . 87)\n  (:start . 79) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 91) (:start . 88)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 97) (:start . 92)\n  (:id . 55))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 103) (:start . 98)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 108)\n  (:start . 104) (:id . 57))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 117)\n  (:start . 109) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s14.149) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504651@unknown@formal@none@1@S@Figure 5 shows the multiplierz-dependent workflow required to evaluate the relative performance improvement for analysis of tryptic peptides derived from whole cell lysate as a function of column size and flow rate (also see Additional File 5).@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "multiplierz-dependent")\n  (:form . "multiplierz-dependent") (:end . 40) (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "workflow") (:form . "workflow") (:end . 49)\n  (:start . 41) (:id . 47))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 58)\n  (:start . 50) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 61) (:start . 59)\n  (:id . 49))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 70)\n  (:start . 62) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 83)\n  (:start . 75) (:id . 52))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 95)\n  (:start . 84) (:id . 53))\n ((:tag . "NN") (:stem . "improvement") (:form . "improvement") (:end . 107)\n  (:start . 96) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 111) (:start . 108)\n  (:id . 55))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 120)\n  (:start . 112) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "tryptic") (:form . "tryptic") (:end . 131)\n  (:start . 124) (:id . 58))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 140)\n  (:start . 132) (:id . 59))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 148)\n  (:start . 141) (:id . 60))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 153) (:start . 149)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 159)\n  (:start . 154) (:id . 62))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 164) (:start . 160)\n  (:id . 63))\n ((:tag . "NN") (:stem . "lysate") (:form . "lysate") (:end . 171)\n  (:start . 165) (:id . 64))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 174) (:start . 172)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 176) (:start . 175)\n  (:id . 66))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 185)\n  (:start . 177) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 188) (:start . 186)\n  (:id . 68))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 195)\n  (:start . 189) (:id . 69))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 200) (:start . 196)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 204) (:start . 201)\n  (:id . 71))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 209) (:start . 205)\n  (:id . 72))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 214) (:start . 210)\n  (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 216) (:start . 215)\n  (:id . 74))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 220) (:start . 216)\n  (:id . 75))\n ((:tag . "VBP") (:stem . "see") (:form . "see") (:end . 224) (:start . 221)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 235)\n  (:start . 225) (:id . 77))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 240) (:start . 236)\n  (:id . 78))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 242) (:start . 241)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 243) (:start . 242)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 244) (:start . 243)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s14.150) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504652@unknown@formal@none@1@S@From approximately 90,000 MS/MS scans encompassing almost 23,000 peptide assignments (combination of sequence, charge state, and modification) multiplierz identified 198 unique peptide sequences and modifications in common across 11 LC-MS acquisitions.@(((:tag . "IN") (:stem . "from") (:form . "From") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "approximately") (:form . "approximately")\n  (:end . 18) (:start . 5) (:id . 43))\n ((:tag . "CD") (:stem . "90,000") (:form . "90,000") (:end . 25)\n  (:start . 19) (:id . 44))\n ((:tag . "NN") (:stem . "ms/ms") (:form . "MS/MS") (:end . 31) (:start . 26)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 37) (:start . 32)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "encompass") (:form . "encompassing") (:end . 50)\n  (:start . 38) (:id . 47))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 57)\n  (:start . 51) (:id . 48))\n ((:tag . "CD") (:stem . "23,000") (:form . "23,000") (:end . 64)\n  (:start . 58) (:id . 49))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 72)\n  (:start . 65) (:id . 50))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 84)\n  (:start . 73) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 52))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 97)\n  (:start . 86) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 100) (:start . 98)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 109)\n  (:start . 101) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 110) (:start . 109)\n  (:id . 56))\n ((:tag . "NN") (:stem . "charge") (:form . "charge") (:end . 117)\n  (:start . 111) (:id . 57))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 123)\n  (:start . 118) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 60))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 141)\n  (:start . 129) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 62))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 154)\n  (:start . 143) (:id . 63))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 165)\n  (:start . 155) (:id . 64))\n ((:tag . "CD") (:stem . "198") (:form . "198") (:end . 169) (:start . 166)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 176)\n  (:start . 170) (:id . 66))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 184)\n  (:start . 177) (:id . 67))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 194)\n  (:start . 185) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 198) (:start . 195)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "modification") (:form . "modifications")\n  (:end . 212) (:start . 199) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 215) (:start . 213)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 222)\n  (:start . 216) (:id . 72))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 229)\n  (:start . 223) (:id . 73))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 232) (:start . 230)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "lc-ms") (:form . "LC-MS") (:end . 238)\n  (:start . 233) (:id . 75))\n ((:tag . "NNS") (:stem . "acquisition") (:form . "acquisitions") (:end . 251)\n  (:start . 239) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s14.151) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504653@unknown@formal@none@1@S@In addition, multiplierz used Mascot-derived peptide identifications to generate RICs, calculate full chromatographic peak width at half-maximum (FWHM), and determine precursor apex intensity.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mascot-derived") (:form . "Mascot-derived")\n  (:end . 44) (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "NNS") (:stem . "identification") (:form . "identifications")\n  (:end . 68) (:start . 53) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 50))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 80)\n  (:start . 72) (:id . 51))\n ((:tag . "NNS") (:stem . "ric") (:form . "RICs") (:end . 85) (:start . 81)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 53))\n ((:tag . "VBP") (:stem . "calculate") (:form . "calculate") (:end . 96)\n  (:start . 87) (:id . 54))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 101) (:start . 97)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "chromatographic") (:form . "chromatographic")\n  (:end . 117) (:start . 102) (:id . 56))\n ((:tag . "JJ") (:stem . "peak") (:form . "peak") (:end . 122) (:start . 118)\n  (:id . 57))\n ((:tag . "NN") (:stem . "width") (:form . "width") (:end . 128)\n  (:start . 123) (:id . 58))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 131) (:start . 129)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "half-maximum") (:form . "half-maximum") (:end . 144)\n  (:start . 132) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "FWHM") (:form . "FWHM") (:end . 150) (:start . 146)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 151) (:start . 150)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 65))\n ((:tag . "NN") (:stem . "determine") (:form . "determine") (:end . 166)\n  (:start . 157) (:id . 66))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 176)\n  (:start . 167) (:id . 67))\n ((:tag . "NN") (:stem . "apex") (:form . "apex") (:end . 181) (:start . 177)\n  (:id . 68))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 191)\n  (:start . 182) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s14.152) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504654@unknown@formal@none@1@S@The entire analysis was performed via the multiplierz GUI.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "entire") (:form . "entire") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 33)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 37) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 53)\n  (:start . 42) (:id . 49))\n ((:tag . "NNP") (:stem . "GUI") (:form . "GUI") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s14.153) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504655@unknown@formal@none@1@S@Finally, the embedded RIC images facilitated rapid validation and comparison of chromatographic features.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "embedded") (:form . "embedded") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "NNP") (:stem . "RIC") (:form . "RIC") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 32)\n  (:start . 26) (:id . 47))\n ((:tag . "VBD") (:stem . "facilitate") (:form . "facilitated") (:end . 44)\n  (:start . 33) (:id . 48))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 61)\n  (:start . 51) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 76)\n  (:start . 66) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "chromatographic") (:form . "chromatographic")\n  (:end . 95) (:start . 80) (:id . 54))\n ((:tag . "NNS") (:stem . "feature") (:form . "features") (:end . 104)\n  (:start . 96) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s14.154) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504656@unknown@formal@none@1@S@Multiplierz -based Workflow for Analysis of LC Column Geometry and Flow Rate.@(((:tag . "JJ") (:stem . "multiplierz") (:form . "Multiplierz") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "-based") (:form . "-based") (:end . 18)\n  (:start . 12) (:id . 43))\n ((:tag . "NNP") (:stem . "Workflow") (:form . "Workflow") (:end . 27)\n  (:start . 19) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 31) (:start . 28)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Analysis") (:form . "Analysis") (:end . 40)\n  (:start . 32) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "LC") (:form . "LC") (:end . 46) (:start . 44)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Column") (:form . "Column") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "NNP") (:stem . "Geometry") (:form . "Geometry") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Flow") (:form . "Flow") (:end . 71) (:start . 67)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Rate") (:form . "Rate") (:end . 76) (:start . 72)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s14.155) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504657@unknown@formal@none@1@S@Relative performance improvement for analysis of peptides derived from whole cell lysate as a function of column size and flow rate (a).@(((:tag . "JJ") (:stem . "relative") (:form . "Relative") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 20)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "improvement") (:form . "improvement") (:end . 32)\n  (:start . 21) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 36) (:start . 33)\n  (:id . 45))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 45)\n  (:start . 37) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 48) (:start . 46)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 57)\n  (:start . 49) (:id . 48))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 65)\n  (:start . 58) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 70) (:start . 66)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "whole") (:form . "whole") (:end . 76) (:start . 71)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cell") (:form . "cell") (:end . 81) (:start . 77)\n  (:id . 52))\n ((:tag . "NN") (:stem . "lysate") (:form . "lysate") (:end . 88)\n  (:start . 82) (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 91) (:start . 89)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 93) (:start . 92)\n  (:id . 55))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 102)\n  (:start . 94) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 57))\n ((:tag . "NN") (:stem . "column") (:form . "column") (:end . 112)\n  (:start . 106) (:id . 58))\n ((:tag . "NN") (:stem . "size") (:form . "size") (:end . 117) (:start . 113)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 121) (:start . 118)\n  (:id . 60))\n ((:tag . "NN") (:stem . "flow") (:form . "flow") (:end . 126) (:start . 122)\n  (:id . 61))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 131) (:start . 127)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 134) (:start . 133)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 135) (:start . 134)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s14.156) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504658@unknown@formal@none@1@S@Original data contained ~90,000 MS/MS scans (b) encompassing almost 23,000 peptide assignments (combination of sequence, charge state, and modification), across 11 LC-MS acquisitions.@(((:tag . "JJ") (:stem . "original") (:form . "Original") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 13) (:start . 9)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "contain") (:form . "contained") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "CD") (:stem . "~90,000") (:form . "~90,000") (:end . 31)\n  (:start . 24) (:id . 45))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 37) (:start . 32)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 43) (:start . 38)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "encompass") (:form . "encompassing") (:end . 60)\n  (:start . 48) (:id . 51))\n ((:tag . "RB") (:stem . "almost") (:form . "almost") (:end . 67)\n  (:start . 61) (:id . 52))\n ((:tag . "CD") (:stem . "23,000") (:form . "23,000") (:end . 74)\n  (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 82)\n  (:start . 75) (:id . 54))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 94)\n  (:start . 83) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 107)\n  (:start . 96) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 110) (:start . 108)\n  (:id . 58))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 119)\n  (:start . 111) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 120) (:start . 119)\n  (:id . 60))\n ((:tag . "NN") (:stem . "charge") (:form . "charge") (:end . 127)\n  (:start . 121) (:id . 61))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 133)\n  (:start . 128) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 138) (:start . 135)\n  (:id . 64))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 151)\n  (:start . 139) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 152) (:start . 151)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 67))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 160)\n  (:start . 154) (:id . 68))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 163) (:start . 161)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "lc-ms") (:form . "LC-MS") (:end . 169)\n  (:start . 164) (:id . 70))\n ((:tag . "NNS") (:stem . "acquisition") (:form . "acquisitions") (:end . 182)\n  (:start . 170) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s14.157) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504659@unknown@formal@none@1@S@In addition, multiplierz used Mascot-derived peptide identifications (c) to generate RICs, calculate full chromatographic peak width at half-maximum (FWHM), and determine precursor apex intensity (d).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 24)\n  (:start . 13) (:id . 45))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "mascot-derived") (:form . "Mascot-derived")\n  (:end . 44) (:start . 30) (:id . 47))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "NNS") (:stem . "identification") (:form . "identifications")\n  (:end . 68) (:start . 53) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 50))\n ((:tag . "NN") (:stem . "c") (:form . "c") (:end . 71) (:start . 70)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 75) (:start . 73)\n  (:id . 53))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 84)\n  (:start . 76) (:id . 54))\n ((:tag . "NNS") (:stem . "ric") (:form . "RICs") (:end . 89) (:start . 85)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "calculate") (:form . "calculate") (:end . 100)\n  (:start . 91) (:id . 57))\n ((:tag . "JJ") (:stem . "full") (:form . "full") (:end . 105) (:start . 101)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "chromatographic") (:form . "chromatographic")\n  (:end . 121) (:start . 106) (:id . 59))\n ((:tag . "JJ") (:stem . "peak") (:form . "peak") (:end . 126) (:start . 122)\n  (:id . 60))\n ((:tag . "NN") (:stem . "width") (:form . "width") (:end . 132)\n  (:start . 127) (:id . 61))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 135) (:start . 133)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "half-maximum") (:form . "half-maximum") (:end . 148)\n  (:start . 136) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "FWHM") (:form . "FWHM") (:end . 154) (:start . 150)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 160) (:start . 157)\n  (:id . 68))\n ((:tag . "NN") (:stem . "determine") (:form . "determine") (:end . 170)\n  (:start . 161) (:id . 69))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 180)\n  (:start . 171) (:id . 70))\n ((:tag . "NN") (:stem . "apex") (:form . "apex") (:end . 185) (:start . 181)\n  (:id . 71))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 195)\n  (:start . 186) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 197) (:start . 196)\n  (:id . 73))\n ((:tag . "NN") (:stem . "d") (:form . "d") (:end . 198) (:start . 197)\n  (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 199) (:start . 198)\n  (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 200) (:start . 199)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s14.158) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504660@unknown@formal@none@1@S@Common peptide sequences and associated analytical metrics are extracted (e) into a final, spreadsheet based report (f).@(((:tag . "JJ") (:stem . "common") (:form . "Common") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 14)\n  (:start . 7) (:id . 43))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 24)\n  (:start . 15) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 39)\n  (:start . 29) (:id . 46))\n ((:tag . "JJ") (:stem . "analytical") (:form . "analytical") (:end . 50)\n  (:start . 40) (:id . 47))\n ((:tag . "NNS") (:stem . "metric") (:form . "metrics") (:end . 58)\n  (:start . 51) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 62) (:start . 59)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "extract") (:form . "extracted") (:end . 72)\n  (:start . 63) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 74) (:start . 73)\n  (:id . 51))\n ((:tag . "NN") (:stem . "e") (:form . "e") (:end . 75) (:start . 74)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n  (:id . 53))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 81) (:start . 77)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 89) (:start . 84)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "VB") (:stem . "spreadsheet") (:form . "spreadsheet") (:end . 102)\n  (:start . 91) (:id . 58))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 108)\n  (:start . 103) (:id . 59))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 115)\n  (:start . 109) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 61))\n ((:tag . "NN") (:stem . "f") (:form . "f") (:end . 118) (:start . 117)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s14.159) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504661@unknown@formal@none@1@S@Figure 2 (see above) shows an example of a multiplierz standard format report.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 13) (:start . 10)\n  (:id . 45))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 19) (:start . 14)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 26) (:start . 21)\n  (:id . 48))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 29) (:start . 27)\n  (:id . 49))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 37)\n  (:start . 30) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 42) (:start . 41)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 54)\n  (:start . 43) (:id . 53))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 63)\n  (:start . 55) (:id . 54))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 70)\n  (:start . 64) (:id . 55))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 77)\n  (:start . 71) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 78) (:start . 77)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s14.160) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504662@unknown@formal@none@1@S@To simplify the display we generated a comparison report (using multiplierz) for the two extremes in the 11 LC-MS acquisitions described above.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "simplify") (:form . "simplify") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "display") (:form . "display") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "comparison") (:form . "comparison") (:end . 49)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 56)\n  (:start . 50) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 63) (:start . 58)\n  (:id . 52))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 75)\n  (:start . 64) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "extreme") (:form . "extremes") (:end . 97)\n  (:start . 89) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 60))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 107) (:start . 105)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "LC-MS") (:form . "LC-MS") (:end . 113)\n  (:start . 108) (:id . 62))\n ((:tag . "NNS") (:stem . "acquisition") (:form . "acquisitions") (:end . 126)\n  (:start . 114) (:id . 63))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 136)\n  (:start . 127) (:id . 64))\n ((:tag . "RB") (:stem . "above") (:form . "above") (:end . 142)\n  (:start . 137) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s14.161) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504663@unknown@formal@none@1@S@The insets show examples of optional embedded images.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "inset") (:form . "insets") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "example") (:form . "examples") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "optional") (:form . "optional") (:end . 36)\n  (:start . 28) (:id . 47))\n ((:tag . "JJ") (:stem . "embedded") (:form . "embedded") (:end . 45)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 52)\n  (:start . 46) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s14.162) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504664@unknown@formal@none@1@S@We note that, unlike many web-based reports that often require frequent page updates, multiplierz images display immediately upon mouse-over, and hence facilitate rapid data validation and interrogation exercises.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "note") (:form . "note") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "IN") (:stem . "unlike") (:form . "unlike") (:end . 20)\n  (:start . 14) (:id . 46))\n ((:tag . "JJ") (:stem . "many") (:form . "many") (:end . 25) (:start . 21)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "web-based") (:form . "web-based") (:end . 35)\n  (:start . 26) (:id . 48))\n ((:tag . "NNS") (:stem . "report") (:form . "reports") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "require") (:form . "require") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "JJ") (:stem . "frequent") (:form . "frequent") (:end . 71)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "page") (:form . "page") (:end . 76) (:start . 72)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "update") (:form . "updates") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 97)\n  (:start . 86) (:id . 57))\n ((:tag . "NNS") (:stem . "image") (:form . "images") (:end . 104)\n  (:start . 98) (:id . 58))\n ((:tag . "VBP") (:stem . "display") (:form . "display") (:end . 112)\n  (:start . 105) (:id . 59))\n ((:tag . "RB") (:stem . "immediately") (:form . "immediately") (:end . 124)\n  (:start . 113) (:id . 60))\n ((:tag . "IN") (:stem . "upon") (:form . "upon") (:end . 129) (:start . 125)\n  (:id . 61))\n ((:tag . "NN") (:stem . "mouse-over") (:form . "mouse-over") (:end . 140)\n  (:start . 130) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 141) (:start . 140)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 64))\n ((:tag . "RB") (:stem . "hence") (:form . "hence") (:end . 151)\n  (:start . 146) (:id . 65))\n ((:tag . "VBP") (:stem . "facilitate") (:form . "facilitate") (:end . 162)\n  (:start . 152) (:id . 66))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 168)\n  (:start . 163) (:id . 67))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 173)\n  (:start . 169) (:id . 68))\n ((:tag . "NN") (:stem . "validation") (:form . "validation") (:end . 184)\n  (:start . 174) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 188) (:start . 185)\n  (:id . 70))\n ((:tag . "NN") (:stem . "interrogation") (:form . "interrogation")\n  (:end . 202) (:start . 189) (:id . 71))\n ((:tag . "NNS") (:stem . "exercise") (:form . "exercises") (:end . 212)\n  (:start . 203) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s14.163) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504665@unknown@formal@none@1@S@Optimization of Phosphopeptide Enrichment Methods@(((:tag . "NN") (:stem . "optimization") (:form . "Optimization") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Phosphopeptide") (:form . "Phosphopeptide")\n  (:end . 30) (:start . 16) (:id . 44))\n ((:tag . "NNP") (:stem . "Enrichment") (:form . "Enrichment") (:end . 41)\n  (:start . 31) (:id . 45))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 49)\n  (:start . 42) (:id . 46)))@@@1@5@((:identifiers (:sid . :s14.164) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504666@unknown@formal@none@1@S@In the aforementioned study, we leveraged the improved performance of our miniaturized LC-electrospray assemblies to elucidate signaling events in embryonic stem cells [20].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "aforementioned") (:form . "aforementioned")\n  (:end . 21) (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 27) (:start . 22)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "leverage") (:form . "leveraged") (:end . 41)\n  (:start . 32) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "improve") (:form . "improved") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 66)\n  (:start . 55) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 52))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "miniaturize") (:form . "miniaturized") (:end . 86)\n  (:start . 74) (:id . 54))\n ((:tag . "NNP") (:stem . "LC-electrospray") (:form . "LC-electrospray")\n  (:end . 102) (:start . 87) (:id . 55))\n ((:tag . "VBZ") (:stem . "assembly") (:form . "assemblies") (:end . 113)\n  (:start . 103) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 116) (:start . 114)\n  (:id . 57))\n ((:tag . "VB") (:stem . "elucidate") (:form . "elucidate") (:end . 126)\n  (:start . 117) (:id . 58))\n ((:tag . "NN") (:stem . "signaling") (:form . "signaling") (:end . 136)\n  (:start . 127) (:id . 59))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 143)\n  (:start . 137) (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 146) (:start . 144)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 156)\n  (:start . 147) (:id . 62))\n ((:tag . "NN") (:stem . "stem") (:form . "stem") (:end . 161) (:start . 157)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 167)\n  (:start . 162) (:id . 64))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 169) (:start . 168)\n  (:id . 65))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 171) (:start . 169)\n  (:id . 66))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 172) (:start . 171)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 173) (:start . 172)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s14.165) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504667@unknown@formal@none@1@S@Our specific choice to focus on tyrosine phosphorylation as a direct probe of the molecular events required for self-renewal and differentiation in these cells required optimization of enrichment protocols for peptides carrying this rare post-translational modification.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "choice") (:form . "choice") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "VB") (:stem . "focus") (:form . "focus") (:end . 28) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "tyrosine") (:form . "tyrosine") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 56) (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "probe") (:form . "probe") (:end . 74) (:start . 69)\n  (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "molecular") (:form . "molecular") (:end . 91)\n  (:start . 82) (:id . 56))\n ((:tag . "NNS") (:stem . "event") (:form . "events") (:end . 98)\n  (:start . 92) (:id . 57))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 107)\n  (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 111) (:start . 108)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "self-renewal") (:form . "self-renewal") (:end . 124)\n  (:start . 112) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 61))\n ((:tag . "NN") (:stem . "differentiation") (:form . "differentiation")\n  (:end . 144) (:start . 129) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 147) (:start . 145)\n  (:id . 63))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 153)\n  (:start . 148) (:id . 64))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 159)\n  (:start . 154) (:id . 65))\n ((:tag . "VBD") (:stem . "require") (:form . "required") (:end . 168)\n  (:start . 160) (:id . 66))\n ((:tag . "NN") (:stem . "optimization") (:form . "optimization") (:end . 181)\n  (:start . 169) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n  (:id . 68))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 195)\n  (:start . 185) (:id . 69))\n ((:tag . "NNS") (:stem . "protocol") (:form . "protocols") (:end . 205)\n  (:start . 196) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 209) (:start . 206)\n  (:id . 71))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 218)\n  (:start . 210) (:id . 72))\n ((:tag . "VBG") (:stem . "carry") (:form . "carrying") (:end . 227)\n  (:start . 219) (:id . 73))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 232) (:start . 228)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "rare") (:form . "rare") (:end . 237) (:start . 233)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "post-translational") (:form . "post-translational")\n  (:end . 256) (:start . 238) (:id . 76))\n ((:tag . "NN") (:stem . "modification") (:form . "modification") (:end . 269)\n  (:start . 257) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 270) (:start . 269)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s14.166) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504668@unknown@formal@none@1@S@A typical strategy would be to simply adjust experimental conditions to yield a maximum number of phosphotyrosine sites subsequent to LC-MS/MS and database search.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "typical") (:form . "typical") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "MD") (:stem . "would") (:form . "would") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "RB") (:stem . "simply") (:form . "simply") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "VB") (:stem . "adjust") (:form . "adjust") (:end . 44)\n  (:start . 38) (:id . 49))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 57)\n  (:start . 45) (:id . 50))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 68)\n  (:start . 58) (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "VB") (:stem . "yield") (:form . "yield") (:end . 77) (:start . 72)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "NN") (:stem . "maximum") (:form . "maximum") (:end . 87)\n  (:start . 80) (:id . 55))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 94)\n  (:start . 88) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "phosphotyrosine") (:form . "phosphotyrosine")\n  (:end . 113) (:start . 98) (:id . 58))\n ((:tag . "NNS") (:stem . "site") (:form . "sites") (:end . 119)\n  (:start . 114) (:id . 59))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 130)\n  (:start . 120) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 133) (:start . 131)\n  (:id . 61))\n ((:tag . "NN") (:stem . "lc-ms/ms") (:form . "LC-MS/MS") (:end . 142)\n  (:start . 134) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 146) (:start . 143)\n  (:id . 63))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 155)\n  (:start . 147) (:id . 64))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 162)\n  (:start . 156) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x14.167.1) (:span 19 24)))\n (:hscopes ((:id . :x14.167.1) (:span 19 162)))\n (:identifiers (:sid . :s14.167) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504669@unknown@formal@none@1@S@However, given the acutely low levels of tyrosine phosphorylation in embryonic stem cells, we chose instead to gauge enrichment efficiency based on the relative fraction of MS/MS scans that contained a phosphotyrosine immonium ion (m/z = 216.04) [21,22], irrespective of any putative peptide sequence assignment.@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "RB") (:stem . "acutely") (:form . "acutely") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "tyrosine") (:form . "tyrosine") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "phosphorylation") (:form . "phosphorylation")\n  (:end . 65) (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "embryonic") (:form . "embryonic") (:end . 78)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "stem") (:form . "stem") (:end . 83) (:start . 79)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "cell") (:form . "cells") (:end . 89) (:start . 84)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 56))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "choose") (:form . "chose") (:end . 99)\n  (:start . 94) (:id . 58))\n ((:tag . "RB") (:stem . "instead") (:form . "instead") (:end . 107)\n  (:start . 100) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 110) (:start . 108)\n  (:id . 60))\n ((:tag . "VB") (:stem . "gauge") (:form . "gauge") (:end . 116)\n  (:start . 111) (:id . 61))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 127)\n  (:start . 117) (:id . 62))\n ((:tag . "NN") (:stem . "efficiency") (:form . "efficiency") (:end . 138)\n  (:start . 128) (:id . 63))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 144)\n  (:start . 139) (:id . 64))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 147) (:start . 145)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "relative") (:form . "relative") (:end . 160)\n  (:start . 152) (:id . 67))\n ((:tag . "NN") (:stem . "fraction") (:form . "fraction") (:end . 169)\n  (:start . 161) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . 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"m/z") (:end . 235) (:start . 232)\n  (:id . 79))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 237) (:start . 236)\n  (:id . 80))\n ((:tag . "CD") (:stem . "216.04") (:form . "216.04") (:end . 244)\n  (:start . 238) (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 245) (:start . 244)\n  (:id . 82))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 247) (:start . 246)\n  (:id . 83))\n ((:tag . "CD") (:stem . "21,22") (:form . "21,22") (:end . 252)\n  (:start . 247) (:id . 84))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 253) (:start . 252)\n  (:id . 85))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 254) (:start . 253)\n  (:id . 86))\n ((:tag . "JJ") (:stem . "irrespective") (:form . "irrespective") (:end . 267)\n  (:start . 255) (:id . 87))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 270) (:start . 268)\n  (:id . 88))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 274) (:start . 271)\n  (:id . 89))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 283)\n  (:start . 275) (:id . 90))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 291)\n  (:start . 284) (:id . 91))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 300)\n  (:start . 292) (:id . 92))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 311)\n  (:start . 301) (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 312) (:start . 311)\n  (:id . 94)))@@@1@53@((:hcues ((:id . :x14.168.1) (:span 275 283)))\n (:hscopes ((:id . :x14.168.1) (:span 275 311)))\n (:identifiers (:sid . :s14.168) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504670@unknown@formal@none@1@S@This strategy allowed us to readily decouple low overall peptide yield from poor enrichment of phosphotyrosine containing peptides in experiments that generally provided modest numbers of peptide identifications (compared to typical large-scale proteomics studies).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "allow") (:form . "allowed") (:end . 21)\n  (:start . 14) (:id . 44))\n ((:tag . "PRP") (:stem . "us") (:form . "us") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 35)\n  (:start . 28) (:id . 47))\n ((:tag . "VB") (:stem . "decouple") (:form . "decouple") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "overall") (:form . "overall") (:end . 56)\n  (:start . 49) (:id . 50))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 64)\n  (:start . 57) (:id . 51))\n ((:tag . "NN") (:stem . "yield") (:form . "yield") (:end . 70) (:start . 65)\n  (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "poor") (:form . "poor") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 91)\n  (:start . 81) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 94) (:start . 92)\n  (:id . 56))\n ((:tag . "NN") (:stem . "phosphotyrosine") (:form . "phosphotyrosine")\n  (:end . 110) (:start . 95) (:id . 57))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 121)\n  (:start . 111) (:id . 58))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 130)\n  (:start . 122) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 133) (:start . 131)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "experiment") (:form . "experiments") (:end . 145)\n  (:start . 134) (:id . 61))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 150) (:start . 146)\n  (:id . 62))\n ((:tag . "RB") (:stem . "generally") (:form . "generally") (:end . 160)\n  (:start . 151) (:id . 63))\n ((:tag . "VBD") (:stem . "provide") (:form . "provided") (:end . 169)\n  (:start . 161) (:id . 64))\n ((:tag . "JJ") (:stem . "modest") (:form . "modest") (:end . 176)\n  (:start . 170) (:id . 65))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 184)\n  (:start . 177) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 187) (:start . 185)\n  (:id . 67))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 195)\n  (:start . 188) (:id . 68))\n ((:tag . "NNS") (:stem . "identification") (:form . "identifications")\n  (:end . 211) (:start . 196) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 213) (:start . 212)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 221)\n  (:start . 213) (:id . 71))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 224) (:start . 222)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "typical") (:form . "typical") (:end . 232)\n  (:start . 225) (:id . 73))\n ((:tag . "JJ") (:stem . "large-scale") (:form . "large-scale") (:end . 244)\n  (:start . 233) (:id . 74))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 255)\n  (:start . 245) (:id . 75))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 263)\n  (:start . 256) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 264) (:start . 263)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s14.169) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504671@unknown@formal@none@1@S@Figure 6a shows the .mz script used to probe MS/MS scans for the presence of a diagnostic fragment ion at m/z = 216.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "6a") (:form . "6a") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . ".mz") (:form . ".mz") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "script") (:form . "script") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "VB") (:stem . "probe") (:form . "probe") (:end . 44) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 50) (:start . 45)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 56) (:start . 51)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 60) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 73)\n  (:start . 65) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 78) (:start . 77)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "diagnostic") (:form . "diagnostic") (:end . 89)\n  (:start . 79) (:id . 58))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 98)\n  (:start . 90) (:id . 59))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . "NN") (:stem . "m/z") (:form . "m/z") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 111) (:start . 110)\n  (:id . 63))\n ((:tag . "CD") (:stem . "216") (:form . "216") (:end . 115) (:start . 112)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s14.170) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504672@unknown@formal@none@1@S@Note that Python's clear and concise syntax is readily accessible, as compared to that encountered with manufacturer libraries and data systems.@(((:tag . "VB") (:stem . "note") (:form . "Note") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 9) (:start . 5)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Python") (:form . "Python") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "clear") (:form . "clear") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "concise") (:form . "concise") (:end . 36)\n  (:start . 29) (:id . 48))\n ((:tag . "NN") (:stem . "syntax") (:form . "syntax") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 54)\n  (:start . 47) (:id . 51))\n ((:tag . "JJ") (:stem . "accessible") (:form . "accessible") (:end . 65)\n  (:start . 55) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 78)\n  (:start . 70) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "encounter") (:form . "encountered") (:end . 98)\n  (:start . 87) (:id . 58))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 103) (:start . 99)\n  (:id . 59))\n ((:tag . "NN") (:stem . "manufacturer") (:form . "manufacturer") (:end . 116)\n  (:start . 104) (:id . 60))\n ((:tag . "NNS") (:stem . "library") (:form . "libraries") (:end . 126)\n  (:start . 117) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 130) (:start . 127)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 135)\n  (:start . 131) (:id . 63))\n ((:tag . "NNS") (:stem . "system") (:form . "systems") (:end . 143)\n  (:start . 136) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 144) (:start . 143)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s14.171) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504673@unknown@formal@none@1@S@Consistent with our reporting strategy, this script outputs a tab delimited file that we readily filter in Excel to generate a histogram view of our phosphotyrosine enrichment efficiency (Figure 6b).@(((:tag . "JJ") (:stem . "consistent") (:form . "Consistent") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 15) (:start . 11)\n  (:id . 43))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "reporting") (:form . "reporting") (:end . 29)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 38)\n  (:start . 30) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "script") (:form . "script") (:end . 51)\n  (:start . 45) (:id . 49))\n ((:tag . "VBZ") (:stem . "output") (:form . "outputs") (:end . 59)\n  (:start . 52) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 61) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "tab") (:form . "tab") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "delimited") (:form . "delimited") (:end . 75)\n  (:start . 66) (:id . 53))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 80) (:start . 76)\n  (:id . 54))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 88) (:start . 86)\n  (:id . 56))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 96)\n  (:start . 89) (:id . 57))\n ((:tag . "VBP") (:stem . "filter") (:form . "filter") (:end . 103)\n  (:start . 97) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Excel") (:form . "Excel") (:end . 112)\n  (:start . 107) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n  (:id . 61))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 124)\n  (:start . 116) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 126) (:start . 125)\n  (:id . 63))\n ((:tag . "NN") (:stem . "histogram") (:form . "histogram") (:end . 136)\n  (:start . 127) (:id . 64))\n ((:tag . "NN") (:stem . "view") (:form . "view") (:end . 141) (:start . 137)\n  (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 144) (:start . 142)\n  (:id . 66))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 148) (:start . 145)\n  (:id . 67))\n ((:tag . "NN") (:stem . "phosphotyrosine") (:form . "phosphotyrosine")\n  (:end . 164) (:start . 149) (:id . 68))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 175)\n  (:start . 165) (:id . 69))\n ((:tag . "NN") (:stem . "efficiency") (:form . "efficiency") (:end . 186)\n  (:start . 176) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 188) (:start . 187)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 194)\n  (:start . 188) (:id . 72))\n ((:tag . "NN") (:stem . "6b") (:form . "6b") (:end . 197) (:start . 195)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 198) (:start . 197)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s14.172) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504674@unknown@formal@none@1@S@User-defined Customization Through .mz Scripts.@(((:tag . "JJ") (:stem . "user-defined") (:form . "User-defined") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "customization") (:form . "Customization")\n  (:end . 26) (:start . 13) (:id . 43))\n ((:tag . "IN") (:stem . "through") (:form . "Through") (:end . 34)\n  (:start . 27) (:id . 44))\n ((:tag . "NN") (:stem . ".mz") (:form . ".mz") (:end . 38) (:start . 35)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "script") (:form . "Scripts") (:end . 46)\n  (:start . 39) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 47) (:start . 46)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s14.173) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504675@unknown@formal@none@1@S@A short .mz script (a) opens each MS/MS spectrum within a given LC-MS acquisition and returns those scans that contain the phosphotyrosine immonium ion (m/z = 216).@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "NN") (:stem . ".mz") (:form . ".mz") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "script") (:form . "script") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "a") (:form . "a") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 22) (:start . 21)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "open") (:form . "opens") (:end . 28) (:start . 23)\n  (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 33) (:start . 29)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 39) (:start . 34)\n  (:id . 51))\n ((:tag . "NN") (:stem . "spectrum") (:form . "spectrum") (:end . 48)\n  (:start . 40) (:id . 52))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 55)\n  (:start . 49) (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 63) (:start . 58)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "LC-MS") (:form . "LC-MS") (:end . 69) (:start . 64)\n  (:id . 56))\n ((:tag . "NN") (:stem . "acquisition") (:form . "acquisition") (:end . 81)\n  (:start . 70) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 85) (:start . 82)\n  (:id . 58))\n ((:tag . "VBZ") (:stem . "return") (:form . "returns") (:end . 93)\n  (:start . 86) (:id . 59))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 99) (:start . 94)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 105)\n  (:start . 100) (:id . 61))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 110) (:start . 106)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 118)\n  (:start . 111) (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 64))\n ((:tag . "NN") (:stem . "phosphotyrosine") (:form . "phosphotyrosine")\n  (:end . 138) (:start . 123) (:id . 65))\n ((:tag . "NN") (:stem . "immonium") (:form . "immonium") (:end . 147)\n  (:start . 139) (:id . 66))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 151) (:start . 148)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . "NN") (:stem . "m/z") (:form . "m/z") (:end . 156) (:start . 153)\n  (:id . 69))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 158) (:start . 157)\n  (:id . 70))\n ((:tag . "CD") (:stem . "216") (:form . "216") (:end . 162) (:start . 159)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 163) (:start . 162)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 164) (:start . 163)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s14.174) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504676@unknown@formal@none@1@S@The tab-delimited multiplierz output is readily opened in Excel and (b) a histogram view facilitates rapid evaluation of enrichment efficiency.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "tab-delimited") (:form . "tab-delimited")\n  (:end . 17) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 29)\n  (:start . 18) (:id . 44))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 36)\n  (:start . 30) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 39) (:start . 37)\n  (:id . 46))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 47)\n  (:start . 40) (:id . 47))\n ((:tag . "VBN") (:stem . "open") (:form . "opened") (:end . 54) (:start . 48)\n  (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Excel") (:form . "Excel") (:end . 63) (:start . 58)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "LS") (:stem . "b") (:form . "b") (:end . 70) (:start . 69)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "histogram") (:form . "histogram") (:end . 83)\n  (:start . 74) (:id . 56))\n ((:tag . "NN") (:stem . "view") (:form . "view") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "facilitate") (:form . "facilitates") (:end . 100)\n  (:start . 89) (:id . 58))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 106)\n  (:start . 101) (:id . 59))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 117)\n  (:start . 107) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 120) (:start . 118)\n  (:id . 61))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 131)\n  (:start . 121) (:id . 62))\n ((:tag . "NN") (:stem . "efficiency") (:form . "efficiency") (:end . 142)\n  (:start . 132) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s14.175) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504677@unknown@formal@none@1@S@In this example, the majority of peptides in the heart of the LC gradient (~25 - 65 min.) contain phosphotyrosine residues as evidenced by the presence of an m/z = 216 immonium ion.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 29)\n  (:start . 21) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 41)\n  (:start . 33) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "NN") (:stem . "heart") (:form . "heart") (:end . 54) (:start . 49)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "LC") (:form . "LC") (:end . 64) (:start . 62)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gradient") (:form . "gradient") (:end . 73)\n  (:start . 65) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . "CD") (:stem . "~25") (:form . "~25") (:end . 78) (:start . 75)\n  (:id . 58))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 80) (:start . 79)\n  (:id . 59))\n ((:tag . "CD") (:stem . "65") (:form . "65") (:end . 83) (:start . 81)\n  (:id . 60))\n ((:tag . "NN") (:stem . "min.") (:form . "min.") (:end . 88) (:start . 84)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "contain") (:form . "contain") (:end . 97)\n  (:start . 90) (:id . 63))\n ((:tag . "NN") (:stem . "phosphotyrosine") (:form . "phosphotyrosine")\n  (:end . 113) (:start . 98) (:id . 64))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 122)\n  (:start . 114) (:id . 65))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 125) (:start . 123)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "evidence") (:form . "evidenced") (:end . 135)\n  (:start . 126) (:id . 67))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 138) (:start . 136)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 142) (:start . 139)\n  (:id . 69))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 151)\n  (:start . 143) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n  (:id . 71))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 157) (:start . 155)\n  (:id . 72))\n ((:tag . "NN") (:stem . "m/z") (:form . "m/z") (:end . 161) (:start . 158)\n  (:id . 73))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 163) (:start . 162)\n  (:id . 74))\n ((:tag . "CD") (:stem . "216") (:form . "216") (:end . 167) (:start . 164)\n  (:id . 75))\n ((:tag . "NN") (:stem . "immonium") (:form . "immonium") (:end . 176)\n  (:start . 168) (:id . 76))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 180) (:start . 177)\n  (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s14.176) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504678@unknown@formal@none@1@S@In a separate report we described the novel application of niobium(V) oxide (Nb2O5) for global enrichment of phosphopeptides from complex, biologically derived mixtures [23].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "separate") (:form . "separate") (:end . 13)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 20)\n  (:start . 14) (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 23) (:start . 21)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "describe") (:form . "described") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "application") (:form . "application") (:end . 55)\n  (:start . 44) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "CD") (:stem . "niobium(V)") (:form . "niobium(V)") (:end . 69)\n  (:start . 59) (:id . 52))\n ((:tag . "NN") (:stem . "oxide") (:form . "oxide") (:end . 75) (:start . 70)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Nb2O5") (:form . "Nb2O5") (:end . 82) (:start . 77)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 87) (:start . 84)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "global") (:form . "global") (:end . 94)\n  (:start . 88) (:id . 58))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 105)\n  (:start . 95) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "phosphopeptide") (:form . "phosphopeptides")\n  (:end . 124) (:start . 109) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 129) (:start . 125)\n  (:id . 62))\n ((:tag . "NN") (:stem . "complex") (:form . "complex") (:end . 137)\n  (:start . 130) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 64))\n ((:tag . "RB") (:stem . "biologically") (:form . "biologically") (:end . 151)\n  (:start . 139) (:id . 65))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 159)\n  (:start . 152) (:id . 66))\n ((:tag . "NNS") (:stem . "mixture") (:form . "mixtures") (:end . 168)\n  (:start . 160) (:id . 67))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 170) (:start . 169)\n  (:id . 68))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 172) (:start . 170)\n  (:id . 69))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 173) (:start . 172)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 174) (:start . 173)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s14.177) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504679@unknown@formal@none@1@S@The "multi-detect" and "multi-filter" tools in multiplierz were used to compare phosphopeptides enriched via Nb2O5 and TiO2, (the current standard), and detected across multiple LC-MS/MS analyses.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "multi-detect") (:form . "multi-detect") (:end . 17)\n  (:start . 5) (:id . 44))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 24) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "multi-filter") (:form . "multi-filter") (:end . 36)\n  (:start . 24) (:id . 48))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "tool") (:form . "tools") (:end . 43) (:start . 38)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 51))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 58)\n  (:start . 47) (:id . 52))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 63) (:start . 59)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 68) (:start . 64)\n  (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 79)\n  (:start . 72) (:id . 56))\n ((:tag . "NNS") (:stem . "phosphopeptide") (:form . "phosphopeptides")\n  (:end . 95) (:start . 80) (:id . 57))\n ((:tag . "VBN") (:stem . "enrich") (:form . "enriched") (:end . 104)\n  (:start . 96) (:id . 58))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Nb2O5") (:form . "Nb2O5") (:end . 114)\n  (:start . 109) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "TiO2") (:form . "TiO2") (:end . 123) (:start . 119)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 129) (:start . 126)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 137)\n  (:start . 130) (:id . 66))\n ((:tag . "NN") (:stem . "standard") (:form . "standard") (:end . 146)\n  (:start . 138) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 147) (:start . 146)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 70))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 161)\n  (:start . 153) (:id . 71))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 168)\n  (:start . 162) (:id . 72))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 177)\n  (:start . 169) (:id . 73))\n ((:tag . "NN") (:stem . "lc-ms/ms") (:form . "LC-MS/MS") (:end . 186)\n  (:start . 178) (:id . 74))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 195)\n  (:start . 187) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 196) (:start . 195)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s14.178) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504680@unknown@formal@none@1@S@Furthermore, to assess potential bias introduced by the stochastic nature of MS/MS, we compared the precursor peak intensities of unique versus commonly detected phosphopeptides that resulted from each method, and confirmed that Nb2O5 and TiO2 exhibited an empirically useful degree of divergence with respect to phosphopeptide enrichment (Figure 7, reprinted from Ficarro et al. [23] by permission from the American Chemical Society).@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "JJ") (:stem . "potential") (:form . "potential") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "bias") (:form . 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"DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 58))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 109)\n  (:start . 100) (:id . 59))\n ((:tag . "NN") (:stem . "peak") (:form . "peak") (:end . 114) (:start . 110)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "intensity") (:form . "intensities") (:end . 126)\n  (:start . 115) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 129) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 136)\n  (:start . 130) (:id . 63))\n ((:tag . "IN") (:stem . "versus") (:form . "versus") (:end . 143)\n  (:start . 137) (:id . 64))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 152)\n  (:start . 144) (:id . 65))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 161)\n  (:start . 153) (:id . 66))\n ((:tag . "NNS") (:stem . "phosphopeptide") (:form . "phosphopeptides")\n  (:end . 177) (:start . 162) (:id . 67))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 182) (:start . 178)\n  (:id . 68))\n ((:tag . "VBD") (:stem . "result") (:form . "resulted") (:end . 191)\n  (:start . 183) (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 196) (:start . 192)\n  (:id . 70))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 201) (:start . 197)\n  (:id . 71))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 208)\n  (:start . 202) (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 209) (:start . 208)\n  (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 213) (:start . 210)\n  (:id . 74))\n ((:tag . "VBD") (:stem . "confirm") (:form . "confirmed") (:end . 223)\n  (:start . 214) (:id . 75))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 228) (:start . 224)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "Nb2O5") (:form . "Nb2O5") (:end . 234)\n  (:start . 229) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 238) (:start . 235)\n  (:id . 78))\n ((:tag . "NN") (:stem . "tio2") (:form . "TiO2") (:end . 243) (:start . 239)\n  (:id . 79))\n ((:tag . "VBD") (:stem . "exhibit") (:form . "exhibited") (:end . 253)\n  (:start . 244) (:id . 80))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 256) (:start . 254)\n  (:id . 81))\n ((:tag . "RB") (:stem . "empirically") (:form . "empirically") (:end . 268)\n  (:start . 257) (:id . 82))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 275)\n  (:start . 269) (:id . 83))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 282)\n  (:start . 276) (:id . 84))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 285) (:start . 283)\n  (:id . 85))\n ((:tag . "NN") (:stem . "divergence") (:form . "divergence") (:end . 296)\n  (:start . 286) (:id . 86))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 301) (:start . 297)\n  (:id . 87))\n ((:tag . "NN") (:stem . "respect") (:form . "respect") (:end . 309)\n  (:start . 302) (:id . 88))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 312) (:start . 310)\n  (:id . 89))\n ((:tag . "NN") (:stem . "phosphopeptide") (:form . "phosphopeptide")\n  (:end . 327) (:start . 313) (:id . 90))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 338)\n  (:start . 328) (:id . 91))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 340) (:start . 339)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 346)\n  (:start . 340) (:id . 93))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 348) (:start . 347)\n  (:id . 94))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 349) (:start . 348)\n  (:id . 95))\n ((:tag . "VBN") (:stem . "reprint") (:form . "reprinted") (:end . 359)\n  (:start . 350) (:id . 96))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 364) (:start . 360)\n  (:id . 97))\n ((:tag . "NNP") (:stem . "Ficarro") (:form . "Ficarro") (:end . 372)\n  (:start . 365) (:id . 98))\n ((:tag . "FW") (:stem . "et") (:form . "et") (:end . 375) (:start . 373)\n  (:id . 99))\n ((:tag . "FW") (:stem . "al.") (:form . "al.") (:end . 379) (:start . 376)\n  (:id . 100))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 381) (:start . 380)\n  (:id . 101))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 383) (:start . 381)\n  (:id . 102))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 384) (:start . 383)\n  (:id . 103))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 387) (:start . 385)\n  (:id . 104))\n ((:tag . "NN") (:stem . "permission") (:form . "permission") (:end . 398)\n  (:start . 388) (:id . 105))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 403) (:start . 399)\n  (:id . 106))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 407) (:start . 404)\n  (:id . 107))\n ((:tag . "NNP") (:stem . "American") (:form . "American") (:end . 416)\n  (:start . 408) (:id . 108))\n ((:tag . "NNP") (:stem . "Chemical") (:form . "Chemical") (:end . 425)\n  (:start . 417) (:id . 109))\n ((:tag . "NNP") (:stem . "Society") (:form . "Society") (:end . 433)\n  (:start . 426) (:id . 110))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 434) (:start . 433)\n  (:id . 111))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 435) (:start . 434)\n  (:id . 112)))@@@1@71@((:identifiers (:sid . :s14.179) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504681@unknown@formal@none@1@S@Quantitative Comparison of Phosphopeptide Enrichment Methods.@(((:tag . "JJ") (:stem . "quantitative") (:form . "Quantitative") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Comparison") (:form . "Comparison") (:end . 23)\n  (:start . 13) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Phosphopeptide") (:form . "Phosphopeptide")\n  (:end . 41) (:start . 27) (:id . 45))\n ((:tag . "NNP") (:stem . "Enrichment") (:form . "Enrichment") (:end . 52)\n  (:start . 42) (:id . 46))\n ((:tag . "NNP") (:stem . "Method") (:form . "Methods") (:end . 60)\n  (:start . 53) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 61) (:start . 60)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s14.180) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504682@unknown@formal@none@1@S@Histogram distributions of peak heights for unique and overlapping phosphopeptides detected in conjunction with (a) (TiO2)-, and (b) (Nb2O5)-based enrichment.@(((:tag . "NNP") (:stem . "Histogram") (:form . "Histogram") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 23) (:start . 10) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 44))\n ((:tag . "NN") (:stem . "peak") (:form . "peak") (:end . 31) (:start . 27)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "height") (:form . "heights") (:end . 39)\n  (:start . 32) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 50)\n  (:start . 44) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "overlap") (:form . "overlapping") (:end . 66)\n  (:start . 55) (:id . 50))\n ((:tag . "NNS") (:stem . "phosphopeptide") (:form . "phosphopeptides")\n  (:end . 82) (:start . 67) (:id . 51))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 91)\n  (:start . 83) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n  (:id . 53))\n ((:tag . "NN") (:stem . "conjunction") (:form . "conjunction") (:end . 106)\n  (:start . 95) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 111) (:start . 107)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 114) (:start . 113)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "TiO2)-") (:form . "TiO2)-") (:end . 123)\n  (:start . 117) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 124) (:start . 123)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 63))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 131) (:start . 130)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 134) (:start . 133)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "Nb2O5)-based") (:form . "Nb2O5)-based") (:end . 146)\n  (:start . 134) (:id . 67))\n ((:tag . "NN") (:stem . "enrichment") (:form . "enrichment") (:end . 157)\n  (:start . 147) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 158) (:start . 157)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s14.181) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504683@unknown@formal@none@1@S@The intensity distributions for phosphopeptides assigned uniquely to either metal oxide did not differ significantly from the intensity distributions for commonly detected phosphopeptides, indicating that the unique precursors were not confined to low signal-to-noise regions.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 27) (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 31) (:start . 28)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "phosphopeptide") (:form . "phosphopeptides")\n  (:end . 47) (:start . 32) (:id . 46))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 56)\n  (:start . 48) (:id . 47))\n ((:tag . "RB") (:stem . "uniquely") (:form . "uniquely") (:end . 65)\n  (:start . 57) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 68) (:start . 66)\n  (:id . 49))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 75)\n  (:start . 69) (:id . 50))\n ((:tag . "NN") (:stem . "metal") (:form . "metal") (:end . 81) (:start . 76)\n  (:id . 51))\n ((:tag . "NN") (:stem . "oxide") (:form . "oxide") (:end . 87) (:start . 82)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 91) (:start . 88)\n  (:id . 53))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 95) (:start . 92)\n  (:id . 54))\n ((:tag . "VB") (:stem . "differ") (:form . "differ") (:end . 102)\n  (:start . 96) (:id . 55))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 116) (:start . 103) (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 121) (:start . 117)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 58))\n ((:tag . "NN") (:stem . "intensity") (:form . "intensity") (:end . 135)\n  (:start . 126) (:id . 59))\n ((:tag . "NNS") (:stem . "distribution") (:form . "distributions")\n  (:end . 149) (:start . 136) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 153) (:start . 150)\n  (:id . 61))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 162)\n  (:start . 154) (:id . 62))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 171)\n  (:start . 163) (:id . 63))\n ((:tag . "NNS") (:stem . "phosphopeptide") (:form . "phosphopeptides")\n  (:end . 187) (:start . 172) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 188) (:start . 187)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "indicate") (:form . "indicating") (:end . 199)\n  (:start . 189) (:id . 66))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 204) (:start . 200)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 208) (:start . 205)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 215)\n  (:start . 209) (:id . 69))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 226)\n  (:start . 216) (:id . 70))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 231) (:start . 227)\n  (:id . 71))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 235) (:start . 232)\n  (:id . 72))\n ((:tag . "VBN") (:stem . "confine") (:form . "confined") (:end . 244)\n  (:start . 236) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 247) (:start . 245)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 251) (:start . 248)\n  (:id . 75))\n ((:tag . "NN") (:stem . "signal-to-noise") (:form . "signal-to-noise")\n  (:end . 267) (:start . 252) (:id . 76))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 275)\n  (:start . 268) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 276) (:start . 275)\n  (:id . 78)))@@@1@37@((:hcues ((:id . :x14.182.1) (:span 189 204)))\n (:hscopes ((:id . :x14.182.1) (:span 189 275)))\n (:identifiers (:sid . :s14.182) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504684@unknown@formal@none@1@S@Reprinted from [23] by permission from the American Chemical Society.@(((:tag . "VBN") (:stem . "reprint") (:form . "Reprinted") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 22) (:start . 20)\n  (:id . 47))\n ((:tag . "NN") (:stem . "permission") (:form . "permission") (:end . 33)\n  (:start . 23) (:id . 48))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "American") (:form . "American") (:end . 51)\n  (:start . 43) (:id . 51))\n ((:tag . "NNP") (:stem . "Chemical") (:form . "Chemical") (:end . 60)\n  (:start . 52) (:id . 52))\n ((:tag . "NNP") (:stem . "Society") (:form . "Society") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s14.183) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504685@unknown@formal@none@1@S@Improved Peptide Sequence Assignment via De-isotoped MS/MS Spectra@(((:tag . "NNP") (:stem . "Improved") (:form . "Improved") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Peptide") (:form . "Peptide") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "NNP") (:stem . "Sequence") (:form . "Sequence") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "NNP") (:stem . "Assignment") (:form . "Assignment") (:end . 36)\n  (:start . 26) (:id . 45))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 40) (:start . 37)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "De-isotoped") (:form . "De-isotoped") (:end . 52)\n  (:start . 41) (:id . 47))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 58) (:start . 53)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Spectra") (:form . "Spectra") (:end . 66)\n  (:start . 59) (:id . 49)))@@@1@8@((:identifiers (:sid . :s14.184) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504686@unknown@formal@none@1@S@In another recent study, we optimized performance of orbitrap HCD MS/MS through systematic exploration of various instrument and post-acquisition parameters [24].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "another") (:form . "another") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "optimize") (:form . "optimized") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 49)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "NN") (:stem . "orbitrap") (:form . "orbitrap") (:end . 61)\n  (:start . 53) (:id . 51))\n ((:tag . "NNP") (:stem . "HCD") (:form . "HCD") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . "IN") (:stem . "through") (:form . "through") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "JJ") (:stem . "systematic") (:form . "systematic") (:end . 90)\n  (:start . 80) (:id . 55))\n ((:tag . "NN") (:stem . "exploration") (:form . "exploration") (:end . 102)\n  (:start . 91) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 113)\n  (:start . 106) (:id . 58))\n ((:tag . "NN") (:stem . "instrument") (:form . "instrument") (:end . 124)\n  (:start . 114) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "post-acquisition") (:form . "post-acquisition")\n  (:end . 145) (:start . 129) (:id . 61))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 156)\n  (:start . 146) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 158) (:start . 157)\n  (:id . 63))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 160) (:start . 158)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 161) (:start . 160)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s14.185) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504687@unknown@formal@none@1@S@In the context of this work, we observed that high charge state (z > 2+) precursors were frequently not assigned to a peptide sequence despite an otherwise high quality fragment ion spectrum.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "context") (:form . "context") (:end . 14)\n  (:start . 7) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "work") (:form . "work") (:end . 27) (:start . 23)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 31) (:start . 29)\n  (:id . 49))\n ((:tag . "VBD") (:stem . "observe") (:form . "observed") (:end . 40)\n  (:start . 32) (:id . 50))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 45) (:start . 41)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 50) (:start . 46)\n  (:id . 52))\n ((:tag . "NN") (:stem . "charge") (:form . "charge") (:end . 57)\n  (:start . 51) (:id . 53))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 63) (:start . 58)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "NN") (:stem . "z") (:form . "z") (:end . 66) (:start . 65)\n  (:id . 56))\n ((:tag . "SYM") (:stem . ">") (:form . ">") (:end . 68) (:start . 67)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "2+") (:form . "2+") (:end . 71) (:start . 69)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 83)\n  (:start . 73) (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 88) (:start . 84)\n  (:id . 61))\n ((:tag . "RB") (:stem . "frequently") (:form . "frequently") (:end . 99)\n  (:start . 89) (:id . 62))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 103) (:start . 100)\n  (:id . 63))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 112)\n  (:start . 104) (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 115) (:start . 113)\n  (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 117) (:start . 116)\n  (:id . 66))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 125)\n  (:start . 118) (:id . 67))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 134)\n  (:start . 126) (:id . 68))\n ((:tag . "IN") (:stem . "despite") (:form . "despite") (:end . 142)\n  (:start . 135) (:id . 69))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 145) (:start . 143)\n  (:id . 70))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 155)\n  (:start . 146) (:id . 71))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 160) (:start . 156)\n  (:id . 72))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 168)\n  (:start . 161) (:id . 73))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 177)\n  (:start . 169) (:id . 74))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 181) (:start . 178)\n  (:id . 75))\n ((:tag . "NN") (:stem . "spectrum") (:form . "spectrum") (:end . 190)\n  (:start . 182) (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 191) (:start . 190)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s14.186) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504688@unknown@formal@none@1@S@We speculated that the presence of multiple isotope peaks per fragment ion in the high resolution Orbitrap MS/MS scans may degrade the sensitivity of the search algorithm, resulting in fewer high-confidence sequence assignments.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "speculate") (:form . "speculated") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "presence") (:form . "presence") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 43)\n  (:start . 35) (:id . 48))\n ((:tag . "NN") (:stem . "isotope") (:form . "isotope") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "peak") (:form . "peaks") (:end . 57) (:start . 52)\n  (:id . 50))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 61) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 74) (:start . 71)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 86) (:start . 82)\n  (:id . 56))\n ((:tag . "NN") (:stem . "resolution") (:form . "resolution") (:end . 97)\n  (:start . 87) (:id . 57))\n ((:tag . "NNP") (:stem . "Orbitrap") (:form . "Orbitrap") (:end . 106)\n  (:start . 98) (:id . 58))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 112)\n  (:start . 107) (:id . 59))\n ((:tag . "NNS") (:stem . "scan") (:form . "scans") (:end . 118)\n  (:start . 113) (:id . 60))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 122) (:start . 119)\n  (:id . 61))\n ((:tag . "VB") (:stem . "degrade") (:form . "degrade") (:end . 130)\n  (:start . 123) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 134) (:start . 131)\n  (:id . 63))\n ((:tag . "NN") (:stem . "sensitivity") (:form . "sensitivity") (:end . 146)\n  (:start . 135) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 149) (:start . 147)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 153) (:start . 150)\n  (:id . 66))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 160)\n  (:start . 154) (:id . 67))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 170)\n  (:start . 161) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 69))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 181)\n  (:start . 172) (:id . 70))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 184) (:start . 182)\n  (:id . 71))\n ((:tag . "JJR") (:stem . "few") (:form . "fewer") (:end . 190) (:start . 185)\n  (:id . 72))\n ((:tag . "NN") (:stem . "high-confidence") (:form . "high-confidence")\n  (:end . 206) (:start . 191) (:id . 73))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 215)\n  (:start . 207) (:id . 74))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 227)\n  (:start . 216) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 228) (:start . 227)\n  (:id . 76)))@@@1@35@((:hcues ((:id . :x14.187.1) (:span 119 122))\n  ((:id . :x14.187.2) (:span 3 13)))\n (:hscopes ((:id . :x14.187.1) (:span 119 170))\n  ((:id . :x14.187.2) (:span 3 227)))\n (:identifiers (:sid . :s14.187) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504689@unknown@formal@none@1@S@Therefore, we generated an .mz Script (see Additional File 2) that de-isotoped [25] each fragment ion cluster and output a charge state reduced peak list for submission to Mascot.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . ".mz") (:form . ".mz") (:end . 30) (:start . 27)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Script") (:form . "Script") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 53)\n  (:start . 43) (:id . 51))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 61) (:start . 60)\n  (:id . 54))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 66) (:start . 62)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "de-isotope") (:form . "de-isotoped") (:end . 78)\n  (:start . 67) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 80) (:start . 79)\n  (:id . 57))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 82) (:start . 80)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 83) (:start . 82)\n  (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 88) (:start . 84)\n  (:id . 60))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 97)\n  (:start . 89) (:id . 61))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 101) (:start . 98)\n  (:id . 62))\n ((:tag . "NN") (:stem . "cluster") (:form . "cluster") (:end . 109)\n  (:start . 102) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 64))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 120)\n  (:start . 114) (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 122) (:start . 121)\n  (:id . 66))\n ((:tag . "NN") (:stem . "charge") (:form . "charge") (:end . 129)\n  (:start . 123) (:id . 67))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 135)\n  (:start . 130) (:id . 68))\n ((:tag . "VBD") (:stem . "reduce") (:form . "reduced") (:end . 143)\n  (:start . 136) (:id . 69))\n ((:tag . "JJ") (:stem . "peak") (:form . "peak") (:end . 148) (:start . 144)\n  (:id . 70))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 153) (:start . 149)\n  (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 157) (:start . 154)\n  (:id . 72))\n ((:tag . "NN") (:stem . "submission") (:form . "submission") (:end . 168)\n  (:start . 158) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 171) (:start . 169)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 178)\n  (:start . 172) (:id . 75))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 76)))@@@1@35@((:identifiers (:sid . :s14.188) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504690@unknown@formal@none@1@S@A variety of parameters can be used to adjust the stringency of spectrum filtering such as maximum charge state, minimum fragment ion mass-to-charge ratio, as well as an option to remove any precursor signal that may remain in the MS/MS spectrum.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "variety") (:form . "variety") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 38) (:start . 36)\n  (:id . 49))\n ((:tag . "VB") (:stem . "adjust") (:form . "adjust") (:end . 45)\n  (:start . 39) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "stringency") (:form . "stringency") (:end . 60)\n  (:start . 50) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "spectrum") (:form . "spectrum") (:end . 72)\n  (:start . 64) (:id . 54))\n ((:tag . "NN") (:stem . "filtering") (:form . "filtering") (:end . 82)\n  (:start . 73) (:id . 55))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 87) (:start . 83)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 90) (:start . 88)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "maximum") (:form . "maximum") (:end . 98)\n  (:start . 91) (:id . 58))\n ((:tag . "NN") (:stem . "charge") (:form . "charge") (:end . 105)\n  (:start . 99) (:id . 59))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 111)\n  (:start . 106) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 61))\n ((:tag . "NN") (:stem . "minimum") (:form . "minimum") (:end . 120)\n  (:start . 113) (:id . 62))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 129)\n  (:start . 121) (:id . 63))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 133) (:start . 130)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "mass-to-charge") (:form . "mass-to-charge")\n  (:end . 148) (:start . 134) (:id . 65))\n ((:tag . "NN") (:stem . "ratio") (:form . "ratio") (:end . 154)\n  (:start . 149) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n  (:id . 67))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 158) (:start . 156)\n  (:id . 68))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 163) (:start . 159)\n  (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 166) (:start . 164)\n  (:id . 70))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 169) (:start . 167)\n  (:id . 71))\n ((:tag . "NN") (:stem . "option") (:form . "option") (:end . 176)\n  (:start . 170) (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 179) (:start . 177)\n  (:id . 73))\n ((:tag . "VB") (:stem . "remove") (:form . "remove") (:end . 186)\n  (:start . 180) (:id . 74))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 190) (:start . 187)\n  (:id . 75))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 200)\n  (:start . 191) (:id . 76))\n ((:tag . "NN") (:stem . "signal") (:form . "signal") (:end . 207)\n  (:start . 201) (:id . 77))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 212) (:start . 208)\n  (:id . 78))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 216) (:start . 213)\n  (:id . 79))\n ((:tag . "VB") (:stem . "remain") (:form . "remain") (:end . 223)\n  (:start . 217) (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 226) (:start . 224)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 230) (:start . 227)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 236)\n  (:start . 231) (:id . 83))\n ((:tag . "NN") (:stem . "spectrum") (:form . "spectrum") (:end . 245)\n  (:start . 237) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 246) (:start . 245)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x14.189.1) (:span 213 216)))\n (:hscopes ((:id . :x14.189.1) (:span 213 245)))\n (:identifiers (:sid . :s14.189) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504691@unknown@formal@none@1@S@Overall we realized an approximate 30% gain in the number of high-confidence (Mascot score > 30) peptide sequence assignments for high charge state precursors (Table 2).@(((:tag . "RB") (:stem . "overall") (:form . "Overall") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "realize") (:form . "realized") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "approximate") (:form . "approximate") (:end . 34)\n  (:start . 23) (:id . 46))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "NN") (:stem . "gain") (:form . "gain") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 46) (:start . 44)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 57)\n  (:start . 51) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "NN") (:stem . "high-confidence") (:form . "high-confidence")\n  (:end . 76) (:start . 61) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 84)\n  (:start . 78) (:id . 56))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "JJR") (:stem . ">") (:form . ">") (:end . 92) (:start . 91)\n  (:id . 58))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 104)\n  (:start . 97) (:id . 61))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 113)\n  (:start . 105) (:id . 62))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 125)\n  (:start . 114) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 129) (:start . 126)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 134) (:start . 130)\n  (:id . 65))\n ((:tag . "NN") (:stem . "charge") (:form . "charge") (:end . 141)\n  (:start . 135) (:id . 66))\n ((:tag . "NN") (:stem . "state") (:form . "state") (:end . 147)\n  (:start . 142) (:id . 67))\n ((:tag . "NNS") (:stem . "precursor") (:form . "precursors") (:end . 158)\n  (:start . 148) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 160) (:start . 159)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 165)\n  (:start . 160) (:id . 70))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 167) (:start . 166)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 168) (:start . 167)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s14.190) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504692@unknown@formal@none@1@S@Improved Peptide Sequence Assignment via De-isotoped MS/MS Spectra.@(((:tag . "NNP") (:stem . "Improved") (:form . "Improved") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Peptide") (:form . "Peptide") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "NNP") (:stem . "Sequence") (:form . "Sequence") (:end . 25)\n  (:start . 17) (:id . 44))\n ((:tag . "NNP") (:stem . "Assignment") (:form . "Assignment") (:end . 36)\n  (:start . 26) (:id . 45))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 40) (:start . 37)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "De-isotoped") (:form . "De-isotoped") (:end . 52)\n  (:start . 41) (:id . 47))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 58) (:start . 53)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Spectra") (:form . "Spectra") (:end . 66)\n  (:start . 59) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s14.191) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504693@unknown@formal@none@1@S@Label-Free Quantitative Proteomics@(((:tag . "JJ") (:stem . "label-free") (:form . "Label-Free") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "quantitative") (:form . "Quantitative") (:end . 23)\n  (:start . 11) (:id . 43))\n ((:tag . "NNPS") (:stem . "Proteomic") (:form . "Proteomics") (:end . 34)\n  (:start . 24) (:id . 44)))@@@1@3@((:identifiers (:sid . :s14.192) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504694@unknown@formal@none@1@S@Relative protein quantitation can be achieved via a label-free approach whereby tryptic digests of protein samples are analyzed without incorporation of stable isotope labels; the resulting peak intensities (or areas) for the constituent peptides are combined and compared across samples as well as within replicates [26].@(((:tag . "JJ") (:stem . "relative") (:form . "Relative") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 16)\n  (:start . 9) (:id . 43))\n ((:tag . "NN") (:stem . "quantitation") (:form . "quantitation") (:end . 29)\n  (:start . 17) (:id . 44))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 33) (:start . 30)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 36) (:start . 34)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 45)\n  (:start . 37) (:id . 47))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "label-free") (:form . "label-free") (:end . 62)\n  (:start . 52) (:id . 50))\n ((:tag . "NN") (:stem . "approach") (:form . "approach") (:end . 71)\n  (:start . 63) (:id . 51))\n ((:tag . "WRB") (:stem . "whereby") (:form . "whereby") (:end . 79)\n  (:start . 72) (:id . 52))\n ((:tag . "JJ") (:stem . "tryptic") (:form . "tryptic") (:end . 87)\n  (:start . 80) (:id . 53))\n ((:tag . "NNS") (:stem . "digest") (:form . "digests") (:end . 95)\n  (:start . 88) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 106)\n  (:start . 99) (:id . 56))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 114)\n  (:start . 107) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 118) (:start . 115)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 127)\n  (:start . 119) (:id . 59))\n ((:tag . "IN") (:stem . "without") (:form . "without") (:end . 135)\n  (:start . 128) (:id . 60))\n ((:tag . "NN") (:stem . "incorporation") (:form . "incorporation")\n  (:end . 149) (:start . 136) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 152) (:start . 150)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "stable") (:form . "stable") (:end . 159)\n  (:start . 153) (:id . 63))\n ((:tag . "NN") (:stem . "isotope") (:form . "isotope") (:end . 167)\n  (:start . 160) (:id . 64))\n ((:tag . "NNS") (:stem . "label") (:form . "labels") (:end . 174)\n  (:start . 168) (:id . 65))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 175) (:start . 174)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 179) (:start . 176)\n  (:id . 67))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 189)\n  (:start . 180) (:id . 68))\n ((:tag . "NN") (:stem . "peak") (:form . "peak") (:end . 194) (:start . 190)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "intensity") (:form . "intensities") (:end . 206)\n  (:start . 195) (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 208) (:start . 207)\n  (:id . 71))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 210) (:start . 208)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "area") (:form . "areas") (:end . 216)\n  (:start . 211) (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 217) (:start . 216)\n  (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 221) (:start . 218)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 225) (:start . 222)\n  (:id . 76))\n ((:tag . "NN") (:stem . "constituent") (:form . "constituent") (:end . 237)\n  (:start . 226) (:id . 77))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 246)\n  (:start . 238) (:id . 78))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 250) (:start . 247)\n  (:id . 79))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 259)\n  (:start . 251) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 263) (:start . 260)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 272)\n  (:start . 264) (:id . 82))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 279)\n  (:start . 273) (:id . 83))\n ((:tag . "NNS") (:stem . "sample") (:form . "samples") (:end . 287)\n  (:start . 280) (:id . 84))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 290) (:start . 288)\n  (:id . 85))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 295) (:start . 291)\n  (:id . 86))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 298) (:start . 296)\n  (:id . 87))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 305)\n  (:start . 299) (:id . 88))\n ((:tag . "NNS") (:stem . "replicate") (:form . "replicates") (:end . 316)\n  (:start . 306) (:id . 89))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 318) (:start . 317)\n  (:id . 90))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 320) (:start . 318)\n  (:id . 91))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 321) (:start . 320)\n  (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 322) (:start . 321)\n  (:id . 93)))@@@1@52@((:hcues ((:id . :x14.193.1) (:span 30 33)))\n (:hscopes ((:id . :x14.193.1) (:span 0 71)))\n (:identifiers (:sid . :s14.193) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504695@unknown@formal@none@1@S@Typically 3-5 replicates of each sample are required to account for non-systematic errors associated with shifts in chromatographic elution time, temperature, electrospray stability, etc.@(((:tag . "RB") (:stem . "typically") (:form . "Typically") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "CD") (:stem . "3-5") (:form . "3-5") (:end . 13) (:start . 10)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "replicate") (:form . "replicates") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sample") (:form . "sample") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "VB") (:stem . "account") (:form . "account") (:end . 63)\n  (:start . 56) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "non-systematic") (:form . "non-systematic")\n  (:end . 82) (:start . 68) (:id . 53))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 89)\n  (:start . 83) (:id . 54))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 100)\n  (:start . 90) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 105) (:start . 101)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "shift") (:form . "shifts") (:end . 112)\n  (:start . 106) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 115) (:start . 113)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "chromatographic") (:form . "chromatographic")\n  (:end . 131) (:start . 116) (:id . 59))\n ((:tag . "NN") (:stem . "elution") (:form . "elution") (:end . 139)\n  (:start . 132) (:id . 60))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 144) (:start . 140)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 62))\n ((:tag . "NN") (:stem . "temperature") (:form . "temperature") (:end . 157)\n  (:start . 146) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 64))\n ((:tag . "NN") (:stem . "electrospray") (:form . "electrospray") (:end . 171)\n  (:start . 159) (:id . 65))\n ((:tag . "NN") (:stem . "stability") (:form . "stability") (:end . 181)\n  (:start . 172) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 182) (:start . 181)\n  (:id . 67))\n ((:tag . "FW") (:stem . "etc") (:form . "etc") (:end . 186) (:start . 183)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s14.194) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504696@unknown@formal@none@1@S@For very large studies, performed across extended periods of time and multiple labs, complex software is typically required to combine, align and analyze the resulting native mass spectrometry files.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "study") (:form . "studies") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "IN") (:stem . "across") (:form . "across") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "VBN") (:stem . "extend") (:form . "extended") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "NNS") (:stem . "period") (:form . "periods") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "time") (:form . "time") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "NNS") (:stem . "lab") (:form . "labs") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "complex") (:form . "complex") (:end . 92)\n  (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 101)\n  (:start . 93) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 104) (:start . 102)\n  (:id . 59))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 114)\n  (:start . 105) (:id . 60))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 123)\n  (:start . 115) (:id . 61))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 126) (:start . 124)\n  (:id . 62))\n ((:tag . "VB") (:stem . "combine") (:form . "combine") (:end . 134)\n  (:start . 127) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 135) (:start . 134)\n  (:id . 64))\n ((:tag . "VB") (:stem . "align") (:form . "align") (:end . 141)\n  (:start . 136) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 145) (:start . 142)\n  (:id . 66))\n ((:tag . "VB") (:stem . "analyze") (:form . "analyze") (:end . 153)\n  (:start . 146) (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 157) (:start . 154)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "result") (:form . "resulting") (:end . 167)\n  (:start . 158) (:id . 69))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 174)\n  (:start . 168) (:id . 70))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 179) (:start . 175)\n  (:id . 71))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 192)\n  (:start . 180) (:id . 72))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 198)\n  (:start . 193) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s14.195) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504697@unknown@formal@none@1@S@In contrast, we demonstrate a strategy similar to the one described by Bondarenko et al. [27], which is deployed entirely within multiplierz: extraction of MS/MS peak lists, X!Tandem based peptide identification, and the generation of common sequences (detected in at least k out of the n RAW files being analyzed) are implemented directly from the multiplierz menu-system.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 27)\n  (:start . 16) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 29) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . 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"at") (:end . 267) (:start . 265)\n  (:id . 89))\n ((:tag . "JJS") (:stem . "least") (:form . "least") (:end . 273)\n  (:start . 268) (:id . 90))\n ((:tag . "NN") (:stem . "k") (:form . "k") (:end . 275) (:start . 274)\n  (:id . 91))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 279) (:start . 276)\n  (:id . 92))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 282) (:start . 280)\n  (:id . 93))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 286) (:start . 283)\n  (:id . 94))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 288) (:start . 287)\n  (:id . 95))\n ((:tag . "NN") (:stem . "raw") (:form . "RAW") (:end . 292) (:start . 289)\n  (:id . 96))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 298)\n  (:start . 293) (:id . 97))\n ((:tag . "VBG") (:stem . "be") (:form . "being") (:end . 304) (:start . 299)\n  (:id . 98))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 313)\n  (:start . 305) (:id . 99))\n ((:tag . 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5504698@unknown@formal@none@1@S@Finally, feature extraction, quantitation, and report generation is performed via an additional mz script (see Additional File 2).@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "NN") (:stem . "feature") (:form . "feature") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "extraction") (:form . "extraction") (:end . 27)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "quantitation") (:form . "quantitation") (:end . 41)\n  (:start . 29) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 53)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "generation") (:form . "generation") (:end . 64)\n  (:start . 54) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "perform") (:form . "performed") (:end . 77)\n  (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "additional") (:form . "additional") (:end . 95)\n  (:start . 85) (:id . 56))\n ((:tag . "NN") (:stem . "mz") (:form . "mz") (:end . 98) (:start . 96)\n  (:id . 57))\n ((:tag . "NN") (:stem . "script") (:form . "script") (:end . 105)\n  (:start . 99) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 59))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 110) (:start . 107)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 121)\n  (:start . 111) (:id . 61))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 126) (:start . 122)\n  (:id . 62))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 128) (:start . 127)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 129) (:start . 128)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s14.197) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504699@unknown@formal@none@1@S@Figure 8 shows an Excel-based report for label-free analysis of two standard protein mixtures (5 proteins each, containing ratios of 1:11, 1:5, 1:1, 2:1 and 5:1, respectively, and analyzed in duplicate).@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 17) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "excel-based") (:form . "Excel-based") (:end . 29)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "label-free") (:form . "label-free") (:end . 51)\n  (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 60)\n  (:start . 52) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 63) (:start . 61)\n  (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 76)\n  (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 84)\n  (:start . 77) (:id . 54))\n ((:tag . "NNS") (:stem . "mixture") (:form . "mixtures") (:end . 93)\n  (:start . 85) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 95) (:start . 94)\n  (:id . 56))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 96) (:start . 95)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 105)\n  (:start . 97) (:id . 58))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 110) (:start . 106)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "contain") (:form . "containing") (:end . 122)\n  (:start . 112) (:id . 61))\n ((:tag . "NNS") (:stem . "ratio") (:form . "ratios") (:end . 129)\n  (:start . 123) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "CD") (:stem . "1:11") (:form . "1:11") (:end . 137) (:start . 133)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 65))\n ((:tag . "CD") (:stem . "1:5") (:form . "1:5") (:end . 142) (:start . 139)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 67))\n ((:tag . "CD") (:stem . "1:1") (:form . "1:1") (:end . 147) (:start . 144)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 69))\n ((:tag . "CD") (:stem . "2:1") (:form . "2:1") (:end . 152) (:start . 149)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 156) (:start . 153)\n  (:id . 71))\n ((:tag . "CD") (:stem . "5:1") (:form . "5:1") (:end . 160) (:start . 157)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 161) (:start . 160)\n  (:id . 73))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 174)\n  (:start . 162) (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "analyze") (:form . "analyzed") (:end . 188)\n  (:start . 180) (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 191) (:start . 189)\n  (:id . 78))\n ((:tag . "NN") (:stem . "duplicate") (:form . "duplicate") (:end . 201)\n  (:start . 192) (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 202) (:start . 201)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 203) (:start . 202)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s14.198) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504700@unknown@formal@none@1@S@Label-Free Relative Protein Quantification.@(((:tag . "JJ") (:stem . "label-free") (:form . "Label-Free") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "relative") (:form . "Relative") (:end . 19)\n  (:start . 11) (:id . 43))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 27)\n  (:start . 20) (:id . 44))\n ((:tag . "NNP") (:stem . "Quantification") (:form . "Quantification")\n  (:end . 42) (:start . 28) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 43) (:start . 42)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s14.199) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504701@unknown@formal@none@1@S@A multiplierz Excel report provides data analytic figures of merit, including: (a) the ratio of each protein across two conditions with an embedded box plot that illustrates the distribution of feature-level ratios, where each feature is defined as a (peptide, modification, charge state) combination; (b) p-value for the significance of the ratio; (c) the number (N) of features underlying the protein quantification; (d) the ratio and embedded RIC plot (showing all RICs used to quantify the peptide - colored by sample source) from the peptide most representative of the final protein ratio; (e) "expected" field is added manually by the user based on the experimental design.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 13)\n  (:start . 2) (:id . 43))\n ((:tag . "NNP") (:stem . "Excel") (:form . 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(:end . 679) (:start . 678)\n  (:id . 175)))@@@1@134@((:identifiers (:sid . :s14.200) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504702@unknown@formal@none@1@S@Users may also generate associated graphs using native plotting capabilities in Excel.@(((:tag . "NNS") (:stem . "user") (:form . "Users") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "VBN") (:stem . "associate") (:form . "associated") (:end . 34)\n  (:start . 24) (:id . 46))\n ((:tag . "NNS") (:stem . "graph") (:form . "graphs") (:end . 41)\n  (:start . 35) (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 47) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 54)\n  (:start . 48) (:id . 49))\n ((:tag . "NN") (:stem . "plotting") (:form . "plotting") (:end . 63)\n  (:start . 55) (:id . 50))\n ((:tag . "NNS") (:stem . "capability") (:form . "capabilities") (:end . 76)\n  (:start . 64) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 79) (:start . 77)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Excel") (:form . "Excel") (:end . 85) (:start . 80)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 54)))@@@1@13@((:hcues ((:id . :x14.201.1) (:span 6 9)))\n (:hscopes ((:id . :x14.201.1) (:span 6 85)))\n (:identifiers (:sid . :s14.201) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504703@unknown@formal@none@1@S@Automated Quality Control of Mass Spectrometer Instrument Performance@(((:tag . "NNP") (:stem . "Automated") (:form . "Automated") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Quality") (:form . "Quality") (:end . 17)\n  (:start . 10) (:id . 43))\n ((:tag . "NNP") (:stem . "Control") (:form . "Control") (:end . 25)\n  (:start . 18) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Mass") (:form . "Mass") (:end . 33) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Spectrometer") (:form . "Spectrometer") (:end . 46)\n  (:start . 34) (:id . 47))\n ((:tag . "NNP") (:stem . "Instrument") (:form . "Instrument") (:end . 57)\n  (:start . 47) (:id . 48))\n ((:tag . "NNP") (:stem . "Performance") (:form . "Performance") (:end . 69)\n  (:start . 58) (:id . 49)))@@@1@8@((:identifiers (:sid . :s14.202) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504704@unknown@formal@none@1@S@High throughput or other core-type operations designed to run in an unattended manner benefit from automated quality control assessment of platform performance.@(((:tag . "JJ") (:stem . "high") (:form . "High") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "throughput") (:form . "throughput") (:end . 15)\n  (:start . 5) (:id . 43))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 18) (:start . 16)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "core-type") (:form . "core-type") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "operation") (:form . "operations") (:end . 45)\n  (:start . 35) (:id . 47))\n ((:tag . "VBN") (:stem . "design") (:form . "designed") (:end . 54)\n  (:start . 46) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 57) (:start . 55)\n  (:id . 49))\n ((:tag . "VB") (:stem . "run") (:form . "run") (:end . 61) (:start . 58)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 67) (:start . 65)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "unattended") (:form . "unattended") (:end . 78)\n  (:start . 68) (:id . 53))\n ((:tag . "NN") (:stem . "manner") (:form . "manner") (:end . 85)\n  (:start . 79) (:id . 54))\n ((:tag . "NN") (:stem . "benefit") (:form . "benefit") (:end . 93)\n  (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 98) (:start . 94)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "automate") (:form . "automated") (:end . 108)\n  (:start . 99) (:id . 57))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 116)\n  (:start . 109) (:id . 58))\n ((:tag . "NN") (:stem . "control") (:form . "control") (:end . 124)\n  (:start . 117) (:id . 59))\n ((:tag . "NN") (:stem . "assessment") (:form . "assessment") (:end . 135)\n  (:start . 125) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 61))\n ((:tag . "NN") (:stem . "platform") (:form . "platform") (:end . 147)\n  (:start . 139) (:id . 62))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 159)\n  (:start . 148) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s14.203) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504705@unknown@formal@none@1@S@For example, periodic confirmation of measured peptide mass accuracy is required to ensure the integrity of instrument calibration routines.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "periodic") (:form . "periodic") (:end . 21)\n  (:start . 13) (:id . 45))\n ((:tag . "NN") (:stem . "confirmation") (:form . "confirmation") (:end . 34)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 46)\n  (:start . 38) (:id . 48))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 68)\n  (:start . 60) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "require") (:form . "required") (:end . 80)\n  (:start . 72) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 83) (:start . 81)\n  (:id . 54))\n ((:tag . "VB") (:stem . "ensure") (:form . "ensure") (:end . 90)\n  (:start . 84) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 56))\n ((:tag . "NN") (:stem . "integrity") (:form . "integrity") (:end . 104)\n  (:start . 95) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 107) (:start . 105)\n  (:id . 58))\n ((:tag . "NN") (:stem . "instrument") (:form . "instrument") (:end . 118)\n  (:start . 108) (:id . 59))\n ((:tag . "NN") (:stem . "calibration") (:form . "calibration") (:end . 130)\n  (:start . 119) (:id . 60))\n ((:tag . "NNS") (:stem . "routine") (:form . "routines") (:end . 139)\n  (:start . 131) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s14.204) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504706@unknown@formal@none@1@S@Towards this end, we created a short .mz script (see Additional File 2), which extracts measured mass-to-charge values for a list of standard peptides from a native data file, and automatically calculates mass errors.@(((:tag . "IN") (:stem . "towards") (:form . "Towards") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "end") (:form . "end") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 20) (:start . 18)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "create") (:form . "created") (:end . 28)\n  (:start . 21) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "short") (:form . "short") (:end . 36) (:start . 31)\n  (:id . 49))\n ((:tag . "NN") (:stem . ".mz") (:form . ".mz") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "script") (:form . "script") (:end . 47)\n  (:start . 41) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 52))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 52) (:start . 49)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 63)\n  (:start . 53) (:id . 54))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 68) (:start . 64)\n  (:id . 55))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 78) (:start . 73)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "extract") (:form . "extracts") (:end . 87)\n  (:start . 79) (:id . 60))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 96)\n  (:start . 88) (:id . 61))\n ((:tag . "JJ") (:stem . "mass-to-charge") (:form . "mass-to-charge")\n  (:end . 111) (:start . 97) (:id . 62))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 118)\n  (:start . 112) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 122) (:start . 119)\n  (:id . 64))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 124) (:start . 123)\n  (:id . 65))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 129) (:start . 125)\n  (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 132) (:start . 130)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 141)\n  (:start . 133) (:id . 68))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 150)\n  (:start . 142) (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 155) (:start . 151)\n  (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 157) (:start . 156)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 164)\n  (:start . 158) (:id . 72))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 169)\n  (:start . 165) (:id . 73))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 174) (:start . 170)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 175) (:start . 174)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n  (:id . 76))\n ((:tag . "RB") (:stem . "automatically") (:form . "automatically")\n  (:end . 193) (:start . 180) (:id . 77))\n ((:tag . "VBZ") (:stem . "calculate") (:form . "calculates") (:end . 204)\n  (:start . 194) (:id . 78))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 209) (:start . 205)\n  (:id . 79))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 216)\n  (:start . 210) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 217) (:start . 216)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s14.205) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504707@unknown@formal@none@1@S@The output is a calibration report (Figure 9) that shows a reconstructed ion chromatogram and experimental mass accuracy for each standard peptide.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "calibration") (:form . "calibration") (:end . 27)\n  (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 42)\n  (:start . 36) (:id . 49))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 51))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 50) (:start . 46)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 56) (:start . 51)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 58) (:start . 57)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "reconstruct") (:form . "reconstructed") (:end . 72)\n  (:start . 59) (:id . 55))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 76) (:start . 73)\n  (:id . 56))\n ((:tag . "NN") (:stem . "chromatogram") (:form . "chromatogram") (:end . 89)\n  (:start . 77) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 106)\n  (:start . 94) (:id . 59))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 111) (:start . 107)\n  (:id . 60))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 120)\n  (:start . 112) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 124) (:start . 121)\n  (:id . 62))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 129) (:start . 125)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 138)\n  (:start . 130) (:id . 64))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 146)\n  (:start . 139) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s14.206) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504708@unknown@formal@none@1@S@The measured mass errors may be used as input for mass tolerance parameters in subsequent database search algorithms (e.g., Mascot, SEQUEST, X!Tandem, etc.) for peptide sequence identification.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "measure") (:form . "measured") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 54) (:start . 50)\n  (:id . 52))\n ((:tag . "NN") (:stem . "tolerance") (:form . "tolerance") (:end . 64)\n  (:start . 55) (:id . 53))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 75)\n  (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "subsequent") (:form . "subsequent") (:end . 89)\n  (:start . 79) (:id . 56))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 98)\n  (:start . 90) (:id . 57))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 105)\n  (:start . 99) (:id . 58))\n ((:tag . "NNS") (:stem . "algorithm") (:form . "algorithms") (:end . 116)\n  (:start . 106) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n  (:id . 60))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 122) (:start . 118)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 123) (:start . 122)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 130)\n  (:start . 124) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "SEQUEST") (:form . "SEQUEST") (:end . 139)\n  (:start . 132) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "X!Tandem") (:form . "X!Tandem") (:end . 149)\n  (:start . 141) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 150) (:start . 149)\n  (:id . 68))\n ((:tag . "LS") (:stem . "etc.") (:form . "etc.") (:end . 155) (:start . 151)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 160) (:start . 157)\n  (:id . 71))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 168)\n  (:start . 161) (:id . 72))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 177)\n  (:start . 169) (:id . 73))\n ((:tag . "NN") (:stem . "identification") (:form . "identification")\n  (:end . 192) (:start . 178) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 193) (:start . 192)\n  (:id . 75)))@@@1@34@((:hcues ((:id . :x14.207.1) (:span 25 28)))\n (:hscopes ((:id . :x14.207.1) (:span 0 192)))\n (:identifiers (:sid . :s14.207) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504709@unknown@formal@none@1@S@Instrument Calibration Quality Control Report.@(((:tag . "NNP") (:stem . "Instrument") (:form . "Instrument") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "Calibration") (:form . "Calibration") (:end . 22)\n  (:start . 11) (:id . 43))\n ((:tag . "NNP") (:stem . "Quality") (:form . "Quality") (:end . 30)\n  (:start . 23) (:id . 44))\n ((:tag . "NNP") (:stem . "Control") (:form . "Control") (:end . 38)\n  (:start . 31) (:id . 45))\n ((:tag . "NNP") (:stem . "Report") (:form . "Report") (:end . 45)\n  (:start . 39) (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s14.208) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504710@unknown@formal@none@1@S@An .mz script is used to automatically generate a spreadsheet report that indicates mass errors (in ppm) for a set of standard peptides.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . ".mz") (:form . ".mz") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "script") (:form . "script") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "RB") (:stem . "automatically") (:form . "automatically")\n  (:end . 38) (:start . 25) (:id . 48))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 47)\n  (:start . 39) (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "spreadsheet") (:form . "spreadsheet") (:end . 61)\n  (:start . 50) (:id . 51))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 83)\n  (:start . 74) (:id . 54))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 95)\n  (:start . 89) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "ppm") (:form . "ppm") (:end . 103) (:start . 100)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 110) (:start . 109)\n  (:id . 62))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 114) (:start . 111)\n  (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 117) (:start . 115)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "standard") (:form . "standard") (:end . 126)\n  (:start . 118) (:id . 65))\n ((:tag . "NNS") (:stem . "peptide") (:form . "peptides") (:end . 135)\n  (:start . 127) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s14.209) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504711@unknown@formal@none@1@S@Images of the precursor isotope distribution and reconstructed ion chromatogram are embedded within the report for rapid confirmation of mass spectrometry and chromatographic performance.@(((:tag . "NNS") (:stem . "image") (:form . "Images") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 23)\n  (:start . 14) (:id . 45))\n ((:tag . "NN") (:stem . "isotope") (:form . "isotope") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 44)\n  (:start . 32) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 48) (:start . 45)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "reconstruct") (:form . "reconstructed") (:end . 62)\n  (:start . 49) (:id . 49))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 66) (:start . 63)\n  (:id . 50))\n ((:tag . "NN") (:stem . "chromatogram") (:form . "chromatogram") (:end . 79)\n  (:start . 67) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 83) (:start . 80)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "embedded") (:form . "embedded") (:end . 92)\n  (:start . 84) (:id . 53))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 99)\n  (:start . 93) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 103) (:start . 100)\n  (:id . 55))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 110)\n  (:start . 104) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 114) (:start . 111)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "rapid") (:form . "rapid") (:end . 120)\n  (:start . 115) (:id . 58))\n ((:tag . "NN") (:stem . "confirmation") (:form . "confirmation") (:end . 133)\n  (:start . 121) (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 60))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 141) (:start . 137)\n  (:id . 61))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 154)\n  (:start . 142) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 158) (:start . 155)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "chromatographic") (:form . "chromatographic")\n  (:end . 174) (:start . 159) (:id . 64))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 186)\n  (:start . 175) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 187) (:start . 186)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s14.210) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504712@unknown@formal@none@1@S@In a second application, we developed a routine for recalibration of MS/MS spectra.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "second") (:form . "second") (:end . 11) (:start . 5)\n  (:id . 44))\n ((:tag . "NN") (:stem . "application") (:form . "application") (:end . 23)\n  (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "develop") (:form . "developed") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "routine") (:form . "routine") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "recalibration") (:form . "recalibration")\n  (:end . 65) (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 68) (:start . 66)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 74) (:start . 69)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "spectrum") (:form . "spectra") (:end . 82)\n  (:start . 75) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 83) (:start . 82)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s14.211) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504713@unknown@formal@none@1@S@It is widely recognized that increased mass accuracy provides for higher stringency searches and yields improved results [28].@(((:tag . "PRP") (:stem . "it") (:form . "It") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "widely") (:form . "widely") (:end . 12) (:start . 6)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "recognize") (:form . "recognized") (:end . 23)\n  (:start . 13) (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 61)\n  (:start . 53) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 72) (:start . 66)\n  (:id . 52))\n ((:tag . "NN") (:stem . "stringency") (:form . "stringency") (:end . 83)\n  (:start . 73) (:id . 53))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 92)\n  (:start . 84) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "yield") (:form . "yields") (:end . 103)\n  (:start . 97) (:id . 56))\n ((:tag . "VBN") (:stem . "improve") (:form . "improved") (:end . 112)\n  (:start . 104) (:id . 57))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 120)\n  (:start . 113) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 122) (:start . 121)\n  (:id . 59))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 124) (:start . 122)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s14.212) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504714@unknown@formal@none@1@S@First, a given set of MS/MS spectra are searched with mass tolerance values based on the most recent mass calibration parameters.@(((:tag . "RB") (:stem . "first") (:form . "First") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 8) (:start . 7)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 14) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 18) (:start . 15)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "MS/MS") (:form . "MS/MS") (:end . 27) (:start . 22)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "spectrum") (:form . "spectra") (:end . 35)\n  (:start . 28) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "search") (:form . "searched") (:end . 48)\n  (:start . 40) (:id . 51))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 58) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "tolerance") (:form . "tolerance") (:end . 68)\n  (:start . 59) (:id . 54))\n ((:tag . "NNS") (:stem . "value") (:form . "values") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 84) (:start . 82)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 58))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 93) (:start . 89)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 100)\n  (:start . 94) (:id . 60))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 105) (:start . 101)\n  (:id . 61))\n ((:tag . "NN") (:stem . "calibration") (:form . "calibration") (:end . 117)\n  (:start . 106) (:id . 62))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 128)\n  (:start . 118) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s14.213) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504715@unknown@formal@none@1@S@Under these conditions we typically observe a monotonic increase in mass error as a function of fragment ion mass (Figure 10a).@(((:tag . "IN") (:stem . "under") (:form . "Under") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "condition") (:form . "conditions") (:end . 22)\n  (:start . 12) (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 35)\n  (:start . 26) (:id . 46))\n ((:tag . "VBP") (:stem . "observe") (:form . "observe") (:end . 43)\n  (:start . 36) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 45) (:start . 44)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "monotonic") (:form . "monotonic") (:end . 55)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "increase") (:form . "increase") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 67) (:start . 65)\n  (:id . 51))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 72) (:start . 68)\n  (:id . 52))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 78) (:start . 73)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 81) (:start . 79)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 92)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 57))\n ((:tag . "NN") (:stem . "fragment") (:form . "fragment") (:end . 104)\n  (:start . 96) (:id . 58))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 113) (:start . 109)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 115) (:start . 114)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 121)\n  (:start . 115) (:id . 62))\n ((:tag . "NN") (:stem . "10a") (:form . "10a") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 126) (:start . 125)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s14.214) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504716@unknown@formal@none@1@S@A high-confidence peptide is selected from the search output, and the corresponding annotated MS/MS spectrum is used to compute the slope and intercept of the linear mass error function.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "high-confidence") (:form . "high-confidence")\n  (:end . 17) (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 25)\n  (:start . 18) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 37)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 42) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 60)\n  (:start . 54) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 61) (:start . 60)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 83)\n  (:start . 70) (:id . 54))\n ((:tag . "VBN") (:stem . "annotate") (:form . "annotated") (:end . 93)\n  (:start . 84) (:id . 55))\n ((:tag . "NN") (:stem . "ms/ms") (:form . "MS/MS") (:end . 99) (:start . 94)\n  (:id . 56))\n ((:tag . "NN") (:stem . "spectrum") (:form . "spectrum") (:end . 108)\n  (:start . 100) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 116) (:start . 112)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 119) (:start . 117)\n  (:id . 60))\n ((:tag . "VB") (:stem . "compute") (:form . "compute") (:end . 127)\n  (:start . 120) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 62))\n ((:tag . "NN") (:stem . "slope") (:form . "slope") (:end . 137)\n  (:start . 132) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 64))\n ((:tag . "NN") (:stem . "intercept") (:form . "intercept") (:end . 151)\n  (:start . 142) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 154) (:start . 152)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "linear") (:form . "linear") (:end . 165)\n  (:start . 159) (:id . 68))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 170) (:start . 166)\n  (:id . 69))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 176)\n  (:start . 171) (:id . 70))\n ((:tag . "NN") (:stem . "function") (:form . "function") (:end . 185)\n  (:start . 177) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s14.215) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504717@unknown@formal@none@1@S@This equation is then used to recalibrate precursor and product ion masses via an .mz script (see Additional File 2).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "equation") (:form . "equation") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "VB") (:stem . "recalibrate") (:form . "recalibrate") (:end . 41)\n  (:start . 30) (:id . 48))\n ((:tag . "NN") (:stem . "precursor") (:form . "precursor") (:end . 51)\n  (:start . 42) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 50))\n ((:tag . "NN") (:stem . "product") (:form . "product") (:end . 63)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 67) (:start . 64)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "mass") (:form . "masses") (:end . 74) (:start . 68)\n  (:id . 53))\n ((:tag . "IN") (:stem . "via") (:form . "via") (:end . 78) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . ".mz") (:form . ".mz") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "NN") (:stem . "script") (:form . "script") (:end . 92)\n  (:start . 86) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 108)\n  (:start . 98) (:id . 60))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 113) (:start . 109)\n  (:id . 61))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 115) (:start . 114)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s14.216) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504718@unknown@formal@none@1@S@Finally, we re-search the newly calibrated dataset with a narrower tolerance, reducing the average mass error (Figure 10b).@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "re-search") (:form . "re-search") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "RB") (:stem . "newly") (:form . "newly") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "calibrate") (:form . "calibrated") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 50)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 57) (:start . 56)\n  (:id . 51))\n ((:tag . "JJR") (:stem . "narrow") (:form . "narrower") (:end . 66)\n  (:start . 58) (:id . 52))\n ((:tag . "NN") (:stem . "tolerance") (:form . "tolerance") (:end . 76)\n  (:start . 67) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "reduce") (:form . "reducing") (:end . 86)\n  (:start . 78) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 98)\n  (:start . 91) (:id . 57))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 103) (:start . 99)\n  (:id . 58))\n ((:tag . "NN") (:stem . "error") (:form . "error") (:end . 109)\n  (:start . 104) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 117)\n  (:start . 111) (:id . 61))\n ((:tag . "CD") (:stem . "10b") (:form . "10b") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 122) (:start . 121)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s14.217) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504719@unknown@formal@none@1@S@Recalibration of Data Acquired on a Quadrupole Time-of-Flight (QTOF) Mass Spectrometer.@(((:tag . "NNP") (:stem . "Recalibration") (:form . "Recalibration")\n  (:end . 13) (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Datum") (:form . "Data") (:end . 21) (:start . 17)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "acquire") (:form . "Acquired") (:end . 30)\n  (:start . 22) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 35) (:start . 34)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Quadrupole") (:form . "Quadrupole") (:end . 46)\n  (:start . 36) (:id . 48))\n ((:tag . "NNP") (:stem . "Time-of-Flight") (:form . "Time-of-Flight")\n  (:end . 61) (:start . 47) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 63) (:start . 62)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "QTOF") (:form . "QTOF") (:end . 67) (:start . 63)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Mass") (:form . "Mass") (:end . 73) (:start . 69)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Spectrometer") (:form . "Spectrometer") (:end . 86)\n  (:start . 74) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 87) (:start . 86)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s14.218) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504720@unknown@formal@none@1@S@Fragment ion mass errors for the peptide ADISSDQIAAIGITNQR (based on Mascot assignment), derived from the protein glycerol kinase (a) before and (b) after recalibration.@(((:tag . "NN") (:stem . "fragment") (:form . "Fragment") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "ion") (:form . "ion") (:end . 12) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "peptide") (:form . "peptide") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "adissdqiaaigitnqr") (:form . "ADISSDQIAAIGITNQR")\n  (:end . 58) (:start . 41) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 68) (:start . 66)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Mascot") (:form . "Mascot") (:end . 75)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "assignment") (:form . "assignment") (:end . 86)\n  (:start . 76) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "derive") (:form . "derived") (:end . 96)\n  (:start . 89) (:id . 57))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 105) (:start . 102)\n  (:id . 59))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 113)\n  (:start . 106) (:id . 60))\n ((:tag . "NN") (:stem . "glycerol") (:form . "glycerol") (:end . 122)\n  (:start . 114) (:id . 61))\n ((:tag . "NNP") (:stem . "kinase") (:form . "kinase") (:end . 129)\n  (:start . 123) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 132) (:start . 131)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 65))\n ((:tag . "IN") (:stem . "before") (:form . "before") (:end . 140)\n  (:start . 134) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 146) (:start . 145)\n  (:id . 68))\n ((:tag . "NN") (:stem . "b") (:form . "b") (:end . 147) (:start . 146)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 148) (:start . 147)\n  (:id . 70))\n ((:tag . "IN") (:stem . "after") (:form . "after") (:end . 154)\n  (:start . 149) (:id . 71))\n ((:tag . "NN") (:stem . "recalibration") (:form . "recalibration")\n  (:end . 168) (:start . 155) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s14.219) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504721@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s14.220) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504722@unknown@formal@none@1@S@We recognize that some aspects of our proposal diverge from current efforts to establish community standards in proteomics.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "recognize") (:form . "recognize") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "some") (:form . "some") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "aspect") (:form . "aspects") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "proposal") (:form . "proposal") (:end . 46)\n  (:start . 38) (:id . 49))\n ((:tag . "VBP") (:stem . "diverge") (:form . "diverge") (:end . 54)\n  (:start . 47) (:id . 50))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "current") (:form . "current") (:end . 67)\n  (:start . 60) (:id . 52))\n ((:tag . "NNS") (:stem . "effort") (:form . "efforts") (:end . 75)\n  (:start . 68) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "VB") (:stem . "establish") (:form . "establish") (:end . 88)\n  (:start . 79) (:id . 55))\n ((:tag . "NN") (:stem . "community") (:form . "community") (:end . 98)\n  (:start . 89) (:id . 56))\n ((:tag . "NNS") (:stem . "standard") (:form . "standards") (:end . 108)\n  (:start . 99) (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 111) (:start . 109)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 122)\n  (:start . 112) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s14.221) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504723@unknown@formal@none@1@S@For example, the use of mzAPI within multiplierz to provide direct access to binary mass spectrometry files does not rely on XML-based surrogate files.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 29) (:start . 24)\n  (:id . 48))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 36)\n  (:start . 30) (:id . 49))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 48)\n  (:start . 37) (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "VB") (:stem . "provide") (:form . "provide") (:end . 59)\n  (:start . 52) (:id . 52))\n ((:tag . "JJ") (:stem . "direct") (:form . "direct") (:end . 66)\n  (:start . 60) (:id . 53))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 73)\n  (:start . 67) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "binary") (:form . "binary") (:end . 83)\n  (:start . 77) (:id . 56))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 101)\n  (:start . 89) (:id . 58))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 107)\n  (:start . 102) (:id . 59))\n ((:tag . "VBZ") (:stem . "do") (:form . "does") (:end . 112) (:start . 108)\n  (:id . 60))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 116) (:start . 113)\n  (:id . 61))\n ((:tag . "VB") (:stem . "rely") (:form . "rely") (:end . 121) (:start . 117)\n  (:id . 62))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "xml-based") (:form . "XML-based") (:end . 134)\n  (:start . 125) (:id . 64))\n ((:tag . "JJ") (:stem . "surrogate") (:form . "surrogate") (:end . 144)\n  (:start . 135) (:id . 65))\n ((:tag . "NNS") (:stem . "file") (:form . "files") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 151) (:start . 150)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s14.222) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504724@unknown@formal@none@1@S@We note however, that the two strategies are not mutually exclusive; that is, support for mzXML [9], or the recently described mzML [29] can be readily incorporated into mzAPI.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "note") (:form . "note") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "RB") (:stem . "however") (:form . "however") (:end . 15)\n  (:start . 8) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 40)\n  (:start . 30) (:id . 49))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 44) (:start . 41)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "RB") (:stem . "mutually") (:form . "mutually") (:end . 57)\n  (:start . 49) (:id . 52))\n ((:tag . "JJ") (:stem . "exclusive") (:form . "exclusive") (:end . 67)\n  (:start . 58) (:id . 53))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 68) (:start . 67)\n  (:id . 54))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 73) (:start . 69)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 57))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 85)\n  (:start . 78) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 89) (:start . 86)\n  (:id . 59))\n ((:tag . "NN") (:stem . "mzxml") (:form . "mzXML") (:end . 95) (:start . 90)\n  (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 98) (:start . 97)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 99) (:start . 98)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 64))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 103) (:start . 101)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 66))\n ((:tag . "RB") (:stem . "recently") (:form . "recently") (:end . 116)\n  (:start . 108) (:id . 67))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 126)\n  (:start . 117) (:id . 68))\n ((:tag . "NN") (:stem . "mzml") (:form . "mzML") (:end . 131) (:start . 127)\n  (:id . 69))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 133) (:start . 132)\n  (:id . 70))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 135) (:start . 133)\n  (:id . 71))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 136) (:start . 135)\n  (:id . 72))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 140) (:start . 137)\n  (:id . 73))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 143) (:start . 141)\n  (:id . 74))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 151)\n  (:start . 144) (:id . 75))\n ((:tag . "VBN") (:stem . "incorporate") (:form . "incorporated") (:end . 164)\n  (:start . 152) (:id . 76))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 169) (:start . 165)\n  (:id . 77))\n ((:tag . "NNP") (:stem . "mzAPI") (:form . "mzAPI") (:end . 175)\n  (:start . 170) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 176) (:start . 175)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x14.223.1) (:span 137 140)))\n (:hscopes ((:id . :x14.223.1) (:span 78 175)))\n (:identifiers (:sid . :s14.223) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504725@unknown@formal@none@1@S@Similarly, output from multiplierz can be readily formatted in pepXML [12].@(((:tag . "RB") (:stem . "similarly") (:form . "Similarly") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 17)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 34)\n  (:start . 23) (:id . 46))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "RB") (:stem . "readily") (:form . "readily") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "VBN") (:stem . "format") (:form . "formatted") (:end . 59)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "pepxml") (:form . "pepXML") (:end . 69)\n  (:start . 63) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "CD") (:stem . "12") (:form . "12") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 75) (:start . 74)\n  (:id . 56)))@@@1@15@((:hcues ((:id . :x14.224.1) (:span 35 38)))\n (:hscopes ((:id . :x14.224.1) (:span 11 69)))\n (:identifiers (:sid . :s14.224) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504726@unknown@formal@none@1@S@In addition, recent discussions focused on data sharing in proteomics suggest that standards may evolve beyond XML-based formats [30,31].@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "recent") (:form . "recent") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "NNS") (:stem . "discussion") (:form . "discussions") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "VBN") (:stem . "focus") (:form . "focused") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "share") (:form . "sharing") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 69)\n  (:start . 59) (:id . 52))\n ((:tag . "VBP") (:stem . "suggest") (:form . "suggest") (:end . 77)\n  (:start . 70) (:id . 53))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 82) (:start . 78)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "standard") (:form . "standards") (:end . 92)\n  (:start . 83) (:id . 55))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 96) (:start . 93)\n  (:id . 56))\n ((:tag . "VB") (:stem . "evolve") (:form . "evolve") (:end . 103)\n  (:start . 97) (:id . 57))\n ((:tag . "IN") (:stem . "beyond") (:form . "beyond") (:end . 110)\n  (:start . 104) (:id . 58))\n ((:tag . "JJ") (:stem . "xml-based") (:form . "XML-based") (:end . 120)\n  (:start . 111) (:id . 59))\n ((:tag . "NNS") (:stem . "format") (:form . "formats") (:end . 128)\n  (:start . 121) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 130) (:start . 129)\n  (:id . 61))\n ((:tag . "CD") (:stem . "30,31") (:form . "30,31") (:end . 135)\n  (:start . 130) (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 136) (:start . 135)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x14.225.1) (:span 93 96)) ((:id . :x14.225.2) (:span 70 77)))\n (:hscopes ((:id . :x14.225.1) (:span 93 128))\n  ((:id . :x14.225.2) (:span 70 128)))\n (:identifiers (:sid . :s14.225) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504727@unknown@formal@none@1@S@Equally important, the emergence of translation layers such as cygwin [32] and Wine [33], continue to blur inter-platform boundaries, such that software solutions amenable to the widest audience may eclipse those based largely on platform independence.@(((:tag . "RB") (:stem . "equally") (:form . "Equally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "important") (:form . "important") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "emergence") (:form . "emergence") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 35) (:start . 33)\n  (:id . 47))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 47)\n  (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "layer") (:form . "layers") (:end . 54)\n  (:start . 48) (:id . 49))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 59) (:start . 55)\n  (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "cygwin") (:form . "cygwin") (:end . 69)\n  (:start . 63) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Wine") (:form . "Wine") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 87) (:start . 85)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 88) (:start . 87)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "continue") (:form . "continue") (:end . 98)\n  (:start . 90) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 101) (:start . 99)\n  (:id . 63))\n ((:tag . "VB") (:stem . "blur") (:form . "blur") (:end . 106) (:start . 102)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "inter-platform") (:form . "inter-platform")\n  (:end . 121) (:start . 107) (:id . 65))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 132)\n  (:start . 122) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 138) (:start . 134)\n  (:id . 68))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 143) (:start . 139)\n  (:id . 69))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 152)\n  (:start . 144) (:id . 70))\n ((:tag . "NNS") (:stem . "solution") (:form . "solutions") (:end . 162)\n  (:start . 153) (:id . 71))\n ((:tag . "JJ") (:stem . "amenable") (:form . "amenable") (:end . 171)\n  (:start . 163) (:id . 72))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 174) (:start . 172)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 74))\n ((:tag . "JJS") (:stem . "wide") (:form . "widest") (:end . 185)\n  (:start . 179) (:id . 75))\n ((:tag . "NN") (:stem . "audience") (:form . "audience") (:end . 194)\n  (:start . 186) (:id . 76))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 198) (:start . 195)\n  (:id . 77))\n ((:tag . "VB") (:stem . "eclipse") (:form . "eclipse") (:end . 206)\n  (:start . 199) (:id . 78))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 212)\n  (:start . 207) (:id . 79))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 218)\n  (:start . 213) (:id . 80))\n ((:tag . "RB") (:stem . "largely") (:form . "largely") (:end . 226)\n  (:start . 219) (:id . 81))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 229) (:start . 227)\n  (:id . 82))\n ((:tag . "NN") (:stem . "platform") (:form . "platform") (:end . 238)\n  (:start . 230) (:id . 83))\n ((:tag . "NN") (:stem . "independence") (:form . "independence") (:end . 251)\n  (:start . 239) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 252) (:start . 251)\n  (:id . 85)))@@@1@44@((:hcues ((:id . :x14.226.1) (:span 195 198)))\n (:hscopes ((:id . :x14.226.1) (:span 195 251)))\n (:identifiers (:sid . :s14.226) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504728@unknown@formal@none@1@S@In fact, our use of Microsoft Excel as the default report output for multiplierz is one such example.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "fact") (:form . "fact") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 12) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "use") (:form . "use") (:end . 16) (:start . 13)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Microsoft") (:form . "Microsoft") (:end . 29)\n  (:start . 20) (:id . 48))\n ((:tag . "NNP") (:stem . "Excel") (:form . "Excel") (:end . 35) (:start . 30)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 51))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 50)\n  (:start . 43) (:id . 52))\n ((:tag . "NN") (:stem . "report") (:form . "report") (:end . 57)\n  (:start . 51) (:id . 53))\n ((:tag . "NN") (:stem . "output") (:form . "output") (:end . 64)\n  (:start . 58) (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n  (:id . 55))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 80)\n  (:start . 69) (:id . 56))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 92) (:start . 88)\n  (:id . 59))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 100)\n  (:start . 93) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 101) (:start . 100)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s14.227) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504729@unknown@formal@none@1@S@Similar image-enhanced spreadsheets may be generated in open formats such as OpenOffice.org XML [34] (see Additional File 4), but our experience to date indicates that the majority of biomedical researchers still opt for commercial spreadsheet solutions, either out of familiarity or because of existing institutional support.@(((:tag . "JJ") (:stem . "similar") (:form . "Similar") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "image-enhanced") (:form . "image-enhanced")\n  (:end . 22) (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "spreadsheet") (:form . "spreadsheets") (:end . 35)\n  (:start . 23) (:id . 44))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 39) (:start . 36)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 42) (:start . 40)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 52)\n  (:start . 43) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 55) (:start . 53)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "open") (:form . "open") (:end . 60) (:start . 56)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "format") (:form . "formats") (:end . 68)\n  (:start . 61) (:id . 50))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 73) (:start . 69)\n  (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 76) (:start . 74)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "OpenOffice.org") (:form . "OpenOffice.org")\n  (:end . 91) (:start . 77) (:id . 53))\n ((:tag . "NNP") (:stem . "XML") (:form . "XML") (:end . 95) (:start . 92)\n  (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 97) (:start . 96)\n  (:id . 55))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 99) (:start . 97)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 100) (:start . 99)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 58))\n ((:tag . "VB") (:stem . "see") (:form . "see") (:end . 105) (:start . 102)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 116)\n  (:start . 106) (:id . 60))\n ((:tag . "NNP") (:stem . "File") (:form . "File") (:end . 121) (:start . 117)\n  (:id . 61))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 123) (:start . 122)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 129) (:start . 126)\n  (:id . 65))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "NN") (:stem . "experience") (:form . "experience") (:end . 144)\n  (:start . 134) (:id . 67))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 147) (:start . 145)\n  (:id . 68))\n ((:tag . "NN") (:stem . "date") (:form . "date") (:end . 152) (:start . 148)\n  (:id . 69))\n ((:tag . "VBZ") (:stem . "indicate") (:form . "indicates") (:end . 162)\n  (:start . 153) (:id . 70))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 167) (:start . 163)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 171) (:start . 168)\n  (:id . 72))\n ((:tag . "NN") (:stem . "majority") (:form . "majority") (:end . 180)\n  (:start . 172) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 183) (:start . 181)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "biomedical") (:form . "biomedical") (:end . 194)\n  (:start . 184) (:id . 75))\n ((:tag . "NNS") (:stem . "researcher") (:form . "researchers") (:end . 206)\n  (:start . 195) (:id . 76))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 212)\n  (:start . 207) (:id . 77))\n ((:tag . "VB") (:stem . "opt") (:form . "opt") (:end . 216) (:start . 213)\n  (:id . 78))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 220) (:start . 217)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "commercial") (:form . "commercial") (:end . 231)\n  (:start . 221) (:id . 80))\n ((:tag . "NN") (:stem . "spreadsheet") (:form . "spreadsheet") (:end . 243)\n  (:start . 232) (:id . 81))\n ((:tag . "NNS") (:stem . "solution") (:form . "solutions") (:end . 253)\n  (:start . 244) (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 254) (:start . 253)\n  (:id . 83))\n ((:tag . "CC") (:stem . "either") (:form . "either") (:end . 261)\n  (:start . 255) (:id . 84))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 265) (:start . 262)\n  (:id . 85))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 268) (:start . 266)\n  (:id . 86))\n ((:tag . "NN") (:stem . "familiarity") (:form . "familiarity") (:end . 280)\n  (:start . 269) (:id . 87))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 283) (:start . 281)\n  (:id . 88))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 291)\n  (:start . 284) (:id . 89))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 294) (:start . 292)\n  (:id . 90))\n ((:tag . "VBG") (:stem . "exist") (:form . "existing") (:end . 303)\n  (:start . 295) (:id . 91))\n ((:tag . "JJ") (:stem . "institutional") (:form . "institutional")\n  (:end . 317) (:start . 304) (:id . 92))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 325)\n  (:start . 318) (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 326) (:start . 325)\n  (:id . 94)))@@@1@53@((:hcues ((:id . :x14.228.1) (:span 153 167))\n  ((:id . :x14.228.2) (:span 36 39)))\n (:hscopes ((:id . :x14.228.1) (:span 153 325))\n  ((:id . :x14.228.2) (:span 0 95)))\n (:identifiers (:sid . :s14.228) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504730@unknown@formal@none@1@S@The multiplierz framework is accessible to a wide range of researchers, and simultaneously provides support for novel algorithm development as well as deployment of automated data pipelines.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 25)\n  (:start . 16) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "accessible") (:form . "accessible") (:end . 39)\n  (:start . 29) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "wide") (:form . "wide") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "range") (:form . "range") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "researcher") (:form . "researchers") (:end . 70)\n  (:start . 59) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "RB") (:stem . "simultaneously") (:form . "simultaneously")\n  (:end . 90) (:start . 76) (:id . 55))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 99)\n  (:start . 91) (:id . 56))\n ((:tag . "NN") (:stem . "support") (:form . "support") (:end . 107)\n  (:start . 100) (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 111) (:start . 108)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "novel") (:form . "novel") (:end . 117)\n  (:start . 112) (:id . 59))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 127)\n  (:start . 118) (:id . 60))\n ((:tag . "NN") (:stem . "development") (:form . "development") (:end . 139)\n  (:start . 128) (:id . 61))\n ((:tag . "RB") (:stem . "as") (:form . "as") (:end . 142) (:start . 140)\n  (:id . 62))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 147) (:start . 143)\n  (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 150) (:start . 148)\n  (:id . 64))\n ((:tag . "NN") (:stem . "deployment") (:form . "deployment") (:end . 161)\n  (:start . 151) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 164) (:start . 162)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "automate") (:form . "automated") (:end . 174)\n  (:start . 165) (:id . 67))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 179)\n  (:start . 175) (:id . 68))\n ((:tag . "NNS") (:stem . "pipeline") (:form . "pipelines") (:end . 189)\n  (:start . 180) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s14.229) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504731@unknown@formal@none@1@S@As a central point of integration for information from publically available databases and native data from proprietary instrument platforms, multiplierz offers compelling addition to the ongoing discourse aimed at identifying an effective means to enable broad access and data exchange in the proteomics community.@(((:tag . "IN") (:stem . "as") (:form . "As") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 4) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "central") (:form . "central") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "point") (:form . "point") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "integration") (:form . "integration") (:end . 33)\n  (:start . 22) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 49)\n  (:start . 38) (:id . 49))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "RB") (:stem . "publically") (:form . "publically") (:end . 65)\n  (:start . 55) (:id . 51))\n ((:tag . "JJ") (:stem . "available") (:form . "available") (:end . 75)\n  (:start . 66) (:id . 52))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 85)\n  (:start . 76) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 96)\n  (:start . 90) (:id . 55))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 101) (:start . 97)\n  (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 106) (:start . 102)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "proprietary") (:form . "proprietary") (:end . 118)\n  (:start . 107) (:id . 58))\n ((:tag . "NN") (:stem . "instrument") (:form . "instrument") (:end . 129)\n  (:start . 119) (:id . 59))\n ((:tag . "NNS") (:stem . "platform") (:form . "platforms") (:end . 139)\n  (:start . 130) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 140) (:start . 139)\n  (:id . 61))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 152)\n  (:start . 141) (:id . 62))\n ((:tag . "VBZ") (:stem . "offer") (:form . "offers") (:end . 159)\n  (:start . 153) (:id . 63))\n ((:tag . "JJ") (:stem . "compelling") (:form . "compelling") (:end . 170)\n  (:start . 160) (:id . 64))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 179)\n  (:start . 171) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 182) (:start . 180)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 186) (:start . 183)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "ongoing") (:form . "ongoing") (:end . 194)\n  (:start . 187) (:id . 68))\n ((:tag . "NN") (:stem . "discourse") (:form . "discourse") (:end . 204)\n  (:start . 195) (:id . 69))\n ((:tag . "VBN") (:stem . "aim") (:form . "aimed") (:end . 210) (:start . 205)\n  (:id . 70))\n ((:tag . "IN") (:stem . "at") (:form . "at") (:end . 213) (:start . 211)\n  (:id . 71))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 225)\n  (:start . 214) (:id . 72))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 228) (:start . 226)\n  (:id . 73))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 238)\n  (:start . 229) (:id . 74))\n ((:tag . "NNS") (:stem . "mean") (:form . "means") (:end . 244)\n  (:start . 239) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 247) (:start . 245)\n  (:id . 76))\n ((:tag . "VB") (:stem . "enable") (:form . "enable") (:end . 254)\n  (:start . 248) (:id . 77))\n ((:tag . "JJ") (:stem . "broad") (:form . "broad") (:end . 260)\n  (:start . 255) (:id . 78))\n ((:tag . "NN") (:stem . "access") (:form . "access") (:end . 267)\n  (:start . 261) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 271) (:start . 268)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 276)\n  (:start . 272) (:id . 81))\n ((:tag . "NN") (:stem . "exchange") (:form . "exchange") (:end . 285)\n  (:start . 277) (:id . 82))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 288) (:start . 286)\n  (:id . 83))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 292) (:start . 289)\n  (:id . 84))\n ((:tag . "NNS") (:stem . "proteomic") (:form . "proteomics") (:end . 303)\n  (:start . 293) (:id . 85))\n ((:tag . "NN") (:stem . "community") (:form . "community") (:end . 313)\n  (:start . 304) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 314) (:start . 313)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s14.230) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504732@unknown@formal@none@1@S@In particular, incorporation of mzAPI into the multiplierz desktop architecture may offer a better impedance match between the rate of proprietary mass spectrometry innovation and researchers' demands for increased autonomy in their data analysis tasks.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "particular") (:form . "particular") (:end . 13)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "incorporation") (:form . "incorporation")\n  (:end . 28) (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 31) (:start . 29)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mzapi") (:form . "mzAPI") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 42) (:start . 38)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "multiplierz") (:form . "multiplierz") (:end . 58)\n  (:start . 47) (:id . 50))\n ((:tag . "NN") (:stem . "desktop") (:form . "desktop") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "architecture") (:form . "architecture") (:end . 79)\n  (:start . 67) (:id . 52))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 83) (:start . 80)\n  (:id . 53))\n ((:tag . "VB") (:stem . "offer") (:form . "offer") (:end . 89) (:start . 84)\n  (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 91) (:start . 90)\n  (:id . 55))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 98) (:start . 92)\n  (:id . 56))\n ((:tag . "NN") (:stem . "impedance") (:form . "impedance") (:end . 108)\n  (:start . 99) (:id . 57))\n ((:tag . "NN") (:stem . "match") (:form . "match") (:end . 114)\n  (:start . 109) (:id . 58))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 122)\n  (:start . 115) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 60))\n ((:tag . "NN") (:stem . "rate") (:form . "rate") (:end . 131) (:start . 127)\n  (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "proprietary") (:form . "proprietary") (:end . 146)\n  (:start . 135) (:id . 63))\n ((:tag . "NN") (:stem . "mass") (:form . "mass") (:end . 151) (:start . 147)\n  (:id . 64))\n ((:tag . "NN") (:stem . "spectrometry") (:form . "spectrometry") (:end . 164)\n  (:start . 152) (:id . 65))\n ((:tag . "NN") (:stem . "innovation") (:form . "innovation") (:end . 175)\n  (:start . 165) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 179) (:start . 176)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "researcher") (:form . "researchers") (:end . 191)\n  (:start . 180) (:id . 68))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 192) (:start . 191)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "demand") (:form . "demands") (:end . 200)\n  (:start . 193) (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 204) (:start . 201)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "increase") (:form . "increased") (:end . 214)\n  (:start . 205) (:id . 72))\n ((:tag . "NN") (:stem . "autonomy") (:form . "autonomy") (:end . 223)\n  (:start . 215) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 226) (:start . 224)\n  (:id . 74))\n ((:tag . "PRP$") (:stem . "their") (:form . "their") (:end . 232)\n  (:start . 227) (:id . 75))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 237)\n  (:start . 233) (:id . 76))\n ((:tag . "NN") (:stem . "analysis") (:form . "analysis") (:end . 246)\n  (:start . 238) (:id . 77))\n ((:tag . "NNS") (:stem . "task") (:form . "tasks") (:end . 252)\n  (:start . 247) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 253) (:start . 252)\n  (:id . 79)))@@@1@38@((:hcues ((:id . :x14.231.1) (:span 80 83)))\n (:hscopes ((:id . :x14.231.1) (:span 80 252)))\n (:identifiers (:sid . :s14.231) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504733@unknown@formal@none@1@S@Availability and Requirements@(((:tag . "NN") (:stem . "availability") (:form . "Availability") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "requirement") (:form . "Requirements") (:end . 29)\n  (:start . 17) (:id . 44)))@@@1@3@((:identifiers (:sid . :s14.232) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504734@unknown@formal@none@1@S@• Project name: multiplierz@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Project") (:form . "Project") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "name") (:form . "name") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "multiplierz") (:form . "multiplierz") (:end . 27)\n  (:start . 16) (:id . 46)))@@@1@5@((:identifiers (:sid . :s14.233) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504735@unknown@formal@none@1@S@• Project home page: http://blais.dfci.harvard.edu/multiplierz@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "Project") (:form . "Project") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "home") (:form . "home") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "page") (:form . "page") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "http://blais.dfci.harvard.edu/multiplierz")\n  (:form . "http://blais.dfci.harvard.edu/multiplierz") (:end . 62)\n  (:start . 21) (:id . 47)))@@@1@6@((:identifiers (:sid . :s14.234) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504736@unknown@formal@none@1@S@• Operating system(s): Microsoft Windows@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "operating") (:form . "Operating") (:end . 11)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "system(s)") (:form . "system(s)") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 22) (:start . 21)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Microsoft") (:form . "Microsoft") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NNP") (:stem . "Windows") (:form . "Windows") (:end . 40)\n  (:start . 33) (:id . 47)))@@@1@6@((:identifiers (:sid . :s14.235) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504737@unknown@formal@none@1@S@• Programming language: Python@(((:tag . "LS") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "programming") (:form . "Programming") (:end . 13)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "Python") (:form . "Python") (:end . 30)\n  (:start . 24) (:id . 46)))@@@1@5@((:identifiers (:sid . :s14.236) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504738@unknown@formal@none@1@S@• License: open source under LGPL@(((:tag . "JJ") (:stem . "•") (:form . "•") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "License") (:form . "License") (:end . 9)\n  (:start . 2) (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "open") (:form . "open") (:end . 15) (:start . 11)\n  (:id . 45))\n ((:tag . "NN") (:stem . "source") (:form . "source") (:end . 22)\n  (:start . 16) (:id . 46))\n ((:tag . "IN") (:stem . "under") (:form . "under") (:end . 28) (:start . 23)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "LGPL") (:form . "LGPL") (:end . 33) (:start . 29)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s14.237) (:did . :pmc2774704) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504739@unknown@formal@none@1@S@(PS)2-v2: template-based protein structure prediction server@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "JJ") (:stem . "template-based") (:form . "template-based")\n  (:end . 24) (:start . 10) (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 32)\n  (:start . 25) (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 53)\n  (:start . 43) (:id . 48))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 60)\n  (:start . 54) (:id . 49)))@@@1@8@((:identifiers (:sid . :s15.1) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Title|)))@oe@9-2-2011
5504740@unknown@formal@none@1@S@Abstract@(((:tag . "NN") (:stem . "abstract") (:form . "Abstract") (:end . 8)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s15.2) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504741@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s15.3) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504742@unknown@formal@none@1@S@Template selection and target-template alignment are critical steps for template-based modeling (TBM) methods.@(((:tag . "NNP") (:stem . "Template") (:form . "Template") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 38) (:start . 23) (:id . 45))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 48)\n  (:start . 39) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 52) (:start . 49)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 61)\n  (:start . 53) (:id . 48))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 67) (:start . 62)\n  (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 71) (:start . 68)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "template-based") (:form . "template-based")\n  (:end . 86) (:start . 72) (:id . 51))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 95)\n  (:start . 87) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 97) (:start . 96)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "TBM") (:form . "TBM") (:end . 100) (:start . 97)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 109)\n  (:start . 102) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s15.4) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504743@unknown@formal@none@1@S@To identify the template for the twilight zone of 15~25% sequence similarity between targets and templates is still difficulty for template-based protein structure prediction.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "twilight") (:form . "twilight") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "zone") (:form . "zone") (:end . 46) (:start . 42)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "CD") (:stem . "15~25") (:form . "15~25") (:end . 55) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 65)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 76)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 92)\n  (:start . 85) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 106)\n  (:start . 97) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 109) (:start . 107)\n  (:id . 59))\n ((:tag . "RB") (:stem . "still") (:form . "still") (:end . 115)\n  (:start . 110) (:id . 60))\n ((:tag . "NN") (:stem . "difficulty") (:form . "difficulty") (:end . 126)\n  (:start . 116) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 130) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "template-based") (:form . "template-based")\n  (:end . 145) (:start . 131) (:id . 63))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 153)\n  (:start . 146) (:id . 64))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 163)\n  (:start . 154) (:id . 65))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 174)\n  (:start . 164) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.5) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504744@unknown@formal@none@1@S@This study presents the (PS)2-v2 server, based on our original server with numerous enhancements and modifications, to improve reliability and applicability.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "present") (:form . "presents") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 39)\n  (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 46) (:start . 41)\n  (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 49) (:start . 47)\n  (:id . 51))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 53) (:start . 50)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 62)\n  (:start . 54) (:id . 53))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 69)\n  (:start . 63) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 74) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "numerous") (:form . "numerous") (:end . 83)\n  (:start . 75) (:id . 56))\n ((:tag . "NNS") (:stem . "enhancement") (:form . "enhancements") (:end . 96)\n  (:start . 84) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "modification") (:form . "modifications")\n  (:end . 114) (:start . 101) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 115) (:start . 114)\n  (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 118) (:start . 116)\n  (:id . 61))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 126)\n  (:start . 119) (:id . 62))\n ((:tag . "NN") (:stem . "reliability") (:form . "reliability") (:end . 138)\n  (:start . 127) (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 142) (:start . 139)\n  (:id . 64))\n ((:tag . "NN") (:stem . "applicability") (:form . "applicability")\n  (:end . 156) (:start . 143) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s15.6) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504745@unknown@formal@none@1@S@Results@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s15.7) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504746@unknown@formal@none@1@S@To detect homologous proteins with remote similarity, the (PS)2-v2 server utilizes the S2A2 matrix, which is a 60 × 60 substitution matrix using the secondary structure propensities of 20 amino acids, and the position-specific sequence profile (PSSM) generated by PSI-BLAST.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "detect") (:form . "detect") (:end . 9) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 20)\n  (:start . 10) (:id . 44))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "remote") (:form . "remote") (:end . 41)\n  (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 52)\n  (:start . 42) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n  (:id . 51))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 66)\n  (:start . 59) (:id . 52))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . "VBZ") (:stem . "utilize") (:form . "utilizes") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 55))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 91) (:start . 87)\n  (:id . 56))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 98)\n  (:start . 92) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 105)\n  (:start . 100) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 110) (:start . 109)\n  (:id . 61))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 113) (:start . 111)\n  (:id . 62))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 115) (:start . 114)\n  (:id . 63))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 118) (:start . 116)\n  (:id . 64))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 131)\n  (:start . 119) (:id . 65))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 138)\n  (:start . 132) (:id . 66))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 144) (:start . 139)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 158)\n  (:start . 149) (:id . 69))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 168)\n  (:start . 159) (:id . 70))\n ((:tag . "NNS") (:stem . "propensity") (:form . "propensities") (:end . 181)\n  (:start . 169) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 184) (:start . 182)\n  (:id . 72))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 187) (:start . 185)\n  (:id . 73))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 193)\n  (:start . 188) (:id . 74))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 199)\n  (:start . 194) (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 204) (:start . 201)\n  (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 208) (:start . 205)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "position-specific") (:form . "position-specific")\n  (:end . 226) (:start . 209) (:id . 79))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 235)\n  (:start . 227) (:id . 80))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 243)\n  (:start . 236) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 245) (:start . 244)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 249) (:start . 245)\n  (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 250) (:start . 249)\n  (:id . 84))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 260)\n  (:start . 251) (:id . 85))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 263) (:start . 261)\n  (:id . 86))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 273)\n  (:start . 264) (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 274) (:start . 273)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s15.8) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504747@unknown@formal@none@1@S@In addition, our server uses multiple templates and multiple models to build and assess models.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "VBZ") (:stem . "use") (:form . "uses") (:end . 28) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 37)\n  (:start . 29) (:id . 48))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 60)\n  (:start . 52) (:id . 51))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 67)\n  (:start . 61) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 70) (:start . 68)\n  (:id . 53))\n ((:tag . "VB") (:stem . "build") (:form . "build") (:end . 76) (:start . 71)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 55))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 87)\n  (:start . 81) (:id . 56))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 94)\n  (:start . 88) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 95) (:start . 94)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s15.9) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504748@unknown@formal@none@1@S@Our method was evaluated on the Lindahl benchmark for fold recognition and ProSup benchmark for sequence alignment.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "evaluate") (:form . "evaluated") (:end . 24)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Lindahl") (:form . "Lindahl") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 58) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 70)\n  (:start . 59) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 53))\n ((:tag . "NN") (:stem . "prosup") (:form . "ProSup") (:end . 81)\n  (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 91)\n  (:start . 82) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 95) (:start . 92)\n  (:id . 56))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 104)\n  (:start . 96) (:id . 57))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 114)\n  (:start . 105) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s15.10) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504749@unknown@formal@none@1@S@Evaluation results indicated that our method outperforms sequence-profile approaches, and had comparable performance to that of structure-based methods on these benchmarks.@(((:tag . "NN") (:stem . "evaluation") (:form . "Evaluation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 18)\n  (:start . 11) (:id . 43))\n ((:tag . "VBD") (:stem . "indicate") (:form . "indicated") (:end . 28)\n  (:start . 19) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 37) (:start . 34)\n  (:id . 46))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 44)\n  (:start . 38) (:id . 47))\n ((:tag . "VBZ") (:stem . "outperform") (:form . "outperforms") (:end . 56)\n  (:start . 45) (:id . 48))\n ((:tag . "JJ") (:stem . "sequence-profile") (:form . "sequence-profile")\n  (:end . 73) (:start . 57) (:id . 49))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 84)\n  (:start . 74) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 93) (:start . 90)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "comparable") (:form . "comparable") (:end . 104)\n  (:start . 94) (:id . 54))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 116)\n  (:start . 105) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 119) (:start . 117)\n  (:id . 56))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 124) (:start . 120)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "structure-based") (:form . "structure-based")\n  (:end . 143) (:start . 128) (:id . 59))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 151)\n  (:start . 144) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 154) (:start . 152)\n  (:id . 61))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 160)\n  (:start . 155) (:id . 62))\n ((:tag . "NNS") (:stem . "benchmark") (:form . "benchmarks") (:end . 171)\n  (:start . 161) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 64)))@@@1@23@((:hcues ((:id . :x15.11.1) (:span 19 33)))\n (:hscopes ((:id . :x15.11.1) (:span 19 171)))\n (:identifiers (:sid . :s15.11) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504750@unknown@formal@none@1@S@Finally, we tested our method using the 154 TBM targets of the CASP8 (Critical Assessment of Techniques for Protein Structure Prediction) dataset.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "test") (:form . "tested") (:end . 18) (:start . 12)\n  (:id . 45))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 29)\n  (:start . 23) (:id . 47))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 43) (:start . 40)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "TBM") (:form . "TBM") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 55)\n  (:start . 48) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 54))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 68) (:start . 63)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "critical") (:form . "Critical") (:end . 78)\n  (:start . 70) (:id . 57))\n ((:tag . "NNP") (:stem . "Assessment") (:form . "Assessment") (:end . 89)\n  (:start . 79) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 92) (:start . 90)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Technique") (:form . "Techniques") (:end . 103)\n  (:start . 93) (:id . 60))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 107) (:start . 104)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Protein") (:form . "Protein") (:end . 115)\n  (:start . 108) (:id . 62))\n ((:tag . "NNP") (:stem . "Structure") (:form . "Structure") (:end . 125)\n  (:start . 116) (:id . 63))\n ((:tag . "NNP") (:stem . "Prediction") (:form . "Prediction") (:end . 136)\n  (:start . 126) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 65))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 145)\n  (:start . 138) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 146) (:start . 145)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.12) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504751@unknown@formal@none@1@S@Experimental results show that (PS)2-v2 is ranked 6th among 72 severs and is faster than the top-rank five serves, which utilize ab initio methods.@(((:tag . "JJ") (:stem . "experimental") (:form . "Experimental") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 20)\n  (:start . 13) (:id . 43))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 25) (:start . 21)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 39)\n  (:start . 32) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 42) (:start . 40)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "rank") (:form . "ranked") (:end . 49) (:start . 43)\n  (:id . 49))\n ((:tag . "RB") (:stem . "6th") (:form . "6th") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "sever") (:form . "severs") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 76) (:start . 74)\n  (:id . 55))\n ((:tag . "JJR") (:stem . "fast") (:form . "faster") (:end . 83) (:start . 77)\n  (:id . 56))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "top-rank") (:form . "top-rank") (:end . 101)\n  (:start . 93) (:id . 59))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "serve") (:form . "serves") (:end . 113)\n  (:start . 107) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 62))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 120)\n  (:start . 115) (:id . 63))\n ((:tag . "VBP") (:stem . "utilize") (:form . "utilize") (:end . 128)\n  (:start . 121) (:id . 64))\n ((:tag . "NN") (:stem . "ab") (:form . "ab") (:end . 131) (:start . 129)\n  (:id . 65))\n ((:tag . "NN") (:stem . "initio") (:form . "initio") (:end . 138)\n  (:start . 132) (:id . 66))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 146)\n  (:start . 139) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s15.13) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504752@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s15.14) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504753@unknown@formal@none@1@S@Experimental results demonstrate that (PS)2-v2 with the S2A2 matrix is useful for template selections and target-template alignments by blending the amino acid and structural propensities.@(((:tag . "JJ") (:stem . "experimental") (:form . "Experimental") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 20)\n  (:start . 13) (:id . 43))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 32)\n  (:start . 21) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 46))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 46)\n  (:start . 39) (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 51) (:start . 47)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 60) (:start . 56)\n  (:id . 50))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 67)\n  (:start . 61) (:id . 51))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 70) (:start . 68)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 77)\n  (:start . 71) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "template") (:form . "template") (:end . 90)\n  (:start . 82) (:id . 55))\n ((:tag . "NNS") (:stem . "selection") (:form . "selections") (:end . 101)\n  (:start . 91) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 121) (:start . 106) (:id . 58))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 132)\n  (:start . 122) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 135) (:start . 133)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "blend") (:form . "blending") (:end . 144)\n  (:start . 136) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 148) (:start . 145)\n  (:id . 62))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 154)\n  (:start . 149) (:id . 63))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 159) (:start . 155)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 163) (:start . 160)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 174)\n  (:start . 164) (:id . 66))\n ((:tag . "NNS") (:stem . "propensity") (:form . "propensities") (:end . 187)\n  (:start . 175) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 188) (:start . 187)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s15.15) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504754@unknown@formal@none@1@S@The multiple-template and multiple-model strategies are able to significantly improve the accuracies for target-template alignments in the twilight zone.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "multiple-template") (:form . "multiple-template")\n  (:end . 21) (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "multiple-model") (:form . "multiple-model")\n  (:end . 40) (:start . 26) (:id . 45))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 51)\n  (:start . 41) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 55) (:start . 52)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 60) (:start . 56)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 49))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 77) (:start . 64) (:id . 50))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 85)\n  (:start . 78) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "accuracy") (:form . "accuracies") (:end . 100)\n  (:start . 90) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 104) (:start . 101)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 120) (:start . 105) (:id . 55))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 131)\n  (:start . 121) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 134) (:start . 132)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 138) (:start . 135)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "twilight") (:form . "twilight") (:end . 147)\n  (:start . 139) (:id . 59))\n ((:tag . "NN") (:stem . "zone") (:form . "zone") (:end . 152) (:start . 148)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s15.16) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504755@unknown@formal@none@1@S@We believe that this server is useful in structure prediction and modeling, especially in detecting homologous templates with sequence similarity in the twilight zone.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "believe") (:form . "believe") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 50)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 61)\n  (:start . 51) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 54))\n ((:tag . "RB") (:stem . "especially") (:form . "especially") (:end . 86)\n  (:start . 76) (:id . 55))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "detect") (:form . "detecting") (:end . 99)\n  (:start . 90) (:id . 57))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 110)\n  (:start . 100) (:id . 58))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 120)\n  (:start . 111) (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 125) (:start . 121)\n  (:id . 60))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 134)\n  (:start . 126) (:id . 61))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 145)\n  (:start . 135) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 148) (:start . 146)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "twilight") (:form . "twilight") (:end . 161)\n  (:start . 153) (:id . 65))\n ((:tag . "NN") (:stem . "zone") (:form . "zone") (:end . 166) (:start . 162)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 67)))@@@1@26@((:hcues ((:id . :x15.17.1) (:span 3 10)))\n (:hscopes ((:id . :x15.17.1) (:span 3 166)))\n (:identifiers (:sid . :s15.17) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504756@unknown@formal@none@1@S@Background@(((:tag . "NN") (:stem . "background") (:form . "Background") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s15.18) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504757@unknown@formal@none@1@S@For template-based modeling (TBM) and fold recognition methods, a prediction model can be built based on the coordinates of the appropriate template(s) [1].@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "template-based") (:form . "template-based")\n  (:end . 18) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 27)\n  (:start . 19) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 29) (:start . 28)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "TBM") (:form . "TBM") (:end . 32) (:start . 29)\n  (:id . 46))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 54)\n  (:start . 43) (:id . 50))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 62)\n  (:start . 55) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 76)\n  (:start . 66) (:id . 54))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 82) (:start . 77)\n  (:id . 55))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 86) (:start . 83)\n  (:id . 56))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 89) (:start . 87)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "build") (:form . "built") (:end . 95) (:start . 90)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "coordinate") (:form . "coordinates") (:end . 120)\n  (:start . 109) (:id . 62))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "appropriate") (:form . "appropriate") (:end . 139)\n  (:start . 128) (:id . 65))\n ((:tag . "NN") (:stem . "template(s)") (:form . "template(s)") (:end . 151)\n  (:start . 140) (:id . 66))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 153) (:start . 152)\n  (:id . 67))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 154) (:start . 153)\n  (:id . 68))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 155) (:start . 154)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 156) (:start . 155)\n  (:id . 70)))@@@1@29@((:hcues ((:id . :x15.19.1) (:span 83 86)))\n (:hscopes ((:id . :x15.19.1) (:span 64 151)))\n (:identifiers (:sid . :s15.19) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504758@unknown@formal@none@1@S@These approaches generally involve four steps: 1) a representative protein structure database is searched to identify a template that is structurally similar to the protein target; 2) an alignment between the target and the template is generated that should align equivalent residues together as in the case of a structural alignment; 3) a prediction structure of the target is built based on the alignment and the selected template structure, and 4) model quality evaluation.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 16)\n  (:start . 6) (:id . 43))\n ((:tag . "RB") (:stem . "generally") (:form . "generally") (:end . 26)\n  (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "involve") (:form . "involve") (:end . 34)\n  (:start . 27) (:id . 45))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 45) (:start . 40)\n  (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 46) (:start . 45)\n  (:id . 48))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 48) (:start . 47)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 51) (:start . 50)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "representative") (:form . "representative")\n  (:end . 66) (:start . 52) (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 74)\n  (:start . 67) (:id . 53))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 84)\n  (:start . 75) (:id . 54))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 93)\n  (:start . 85) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 96) (:start . 94)\n  (:id . 56))\n ((:tag . "VBN") (:stem . "search") (:form . "searched") (:end . 105)\n  (:start . 97) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 58))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 117)\n  (:start . 109) (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 119) (:start . 118)\n  (:id . 60))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 128)\n  (:start . 120) (:id . 61))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 133) (:start . 129)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 136) (:start . 134)\n  (:id . 63))\n ((:tag . "RB") (:stem . "structurally") (:form . "structurally") (:end . 149)\n  (:start . 137) (:id . 64))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 157)\n  (:start . 150) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 160) (:start . 158)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 164) (:start . 161)\n  (:id . 67))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 172)\n  (:start . 165) (:id . 68))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 179)\n  (:start . 173) (:id . 69))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 180) (:start . 179)\n  (:id . 70))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 182) (:start . 181)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n  (:id . 72))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 186) (:start . 184)\n  (:id . 73))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 196)\n  (:start . 187) (:id . 74))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 204)\n  (:start . 197) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 208) (:start . 205)\n  (:id . 76))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 215)\n  (:start . 209) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 219) (:start . 216)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 223) (:start . 220)\n  (:id . 79))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 232)\n  (:start . 224) (:id . 80))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 235) (:start . 233)\n  (:id . 81))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 245)\n  (:start . 236) (:id . 82))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 250) (:start . 246)\n  (:id . 83))\n ((:tag . "MD") (:stem . "should") (:form . "should") (:end . 257)\n  (:start . 251) (:id . 84))\n ((:tag . "VB") (:stem . "align") (:form . "align") (:end . 263)\n  (:start . 258) (:id . 85))\n ((:tag . "JJ") (:stem . "equivalent") (:form . "equivalent") (:end . 274)\n  (:start . 264) (:id . 86))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 283)\n  (:start . 275) (:id . 87))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 292)\n  (:start . 284) (:id . 88))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 295) (:start . 293)\n  (:id . 89))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 298) (:start . 296)\n  (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 302) (:start . 299)\n  (:id . 91))\n ((:tag . "NN") (:stem . "case") (:form . "case") (:end . 307) (:start . 303)\n  (:id . 92))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 310) (:start . 308)\n  (:id . 93))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 312) (:start . 311)\n  (:id . 94))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 323)\n  (:start . 313) (:id . 95))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 333)\n  (:start . 324) (:id . 96))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 334) (:start . 333)\n  (:id . 97))\n ((:tag . "LS") (:stem . "3") (:form . "3") (:end . 336) (:start . 335)\n  (:id . 98))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 337) (:start . 336)\n  (:id . 99))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 339) (:start . 338)\n  (:id . 100))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 350)\n  (:start . 340) (:id . 101))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 360)\n  (:start . 351) (:id . 102))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 363) (:start . 361)\n  (:id . 103))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 367) (:start . 364)\n  (:id . 104))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 374)\n  (:start . 368) (:id . 105))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 377) (:start . 375)\n  (:id . 106))\n ((:tag . "VBN") (:stem . "build") (:form . "built") (:end . 383)\n  (:start . 378) (:id . 107))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 389)\n  (:start . 384) (:id . 108))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 392) (:start . 390)\n  (:id . 109))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 396) (:start . 393)\n  (:id . 110))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 406)\n  (:start . 397) (:id . 111))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 410) (:start . 407)\n  (:id . 112))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 414) (:start . 411)\n  (:id . 113))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 423)\n  (:start . 415) (:id . 114))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 432)\n  (:start . 424) (:id . 115))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 442)\n  (:start . 433) (:id . 116))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 443) (:start . 442)\n  (:id . 117))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 447) (:start . 444)\n  (:id . 118))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 449) (:start . 448)\n  (:id . 119))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 450) (:start . 449)\n  (:id . 120))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 456)\n  (:start . 451) (:id . 121))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 464)\n  (:start . 457) (:id . 122))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 475)\n  (:start . 465) (:id . 123))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 476) (:start . 475)\n  (:id . 124)))@@@1@83@((:hcues ((:id . :x15.20.1) (:span 251 257)))\n (:hscopes ((:id . :x15.20.1) (:span 251 333)))\n (:identifiers (:sid . :s15.20) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504759@unknown@formal@none@1@S@The first two steps significantly affect the quality of the final model prediction in TBM methods.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 19) (:start . 14)\n  (:id . 45))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 33) (:start . 20) (:id . 46))\n ((:tag . "VBP") (:stem . "affect") (:form . "affect") (:end . 40)\n  (:start . 34) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 52)\n  (:start . 45) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 55) (:start . 53)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 65) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 82)\n  (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 85) (:start . 83)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "TBM") (:form . "TBM") (:end . 89) (:start . 86)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 97)\n  (:start . 90) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 98) (:start . 97)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s15.21) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504760@unknown@formal@none@1@S@The secondary structure of a protein is often more conserved than the amino acid sequence, and the prediction accuracy of the secondary structure has been achieved ~80% on average.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 23)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 60)\n  (:start . 51) (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 75) (:start . 70)\n  (:id . 54))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 89)\n  (:start . 81) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 59))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 109)\n  (:start . 99) (:id . 60))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 118)\n  (:start . 110) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 121) (:start . 119)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 135)\n  (:start . 126) (:id . 64))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 145)\n  (:start . 136) (:id . 65))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 149) (:start . 146)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 154) (:start . 150)\n  (:id . 67))\n ((:tag . "VBN") (:stem . "achieve") (:form . "achieved") (:end . 163)\n  (:start . 155) (:id . 68))\n ((:tag . "CD") (:stem . "~80") (:form . "~80") (:end . 167) (:start . 164)\n  (:id . 69))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 168) (:start . 167)\n  (:id . 70))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 171) (:start . 169)\n  (:id . 71))\n ((:tag . "NN") (:stem . "average") (:form . "average") (:end . 179)\n  (:start . 172) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s15.22) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504761@unknown@formal@none@1@S@Recently, a number of methods, integrating secondary structures (i.e., α-helix, ß-strand and coil) with primary amino acid sequences, have successfully detected the homologs with remote similarity for automated comparative modeling [2-6] and fold recognition [7-12].@(((:tag . "RB") (:stem . "recently") (:form . "Recently") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 29)\n  (:start . 22) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "integrate") (:form . "integrating") (:end . 42)\n  (:start . 31) (:id . 49))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 63)\n  (:start . 53) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 52))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "α-helix") (:form . "α-helix") (:end . 78)\n  (:start . 71) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "ß-strand") (:form . "ß-strand") (:end . 88)\n  (:start . 80) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "NN") (:stem . "coil") (:form . "coil") (:end . 97) (:start . 93)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 103) (:start . 99)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 111)\n  (:start . 104) (:id . 62))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 117)\n  (:start . 112) (:id . 63))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 122) (:start . 118)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 132)\n  (:start . 123) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 66))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 138) (:start . 134)\n  (:id . 67))\n ((:tag . "RB") (:stem . "successfully") (:form . "successfully") (:end . 151)\n  (:start . 139) (:id . 68))\n ((:tag . "VBN") (:stem . "detect") (:form . "detected") (:end . 160)\n  (:start . 152) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 164) (:start . 161)\n  (:id . 70))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 173)\n  (:start . 165) (:id . 71))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 178) (:start . 174)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "remote") (:form . "remote") (:end . 185)\n  (:start . 179) (:id . 73))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 196)\n  (:start . 186) (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 200) (:start . 197)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "automated") (:form . "automated") (:end . 210)\n  (:start . 201) (:id . 76))\n ((:tag . "JJ") (:stem . "comparative") (:form . "comparative") (:end . 222)\n  (:start . 211) (:id . 77))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 231)\n  (:start . 223) (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 233) (:start . 232)\n  (:id . 79))\n ((:tag . "CD") (:stem . "2-6") (:form . "2-6") (:end . 236) (:start . 233)\n  (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 237) (:start . 236)\n  (:id . 81))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 241) (:start . 238)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 246) (:start . 242)\n  (:id . 83))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 258)\n  (:start . 247) (:id . 84))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 260) (:start . 259)\n  (:id . 85))\n ((:tag . "NN") (:stem . "7-12") (:form . "7-12") (:end . 264) (:start . 260)\n  (:id . 86))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 265) (:start . 264)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 266) (:start . 265)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s15.23) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504762@unknown@formal@none@1@S@These methods often used two separated substitution matrices [9,10,13] to score secondary structures and primary amino acids, respectively, for aligning a residue pair.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 19) (:start . 14)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "separate") (:form . "separated") (:end . 38)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 51)\n  (:start . 39) (:id . 48))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 60)\n  (:start . 52) (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 62) (:start . 61)\n  (:id . 50))\n ((:tag . "CD") (:stem . "9,10,13") (:form . "9,10,13") (:end . 69)\n  (:start . 62) (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 70) (:start . 69)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 53))\n ((:tag . "VB") (:stem . "score") (:form . "score") (:end . 79) (:start . 74)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 89)\n  (:start . 80) (:id . 55))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 100)\n  (:start . 90) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 104) (:start . 101)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "primary") (:form . "primary") (:end . 112)\n  (:start . 105) (:id . 58))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 118)\n  (:start . 113) (:id . 59))\n ((:tag . "NNS") (:stem . "acid") (:form . "acids") (:end . 124)\n  (:start . 119) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 125) (:start . 124)\n  (:id . 61))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 138)\n  (:start . 126) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 143) (:start . 140)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "align") (:form . "aligning") (:end . 152)\n  (:start . 144) (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 154) (:start . 153)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "residue") (:form . "residue") (:end . 162)\n  (:start . 155) (:id . 67))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 167) (:start . 163)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s15.24) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504763@unknown@formal@none@1@S@The separated matrices are unable to reflect the real score because the amino acid type often prefers to a specific secondary structure.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "separated") (:form . "separated") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "unable") (:form . "unable") (:end . 33)\n  (:start . 27) (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "VB") (:stem . "reflect") (:form . "reflect") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "real") (:form . "real") (:end . 53) (:start . 49)\n  (:id . 50))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 59) (:start . 54)\n  (:id . 51))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 67)\n  (:start . 60) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 77) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 82) (:start . 78)\n  (:id . 55))\n ((:tag . "NN") (:stem . "type") (:form . "type") (:end . 87) (:start . 83)\n  (:id . 56))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 93) (:start . 88)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "prefer") (:form . "prefers") (:end . 101)\n  (:start . 94) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 104) (:start . 102)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 115)\n  (:start . 107) (:id . 61))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 125)\n  (:start . 116) (:id . 62))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 135)\n  (:start . 126) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s15.25) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504764@unknown@formal@none@1@S@Here, we have developed a substitution matrix, called S2A2, which considers the properties of the secondary structures and amino acid types.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 13) (:start . 9)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "develop") (:form . "developed") (:end . 23)\n  (:start . 14) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 38)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 45)\n  (:start . 39) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "call") (:form . "called") (:end . 53) (:start . 47)\n  (:id . 51))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 65) (:start . 60)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "consider") (:form . "considers") (:end . 75)\n  (:start . 66) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 79) (:start . 76)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 90)\n  (:start . 80) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 107)\n  (:start . 98) (:id . 60))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 118)\n  (:start . 108) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 128)\n  (:start . 123) (:id . 63))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 133) (:start . 129)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 139)\n  (:start . 134) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s15.26) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504765@unknown@formal@none@1@S@The S2A2 is a 60 × 60 matrix that considers all possible pair combination of 20 amino acid types and three secondary structure elements.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 16) (:start . 14)\n  (:id . 46))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 18) (:start . 17)\n  (:id . 47))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 21) (:start . 19)\n  (:id . 48))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 28)\n  (:start . 22) (:id . 49))\n ((:tag . "WDT") (:stem . "that") (:form . "that") (:end . 33) (:start . 29)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "consider") (:form . "considers") (:end . 43)\n  (:start . 34) (:id . 51))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 47) (:start . 44)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "possible") (:form . "possible") (:end . 56)\n  (:start . 48) (:id . 53))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . "NN") (:stem . "combination") (:form . "combination") (:end . 73)\n  (:start . 62) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 76) (:start . 74)\n  (:id . 56))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 85) (:start . 80)\n  (:id . 58))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 90) (:start . 86)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 96) (:start . 91)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 100) (:start . 97)\n  (:id . 61))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 106)\n  (:start . 101) (:id . 62))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 116)\n  (:start . 107) (:id . 63))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 126)\n  (:start . 117) (:id . 64))\n ((:tag . "NNS") (:stem . "element") (:form . "elements") (:end . 135)\n  (:start . 127) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 136) (:start . 135)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x15.27.1) (:span 48 56)))\n (:hscopes ((:id . :x15.27.1) (:span 48 135)))\n (:identifiers (:sid . :s15.27) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504766@unknown@formal@none@1@S@This matrix was evaluated on the Lindahl benchmark [14] for fold recognition and the ProSup benchmark [15] for alignment accuracies.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "evaluate") (:form . "evaluated") (:end . 25)\n  (:start . 16) (:id . 45))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 28) (:start . 26)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Lindahl") (:form . "Lindahl") (:end . 40)\n  (:start . 33) (:id . 48))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 52) (:start . 51)\n  (:id . 50))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 64) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 76)\n  (:start . 65) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "ProSup") (:form . "ProSup") (:end . 91)\n  (:start . 85) (:id . 58))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 101)\n  (:start . 92) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 105) (:start . 103)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 106) (:start . 105)\n  (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 110) (:start . 107)\n  (:id . 63))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 120)\n  (:start . 111) (:id . 64))\n ((:tag . "NNS") (:stem . "accuracy") (:form . "accuracies") (:end . 131)\n  (:start . 121) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s15.28) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504767@unknown@formal@none@1@S@According to these evaluation results, the S2A2 matrix has higher accuracy than position specific scoring matrix (PSSM) generated by PSI-BLAST and prof_sim for fold recognition and sequence alignments.@(((:tag . "VBG") (:stem . "accord") (:form . "According") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 37)\n  (:start . 30) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 54)\n  (:start . 48) (:id . 50))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 65) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 79) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "position") (:form . "position") (:end . 88)\n  (:start . 80) (:id . 55))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 97)\n  (:start . 89) (:id . 56))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 105)\n  (:start . 98) (:id . 57))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 112)\n  (:start . 106) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 118) (:start . 114)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 119) (:start . 118)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 129)\n  (:start . 120) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 132) (:start . 130)\n  (:id . 63))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 142)\n  (:start . 133) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 146) (:start . 143)\n  (:id . 65))\n ((:tag . "NN") (:stem . "prof_sim") (:form . "prof_sim") (:end . 155)\n  (:start . 147) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 159) (:start . 156)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 164) (:start . 160)\n  (:id . 68))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 176)\n  (:start . 165) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 180) (:start . 177)\n  (:id . 70))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 189)\n  (:start . 181) (:id . 71))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 200)\n  (:start . 190) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 201) (:start . 200)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s15.29) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504768@unknown@formal@none@1@S@By integrating the S2A2 matrix and PSSM, each having a unique scoring mechanism, the (PS)2-v2 server blends the sequence profile and secondary structure information so that they work cooperatively.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "integrate") (:form . "integrating") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 45) (:start . 41)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "have") (:form . "having") (:end . 52) (:start . 46)\n  (:id . 51))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "unique") (:form . "unique") (:end . 61)\n  (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 69)\n  (:start . 62) (:id . 54))\n ((:tag . "NN") (:stem . "mechanism") (:form . "mechanism") (:end . 79)\n  (:start . 70) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 93)\n  (:start . 86) (:id . 59))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 100)\n  (:start . 94) (:id . 60))\n ((:tag . "VBZ") (:stem . "blend") (:form . "blends") (:end . 107)\n  (:start . 101) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 62))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 120)\n  (:start . 112) (:id . 63))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 128)\n  (:start . 121) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 132) (:start . 129)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 142)\n  (:start . 133) (:id . 66))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 152)\n  (:start . 143) (:id . 67))\n ((:tag . "NN") (:stem . "information") (:form . "information") (:end . 164)\n  (:start . 153) (:id . 68))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 167) (:start . 165)\n  (:id . 69))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 172) (:start . 168)\n  (:id . 70))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 177) (:start . 173)\n  (:id . 71))\n ((:tag . "VBP") (:stem . "work") (:form . "work") (:end . 182) (:start . 178)\n  (:id . 72))\n ((:tag . "RB") (:stem . "cooperatively") (:form . "cooperatively")\n  (:end . 196) (:start . 183) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 197) (:start . 196)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s15.30) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504769@unknown@formal@none@1@S@Numerous enhancements and modifications were applied to original (PS)2 servers (namely (PS)2-original) [16] and (PS)2-CASP8 [17] which participates the CASP8 experiment, thereby improving the reliability and applicability of the method.@(((:tag . "JJ") (:stem . "numerous") (:form . "Numerous") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "enhancement") (:form . "enhancements") (:end . 21)\n  (:start . 9) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 25) (:start . 22)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "modification") (:form . "modifications")\n  (:end . 39) (:start . 26) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 44) (:start . 40)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 52)\n  (:start . 45) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 55) (:start . 53)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 64)\n  (:start . 56) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "PS)2") (:form . "PS)2") (:end . 70) (:start . 66)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 78)\n  (:start . 71) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 80) (:start . 79)\n  (:id . 53))\n ((:tag . "RB") (:stem . "namely") (:form . "namely") (:end . 86)\n  (:start . 80) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 88) (:start . 87)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 101) (:start . 88) (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 102) (:start . 101)\n  (:id . 57))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 104) (:start . 103)\n  (:id . 58))\n ((:tag . "CD") (:stem . "16") (:form . "16") (:end . 106) (:start . 104)\n  (:id . 59))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 107) (:start . 106)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 113) (:start . 112)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 123)\n  (:start . 113) (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 125) (:start . 124)\n  (:id . 64))\n ((:tag . "CD") (:stem . "17") (:form . "17") (:end . 127) (:start . 125)\n  (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 128) (:start . 127)\n  (:id . 66))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 134)\n  (:start . 129) (:id . 67))\n ((:tag . "VBZ") (:stem . "participate") (:form . "participates") (:end . 147)\n  (:start . 135) (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 151) (:start . 148)\n  (:id . 69))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 157)\n  (:start . 152) (:id . 70))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 168)\n  (:start . 158) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 169) (:start . 168)\n  (:id . 72))\n ((:tag . "RB") (:stem . "thereby") (:form . "thereby") (:end . 177)\n  (:start . 170) (:id . 73))\n ((:tag . "VBG") (:stem . "improve") (:form . "improving") (:end . 187)\n  (:start . 178) (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 191) (:start . 188)\n  (:id . 75))\n ((:tag . "NN") (:stem . "reliability") (:form . "reliability") (:end . 203)\n  (:start . 192) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 207) (:start . 204)\n  (:id . 77))\n ((:tag . "NN") (:stem . "applicability") (:form . "applicability")\n  (:end . 221) (:start . 208) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 224) (:start . 222)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 228) (:start . 225)\n  (:id . 80))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 235)\n  (:start . 229) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 236) (:start . 235)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s15.31) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504770@unknown@formal@none@1@S@There are four main differences in methodology between the present server ((PS)2-v2) and our previous works (Table 1).@(((:tag . "EX") (:stem . "there") (:form . "There") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 14) (:start . 10)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "main") (:form . "main") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 31)\n  (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 34) (:start . 32)\n  (:id . 47))\n ((:tag . "NN") (:stem . "methodology") (:form . "methodology") (:end . 46)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 54)\n  (:start . 47) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "present") (:form . "present") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 73)\n  (:start . 67) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 83)\n  (:start . 76) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 84) (:start . 83)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 101)\n  (:start . 93) (:id . 59))\n ((:tag . "NNS") (:stem . "work") (:form . "works") (:end . 107)\n  (:start . 102) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 114)\n  (:start . 109) (:id . 62))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 116) (:start . 115)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 117) (:start . 116)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s15.32) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504771@unknown@formal@none@1@S@First, (PS)2-v2 integrates S2A2 matrix and PSSM for the template selection and the target-template alignment to replace a consensus strategy applied in the (PS)2-original server.@(((:tag . "RB") (:stem . "first") (:form . "First") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 15)\n  (:start . 8) (:id . 45))\n ((:tag . "VBZ") (:stem . "integrate") (:form . "integrates") (:end . 26)\n  (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 64)\n  (:start . 56) (:id . 53))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 74)\n  (:start . 65) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 98) (:start . 83) (:id . 57))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 108)\n  (:start . 99) (:id . 58))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . "VB") (:stem . "replace") (:form . "replace") (:end . 119)\n  (:start . 112) (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 121) (:start . 120)\n  (:id . 61))\n ((:tag . "NN") (:stem . "consensus") (:form . "consensus") (:end . 131)\n  (:start . 122) (:id . 62))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 140)\n  (:start . 132) (:id . 63))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 148)\n  (:start . 141) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 151) (:start . 149)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 157) (:start . 156)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 170) (:start . 157) (:id . 68))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 177)\n  (:start . 171) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 178) (:start . 177)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s15.33) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504772@unknown@formal@none@1@S@Second, we modified the SSEARCH [18] search method to replace the PSI-BLAST search method and Smith-Waterman algorithm applied in the (PS)2-original server and (PS)2-CASP8, respectively.@(((:tag . "RB") (:stem . "second") (:form . "Second") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 7) (:start . 6) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "modify") (:form . "modified") (:end . 19)\n  (:start . 11) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "SSEARCH") (:form . "SSEARCH") (:end . 31)\n  (:start . 24) (:id . 47))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 35) (:start . 33)\n  (:id . 49))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 43)\n  (:start . 37) (:id . 51))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 50)\n  (:start . 44) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 53) (:start . 51)\n  (:id . 53))\n ((:tag . "VB") (:stem . "replace") (:form . "replace") (:end . 61)\n  (:start . 54) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 55))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 75)\n  (:start . 66) (:id . 56))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 82)\n  (:start . 76) (:id . 57))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 89)\n  (:start . 83) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "Smith-Waterman") (:form . "Smith-Waterman")\n  (:end . 108) (:start . 94) (:id . 60))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 118)\n  (:start . 109) (:id . 61))\n ((:tag . "VBD") (:stem . "apply") (:form . "applied") (:end . 126)\n  (:start . 119) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 129) (:start . 127)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 135) (:start . 134)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 148) (:start . 135) (:id . 66))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 155)\n  (:start . 149) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 159) (:start . 156)\n  (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 161) (:start . 160)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 171)\n  (:start . 161) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 71))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 185)\n  (:start . 173) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s15.34) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504773@unknown@formal@none@1@S@Third, (PS)2-v2 utilized a new multiple template method for modeling different domains of the target sequence.@(((:tag . "JJ") (:stem . "third") (:form . "Third") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 6) (:start . 5) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 8) (:start . 7) (:id . 44))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 15)\n  (:start . 8) (:id . 45))\n ((:tag . "VBD") (:stem . "utilize") (:form . "utilized") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 39)\n  (:start . 31) (:id . 49))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "model") (:form . "modeling") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 78)\n  (:start . 69) (:id . 54))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 86)\n  (:start . 79) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 57))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 100)\n  (:start . 94) (:id . 58))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 109)\n  (:start . 101) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.35) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504774@unknown@formal@none@1@S@Finally, (PS)2-v2 added a multiple model strategy and utilized ProQ [19] to assess and select the final model.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 17)\n  (:start . 10) (:id . 45))\n ((:tag . "VBD") (:stem . "add") (:form . "added") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 34)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 40) (:start . 35)\n  (:id . 49))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 49)\n  (:start . 41) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "utilize") (:form . "utilized") (:end . 62)\n  (:start . 54) (:id . 52))\n ((:tag . "NNP") (:stem . "ProQ") (:form . "ProQ") (:end . 67) (:start . 63)\n  (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 69) (:start . 68)\n  (:id . 54))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 75) (:start . 73)\n  (:id . 57))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 82)\n  (:start . 76) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 59))\n ((:tag . "VB") (:stem . "select") (:form . "select") (:end . 93)\n  (:start . 87) (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 103) (:start . 98)\n  (:id . 62))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 109)\n  (:start . 104) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s15.36) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504775@unknown@formal@none@1@S@We have assessed the prediction accuracy of the (PS)2-v2 server based on the 154 TBM targets of the CASP8 dataset.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 31)\n  (:start . 21) (:id . 46))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 43) (:start . 41)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 49) (:start . 48)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 56)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 69) (:start . 64)\n  (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 72) (:start . 70)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "TBM") (:form . "TBM") (:end . 84) (:start . 81)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 92)\n  (:start . 85) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 60))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 105)\n  (:start . 100) (:id . 61))\n ((:tag . "NN") (:stem . "dataset") (:form . "dataset") (:end . 113)\n  (:start . 106) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s15.37) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504776@unknown@formal@none@1@S@The experimental results show that the S2A2 matrix, multiple-template and multiple-model strategies are able to significantly improve the accuracies for protein structure prediction and modeling when the sequence similarity between the template and the target is in the twilight zone.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "experimental") (:form . "experimental") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 24)\n  (:start . 17) (:id . 44))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 34) (:start . 30)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "multiple-template") (:form . "multiple-template")\n  (:end . 69) (:start . 52) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "multiple-model") (:form . "multiple-model")\n  (:end . 88) (:start . 74) (:id . 53))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 99)\n  (:start . 89) (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 103) (:start . 100)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 108) (:start . 104)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n  (:id . 57))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 125) (:start . 112) (:id . 58))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 133)\n  (:start . 126) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 137) (:start . 134)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "accuracy") (:form . "accuracies") (:end . 148)\n  (:start . 138) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 152) (:start . 149)\n  (:id . 62))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 160)\n  (:start . 153) (:id . 63))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 170)\n  (:start . 161) (:id . 64))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 181)\n  (:start . 171) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 185) (:start . 182)\n  (:id . 66))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 194)\n  (:start . 186) (:id . 67))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 199) (:start . 195)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n  (:id . 69))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 212)\n  (:start . 204) (:id . 70))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 223)\n  (:start . 213) (:id . 71))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 231)\n  (:start . 224) (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 235) (:start . 232)\n  (:id . 73))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 244)\n  (:start . 236) (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 248) (:start . 245)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 252) (:start . 249)\n  (:id . 76))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 259)\n  (:start . 253) (:id . 77))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 262) (:start . 260)\n  (:id . 78))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 265) (:start . 263)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 269) (:start . 266)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "twilight") (:form . "twilight") (:end . 278)\n  (:start . 270) (:id . 81))\n ((:tag . "NN") (:stem . "zone") (:form . "zone") (:end . 283) (:start . 279)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 284) (:start . 283)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s15.38) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504777@unknown@formal@none@1@S@The essential differences of (PS)2-original, (PS)2-CASP8 and (PS)2-v2@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "difference") (:form . "differences") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 28) (:start . 26)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 43) (:start . 30) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 69)\n  (:start . 62) (:id . 53)))@@@1@12@((:identifiers (:sid . :s15.39) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504778@unknown@formal@none@1@S@Methods@(((:tag . "NNS") (:stem . "method") (:form . "Methods") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s15.40) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504779@unknown@formal@none@1@S@Figures 1 and 2 show the framework of the (PS)2-v2 server for protein structure prediction.@(((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 9) (:start . 8)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 15) (:start . 14)\n  (:id . 45))\n ((:tag . "VBP") (:stem . "show") (:form . "show") (:end . 20) (:start . 16)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 34)\n  (:start . 25) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 50)\n  (:start . 43) (:id . 52))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 57)\n  (:start . 51) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 61) (:start . 58)\n  (:id . 54))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 69)\n  (:start . 62) (:id . 55))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 79)\n  (:start . 70) (:id . 56))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 90)\n  (:start . 80) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s15.41) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504780@unknown@formal@none@1@S@(PS)2-v2 uses the S2A2 matrix and the PSSM for the template selection and the target-template alignment.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . "VBZ") (:stem . "use") (:form . "uses") (:end . 13) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 29)\n  (:start . 23) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 42) (:start . 38)\n  (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 50) (:start . 47)\n  (:id . 52))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 59)\n  (:start . 51) (:id . 53))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 69)\n  (:start . 60) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 93) (:start . 78) (:id . 57))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 103)\n  (:start . 94) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s15.42) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504781@unknown@formal@none@1@S@(PS)2-v2 first applied the query sequence to generate a PSSM by running three iterations of PSI-BLAST against a non-redundant sequence UniRef90 [20] with an E-value cutoff of 0.001.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "apply") (:form . "applied") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 55) (:start . 54)\n  (:id . 51))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "run") (:form . "running") (:end . 71) (:start . 64)\n  (:id . 54))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "iteration") (:form . "iterations") (:end . 88)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 101)\n  (:start . 92) (:id . 58))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 109)\n  (:start . 102) (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 111) (:start . 110)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "non-redundant") (:form . "non-redundant")\n  (:end . 125) (:start . 112) (:id . 61))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 134)\n  (:start . 126) (:id . 62))\n ((:tag . "NN") (:stem . "uniref90") (:form . "UniRef90") (:end . 143)\n  (:start . 135) (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 145) (:start . 144)\n  (:id . 64))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 147) (:start . 145)\n  (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 148) (:start . 147)\n  (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 153) (:start . 149)\n  (:id . 67))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 156) (:start . 154)\n  (:id . 68))\n ((:tag . "NN") (:stem . "e-value") (:form . "E-value") (:end . 164)\n  (:start . 157) (:id . 69))\n ((:tag . "NN") (:stem . "cutoff") (:form . "cutoff") (:end . 171)\n  (:start . 165) (:id . 70))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 174) (:start . 172)\n  (:id . 71))\n ((:tag . "CD") (:stem . "0.001") (:form . "0.001") (:end . 180)\n  (:start . 175) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s15.43) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504782@unknown@formal@none@1@S@The PSSM was then used as the input for the PSIPRED [21] tool to predict the secondary structure of this query.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 22) (:start . 18)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "input") (:form . "input") (:end . 35) (:start . 30)\n  (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "psipred") (:form . "PSIPRED") (:end . 51)\n  (:start . 44) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 53) (:start . 52)\n  (:id . 53))\n ((:tag . "CD") (:stem . "21") (:form . "21") (:end . 55) (:start . 53)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 56) (:start . 55)\n  (:id . 55))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 61) (:start . 57)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 57))\n ((:tag . "VB") (:stem . "predict") (:form . "predict") (:end . 72)\n  (:start . 65) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 86)\n  (:start . 77) (:id . 60))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 96)\n  (:start . 87) (:id . 61))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 99) (:start . 97)\n  (:id . 62))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 104) (:start . 100)\n  (:id . 63))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 110)\n  (:start . 105) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s15.44) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504783@unknown@formal@none@1@S@We then modified the SSEARCH [18] search method, using the S2A2 matrix and the PSSM as the scoring matrices, to identify the template(s) from the protein structure library, and to generate the target-template alignment(s).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "modify") (:form . "modified") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "SSEARCH") (:form . "SSEARCH") (:end . 28)\n  (:start . 21) (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 32) (:start . 30)\n  (:id . 48))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 33) (:start . 32)\n  (:id . 49))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 40)\n  (:start . 34) (:id . 50))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 47)\n  (:start . 41) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 48) (:start . 47)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 54) (:start . 49)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 54))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 63) (:start . 59)\n  (:id . 55))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 70)\n  (:start . 64) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 58))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 83) (:start . 79)\n  (:id . 59))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 86) (:start . 84)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 90) (:start . 87)\n  (:id . 61))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 98)\n  (:start . 91) (:id . 62))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 107)\n  (:start . 99) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 108) (:start . 107)\n  (:id . 64))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 111) (:start . 109)\n  (:id . 65))\n ((:tag . "VB") (:stem . "identify") (:form . "identify") (:end . 120)\n  (:start . 112) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 124) (:start . 121)\n  (:id . 67))\n ((:tag . "NN") (:stem . "template(s)") (:form . "template(s)") (:end . 136)\n  (:start . 125) (:id . 68))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 141) (:start . 137)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 70))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 153)\n  (:start . 146) (:id . 71))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 163)\n  (:start . 154) (:id . 72))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 171)\n  (:start . 164) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 172) (:start . 171)\n  (:id . 74))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n  (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 179) (:start . 177)\n  (:id . 76))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 188)\n  (:start . 180) (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 192) (:start . 189)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 208) (:start . 193) (:id . 79))\n ((:tag . "JJ") (:stem . "alignment(s)") (:form . "alignment(s)") (:end . 221)\n  (:start . 209) (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 222) (:start . 221)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s15.45) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504784@unknown@formal@none@1@S@The library consists of 20,982 non-redundant structures (April, 2008) selected from protein data bank (PDB) [22].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "CD") (:stem . "20,982") (:form . "20,982") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "JJ") (:stem . "non-redundant") (:form . "non-redundant")\n  (:end . 44) (:start . 31) (:id . 47))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 55)\n  (:start . 45) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 57) (:start . 56)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "April") (:form . "April") (:end . 62) (:start . 57)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 51))\n ((:tag . "CD") (:stem . "2008") (:form . "2008") (:end . 68) (:start . 64)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 78)\n  (:start . 70) (:id . 54))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 83) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 91)\n  (:start . 84) (:id . 56))\n ((:tag . "NNS") (:stem . "datum") (:form . "data") (:end . 96) (:start . 92)\n  (:id . 57))\n ((:tag . "NN") (:stem . "bank") (:form . "bank") (:end . 101) (:start . 97)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 106) (:start . 103)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 109) (:start . 108)\n  (:id . 62))\n ((:tag . "CD") (:stem . "22") (:form . "22") (:end . 111) (:start . 109)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s15.46) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504785@unknown@formal@none@1@S@The secondary structures of each structure in the library were assigned using DSSP [23].@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 42)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 45) (:start . 43)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 57)\n  (:start . 50) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "assign") (:form . "assigned") (:end . 71)\n  (:start . 63) (:id . 52))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 77) (:start . 72)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "DSSP") (:form . "DSSP") (:end . 82) (:start . 78)\n  (:id . 54))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 84) (:start . 83)\n  (:id . 55))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 86) (:start . 84)\n  (:id . 56))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 87) (:start . 86)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s15.47) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504786@unknown@formal@none@1@S@Based on various target-template alignments of top-ranking 5 selected templates, (PS)2-v2 generates 30 protein structures using MODELLER [24].@(((:tag . "VBN") (:stem . "base") (:form . "Based") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "various") (:form . "various") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 32) (:start . 17) (:id . 45))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 43)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "top-ranking") (:form . "top-ranking") (:end . 58)\n  (:start . 47) (:id . 48))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 60) (:start . 59)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 69)\n  (:start . 61) (:id . 50))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 79)\n  (:start . 70) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 89)\n  (:start . 82) (:id . 54))\n ((:tag . "VBZ") (:stem . "generate") (:form . "generates") (:end . 99)\n  (:start . 90) (:id . 55))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 102) (:start . 100)\n  (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 110)\n  (:start . 103) (:id . 57))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 121)\n  (:start . 111) (:id . 58))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 127) (:start . 122)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "MODELLER") (:form . "MODELLER") (:end . 136)\n  (:start . 128) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 138) (:start . 137)\n  (:id . 61))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 140) (:start . 138)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 141) (:start . 140)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s15.48) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504787@unknown@formal@none@1@S@Finally, the program ProQ was used to evaluate these models and to select the final model for the target.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 12) (:start . 9)\n  (:id . 44))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 20)\n  (:start . 13) (:id . 45))\n ((:tag . "NNP") (:stem . "ProQ") (:form . "ProQ") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 37) (:start . 35)\n  (:id . 49))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 52) (:start . 47)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 63) (:start . 60)\n  (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 66) (:start . 64)\n  (:id . 54))\n ((:tag . "VB") (:stem . "select") (:form . "select") (:end . 73)\n  (:start . 67) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 83) (:start . 78)\n  (:id . 57))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 89) (:start . 84)\n  (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 60))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 104)\n  (:start . 98) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s15.49) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504788@unknown@formal@none@1@S@The S2A2 matrix, the aligned method, the modeling process and the final model selection are described in the following subsections.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "aligned") (:form . "aligned") (:end . 28)\n  (:start . 21) (:id . 47))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 35)\n  (:start . 29) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 50))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 49)\n  (:start . 41) (:id . 51))\n ((:tag . "NN") (:stem . "process") (:form . "process") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 61) (:start . 58)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 71) (:start . 66)\n  (:id . 55))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 77) (:start . 72)\n  (:id . 56))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 87)\n  (:start . 78) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "describe") (:form . "described") (:end . 101)\n  (:start . 92) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 104) (:start . 102)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 118)\n  (:start . 109) (:id . 62))\n ((:tag . "NNS") (:stem . "subsection") (:form . "subsections") (:end . 130)\n  (:start . 119) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s15.50) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504789@unknown@formal@none@1@S@The components of the (PS)2-v2 server were built using C, Perl and PHP (Additional file 1).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 30)\n  (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "build") (:form . "built") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Perl") (:form . "Perl") (:end . 62) (:start . 58)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PHP") (:form . "PHP") (:end . 70) (:start . 67)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 82)\n  (:start . 72) (:id . 58))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 87) (:start . 83)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 89) (:start . 88)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 91) (:start . 90)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s15.51) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504790@unknown@formal@none@1@S@The framework of the (PS)2-v2 server for protein structure prediction.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "framework") (:form . "framework") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 16) (:start . 14)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 29)\n  (:start . 22) (:id . 47))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 36)\n  (:start . 30) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 69)\n  (:start . 59) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s15.52) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504791@unknown@formal@none@1@S@Overview of the (PS)2-v2 server.@(((:tag . "NNP") (:stem . "Overview") (:form . "Overview") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 24)\n  (:start . 17) (:id . 46))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 31)\n  (:start . 25) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 32) (:start . 31)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s15.53) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504792@unknown@formal@none@1@S@The protein sequence of telomere replication protein Est3 (UniProt Q03096) in Saccharomyces cerevisiae was used as the query.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 20)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 23) (:start . 21)\n  (:id . 45))\n ((:tag . "NN") (:stem . "telomere") (:form . "telomere") (:end . 32)\n  (:start . 24) (:id . 46))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 44)\n  (:start . 33) (:id . 47))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 52)\n  (:start . 45) (:id . 48))\n ((:tag . "NNP") (:stem . "Est3") (:form . "Est3") (:end . 57) (:start . 53)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "UniProt") (:form . "UniProt") (:end . 66)\n  (:start . 59) (:id . 51))\n ((:tag . "NNP") (:stem . "Q03096") (:form . "Q03096") (:end . 73)\n  (:start . 67) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 74) (:start . 73)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Saccharomyces") (:form . "Saccharomyces")\n  (:end . 91) (:start . 78) (:id . 55))\n ((:tag . "NNP") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 102)\n  (:start . 92) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 106) (:start . 103)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 111) (:start . 107)\n  (:id . 58))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 114) (:start . 112)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 60))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 124)\n  (:start . 119) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s15.54) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504793@unknown@formal@none@1@S@(A) Input format of the (PS)2-v2 server.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NN") (:stem . "input") (:form . "Input") (:end . 9) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 16)\n  (:start . 10) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 32)\n  (:start . 25) (:id . 50))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 39)\n  (:start . 33) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 40) (:start . 39)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s15.55) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504794@unknown@formal@none@1@S@(B) Search results of a query protein, comprising target name, sequence, predicted secondary structure, the graph of the aligned regions and the hits list of the templates of the query.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "NNP") (:stem . "Search") (:form . "Search") (:end . 10)\n  (:start . 4) (:id . 45))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 18)\n  (:start . 11) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 21) (:start . 19)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 23) (:start . 22)\n  (:id . 48))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 29) (:start . 24)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 37)\n  (:start . 30) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "comprise") (:form . "comprising") (:end . 49)\n  (:start . 39) (:id . 52))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 56)\n  (:start . 50) (:id . 53))\n ((:tag . "NN") (:stem . "name") (:form . "name") (:end . 61) (:start . 57)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 55))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 71)\n  (:start . 63) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 72) (:start . 71)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "predict") (:form . "predicted") (:end . 82)\n  (:start . 73) (:id . 58))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 92)\n  (:start . 83) (:id . 59))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 102)\n  (:start . 93) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 62))\n ((:tag . "NN") (:stem . "graph") (:form . "graph") (:end . 113)\n  (:start . 108) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 120) (:start . 117)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 128)\n  (:start . 121) (:id . 66))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 136)\n  (:start . 129) (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 144) (:start . 141)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "hit") (:form . "hits") (:end . 149) (:start . 145)\n  (:id . 70))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 154) (:start . 150)\n  (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 157) (:start . 155)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 161) (:start . 158)\n  (:id . 73))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 171)\n  (:start . 162) (:id . 74))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 174) (:start . 172)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 178) (:start . 175)\n  (:id . 76))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 184)\n  (:start . 179) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 185) (:start . 184)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s15.56) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504795@unknown@formal@none@1@S@(C) The selected template, target-template alignment and prediction structure of Est3.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 16)\n  (:start . 8) (:id . 46))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 25)\n  (:start . 17) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 42) (:start . 27) (:id . 49))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 52)\n  (:start . 43) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 67)\n  (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 77)\n  (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 80) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Est3") (:form . "Est3") (:end . 85) (:start . 81)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 86) (:start . 85)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s15.57) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504796@unknown@formal@none@1@S@(D) The visualization of the predicted structure for Est3.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "visualization") (:form . "visualization")\n  (:end . 21) (:start . 8) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 38)\n  (:start . 29) (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 48)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Est3") (:form . "Est3") (:end . 57) (:start . 53)\n  (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s15.58) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504797@unknown@formal@none@1@S@(E) The model quality assessment.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 13) (:start . 8)\n  (:id . 46))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 21)\n  (:start . 14) (:id . 47))\n ((:tag . "NN") (:stem . "assessment") (:form . "assessment") (:end . 32)\n  (:start . 22) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 33) (:start . 32)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s15.59) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504798@unknown@formal@none@1@S@S2A2 matrix@(((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 11) (:start . 5)\n  (:id . 43)))@@@1@2@((:identifiers (:sid . :s15.60) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504799@unknown@formal@none@1@S@A substitution matrix is the key component of protein sequence alignment methods.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 14)\n  (:start . 2) (:id . 43))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "key") (:form . "key") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "component") (:form . "component") (:end . 42)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 53)\n  (:start . 46) (:id . 50))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 62)\n  (:start . 54) (:id . 51))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 80)\n  (:start . 73) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 81) (:start . 80)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s15.61) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504800@unknown@formal@none@1@S@We developed the S2A2 substitution matrix (Figure 3 and Figure S1 in Additional file 2) applying a general mathematical structure [25].@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "develop") (:form . "developed") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 34)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 41)\n  (:start . 35) (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "NN") (:stem . "s1") (:form . "S1") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 79)\n  (:start . 69) (:id . 55))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 84) (:start . 80)\n  (:id . 56))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "apply") (:form . "applying") (:end . 96)\n  (:start . 88) (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 98) (:start . 97)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 106)\n  (:start . 99) (:id . 61))\n ((:tag . "JJ") (:stem . "mathematical") (:form . "mathematical") (:end . 119)\n  (:start . 107) (:id . 62))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 129)\n  (:start . 120) (:id . 63))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 131) (:start . 130)\n  (:id . 64))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 133) (:start . 131)\n  (:id . 65))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 134) (:start . 133)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.62) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504801@unknown@formal@none@1@S@To calculate the S2A2, 674 structural pairs (1,348 proteins) [26], which are structurally similar and with low sequence identity, were selected from SCOP 1.65 [27] based on two criteria: 1) the root-mean-square deviation (rmsd) of a protein pair was be less than 3.5 A, with more than 70% of aligned residues included in the rmsd calculation, and 2) the sequence identity of a pair is less than 40%.@(((:tag . "TO") (:stem . "to") (:form . "To") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VB") (:stem . "calculate") (:form . "calculate") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 21) (:start . 17)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "CD") (:stem . "674") (:form . "674") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 37)\n  (:start . 27) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 43) (:start . 38)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 50))\n ((:tag . "CD") (:stem . "1,348") (:form . "1,348") (:end . 50) (:start . 45)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 59)\n  (:start . 51) (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 60) (:start . 59)\n  (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 64) (:start . 62)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 65) (:start . 64)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 57))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 72) (:start . 67)\n  (:id . 58))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 76) (:start . 73)\n  (:id . 59))\n ((:tag . "RB") (:stem . "structurally") (:form . "structurally") (:end . 89)\n  (:start . 77) (:id . 60))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 97)\n  (:start . 90) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 106) (:start . 102)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 110) (:start . 107)\n  (:id . 64))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 119)\n  (:start . 111) (:id . 65))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 128)\n  (:start . 120) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 129) (:start . 128)\n  (:id . 67))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 134) (:start . 130)\n  (:id . 68))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 143)\n  (:start . 135) (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 148) (:start . 144)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "SCOP") (:form . "SCOP") (:end . 153) (:start . 149)\n  (:id . 71))\n ((:tag . "CD") (:stem . "1.65") (:form . "1.65") (:end . 158) (:start . 154)\n  (:id . 72))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 160) (:start . 159)\n  (:id . 73))\n ((:tag . "CD") (:stem . "27") (:form . "27") (:end . 162) (:start . 160)\n  (:id . 74))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 163) (:start . 162)\n  (:id . 75))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 169)\n  (:start . 164) (:id . 76))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 172) (:start . 170)\n  (:id . 77))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 176) (:start . 173)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "criterion") (:form . "criteria") (:end . 185)\n  (:start . 177) (:id . 79))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 186) (:start . 185)\n  (:id . 80))\n ((:tag . "LS") (:stem . "1") (:form . "1") (:end . 188) (:start . 187)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 82))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 193) (:start . 190)\n  (:id . 83))\n ((:tag . "NN") (:stem . "root-mean-square") (:form . "root-mean-square")\n  (:end . 210) (:start . 194) (:id . 84))\n ((:tag . "NN") (:stem . "deviation") (:form . "deviation") (:end . 220)\n  (:start . 211) (:id . 85))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 222) (:start . 221)\n  (:id . 86))\n ((:tag . "NN") (:stem . "rmsd") (:form . "rmsd") (:end . 226) (:start . 222)\n  (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 227) (:start . 226)\n  (:id . 88))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 230) (:start . 228)\n  (:id . 89))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 232) (:start . 231)\n  (:id . 90))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 240)\n  (:start . 233) (:id . 91))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 245) (:start . 241)\n  (:id . 92))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 249) (:start . 246)\n  (:id . 93))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 252) (:start . 250)\n  (:id . 94))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 257) (:start . 253)\n  (:id . 95))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 262) (:start . 258)\n  (:id . 96))\n ((:tag . "CD") (:stem . "3.5") (:form . "3.5") (:end . 266) (:start . 263)\n  (:id . 97))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 268) (:start . 267)\n  (:id . 98))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 269) (:start . 268)\n  (:id . 99))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 274) (:start . 270)\n  (:id . 100))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 279) (:start . 275)\n  (:id . 101))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 284) (:start . 280)\n  (:id . 102))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 287) (:start . 285)\n  (:id . 103))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 288) (:start . 287)\n  (:id . 104))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 291) (:start . 289)\n  (:id . 105))\n ((:tag . "JJ") (:stem . "aligned") (:form . "aligned") (:end . 299)\n  (:start . 292) (:id . 106))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 308)\n  (:start . 300) (:id . 107))\n ((:tag . "VBN") (:stem . "include") (:form . "included") (:end . 317)\n  (:start . 309) (:id . 108))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 320) (:start . 318)\n  (:id . 109))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 324) (:start . 321)\n  (:id . 110))\n ((:tag . "NN") (:stem . "rmsd") (:form . "rmsd") (:end . 329) (:start . 325)\n  (:id . 111))\n ((:tag . "NN") (:stem . "calculation") (:form . "calculation") (:end . 341)\n  (:start . 330) (:id . 112))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 342) (:start . 341)\n  (:id . 113))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 346) (:start . 343)\n  (:id . 114))\n ((:tag . "LS") (:stem . "2") (:form . "2") (:end . 348) (:start . 347)\n  (:id . 115))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 349) (:start . 348)\n  (:id . 116))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 353) (:start . 350)\n  (:id . 117))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 362)\n  (:start . 354) (:id . 118))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 371)\n  (:start . 363) (:id . 119))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 374) (:start . 372)\n  (:id . 120))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 376) (:start . 375)\n  (:id . 121))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 381) (:start . 377)\n  (:id . 122))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 384) (:start . 382)\n  (:id . 123))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 389) (:start . 385)\n  (:id . 124))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 394) (:start . 390)\n  (:id . 125))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 397) (:start . 395)\n  (:id . 126))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 398) (:start . 397)\n  (:id . 127))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 399) (:start . 398)\n  (:id . 128)))@@@1@87@((:identifiers (:sid . :s15.63) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504802@unknown@formal@none@1@S@The selected protein pairs had an average sequence identity of 26%, an average rmsd of 2.3 A and average aligned residues of 90% (207,492 aligned residues out of 230,915 residues).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 20)\n  (:start . 13) (:id . 44))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 26) (:start . 21)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 41)\n  (:start . 34) (:id . 48))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 50)\n  (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 59)\n  (:start . 51) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 62) (:start . 60)\n  (:id . 51))\n ((:tag . "CD") (:stem . "26") (:form . "26") (:end . 65) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 66) (:start . 65)\n  (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 70) (:start . 68)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 78)\n  (:start . 71) (:id . 56))\n ((:tag . "NN") (:stem . "rmsd") (:form . "rmsd") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 86) (:start . 84)\n  (:id . 58))\n ((:tag . "CD") (:stem . "2.3") (:form . "2.3") (:end . 90) (:start . 87)\n  (:id . 59))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 92) (:start . 91)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 104)\n  (:start . 97) (:id . 62))\n ((:tag . "JJ") (:stem . "aligned") (:form . "aligned") (:end . 112)\n  (:start . 105) (:id . 63))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 121)\n  (:start . 113) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 124) (:start . 122)\n  (:id . 65))\n ((:tag . "CD") (:stem . "90") (:form . "90") (:end . 127) (:start . 125)\n  (:id . 66))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 128) (:start . 127)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 68))\n ((:tag . "CD") (:stem . "207,492") (:form . "207,492") (:end . 137)\n  (:start . 130) (:id . 69))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 145)\n  (:start . 138) (:id . 70))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 154)\n  (:start . 146) (:id . 71))\n ((:tag . "IN") (:stem . "out") (:form . "out") (:end . 158) (:start . 155)\n  (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 161) (:start . 159)\n  (:id . 73))\n ((:tag . "CD") (:stem . "230,915") (:form . "230,915") (:end . 169)\n  (:start . 162) (:id . 74))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 178)\n  (:start . 170) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 179) (:start . 178)\n  (:id . 76))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 77)))@@@1@36@((:identifiers (:sid . :s15.64) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504803@unknown@formal@none@1@S@The program DSSP was used to assign the secondary structure for each residue of these 674 structural pairs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "DSSP") (:form . "DSSP") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 35)\n  (:start . 29) (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 39) (:start . 36)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 49)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 59)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n  (:id . 52))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 76)\n  (:start . 69) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 79) (:start . 77)\n  (:id . 55))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 85) (:start . 80)\n  (:id . 56))\n ((:tag . "CD") (:stem . "674") (:form . "674") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 100)\n  (:start . 90) (:id . 58))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 106)\n  (:start . 101) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.65) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504804@unknown@formal@none@1@S@The eight types of the secondary structure used in DSSP were reduced to three commonly accepted types (H (helix), E (strand) and C (coil)) according to the following scheme: (H, G, I) › H; (E, B) › E; (T, S, blank) › C.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "eight") (:form . "eight") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 32)\n  (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 42)\n  (:start . 33) (:id . 48))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 47) (:start . 43)\n  (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "DSSP") (:form . "DSSP") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "reduce") (:form . "reduced") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "RB") (:stem . "commonly") (:form . "commonly") (:end . 86)\n  (:start . 78) (:id . 56))\n ((:tag . "VBN") (:stem . "accept") (:form . "accepted") (:end . 95)\n  (:start . 87) (:id . 57))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 101) (:start . 96)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 61))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 111)\n  (:start . 106) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 113) (:start . 112)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 115) (:start . 114)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 117) (:start . 116)\n  (:id . 66))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 123)\n  (:start . 117) (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 124) (:start . 123)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 128) (:start . 125)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 130) (:start . 129)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 132) (:start . 131)\n  (:id . 71))\n ((:tag . "NN") (:stem . "coil") (:form . "coil") (:end . 136) (:start . 132)\n  (:id . 72))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 137) (:start . 136)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 74))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 148)\n  (:start . 139) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 151) (:start . 149)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 77))\n ((:tag . "VBG") (:stem . "follow") (:form . "following") (:end . 165)\n  (:start . 156) (:id . 78))\n ((:tag . "NN") (:stem . "scheme") (:form . "scheme") (:end . 172)\n  (:start . 166) (:id . 79))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 173) (:start . 172)\n  (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 175) (:start . 174)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 176) (:start . 175)\n  (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 177) (:start . 176)\n  (:id . 83))\n ((:tag . "NNP") (:stem . "G") (:form . "G") (:end . 179) (:start . 178)\n  (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 180) (:start . 179)\n  (:id . 85))\n ((:tag . "PRP") (:stem . "i") (:form . "I") (:end . 182) (:start . 181)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n  (:id . 87))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 183) (:start . 183)\n  (:id . 88))\n ((:tag . "NNP") (:stem . "H") (:form . "H") (:end . 187) (:start . 186)\n  (:id . 89))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 188) (:start . 187)\n  (:id . 90))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 190) (:start . 189)\n  (:id . 91))\n ((:tag . "NNP") (:stem . "E") (:form . "E") (:end . 191) (:start . 190)\n  (:id . 92))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 192) (:start . 191)\n  (:id . 93))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 194) (:start . 193)\n  (:id . 94))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 95))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 195) (:start . 195)\n  (:id . 96))\n ((:tag . "NN") (:stem . "e") (:form . "E") (:end . 199) (:start . 198)\n  (:id . 97))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 200) (:start . 199)\n  (:id . 98))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 202) (:start . 201)\n  (:id . 99))\n ((:tag . "NN") (:stem . "t") (:form . "T") (:end . 203) (:start . 202)\n  (:id . 100))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 204) (:start . 203)\n  (:id . 101))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 206) (:start . 205)\n  (:id . 102))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 207) (:start . 206)\n  (:id . 103))\n ((:tag . "JJ") (:stem . "blank") (:form . "blank") (:end . 213)\n  (:start . 208) (:id . 104))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 214) (:start . 213)\n  (:id . 105))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 214) (:start . 214)\n  (:id . 106))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 218) (:start . 217)\n  (:id . 107))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 219) (:start . 218)\n  (:id . 108)))@@@1@67@((:identifiers (:sid . :s15.66) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504805@unknown@formal@none@1@S@The 20 amino acid types and 3 secondary structure types were converted into 60 residue-structure (RS) types.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 23) (:start . 18)\n  (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 39)\n  (:start . 30) (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 49)\n  (:start . 40) (:id . 50))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 55) (:start . 50)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 60) (:start . 56)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "convert") (:form . "converted") (:end . 70)\n  (:start . 61) (:id . 53))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 75) (:start . 71)\n  (:id . 54))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 78) (:start . 76)\n  (:id . 55))\n ((:tag . "NN") (:stem . "residue-structure") (:form . "residue-structure")\n  (:end . 96) (:start . 79) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 98) (:start . 97)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "RS") (:form . "RS") (:end . 100) (:start . 98)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 107)\n  (:start . 102) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s15.67) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504806@unknown@formal@none@1@S@The S2A2 substitution matrix.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 21)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 28)\n  (:start . 22) (:id . 45))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 29) (:start . 28)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s15.68) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504807@unknown@formal@none@1@S@The scores are high if the residue-structure (RS) letters with similar residue types and the same secondary structure are aligned (red blocks).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "NN") (:stem . "residue-structure") (:form . "residue-structure")\n  (:end . 44) (:start . 27) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "RS") (:form . "RS") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 49) (:start . 48)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 62) (:start . 58)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 70)\n  (:start . 63) (:id . 54))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 78)\n  (:start . 71) (:id . 55))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 84) (:start . 79)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 88) (:start . 85)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 97) (:start . 93)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 107)\n  (:start . 98) (:id . 60))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 117)\n  (:start . 108) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 129)\n  (:start . 122) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 131) (:start . 130)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "red") (:form . "red") (:end . 134) (:start . 131)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "block") (:form . "blocks") (:end . 141)\n  (:start . 135) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s15.69) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504808@unknown@formal@none@1@S@When two identical RS letters (e.g. diagonal entries) are aligned, the substitution scores are very high.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "rs") (:form . "RS") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 35) (:start . 31)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "diagonal") (:form . "diagonal") (:end . 44)\n  (:start . 36) (:id . 49))\n ((:tag . "NNS") (:stem . "entry") (:form . "entries") (:end . 52)\n  (:start . 45) (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 57) (:start . 54)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 65)\n  (:start . 58) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 55))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 83)\n  (:start . 71) (:id . 56))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 90)\n  (:start . 84) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 99) (:start . 95)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 104) (:start . 100)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s15.70) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504809@unknown@formal@none@1@S@In contrast, the scores are low when helix letters are aligned with strand letters (blue blocks).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 23)\n  (:start . 17) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 36) (:start . 32)\n  (:id . 49))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 42) (:start . 37)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 50)\n  (:start . 43) (:id . 51))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 62)\n  (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 74)\n  (:start . 68) (:id . 55))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 82)\n  (:start . 75) (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 88) (:start . 84)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "block") (:form . "blocks") (:end . 95)\n  (:start . 89) (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s15.71) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504810@unknown@formal@none@1@S@The S2A2 matrix (60 × 60) reveals substitution preferences between homologs with low sequence identity, and was developed in a similar way to BLOSUM62 [25] based on these 674 structural pairs.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 24) (:start . 22)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "reveal") (:form . "reveals") (:end . 33)\n  (:start . 26) (:id . 50))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 46)\n  (:start . 34) (:id . 51))\n ((:tag . "NNS") (:stem . "preference") (:form . "preferences") (:end . 58)\n  (:start . 47) (:id . 52))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 66)\n  (:start . 59) (:id . 53))\n ((:tag . "NNS") (:stem . "homolog") (:form . "homologs") (:end . 75)\n  (:start . 67) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 80) (:start . 76)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 93)\n  (:start . 85) (:id . 57))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 102)\n  (:start . 94) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 107) (:start . 104)\n  (:id . 60))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 111) (:start . 108)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "develop") (:form . "developed") (:end . 121)\n  (:start . 112) (:id . 62))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 124) (:start . 122)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 126) (:start . 125)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 134)\n  (:start . 127) (:id . 65))\n ((:tag . "NN") (:stem . "way") (:form . "way") (:end . 138) (:start . 135)\n  (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 141) (:start . 139)\n  (:id . 67))\n ((:tag . "NN") (:stem . "blosum62") (:form . "BLOSUM62") (:end . 150)\n  (:start . 142) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 152) (:start . 151)\n  (:id . 69))\n ((:tag . "CD") (:stem . "25") (:form . "25") (:end . 154) (:start . 152)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 155) (:start . 154)\n  (:id . 71))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 161)\n  (:start . 156) (:id . 72))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 164) (:start . 162)\n  (:id . 73))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 170)\n  (:start . 165) (:id . 74))\n ((:tag . "CD") (:stem . "674") (:form . "674") (:end . 174) (:start . 171)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 185)\n  (:start . 175) (:id . 76))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 191)\n  (:start . 186) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 192) (:start . 191)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s15.72) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504811@unknown@formal@none@1@S@The entry (Sij), which is the substitution score for aligning a RS letter i, j pair (1 ≤ i, j ≤ 60), of the S2A2 matrix is defined as Sij = λlog2(qij/eij), where λ is a scale factor, and qij and eij are the observed and expected probabilities, respectively, of the occurrence of each i, j pair.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "entry") (:form . "entry") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sij") (:form . "Sij") (:end . 14) (:start . 11)\n  (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 47))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 22) (:start . 17)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 50))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 42)\n  (:start . 30) (:id . 51))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 48) (:start . 43)\n  (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 52) (:start . 49)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "align") (:form . "aligning") (:end . 61)\n  (:start . 53) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 63) (:start . 62)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "RS") (:form . "RS") (:end . 66) (:start . 64)\n  (:id . 56))\n ((:tag . "NN") (:stem . "letter") (:form . "letter") (:end . 73)\n  (:start . 67) (:id . 57))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 75) (:start . 74)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 59))\n ((:tag . "NN") (:stem . "j") (:form . "j") (:end . 78) (:start . 77)\n  (:id . 60))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 83) (:start . 79)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 62))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 86) (:start . 85)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 88) (:start . 87)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 90) (:start . 89)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "j") (:form . "j") (:end . 93) (:start . 92)\n  (:id . 67))\n ((:tag . "NN") (:stem . "≤") (:form . "≤") (:end . 95) (:start . 94)\n  (:id . 68))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 98) (:start . 96)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 100) (:start . 99)\n  (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 73))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 112) (:start . 108)\n  (:id . 74))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 119)\n  (:start . 113) (:id . 75))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 122) (:start . 120)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "define") (:form . "defined") (:end . 130)\n  (:start . 123) (:id . 77))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 133) (:start . 131)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Sij") (:form . "Sij") (:end . 137) (:start . 134)\n  (:id . 79))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 139) (:start . 138)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "λlog2(qij/eij)") (:form . "λlog2(qij/eij)")\n  (:end . 154) (:start . 140) (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 155) (:start . 154)\n  (:id . 82))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 161)\n  (:start . 156) (:id . 83))\n ((:tag . "NNP") (:stem . "λ") (:form . "λ") (:end . 163) (:start . 162)\n  (:id . 84))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 166) (:start . 164)\n  (:id . 85))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 168) (:start . 167)\n  (:id . 86))\n ((:tag . "NN") (:stem . "scale") (:form . "scale") (:end . 174)\n  (:start . 169) (:id . 87))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 181)\n  (:start . 175) (:id . 88))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 182) (:start . 181)\n  (:id . 89))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 186) (:start . 183)\n  (:id . 90))\n ((:tag . "NNP") (:stem . "qij") (:form . "qij") (:end . 190) (:start . 187)\n  (:id . 91))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 194) (:start . 191)\n  (:id . 92))\n ((:tag . "NNP") (:stem . "eij") (:form . "eij") (:end . 198) (:start . 195)\n  (:id . 93))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 202) (:start . 199)\n  (:id . 94))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 206) (:start . 203)\n  (:id . 95))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 215)\n  (:start . 207) (:id . 96))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 219) (:start . 216)\n  (:id . 97))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 228)\n  (:start . 220) (:id . 98))\n ((:tag . "NNS") (:stem . "probability") (:form . "probabilities")\n  (:end . 242) (:start . 229) (:id . 99))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 243) (:start . 242)\n  (:id . 100))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 256)\n  (:start . 244) (:id . 101))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 257) (:start . 256)\n  (:id . 102))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 260) (:start . 258)\n  (:id . 103))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 264) (:start . 261)\n  (:id . 104))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 275)\n  (:start . 265) (:id . 105))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 278) (:start . 276)\n  (:id . 106))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 283) (:start . 279)\n  (:id . 107))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 285) (:start . 284)\n  (:id . 108))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 286) (:start . 285)\n  (:id . 109))\n ((:tag . "NN") (:stem . "j") (:form . "j") (:end . 288) (:start . 287)\n  (:id . 110))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 293) (:start . 289)\n  (:id . 111))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 294) (:start . 293)\n  (:id . 112)))@@@1@71@((:identifiers (:sid . :s15.73) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504812@unknown@formal@none@1@S@The observed probability is given by , where fij is the total number of aligning i, j pairs in these 207,492 RS letters.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 24)\n  (:start . 13) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 27) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 33) (:start . 28)\n  (:id . 46))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "fij") (:form . "fij") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 61) (:start . 56)\n  (:id . 53))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 68)\n  (:start . 62) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 71) (:start . 69)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "align") (:form . "aligning") (:end . 80)\n  (:start . 72) (:id . 56))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 58))\n ((:tag . "NN") (:stem . "j") (:form . "j") (:end . 85) (:start . 84)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 91) (:start . 86)\n  (:id . 60))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 94) (:start . 92)\n  (:id . 61))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 100) (:start . 95)\n  (:id . 62))\n ((:tag . "CD") (:stem . "207,492") (:form . "207,492") (:end . 108)\n  (:start . 101) (:id . 63))\n ((:tag . "NN") (:stem . "rs") (:form . "RS") (:end . 111) (:start . 109)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 119)\n  (:start . 112) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s15.74) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504813@unknown@formal@none@1@S@The factor eij = pipj if i = j; otherwise, eij = 2pipj (if i ≠ j), where pi is the background probability of occurrence of the letter i, and equals .@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "eij") (:form . "eij") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "=") (:form . "=") (:end . 16) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "pipj") (:form . "pipj") (:end . 21) (:start . 17)\n  (:id . 46))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 24) (:start . 22)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 26) (:start . 25)\n  (:id . 48))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 28) (:start . 27)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "j") (:form . "j") (:end . 30) (:start . 29)\n  (:id . 50))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 31) (:start . 30)\n  (:id . 51))\n ((:tag . "RB") (:stem . "otherwise") (:form . "otherwise") (:end . 41)\n  (:start . 32) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 53))\n ((:tag . "NN") (:stem . "eij") (:form . "eij") (:end . 46) (:start . 43)\n  (:id . 54))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 48) (:start . 47)\n  (:id . 55))\n ((:tag . "NN") (:stem . "2pipj") (:form . "2pipj") (:end . 54) (:start . 49)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 57))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 58) (:start . 56)\n  (:id . 58))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 60) (:start . 59)\n  (:id . 59))\n ((:tag . "NN") (:stem . "≠") (:form . "≠") (:end . 62) (:start . 61)\n  (:id . 60))\n ((:tag . "NN") (:stem . "j") (:form . "j") (:end . 64) (:start . 63)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 65) (:start . 64)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 66) (:start . 65)\n  (:id . 63))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 72) (:start . 67)\n  (:id . 64))\n ((:tag . "NN") (:stem . "pi") (:form . "pi") (:end . 75) (:start . 73)\n  (:id . 65))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 78) (:start . 76)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 67))\n ((:tag . "NN") (:stem . "background") (:form . "background") (:end . 93)\n  (:start . 83) (:id . 68))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 105)\n  (:start . 94) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 108) (:start . 106)\n  (:id . 70))\n ((:tag . "NN") (:stem . "occurrence") (:form . "occurrence") (:end . 119)\n  (:start . 109) (:id . 71))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 122) (:start . 120)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 73))\n ((:tag . "NN") (:stem . "letter") (:form . "letter") (:end . 133)\n  (:start . 127) (:id . 74))\n ((:tag . "NN") (:stem . "i") (:form . "i") (:end . 135) (:start . 134)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 140) (:start . 137)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "equal") (:form . "equals") (:end . 147)\n  (:start . 141) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 149) (:start . 148)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s15.75) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504814@unknown@formal@none@1@S@The substitution score is greater than zero (Sij > 0) if the observed probability is greater than the expected probability.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 22) (:start . 17)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 25) (:start . 23)\n  (:id . 45))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 33)\n  (:start . 26) (:id . 46))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "CD") (:stem . "zero") (:form . "zero") (:end . 43) (:start . 39)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Sij") (:form . "Sij") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "SYM") (:stem . ">") (:form . ">") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 52) (:start . 51)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 53) (:start . 52)\n  (:id . 53))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 56) (:start . 54)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "observe") (:form . "observed") (:end . 69)\n  (:start . 61) (:id . 56))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 81)\n  (:start . 70) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 92)\n  (:start . 85) (:id . 59))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 97) (:start . 93)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "expect") (:form . "expected") (:end . 110)\n  (:start . 102) (:id . 62))\n ((:tag . "NN") (:stem . "probability") (:form . "probability") (:end . 122)\n  (:start . 111) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 123) (:start . 122)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s15.76) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504815@unknown@formal@none@1@S@By contrast, Sij < 0 if qij <eij.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "Sij") (:form . "Sij") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 20) (:start . 19)\n  (:id . 47))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 23) (:start . 21)\n  (:id . 48))\n ((:tag . "NN") (:stem . "qij") (:form . "qij") (:end . 27) (:start . 24)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "<eij") (:form . "<eij") (:end . 32) (:start . 28)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 33) (:start . 32)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s15.77) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504816@unknown@formal@none@1@S@The λ is optimized by the SALIGN set [28], and is set to 1.6 according to the performance and efficiency.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "λ") (:form . "λ") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "optimize") (:form . "optimized") (:end . 18)\n  (:start . 9) (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "SALIGN") (:form . "SALIGN") (:end . 32)\n  (:start . 26) (:id . 48))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 36) (:start . 33)\n  (:id . 49))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 38) (:start . 37)\n  (:id . 50))\n ((:tag . "CD") (:stem . "28") (:form . "28") (:end . 40) (:start . 38)\n  (:id . 51))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 41) (:start . 40)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 46) (:start . 43)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 49) (:start . 47)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 53) (:start . 50)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 56) (:start . 54)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1.6") (:form . "1.6") (:end . 60) (:start . 57)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 70)\n  (:start . 61) (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 73) (:start . 71)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 77) (:start . 74)\n  (:id . 61))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 89)\n  (:start . 78) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 93) (:start . 90)\n  (:id . 63))\n ((:tag . "NN") (:stem . "efficiency") (:form . "efficiency") (:end . 104)\n  (:start . 94) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s15.78) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504817@unknown@formal@none@1@S@Scoring and alignment methods@(((:tag . "NNP") (:stem . "Scoring") (:form . "Scoring") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 21)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 29)\n  (:start . 22) (:id . 45)))@@@1@4@((:identifiers (:sid . :s15.79) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504818@unknown@formal@none@1@S@We modified the SSEARCH program [18], which used a rigorous Smith-Waterman algorithm [29], to search for similarity between a query sequence and template sequences in a library.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "modify") (:form . "modified") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "SSEARCH") (:form . "SSEARCH") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "CD") (:stem . "18") (:form . "18") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 50))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 43) (:start . 38)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 48) (:start . 44)\n  (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 50) (:start . 49)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "rigorous") (:form . "rigorous") (:end . 59)\n  (:start . 51) (:id . 54))\n ((:tag . "JJ") (:stem . "smith-waterman") (:form . "Smith-Waterman")\n  (:end . 74) (:start . 60) (:id . 55))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 84)\n  (:start . 75) (:id . 56))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 86) (:start . 85)\n  (:id . 57))\n ((:tag . "CD") (:stem . "29") (:form . "29") (:end . 88) (:start . 86)\n  (:id . 58))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 89) (:start . 88)\n  (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 93) (:start . 91)\n  (:id . 61))\n ((:tag . "VB") (:stem . "search") (:form . "search") (:end . 100)\n  (:start . 94) (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 104) (:start . 101)\n  (:id . 63))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 115)\n  (:start . 105) (:id . 64))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 123)\n  (:start . 116) (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 125) (:start . 124)\n  (:id . 66))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 131)\n  (:start . 126) (:id . 67))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 140)\n  (:start . 132) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n  (:id . 69))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 153)\n  (:start . 145) (:id . 70))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 163)\n  (:start . 154) (:id . 71))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 166) (:start . 164)\n  (:id . 72))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 168) (:start . 167)\n  (:id . 73))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 176)\n  (:start . 169) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 177) (:start . 176)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s15.80) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504819@unknown@formal@none@1@S@We optimized the score between the query and template(s) using both S2A2 and PSSM matrices based on alignment accuracies on the SALIGN set.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "optimize") (:form . "optimized") (:end . 12)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 30)\n  (:start . 23) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 40) (:start . 35)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "template(s)") (:form . "template(s)") (:end . 56)\n  (:start . 45) (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 62) (:start . 57)\n  (:id . 51))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 81) (:start . 77)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 90)\n  (:start . 82) (:id . 56))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 96) (:start . 91)\n  (:id . 57))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 99) (:start . 97)\n  (:id . 58))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 109)\n  (:start . 100) (:id . 59))\n ((:tag . "NNS") (:stem . "accuracy") (:form . "accuracies") (:end . 120)\n  (:start . 110) (:id . 60))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 123) (:start . 121)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 127) (:start . 124)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "SALIGN") (:form . "SALIGN") (:end . 134)\n  (:start . 128) (:id . 63))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 138) (:start . 135)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s15.81) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504820@unknown@formal@none@1@S@The score is given as where i and j are RS letters on the query and the template, respectively; wstru(i, j) is a structure-dependent scoring weight, and is set to 1.3, 1.7 and 0.8 for α-helix, ß-strand and coil, respectively; wS2A2 (here, wS2A2 is set to 0.64) is the weight of the S2A2 matrix; S2A2(i, j) and PSSMquery(i, j) are the scores of S2A2 and PSSM matrices, respectively, when the RS letter i is aligned to the RS letter j.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 12) (:start . 10)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 18) (:start . 13)\n  (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 27) (:start . 22)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 29) (:start . 28)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 49))\n ((:tag . "NN") (:stem . "j") (:form . "j") (:end . 35) (:start . 34)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 39) (:start . 36)\n  (:id . 51))\n ((:tag . "NN") (:stem . "rs") (:form . "RS") (:end . 42) (:start . 40)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 50)\n  (:start . 43) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 53) (:start . 51)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 57) (:start . 54)\n  (:id . 55))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 63) (:start . 58)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 67) (:start . 64)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 58))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 80)\n  (:start . 72) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 60))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 94)\n  (:start . 82) (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 95) (:start . 94)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "wstru(i") (:form . "wstru(i") (:end . 103)\n  (:start . 96) (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "j") (:form . "j") (:end . 106) (:start . 105)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 107) (:start . 106)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 110) (:start . 108)\n  (:id . 67))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 112) (:start . 111)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "structure-dependent")\n  (:form . "structure-dependent") (:end . 132) (:start . 113) (:id . 69))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 140)\n  (:start . 133) (:id . 70))\n ((:tag . "NN") (:stem . "weight") (:form . "weight") (:end . 147)\n  (:start . 141) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 148) (:start . 147)\n  (:id . 72))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 73))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 155) (:start . 153)\n  (:id . 74))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 159) (:start . 156)\n  (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 162) (:start . 160)\n  (:id . 76))\n ((:tag . "CD") (:stem . "1.3") (:form . "1.3") (:end . 166) (:start . 163)\n  (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 78))\n ((:tag . "CD") (:stem . "1.7") (:form . "1.7") (:end . 171) (:start . 168)\n  (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 175) (:start . 172)\n  (:id . 80))\n ((:tag . "CD") (:stem . "0.8") (:form . "0.8") (:end . 179) (:start . 176)\n  (:id . 81))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 183) (:start . 180)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "α-helix") (:form . "α-helix") (:end . 191)\n  (:start . 184) (:id . 83))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 192) (:start . 191)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "ß-strand") (:form . "ß-strand") (:end . 201)\n  (:start . 193) (:id . 85))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 205) (:start . 202)\n  (:id . 86))\n ((:tag . "NN") (:stem . "coil") (:form . "coil") (:end . 210) (:start . 206)\n  (:id . 87))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 211) (:start . 210)\n  (:id . 88))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 224)\n  (:start . 212) (:id . 89))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 225) (:start . 224)\n  (:id . 90))\n ((:tag . "NN") (:stem . "ws2a2") (:form . "wS2A2") (:end . 231)\n  (:start . 226) (:id . 91))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 233) (:start . 232)\n  (:id . 92))\n ((:tag . "RB") (:stem . "here") (:form . "here") (:end . 237) (:start . 233)\n  (:id . 93))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 238) (:start . 237)\n  (:id . 94))\n ((:tag . "NN") (:stem . "ws2a2") (:form . "wS2A2") (:end . 244)\n  (:start . 239) (:id . 95))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 247) (:start . 245)\n  (:id . 96))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 251) (:start . 248)\n  (:id . 97))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 254) (:start . 252)\n  (:id . 98))\n ((:tag . "CD") (:stem . "0.64") (:form . "0.64") (:end . 259) (:start . 255)\n  (:id . 99))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 260) (:start . 259)\n  (:id . 100))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 263) (:start . 261)\n  (:id . 101))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 267) (:start . 264)\n  (:id . 102))\n ((:tag . "NN") (:stem . "weight") (:form . "weight") (:end . 274)\n  (:start . 268) (:id . 103))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 277) (:start . 275)\n  (:id . 104))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 281) (:start . 278)\n  (:id . 105))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 286) (:start . 282)\n  (:id . 106))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 293)\n  (:start . 287) (:id . 107))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 294) (:start . 293)\n  (:id . 108))\n ((:tag . "NNP") (:stem . "S2A2(i") (:form . "S2A2(i") (:end . 301)\n  (:start . 295) (:id . 109))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 302) (:start . 301)\n  (:id . 110))\n ((:tag . "NNP") (:stem . "j") (:form . "j") (:end . 304) (:start . 303)\n  (:id . 111))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 305) (:start . 304)\n  (:id . 112))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 309) (:start . 306)\n  (:id . 113))\n ((:tag . "NNP") (:stem . "PSSMquery(i") (:form . "PSSMquery(i") (:end . 321)\n  (:start . 310) (:id . 114))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 322) (:start . 321)\n  (:id . 115))\n ((:tag . "NNP") (:stem . "j") (:form . "j") (:end . 324) (:start . 323)\n  (:id . 116))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 325) (:start . 324)\n  (:id . 117))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 329) (:start . 326)\n  (:id . 118))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 333) (:start . 330)\n  (:id . 119))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 340)\n  (:start . 334) (:id . 120))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 343) (:start . 341)\n  (:id . 121))\n ((:tag . "NNP") (:stem . "S2A2") (:form . "S2A2") (:end . 348) (:start . 344)\n  (:id . 122))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 352) (:start . 349)\n  (:id . 123))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 357) (:start . 353)\n  (:id . 124))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 366)\n  (:start . 358) (:id . 125))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 367) (:start . 366)\n  (:id . 126))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 380)\n  (:start . 368) (:id . 127))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 381) (:start . 380)\n  (:id . 128))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 386) (:start . 382)\n  (:id . 129))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 390) (:start . 387)\n  (:id . 130))\n ((:tag . "NNP") (:stem . "RS") (:form . "RS") (:end . 393) (:start . 391)\n  (:id . 131))\n ((:tag . "NN") (:stem . "letter") (:form . "letter") (:end . 400)\n  (:start . 394) (:id . 132))\n ((:tag . "NNP") (:stem . "i") (:form . "i") (:end . 402) (:start . 401)\n  (:id . 133))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 405) (:start . 403)\n  (:id . 134))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 413)\n  (:start . 406) (:id . 135))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 416) (:start . 414)\n  (:id . 136))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 420) (:start . 417)\n  (:id . 137))\n ((:tag . "NNP") (:stem . "RS") (:form . "RS") (:end . 423) (:start . 421)\n  (:id . 138))\n ((:tag . "NN") (:stem . "letter") (:form . "letter") (:end . 430)\n  (:start . 424) (:id . 139))\n ((:tag . "NN") (:stem . "j") (:form . "j") (:end . 432) (:start . 431)\n  (:id . 140))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 433) (:start . 432)\n  (:id . 141)))@@@1@100@((:identifiers (:sid . :s15.82) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504821@unknown@formal@none@1@S@In addition, we considered structure-dependent gap penalty.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 15) (:start . 13)\n  (:id . 45))\n ((:tag . "VBD") (:stem . "consider") (:form . "considered") (:end . 26)\n  (:start . 16) (:id . 46))\n ((:tag . "JJ") (:stem . "structure-dependent")\n  (:form . "structure-dependent") (:end . 46) (:start . 27) (:id . 47))\n ((:tag . "NN") (:stem . "gap") (:form . "gap") (:end . 50) (:start . 47)\n  (:id . 48))\n ((:tag . "NN") (:stem . "penalty") (:form . "penalty") (:end . 58)\n  (:start . 51) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 59) (:start . 58)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s15.83) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504822@unknown@formal@none@1@S@Here, wgap is a structure-dependent gapping weight, set to 2.0 (α-helix), 2.0 (ß-strand) and 0.15 (coil), respectively; gS2A2 is the gap opening penalty (set to 7.2) and the gap extension (set to 1.2) for the S2A2 matrix.@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "wgap") (:form . "wgap") (:end . 10) (:start . 6)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "structure-dependent")\n  (:form . "structure-dependent") (:end . 35) (:start . 16) (:id . 47))\n ((:tag . "NN") (:stem . "gapping") (:form . "gapping") (:end . 43)\n  (:start . 36) (:id . 48))\n ((:tag . "NN") (:stem . "weight") (:form . "weight") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 55) (:start . 52)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "CD") (:stem . "2.0") (:form . "2.0") (:end . 62) (:start . 59)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "α-helix") (:form . "α-helix") (:end . 71)\n  (:start . 64) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 72) (:start . 71)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2.0") (:form . "2.0") (:end . 77) (:start . 74)\n  (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "ß-strand") (:form . "ß-strand") (:end . 87)\n  (:start . 79) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 88) (:start . 87)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 62))\n ((:tag . "CD") (:stem . "0.15") (:form . "0.15") (:end . 97) (:start . 93)\n  (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n  (:id . 64))\n ((:tag . "NN") (:stem . "coil") (:form . "coil") (:end . 103) (:start . 99)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 104) (:start . 103)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 67))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 118)\n  (:start . 106) (:id . 68))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 119) (:start . 118)\n  (:id . 69))\n ((:tag . "NN") (:stem . "gs2a2") (:form . "gS2A2") (:end . 125)\n  (:start . 120) (:id . 70))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 128) (:start . 126)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 72))\n ((:tag . "NN") (:stem . "gap") (:form . "gap") (:end . 136) (:start . 133)\n  (:id . 73))\n ((:tag . "NN") (:stem . "opening") (:form . "opening") (:end . 144)\n  (:start . 137) (:id . 74))\n ((:tag . "NN") (:stem . "penalty") (:form . "penalty") (:end . 152)\n  (:start . 145) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 154) (:start . 153)\n  (:id . 76))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 157) (:start . 154)\n  (:id . 77))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 160) (:start . 158)\n  (:id . 78))\n ((:tag . "CD") (:stem . "7.2") (:form . "7.2") (:end . 164) (:start . 161)\n  (:id . 79))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 165) (:start . 164)\n  (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 169) (:start . 166)\n  (:id . 81))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 173) (:start . 170)\n  (:id . 82))\n ((:tag . "NN") (:stem . "gap") (:form . "gap") (:end . 177) (:start . 174)\n  (:id . 83))\n ((:tag . "NN") (:stem . "extension") (:form . "extension") (:end . 187)\n  (:start . 178) (:id . 84))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 189) (:start . 188)\n  (:id . 85))\n ((:tag . "VBN") (:stem . "set") (:form . "set") (:end . 192) (:start . 189)\n  (:id . 86))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 195) (:start . 193)\n  (:id . 87))\n ((:tag . "CD") (:stem . "1.2") (:form . "1.2") (:end . 199) (:start . 196)\n  (:id . 88))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 200) (:start . 199)\n  (:id . 89))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 204) (:start . 201)\n  (:id . 90))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 208) (:start . 205)\n  (:id . 91))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 213) (:start . 209)\n  (:id . 92))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 220)\n  (:start . 214) (:id . 93))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 221) (:start . 220)\n  (:id . 94)))@@@1@53@((:identifiers (:sid . :s15.84) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504823@unknown@formal@none@1@S@These weights were optimized based on the SALIGN set.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "weight") (:form . "weights") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "optimize") (:form . "optimized") (:end . 28)\n  (:start . 19) (:id . 45))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 34) (:start . 29)\n  (:id . 46))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "SALIGN") (:form . "SALIGN") (:end . 48)\n  (:start . 42) (:id . 49))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 53) (:start . 52)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s15.85) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504824@unknown@formal@none@1@S@gpssm refers to the PSSM, where the gap opening penalty is 11 and gap extension is 1 according to the default parameters of PSI-BLAST.@(((:tag . "NN") (:stem . "gpssm") (:form . "gpssm") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBZ") (:stem . "refer") (:form . "refers") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 31) (:start . 26)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "NN") (:stem . "gap") (:form . "gap") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "NN") (:stem . "opening") (:form . "opening") (:end . 47)\n  (:start . 40) (:id . 51))\n ((:tag . "NN") (:stem . "penalty") (:form . "penalty") (:end . 55)\n  (:start . 48) (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 58) (:start . 56)\n  (:id . 53))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 61) (:start . 59)\n  (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 55))\n ((:tag . "NN") (:stem . "gap") (:form . "gap") (:end . 69) (:start . 66)\n  (:id . 56))\n ((:tag . "NN") (:stem . "extension") (:form . "extension") (:end . 79)\n  (:start . 70) (:id . 57))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 82) (:start . 80)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 84) (:start . 83)\n  (:id . 59))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 94)\n  (:start . 85) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 97) (:start . 95)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 101) (:start . 98)\n  (:id . 62))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 109)\n  (:start . 102) (:id . 63))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 120)\n  (:start . 110) (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 65))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 133)\n  (:start . 124) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 134) (:start . 133)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.86) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504825@unknown@formal@none@1@S@Statistics and template selection@(((:tag . "NNPS") (:stem . "Statistic") (:form . "Statistics") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "VB") (:stem . "template") (:form . "template") (:end . 23)\n  (:start . 15) (:id . 44))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 33)\n  (:start . 24) (:id . 45)))@@@1@4@((:identifiers (:sid . :s15.87) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504826@unknown@formal@none@1@S@SSEARCH provides the statistical significance for library searches.@(((:tag . "NN") (:stem . "ssearch") (:form . "SSEARCH") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 16)\n  (:start . 8) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "statistical") (:form . "statistical") (:end . 32)\n  (:start . 21) (:id . 45))\n ((:tag . "NN") (:stem . "significance") (:form . "significance") (:end . 45)\n  (:start . 33) (:id . 46))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 49) (:start . 46)\n  (:id . 47))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 57)\n  (:start . 50) (:id . 48))\n ((:tag . "NNS") (:stem . "search") (:form . "searches") (:end . 66)\n  (:start . 58) (:id . 49))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 50)))@@@1@9@((:identifiers (:sid . :s15.88) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504827@unknown@formal@none@1@S@The local sequence similarity score (S) follows the extreme value distribution, so that P(S > x) = 1 - exp(-Kmn exp(-λx)) where m, n are the lengths of the query and library sequence.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "local") (:form . "local") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 18)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 29)\n  (:start . 19) (:id . 45))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "S") (:form . "S") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "follow") (:form . "follows") (:end . 47)\n  (:start . 40) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "extreme") (:form . "extreme") (:end . 59)\n  (:start . 52) (:id . 52))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 78)\n  (:start . 66) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 79) (:start . 78)\n  (:id . 55))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 82) (:start . 80)\n  (:id . 56))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 87) (:start . 83)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "P(S") (:form . "P(S") (:end . 91) (:start . 88)\n  (:id . 58))\n ((:tag . "SYM") (:stem . ">") (:form . ">") (:end . 93) (:start . 92)\n  (:id . 59))\n ((:tag . "SYM") (:stem . "x") (:form . "x") (:end . 95) (:start . 94)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 61))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 98) (:start . 97)\n  (:id . 62))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 100) (:start . 99)\n  (:id . 63))\n ((:tag . "HYPH") (:stem . "-") (:form . "-") (:end . 102) (:start . 101)\n  (:id . 64))\n ((:tag . "NN") (:stem . "exp(-Kmn") (:form . "exp(-Kmn") (:end . 111)\n  (:start . 103) (:id . 65))\n ((:tag . "NN") (:stem . "exp(-λx))") (:form . "exp(-λx))") (:end . 121)\n  (:start . 112) (:id . 66))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 127)\n  (:start . 122) (:id . 67))\n ((:tag . "NN") (:stem . "m") (:form . "m") (:end . 129) (:start . 128)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 130) (:start . 129)\n  (:id . 69))\n ((:tag . "NN") (:stem . "n") (:form . "n") (:end . 132) (:start . 131)\n  (:id . 70))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 136) (:start . 133)\n  (:id . 71))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 140) (:start . 137)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "length") (:form . "lengths") (:end . 148)\n  (:start . 141) (:id . 73))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 151) (:start . 149)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 155) (:start . 152)\n  (:id . 75))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 161)\n  (:start . 156) (:id . 76))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 165) (:start . 162)\n  (:id . 77))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 173)\n  (:start . 166) (:id . 78))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 182)\n  (:start . 174) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 183) (:start . 182)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s15.89) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504828@unknown@formal@none@1@S@The score shows that the average score for an unrelated library sequence increases with the logarithm of the length of the library sequence.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 38) (:start . 33)\n  (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 45) (:start . 43)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "unrelated") (:form . "unrelated") (:end . 55)\n  (:start . 46) (:id . 51))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 63)\n  (:start . 56) (:id . 52))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 72)\n  (:start . 64) (:id . 53))\n ((:tag . "VBZ") (:stem . "increase") (:form . "increases") (:end . 82)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 87) (:start . 83)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "NN") (:stem . "logarithm") (:form . "logarithm") (:end . 101)\n  (:start . 92) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 104) (:start . 102)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 59))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 115)\n  (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 118) (:start . 116)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 122) (:start . 119)\n  (:id . 62))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 130)\n  (:start . 123) (:id . 63))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 139)\n  (:start . 131) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s15.90) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504829@unknown@formal@none@1@S@SSEARCH uses simple linear regression against the log of the library sequence length to calculate a normalized "z-score" with mean 50, regardless of library sequence length, and variance 10.@(((:tag . "NN") (:stem . "ssearch") (:form . "SSEARCH") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "VBZ") (:stem . "use") (:form . "uses") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "simple") (:form . "simple") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "JJ") (:stem . "linear") (:form . "linear") (:end . 26)\n  (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "regression") (:form . "regression") (:end . 37)\n  (:start . 27) (:id . 46))\n ((:tag . "IN") (:stem . "against") (:form . "against") (:end . 45)\n  (:start . 38) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "NN") (:stem . "log") (:form . "log") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 56) (:start . 54)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 68)\n  (:start . 61) (:id . 52))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 84)\n  (:start . 78) (:id . 54))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "VB") (:stem . "calculate") (:form . "calculate") (:end . 97)\n  (:start . 88) (:id . 56))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 99) (:start . 98)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "normalized") (:form . "normalized") (:end . 110)\n  (:start . 100) (:id . 58))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 112) (:start . 111)\n  (:id . 59))\n ((:tag . "NN") (:stem . "z-score") (:form . "z-score") (:end . 119)\n  (:start . 112) (:id . 60))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 120) (:start . 119)\n  (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 125) (:start . 121)\n  (:id . 62))\n ((:tag . "NN") (:stem . "mean") (:form . "mean") (:end . 130) (:start . 126)\n  (:id . 63))\n ((:tag . "CD") (:stem . "50") (:form . "50") (:end . 133) (:start . 131)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 134) (:start . 133)\n  (:id . 65))\n ((:tag . "RB") (:stem . "regardless") (:form . "regardless") (:end . 145)\n  (:start . 135) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 148) (:start . 146)\n  (:id . 67))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 156)\n  (:start . 149) (:id . 68))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 165)\n  (:start . 157) (:id . 69))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 172)\n  (:start . 166) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 173) (:start . 172)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 177) (:start . 174)\n  (:id . 72))\n ((:tag . "NN") (:stem . "variance") (:form . "variance") (:end . 186)\n  (:start . 178) (:id . 73))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 189) (:start . 187)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 190) (:start . 189)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s15.91) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504830@unknown@formal@none@1@S@These z-scores can then be used with the extreme value distribution and the Poisson distribution to calculate the number of library sequences to obtain a score (i.e. E-value) greater than or equal to the score obtained in the search.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "z-score") (:form . "z-scores") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "extreme") (:form . "extreme") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "value") (:form . "value") (:end . 54) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 67)\n  (:start . 55) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Poisson") (:form . "Poisson") (:end . 83)\n  (:start . 76) (:id . 55))\n ((:tag . "NN") (:stem . "distribution") (:form . "distribution") (:end . 96)\n  (:start . 84) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 99) (:start . 97)\n  (:id . 57))\n ((:tag . "VB") (:stem . "calculate") (:form . "calculate") (:end . 109)\n  (:start . 100) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 113) (:start . 110)\n  (:id . 59))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 120)\n  (:start . 114) (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 123) (:start . 121)\n  (:id . 61))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 131)\n  (:start . 124) (:id . 62))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 141)\n  (:start . 132) (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 144) (:start . 142)\n  (:id . 64))\n ((:tag . "VB") (:stem . "obtain") (:form . "obtain") (:end . 151)\n  (:start . 145) (:id . 65))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 153) (:start . 152)\n  (:id . 66))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 159)\n  (:start . 154) (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 161) (:start . 160)\n  (:id . 68))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 165) (:start . 161)\n  (:id . 69))\n ((:tag . "NN") (:stem . "e-value") (:form . "E-value") (:end . 173)\n  (:start . 166) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 174) (:start . 173)\n  (:id . 71))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 182)\n  (:start . 175) (:id . 72))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 187) (:start . 183)\n  (:id . 73))\n ((:tag . "CC") (:stem . "or") (:form . "or") (:end . 190) (:start . 188)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "equal") (:form . "equal") (:end . 196)\n  (:start . 191) (:id . 75))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 199) (:start . 197)\n  (:id . 76))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 203) (:start . 200)\n  (:id . 77))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 209)\n  (:start . 204) (:id . 78))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 218)\n  (:start . 210) (:id . 79))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 221) (:start . 219)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 225) (:start . 222)\n  (:id . 81))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 232)\n  (:start . 226) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 233) (:start . 232)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s15.92) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504831@unknown@formal@none@1@S@The top-ranking 5 templates with the lowest E-values were considered as the templates if the E-values < 0.1.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "top-ranking") (:form . "top-ranking") (:end . 15)\n  (:start . 4) (:id . 43))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 17) (:start . 16)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 32) (:start . 28)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 47))\n ((:tag . "JJS") (:stem . "low") (:form . "lowest") (:end . 43) (:start . 37)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "e-value") (:form . "E-values") (:end . 52)\n  (:start . 44) (:id . 49))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 57) (:start . 53)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 68)\n  (:start . 58) (:id . 51))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 71) (:start . 69)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 85)\n  (:start . 76) (:id . 54))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-values") (:end . 101)\n  (:start . 93) (:id . 57))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 103) (:start . 102)\n  (:id . 58))\n ((:tag . "CD") (:stem . "0.1") (:form . "0.1") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.93) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504832@unknown@formal@none@1@S@For each structure in the top-ranking 5 templates, The (PS)2-v2 server generated six alternative target-template alignments by using different S2A2-matrix (wS2A2) weights, including 0, 0.2, 0.4, 0.64, 0.8 and 1.0.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 18)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 21) (:start . 19)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "top-ranking") (:form . "top-ranking") (:end . 37)\n  (:start . 26) (:id . 47))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 63)\n  (:start . 56) (:id . 53))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 70)\n  (:start . 64) (:id . 54))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 80)\n  (:start . 71) (:id . 55))\n ((:tag . "CD") (:stem . "six") (:form . "six") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 96)\n  (:start . 85) (:id . 57))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 112) (:start . 97) (:id . 58))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 123)\n  (:start . 113) (:id . 59))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 126) (:start . 124)\n  (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 132) (:start . 127)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 142)\n  (:start . 133) (:id . 62))\n ((:tag . "NNP") (:stem . "S2A2-matrix") (:form . "S2A2-matrix") (:end . 154)\n  (:start . 143) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 64))\n ((:tag . "NN") (:stem . "ws2a2") (:form . "wS2A2") (:end . 161)\n  (:start . 156) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "weight") (:form . "weights") (:end . 170)\n  (:start . 163) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 181)\n  (:start . 172) (:id . 69))\n ((:tag . "CD") (:stem . "0") (:form . "0") (:end . 183) (:start . 182)\n  (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 184) (:start . 183)\n  (:id . 71))\n ((:tag . "CD") (:stem . "0.2") (:form . "0.2") (:end . 188) (:start . 185)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 189) (:start . 188)\n  (:id . 73))\n ((:tag . "CD") (:stem . "0.4") (:form . "0.4") (:end . 193) (:start . 190)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 194) (:start . 193)\n  (:id . 75))\n ((:tag . "CD") (:stem . "0.64") (:form . "0.64") (:end . 199) (:start . 195)\n  (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 200) (:start . 199)\n  (:id . 77))\n ((:tag . "CD") (:stem . "0.8") (:form . "0.8") (:end . 204) (:start . 201)\n  (:id . 78))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 208) (:start . 205)\n  (:id . 79))\n ((:tag . "CD") (:stem . "1.0") (:form . "1.0") (:end . 212) (:start . 209)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 213) (:start . 212)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s15.94) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504833@unknown@formal@none@1@S@Finally, we yielded 30 target-template alignments for a target protein.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "yield") (:form . "yielded") (:end . 19)\n  (:start . 12) (:id . 45))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 38) (:start . 23) (:id . 47))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 49)\n  (:start . 39) (:id . 48))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 55) (:start . 54)\n  (:id . 50))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 62)\n  (:start . 56) (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 70)\n  (:start . 63) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 71) (:start . 70)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s15.95) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504834@unknown@formal@none@1@S@Model building and evaluation@(((:tag . "NNP") (:stem . "Model") (:form . "Model") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "building") (:form . "building") (:end . 14)\n  (:start . 6) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 29)\n  (:start . 19) (:id . 45)))@@@1@4@((:identifiers (:sid . :s15.96) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504835@unknown@formal@none@1@S@Protein structure models were built using the homology modeling tool, MODELLER [24] according to the selected template(s) and target-template alignment(s) and then the ability to discriminate a correct protein model from incorrect models is critical when a server used multiple model methods.@(((:tag . "NN") (:stem . "protein") (:form . "Protein") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 17)\n  (:start . 8) (:id . 43))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 24)\n  (:start . 18) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "build") (:form . "built") (:end . 35) (:start . 30)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 41) (:start . 36)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 45) (:start . 42)\n  (:id . 48))\n ((:tag . "NN") (:stem . "homology") (:form . "homology") (:end . 54)\n  (:start . 46) (:id . 49))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 63)\n  (:start . 55) (:id . 50))\n ((:tag . "NN") (:stem . "tool") (:form . "tool") (:end . 68) (:start . 64)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 69) (:start . 68)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "MODELLER") (:form . "MODELLER") (:end . 78)\n  (:start . 70) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 80) (:start . 79)\n  (:id . 54))\n ((:tag . "CD") (:stem . "24") (:form . "24") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "accord") (:form . "according") (:end . 93)\n  (:start . 84) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 96) (:start . 94)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 100) (:start . 97)\n  (:id . 59))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 109)\n  (:start . 101) (:id . 60))\n ((:tag . "NN") (:stem . "template(s)") (:form . "template(s)") (:end . 121)\n  (:start . 110) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 125) (:start . 122)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 141) (:start . 126) (:id . 63))\n ((:tag . "JJ") (:stem . "alignment(s)") (:form . "alignment(s)") (:end . 154)\n  (:start . 142) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 158) (:start . 155)\n  (:id . 65))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 163) (:start . 159)\n  (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 67))\n ((:tag . "NN") (:stem . "ability") (:form . "ability") (:end . 175)\n  (:start . 168) (:id . 68))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 178) (:start . 176)\n  (:id . 69))\n ((:tag . "VB") (:stem . "discriminate") (:form . "discriminate") (:end . 191)\n  (:start . 179) (:id . 70))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 193) (:start . 192)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "correct") (:form . "correct") (:end . 201)\n  (:start . 194) (:id . 72))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 209)\n  (:start . 202) (:id . 73))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 215)\n  (:start . 210) (:id . 74))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 220) (:start . 216)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "incorrect") (:form . "incorrect") (:end . 230)\n  (:start . 221) (:id . 76))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 237)\n  (:start . 231) (:id . 77))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 240) (:start . 238)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 249)\n  (:start . 241) (:id . 79))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 254) (:start . 250)\n  (:id . 80))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 256) (:start . 255)\n  (:id . 81))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 263)\n  (:start . 257) (:id . 82))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 268) (:start . 264)\n  (:id . 83))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 277)\n  (:start . 269) (:id . 84))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 283)\n  (:start . 278) (:id . 85))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 291)\n  (:start . 284) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 292) (:start . 291)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s15.97) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504836@unknown@formal@none@1@S@Here, we utilized the program ProQ [19] to assess the quality of protein models based on the LGscore [30] and a model was considered correct if the LGscore was greater than 1.5 [19].@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "utilize") (:form . "utilized") (:end . 17)\n  (:start . 9) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 29)\n  (:start . 22) (:id . 47))\n ((:tag . "NNP") (:stem . "ProQ") (:form . "ProQ") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 36) (:start . 35)\n  (:id . 49))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 39) (:start . 38)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 42) (:start . 40)\n  (:id . 52))\n ((:tag . "VB") (:stem . "assess") (:form . "assess") (:end . 49)\n  (:start . 43) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 54))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 61)\n  (:start . 54) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 64) (:start . 62)\n  (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 72)\n  (:start . 65) (:id . 57))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 79)\n  (:start . 73) (:id . 58))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 85) (:start . 80)\n  (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 88) (:start . 86)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "LGscore") (:form . "LGscore") (:end . 100)\n  (:start . 93) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 102) (:start . 101)\n  (:id . 63))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 104) (:start . 102)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 105) (:start . 104)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 66))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 111) (:start . 110)\n  (:id . 67))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 117)\n  (:start . 112) (:id . 68))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 121) (:start . 118)\n  (:id . 69))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 132)\n  (:start . 122) (:id . 70))\n ((:tag . "JJ") (:stem . "correct") (:form . "correct") (:end . 140)\n  (:start . 133) (:id . 71))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 143) (:start . 141)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 147) (:start . 144)\n  (:id . 73))\n ((:tag . "NN") (:stem . "lgscore") (:form . "LGscore") (:end . 155)\n  (:start . 148) (:id . 74))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 159) (:start . 156)\n  (:id . 75))\n ((:tag . "JJR") (:stem . "great") (:form . "greater") (:end . 167)\n  (:start . 160) (:id . 76))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 172) (:start . 168)\n  (:id . 77))\n ((:tag . "CD") (:stem . "1.5") (:form . "1.5") (:end . 176) (:start . 173)\n  (:id . 78))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 178) (:start . 177)\n  (:id . 79))\n ((:tag . "CD") (:stem . "19") (:form . "19") (:end . 180) (:start . 178)\n  (:id . 80))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 181) (:start . 180)\n  (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s15.98) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504837@unknown@formal@none@1@S@The (PS)2-v2 server first selected the protein model, generated by the first rank template with wS2A2 = 0.64 as the seed model.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 46)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 52) (:start . 47)\n  (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "first") (:form . "first") (:end . 76) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "rank") (:form . "rank") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 90)\n  (:start . 82) (:id . 57))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "ws2a2") (:form . "wS2A2") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 103) (:start . 102)\n  (:id . 60))\n ((:tag . "CD") (:stem . "0.64") (:form . "0.64") (:end . 108) (:start . 104)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 111) (:start . 109)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 115) (:start . 112)\n  (:id . 63))\n ((:tag . "NN") (:stem . "seed") (:form . "seed") (:end . 120) (:start . 116)\n  (:id . 64))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 126)\n  (:start . 121) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 127) (:start . 126)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s15.99) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504838@unknown@formal@none@1@S@The LGscore of the seed model was then compared with those of the other models based on the top-rank 5 templates with different wS2A2 weights.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "lgscore") (:form . "LGscore") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "seed") (:form . "seed") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 47)\n  (:start . 39) (:id . 50))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 71) (:start . 66)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 78)\n  (:start . 72) (:id . 56))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 84) (:start . 79)\n  (:id . 57))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 87) (:start . 85)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "top-rank") (:form . "top-rank") (:end . 100)\n  (:start . 92) (:id . 60))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 112)\n  (:start . 103) (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 117) (:start . 113)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 127)\n  (:start . 118) (:id . 64))\n ((:tag . "NN") (:stem . "ws2a2") (:form . "wS2A2") (:end . 133)\n  (:start . 128) (:id . 65))\n ((:tag . "NNS") (:stem . "weight") (:form . "weights") (:end . 141)\n  (:start . 134) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 142) (:start . 141)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.100) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504839@unknown@formal@none@1@S@A model was chosen as the final one if it had the highest LGscore and its LGscore (> 0.7) was significantly better than that of the seed model.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 7) (:start . 2)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "choose") (:form . "chosen") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 21) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 31) (:start . 26)\n  (:id . 48))\n ((:tag . "CD") (:stem . "one") (:form . "one") (:end . 35) (:start . 32)\n  (:id . 49))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 38) (:start . 36)\n  (:id . 50))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 41) (:start . 39)\n  (:id . 51))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 45) (:start . 42)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 49) (:start . 46)\n  (:id . 53))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 57)\n  (:start . 50) (:id . 54))\n ((:tag . "NN") (:stem . "lgscore") (:form . "LGscore") (:end . 65)\n  (:start . 58) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 69) (:start . 66)\n  (:id . 56))\n ((:tag . "PRP$") (:stem . "its") (:form . "its") (:end . 73) (:start . 70)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "LGscore") (:form . "LGscore") (:end . 81)\n  (:start . 74) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 59))\n ((:tag . "SYM") (:stem . ">") (:form . ">") (:end . 84) (:start . 83)\n  (:id . 60))\n ((:tag . "CD") (:stem . "0.7") (:form . "0.7") (:end . 88) (:start . 85)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 62))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 93) (:start . 90)\n  (:id . 63))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 107) (:start . 94) (:id . 64))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 114)\n  (:start . 108) (:id . 65))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 119) (:start . 115)\n  (:id . 66))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 124) (:start . 120)\n  (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 127) (:start . 125)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 69))\n ((:tag . "NN") (:stem . "seed") (:form . "seed") (:end . 136) (:start . 132)\n  (:id . 70))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 142)\n  (:start . 137) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s15.101) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504840@unknown@formal@none@1@S@Otherwise, the server selected the seed model as the final model.@(((:tag . "RB") (:stem . "otherwise") (:form . "Otherwise") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 30)\n  (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "seed") (:form . "seed") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 45) (:start . 40)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 64) (:start . 59)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s15.102) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504841@unknown@formal@none@1@S@Multiple-template method@(((:tag . "JJ") (:stem . "multiple-template") (:form . "Multiple-template")\n  (:end . 17) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 24)\n  (:start . 18) (:id . 43)))@@@1@2@((:identifiers (:sid . :s15.103) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504842@unknown@formal@none@1@S@(PS)2-v2 considered a target as a multiple domain protein if any region with >40 residues has non-aligned residues to the template(s) when using above "model building and evaluation" steps.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 19)\n  (:start . 9) (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 31) (:start . 29)\n  (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 42)\n  (:start . 34) (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 49)\n  (:start . 43) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 57)\n  (:start . 50) (:id . 51))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 60) (:start . 58)\n  (:id . 52))\n ((:tag . "DT") (:stem . "any") (:form . "any") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "region") (:form . "region") (:end . 71)\n  (:start . 65) (:id . 54))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 76) (:start . 72)\n  (:id . 55))\n ((:tag . "CD") (:stem . ">40") (:form . ">40") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 89)\n  (:start . 81) (:id . 57))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 93) (:start . 90)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "non-aligned") (:form . "non-aligned") (:end . 105)\n  (:start . 94) (:id . 59))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 114)\n  (:start . 106) (:id . 60))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 117) (:start . 115)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "NN") (:stem . "template(s)") (:form . "template(s)") (:end . 133)\n  (:start . 122) (:id . 63))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 138) (:start . 134)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 144) (:start . 139)\n  (:id . 65))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 150)\n  (:start . 145) (:id . 66))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 152) (:start . 151)\n  (:id . 67))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 157)\n  (:start . 152) (:id . 68))\n ((:tag . "NN") (:stem . "building") (:form . "building") (:end . 166)\n  (:start . 158) (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 170) (:start . 167)\n  (:id . 70))\n ((:tag . "NN") (:stem . "evaluation") (:form . "evaluation") (:end . 181)\n  (:start . 171) (:id . 71))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 182) (:start . 181)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 188)\n  (:start . 183) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 189) (:start . 188)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s15.104) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504843@unknown@formal@none@1@S@For a multiple domain protein, (PS)2-v2 automatically decided domain boundaries based on the borders of the large gaps between the target and the template(s), and repeatedly executed above steps to model the structures of the non-aligned residues (Figure 1).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 14)\n  (:start . 6) (:id . 44))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 39)\n  (:start . 32) (:id . 49))\n ((:tag . "RB") (:stem . "automatically") (:form . "automatically")\n  (:end . 53) (:start . 40) (:id . 50))\n ((:tag . "VBD") (:stem . "decide") (:form . "decided") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 68)\n  (:start . 62) (:id . 52))\n ((:tag . "NNS") (:stem . "boundary") (:form . "boundaries") (:end . 79)\n  (:start . 69) (:id . 53))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 85) (:start . 80)\n  (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 88) (:start . 86)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 92) (:start . 89)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "border") (:form . "borders") (:end . 100)\n  (:start . 93) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 103) (:start . 101)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 107) (:start . 104)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 113)\n  (:start . 108) (:id . 60))\n ((:tag . "NNS") (:stem . "gap") (:form . "gaps") (:end . 118) (:start . 114)\n  (:id . 61))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 126)\n  (:start . 119) (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 63))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 137)\n  (:start . 131) (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 141) (:start . 138)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 66))\n ((:tag . "NN") (:stem . "template(s)") (:form . "template(s)") (:end . 157)\n  (:start . 146) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 158) (:start . 157)\n  (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 162) (:start . 159)\n  (:id . 69))\n ((:tag . "RB") (:stem . "repeatedly") (:form . "repeatedly") (:end . 173)\n  (:start . 163) (:id . 70))\n ((:tag . "VBN") (:stem . "execute") (:form . "executed") (:end . 182)\n  (:start . 174) (:id . 71))\n ((:tag . "IN") (:stem . "above") (:form . "above") (:end . 188)\n  (:start . 183) (:id . 72))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 194)\n  (:start . 189) (:id . 73))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 197) (:start . 195)\n  (:id . 74))\n ((:tag . "VB") (:stem . "model") (:form . "model") (:end . 203)\n  (:start . 198) (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 207) (:start . 204)\n  (:id . 76))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 218)\n  (:start . 208) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 221) (:start . 219)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 225) (:start . 222)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "non-aligned") (:form . "non-aligned") (:end . 237)\n  (:start . 226) (:id . 80))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 246)\n  (:start . 238) (:id . 81))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 248) (:start . 247)\n  (:id . 82))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 254)\n  (:start . 248) (:id . 83))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 256) (:start . 255)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 257) (:start . 256)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 258) (:start . 257)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s15.105) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504844@unknown@formal@none@1@S@Finally, these multiple models were then used as structure templates to generate the full-length final model for the query protein.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 23)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 40) (:start . 36)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "VBZ") (:stem . "template") (:form . "templates") (:end . 68)\n  (:start . 59) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 53))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 80)\n  (:start . 72) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "full-length") (:form . "full-length") (:end . 96)\n  (:start . 85) (:id . 56))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 102) (:start . 97)\n  (:id . 57))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 108)\n  (:start . 103) (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 112) (:start . 109)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 60))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 122)\n  (:start . 117) (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 130)\n  (:start . 123) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 131) (:start . 130)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s15.106) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504845@unknown@formal@none@1@S@Utility@(((:tag . "NNP") (:stem . "Utility") (:form . "Utility") (:end . 7)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s15.107) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504846@unknown@formal@none@1@S@Input format@(((:tag . "NN") (:stem . "input") (:form . "Input") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 12) (:start . 6)\n  (:id . 43)))@@@1@2@((:identifiers (:sid . :s15.108) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504847@unknown@formal@none@1@S@The (PS)2-v2 server is an easy-to-use web server (Figure 2).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 22) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "easy-to-use") (:form . "easy-to-use") (:end . 37)\n  (:start . 26) (:id . 48))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 48)\n  (:start . 42) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 56)\n  (:start . 50) (:id . 52))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 58) (:start . 57)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 59) (:start . 58)\n  (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 60) (:start . 59)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s15.109) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504848@unknown@formal@none@1@S@Users input the query protein sequence in FASTA format.@(((:tag . "NNS") (:stem . "user") (:form . "Users") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "input") (:form . "input") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 38)\n  (:start . 30) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "FASTA") (:form . "FASTA") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 54)\n  (:start . 48) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 55) (:start . 54)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s15.110) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504849@unknown@formal@none@1@S@The server provides three modes (Automatic, Manual and 'Use this template') for choosing template(s) (Figure 2A).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 25) (:start . 20)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "mode") (:form . "modes") (:end . 31) (:start . 26)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 33) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Automatic") (:form . "Automatic") (:end . 42)\n  (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Manual") (:form . "Manual") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "VB") (:stem . "Use") (:form . "Use") (:end . 59) (:start . 56)\n  (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 64) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 73)\n  (:start . 65) (:id . 55))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 79) (:start . 76)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "choose") (:form . "choosing") (:end . 88)\n  (:start . 80) (:id . 59))\n ((:tag . "NNP") (:stem . "template(s)") (:form . "template(s)") (:end . 100)\n  (:start . 89) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 108)\n  (:start . 102) (:id . 62))\n ((:tag . "NN") (:stem . "2a") (:form . "2A") (:end . 111) (:start . 109)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 112) (:start . 111)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s15.111) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504850@unknown@formal@none@1@S@The default mode is 'Automatic'.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "default") (:form . "default") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "mode") (:form . "mode") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "Automatic") (:form . "Automatic") (:end . 30)\n  (:start . 21) (:id . 47))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 32) (:start . 31)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s15.112) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504851@unknown@formal@none@1@S@In this mode, (PS)2-v2 automatically selects the modeling template(s).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "mode") (:form . "mode") (:end . 12) (:start . 8)\n  (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 22)\n  (:start . 15) (:id . 47))\n ((:tag . "RB") (:stem . "automatically") (:form . "automatically")\n  (:end . 36) (:start . 23) (:id . 48))\n ((:tag . "VBZ") (:stem . "select") (:form . "selects") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 57)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "template(s)") (:form . "template(s)") (:end . 69)\n  (:start . 58) (:id . 52))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s15.113) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504852@unknown@formal@none@1@S@For the 'Manual' mode, our server enables users to assign specific template(s) from a list of candidates (Figure 2B).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 9) (:start . 8)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "Manual") (:form . "Manual") (:end . 15) (:start . 9)\n  (:id . 45))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 16) (:start . 15)\n  (:id . 46))\n ((:tag . "NN") (:stem . "mode") (:form . "mode") (:end . 21) (:start . 17)\n  (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 48))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 26) (:start . 23)\n  (:id . 49))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 33)\n  (:start . 27) (:id . 50))\n ((:tag . "VBZ") (:stem . "enable") (:form . "enables") (:end . 41)\n  (:start . 34) (:id . 51))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 47) (:start . 42)\n  (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 53))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 57)\n  (:start . 51) (:id . 54))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 66)\n  (:start . 58) (:id . 55))\n ((:tag . "NNS") (:stem . "template(s)") (:form . "template(s)") (:end . 78)\n  (:start . 67) (:id . 56))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 90) (:start . 86)\n  (:id . 59))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "candidate") (:form . "candidates") (:end . 104)\n  (:start . 94) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 112)\n  (:start . 106) (:id . 63))\n ((:tag . "NN") (:stem . "2b") (:form . "2B") (:end . 115) (:start . 113)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s15.114) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504853@unknown@formal@none@1@S@The 'Use this template' mode allows users to assign a specific protein structure as the template.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 5) (:start . 4)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Use") (:form . "Use") (:end . 8) (:start . 5)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 13) (:start . 9)\n  (:id . 45))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 22)\n  (:start . 14) (:id . 46))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "NN") (:stem . "mode") (:form . "mode") (:end . 28) (:start . 24)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "allow") (:form . "allows") (:end . 35)\n  (:start . 29) (:id . 49))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 41) (:start . 36)\n  (:id . 50))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 44) (:start . 42)\n  (:id . 51))\n ((:tag . "VB") (:stem . "assign") (:form . "assign") (:end . 51)\n  (:start . 45) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 53) (:start . 52)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "specific") (:form . "specific") (:end . 62)\n  (:start . 54) (:id . 54))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 70)\n  (:start . 63) (:id . 55))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 80)\n  (:start . 71) (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 83) (:start . 81)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 87) (:start . 84)\n  (:id . 58))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 96)\n  (:start . 88) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.115) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504854@unknown@formal@none@1@S@Finally, (PS)2-v2 transmits the predicted results to the users by email addresses.@(((:tag . "RB") (:stem . "finally") (:form . "Finally") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 10) (:start . 9)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 17)\n  (:start . 10) (:id . 45))\n ((:tag . "VBZ") (:stem . "transmit") (:form . "transmits") (:end . 27)\n  (:start . 18) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 41)\n  (:start . 32) (:id . 48))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 49)\n  (:start . 42) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "user") (:form . "users") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "email") (:form . "email") (:end . 71) (:start . 66)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "address") (:form . "addresses") (:end . 81)\n  (:start . 72) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s15.116) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504855@unknown@formal@none@1@S@Output format@(((:tag . "NN") (:stem . "output") (:form . "Output") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 13) (:start . 7)\n  (:id . 43)))@@@1@2@((:identifiers (:sid . :s15.117) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504856@unknown@formal@none@1@S@The (PS)2-v2 server typically yields a predicted structure within 7 minutes if the query sequence length is ~200.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "RB") (:stem . "typically") (:form . "typically") (:end . 29)\n  (:start . 20) (:id . 46))\n ((:tag . "VBZ") (:stem . "yield") (:form . "yields") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 38) (:start . 37)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 48)\n  (:start . 39) (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 58)\n  (:start . 49) (:id . 50))\n ((:tag . "IN") (:stem . "within") (:form . "within") (:end . 65)\n  (:start . 59) (:id . 51))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 67) (:start . 66)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "minute") (:form . "minutes") (:end . 75)\n  (:start . 68) (:id . 53))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 78) (:start . 76)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 55))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 88) (:start . 83)\n  (:id . 56))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 97)\n  (:start . 89) (:id . 57))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 104)\n  (:start . 98) (:id . 58))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 107) (:start . 105)\n  (:id . 59))\n ((:tag . "CD") (:stem . "~200") (:form . "~200") (:end . 112) (:start . 108)\n  (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s15.118) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504857@unknown@formal@none@1@S@The server shows a list of templates, selected template(s), target-template alignment(s), predicted structure(s) and structure evaluations (Figures 2B and 2C).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "list") (:form . "list") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 36)\n  (:start . 27) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 37) (:start . 36)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 46)\n  (:start . 38) (:id . 50))\n ((:tag . "NNS") (:stem . "template(s)") (:form . "template(s)") (:end . 58)\n  (:start . 47) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 75) (:start . 60) (:id . 53))\n ((:tag . "JJ") (:stem . "alignment(s)") (:form . "alignment(s)") (:end . 88)\n  (:start . 76) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 99)\n  (:start . 90) (:id . 56))\n ((:tag . "NN") (:stem . "structure(s)") (:form . "structure(s)") (:end . 112)\n  (:start . 100) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 116) (:start . 113)\n  (:id . 58))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 126)\n  (:start . 117) (:id . 59))\n ((:tag . "NNS") (:stem . "evaluation") (:form . "evaluations") (:end . 138)\n  (:start . 127) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 140) (:start . 139)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "figure") (:form . "Figures") (:end . 147)\n  (:start . 140) (:id . 62))\n ((:tag . "NN") (:stem . "2b") (:form . "2B") (:end . 150) (:start . 148)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 154) (:start . 151)\n  (:id . 64))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 157) (:start . 155)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 158) (:start . 157)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 159) (:start . 158)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.119) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504858@unknown@formal@none@1@S@The predicted structures are visualized in PNG format generated by the MolScript [31] and Raster3D [32] packages.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 24)\n  (:start . 14) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 28) (:start . 25)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "visualize") (:form . "visualized") (:end . 39)\n  (:start . 29) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "NN") (:stem . "png") (:form . "PNG") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 53)\n  (:start . 47) (:id . 49))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 63)\n  (:start . 54) (:id . 50))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 66) (:start . 64)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "MolScript") (:form . "MolScript") (:end . 80)\n  (:start . 71) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 82) (:start . 81)\n  (:id . 54))\n ((:tag . "CD") (:stem . "31") (:form . "31") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Raster3D") (:form . "Raster3D") (:end . 98)\n  (:start . 90) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 100) (:start . 99)\n  (:id . 59))\n ((:tag . "CD") (:stem . "32") (:form . "32") (:end . 102) (:start . 100)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 103) (:start . 102)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "package") (:form . "packages") (:end . 112)\n  (:start . 104) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s15.120) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504859@unknown@formal@none@1@S@If the user clicks a PNG picture, then the corresponding protein 3D structure is also displayed on the AstexViewer [33] (Figure 2D).@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "click") (:form . "clicks") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "png") (:form . "PNG") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "NN") (:stem . "picture") (:form . "picture") (:end . 32)\n  (:start . 25) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 33) (:start . 32)\n  (:id . 49))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 38) (:start . 34)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 51))\n ((:tag . "VBG") (:stem . "correspond") (:form . "corresponding") (:end . 56)\n  (:start . 43) (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 64)\n  (:start . 57) (:id . 53))\n ((:tag . "NN") (:stem . "3d") (:form . "3D") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 77)\n  (:start . 68) (:id . 55))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 80) (:start . 78)\n  (:id . 56))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 85) (:start . 81)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "display") (:form . "displayed") (:end . 95)\n  (:start . 86) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 98) (:start . 96)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "AstexViewer") (:form . "AstexViewer") (:end . 114)\n  (:start . 103) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 116) (:start . 115)\n  (:id . 62))\n ((:tag . "CD") (:stem . "33") (:form . "33") (:end . 118) (:start . 116)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 119) (:start . 118)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 121) (:start . 120)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 127)\n  (:start . 121) (:id . 66))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 130) (:start . 128)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s15.121) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504860@unknown@formal@none@1@S@A user can download the predicted structure coordinates in the PDB format.@(((:tag . "DT") (:stem . "a") (:form . "A") (:end . 1) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "user") (:form . "user") (:end . 6) (:start . 2)\n  (:id . 43))\n ((:tag . "MD") (:stem . "can") (:form . "can") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "VB") (:stem . "download") (:form . "download") (:end . 19)\n  (:start . 11) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "VBZ") (:stem . "coordinate") (:form . "coordinates") (:end . 55)\n  (:start . 44) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 58) (:start . 56)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 66) (:start . 63)\n  (:id . 52))\n ((:tag . "NN") (:stem . "format") (:form . "format") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s15.122) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504861@unknown@formal@none@1@S@The server also provides the target-template alignments and the structure quality factors (Figure 2E).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "provide") (:form . "provides") (:end . 24)\n  (:start . 16) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 44) (:start . 29) (:id . 47))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 55)\n  (:start . 45) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 59) (:start . 56)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 50))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 73)\n  (:start . 64) (:id . 51))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 81)\n  (:start . 74) (:id . 52))\n ((:tag . "NNS") (:stem . "factor") (:form . "factors") (:end . 89)\n  (:start . 82) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 97)\n  (:start . 91) (:id . 55))\n ((:tag . "NN") (:stem . "2e") (:form . "2E") (:end . 100) (:start . 98)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 102) (:start . 101)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s15.123) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504862@unknown@formal@none@1@S@Modeling of ever shorter telomeres 3@(((:tag . "NN") (:stem . "modeling") (:form . "Modeling") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 11) (:start . 9)\n  (:id . 43))\n ((:tag . "RB") (:stem . "ever") (:form . "ever") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "JJR") (:stem . "short") (:form . "shorter") (:end . 24)\n  (:start . 17) (:id . 45))\n ((:tag . "VBZ") (:stem . "telomere") (:form . "telomeres") (:end . 34)\n  (:start . 25) (:id . 46))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 36) (:start . 35)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s15.124) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504863@unknown@formal@none@1@S@The ever shorter telomeres 3 (Est3, UniProt Q03096), which is essential for telomere replication in vivo, is a small regulatory subunit of telomerase from Saccharomyces cerevisiae.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "RB") (:stem . "ever") (:form . "ever") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "JJR") (:stem . "short") (:form . "shorter") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "telomere") (:form . "telomeres") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "Est3") (:form . "Est3") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 35) (:start . 34)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "UniProt") (:form . "UniProt") (:end . 43)\n  (:start . 36) (:id . 50))\n ((:tag . "NNP") (:stem . "Q03096") (:form . "Q03096") (:end . 50)\n  (:start . 44) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 58) (:start . 53)\n  (:id . 54))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 61) (:start . 59)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "essential") (:form . "essential") (:end . 71)\n  (:start . 62) (:id . 56))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 75) (:start . 72)\n  (:id . 57))\n ((:tag . "NN") (:stem . "telomere") (:form . "telomere") (:end . 84)\n  (:start . 76) (:id . 58))\n ((:tag . "NN") (:stem . "replication") (:form . "replication") (:end . 96)\n  (:start . 85) (:id . 59))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 99) (:start . 97)\n  (:id . 60))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 104) (:start . 100)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 105) (:start . 104)\n  (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 108) (:start . 106)\n  (:id . 63))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 110) (:start . 109)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "small") (:form . "small") (:end . 116)\n  (:start . 111) (:id . 65))\n ((:tag . "JJ") (:stem . "regulatory") (:form . "regulatory") (:end . 127)\n  (:start . 117) (:id . 66))\n ((:tag . "NN") (:stem . "subunit") (:form . "subunit") (:end . 135)\n  (:start . 128) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 138) (:start . 136)\n  (:id . 68))\n ((:tag . "NN") (:stem . "telomerase") (:form . "telomerase") (:end . 149)\n  (:start . 139) (:id . 69))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 154) (:start . 150)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "Saccharomyces") (:form . "Saccharomyces")\n  (:end . 168) (:start . 155) (:id . 71))\n ((:tag . "NNP") (:stem . "cerevisiae") (:form . "cerevisiae") (:end . 179)\n  (:start . 169) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 180) (:start . 179)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s15.125) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504864@unknown@formal@none@1@S@According to structure prediction combined with in vivo characterization, it has been reported that Est3 consists of a predicted OB-fold (oligosaccharide/oligonucleotide binding) with structurally similar to the OB-fold of the human Tpp1 protein [34].@(((:tag . "VBG") (:stem . "accord") (:form . "According") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 22)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 33)\n  (:start . 23) (:id . 45))\n ((:tag . "VBN") (:stem . "combine") (:form . "combined") (:end . 42)\n  (:start . 34) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 47) (:start . 43)\n  (:id . 47))\n ((:tag . "FW") (:stem . "in") (:form . "in") (:end . 50) (:start . 48)\n  (:id . 48))\n ((:tag . "FW") (:stem . "vivo") (:form . "vivo") (:end . 55) (:start . 51)\n  (:id . 49))\n ((:tag . "NN") (:stem . "characterization") (:form . "characterization")\n  (:end . 72) (:start . 56) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 73) (:start . 72)\n  (:id . 51))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 76) (:start . 74)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 80) (:start . 77)\n  (:id . 53))\n ((:tag . "VBN") (:stem . "be") (:form . "been") (:end . 85) (:start . 81)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 94)\n  (:start . 86) (:id . 55))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 99) (:start . 95)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Est3") (:form . "Est3") (:end . 104) (:start . 100)\n  (:id . 57))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 113)\n  (:start . 105) (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 116) (:start . 114)\n  (:id . 59))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 118) (:start . 117)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 128)\n  (:start . 119) (:id . 61))\n ((:tag . "JJ") (:stem . "ob-fold") (:form . "OB-fold") (:end . 136)\n  (:start . 129) (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 138) (:start . 137)\n  (:id . 63))\n ((:tag . "NN") (:stem . "oligosaccharide/oligonucleotide")\n  (:form . "oligosaccharide/oligonucleotide") (:end . 169) (:start . 138)\n  (:id . 64))\n ((:tag . "NN") (:stem . "binding") (:form . "binding") (:end . 177)\n  (:start . 170) (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 178) (:start . 177)\n  (:id . 66))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 183) (:start . 179)\n  (:id . 67))\n ((:tag . "RB") (:stem . "structurally") (:form . "structurally") (:end . 196)\n  (:start . 184) (:id . 68))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 204)\n  (:start . 197) (:id . 69))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 207) (:start . 205)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 211) (:start . 208)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "OB-fold") (:form . "OB-fold") (:end . 219)\n  (:start . 212) (:id . 72))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 222) (:start . 220)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 226) (:start . 223)\n  (:id . 74))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 232)\n  (:start . 227) (:id . 75))\n ((:tag . "NN") (:stem . "tpp1") (:form . "Tpp1") (:end . 237) (:start . 233)\n  (:id . 76))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 245)\n  (:start . 238) (:id . 77))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 247) (:start . 246)\n  (:id . 78))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 249) (:start . 247)\n  (:id . 79))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 250) (:start . 249)\n  (:id . 80))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 251) (:start . 250)\n  (:id . 81)))@@@1@40@((:identifiers (:sid . :s15.126) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504865@unknown@formal@none@1@S@Because of the limited degree of conservation between these two protein families, these two proteins could not be recognized from simple sequence profile methods.@(((:tag . "IN") (:stem . "because") (:form . "Because") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "limited") (:form . "limited") (:end . 22)\n  (:start . 15) (:id . 45))\n ((:tag . "NN") (:stem . "degree") (:form . "degree") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 45)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 53)\n  (:start . 46) (:id . 49))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 59) (:start . 54)\n  (:id . 50))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 63) (:start . 60)\n  (:id . 51))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 71)\n  (:start . 64) (:id . 52))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 80)\n  (:start . 72) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 54))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 87) (:start . 82)\n  (:id . 55))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 91) (:start . 88)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 100)\n  (:start . 92) (:id . 57))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 106)\n  (:start . 101) (:id . 58))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 110) (:start . 107)\n  (:id . 59))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 113) (:start . 111)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "recognize") (:form . "recognized") (:end . 124)\n  (:start . 114) (:id . 61))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 129) (:start . 125)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "simple") (:form . "simple") (:end . 136)\n  (:start . 130) (:id . 63))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 145)\n  (:start . 137) (:id . 64))\n ((:tag . "NN") (:stem . "profile") (:form . "profile") (:end . 153)\n  (:start . 146) (:id . 65))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 161)\n  (:start . 154) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 162) (:start . 161)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.127) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504866@unknown@formal@none@1@S@Additionally, the original (PS)2 -v2 server could not recognize them.@(((:tag . "RB") (:stem . "additionally") (:form . "Additionally") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 13) (:start . 12)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "PS)2") (:form . "PS)2") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "CD") (:stem . "-v2") (:form . "-v2") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 43)\n  (:start . 37) (:id . 49))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 49) (:start . 44)\n  (:id . 50))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 53) (:start . 50)\n  (:id . 51))\n ((:tag . "VB") (:stem . "recognize") (:form . "recognize") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 68) (:start . 64)\n  (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 69) (:start . 68)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s15.128) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504867@unknown@formal@none@1@S@For the target Est3, the (PS)2 -v2 server selected the OB-fold domain of the Tpp1 protein (PDB code 2i46) from Homo sapiens as the template [35], with an E-value of 0.014.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "est3") (:form . "Est3") (:end . 19) (:start . 15)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 48))\n ((:tag . "NN") (:stem . "PS)2") (:form . "PS)2") (:end . 30) (:start . 26)\n  (:id . 49))\n ((:tag . "CD") (:stem . "-v2") (:form . "-v2") (:end . 34) (:start . 31)\n  (:id . 50))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 41)\n  (:start . 35) (:id . 51))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 50)\n  (:start . 42) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "ob-fold") (:form . "OB-fold") (:end . 62)\n  (:start . 55) (:id . 54))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 69)\n  (:start . 63) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 72) (:start . 70)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 57))\n ((:tag . "NN") (:stem . "tpp1") (:form . "Tpp1") (:end . 81) (:start . 77)\n  (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 89)\n  (:start . 82) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 91) (:start . 90)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 94) (:start . 91)\n  (:id . 61))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 99) (:start . 95)\n  (:id . 62))\n ((:tag . "CD") (:stem . "2i46") (:form . "2i46") (:end . 104) (:start . 100)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 105) (:start . 104)\n  (:id . 64))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 110) (:start . 106)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Homo") (:form . "Homo") (:end . 115) (:start . 111)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "sapien") (:form . "sapiens") (:end . 123)\n  (:start . 116) (:id . 67))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 126) (:start . 124)\n  (:id . 68))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 130) (:start . 127)\n  (:id . 69))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 139)\n  (:start . 131) (:id . 70))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 141) (:start . 140)\n  (:id . 71))\n ((:tag . "CD") (:stem . "35") (:form . "35") (:end . 143) (:start . 141)\n  (:id . 72))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 144) (:start . 143)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 145) (:start . 144)\n  (:id . 74))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 150) (:start . 146)\n  (:id . 75))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 153) (:start . 151)\n  (:id . 76))\n ((:tag . "NN") (:stem . "e-value") (:form . "E-value") (:end . 161)\n  (:start . 154) (:id . 77))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 164) (:start . 162)\n  (:id . 78))\n ((:tag . "CD") (:stem . "0.014") (:form . "0.014") (:end . 170)\n  (:start . 165) (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s15.129) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504868@unknown@formal@none@1@S@This template shared only 17.6% sequence identity with the query sequence.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 13)\n  (:start . 5) (:id . 43))\n ((:tag . "VBD") (:stem . "share") (:form . "shared") (:end . 20)\n  (:start . 14) (:id . 44))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 25) (:start . 21)\n  (:id . 45))\n ((:tag . "CD") (:stem . "17.6") (:form . "17.6") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 31) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 40)\n  (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 49)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 54) (:start . 50)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 64) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 73)\n  (:start . 65) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 74) (:start . 73)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s15.130) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504869@unknown@formal@none@1@S@Figure 2C shows the target-template alignment.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 35) (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 45)\n  (:start . 36) (:id . 47))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n  (:id . 48)))@@@1@7@((:identifiers (:sid . :s15.131) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504870@unknown@formal@none@1@S@The server successfully recognized Tpp1 as the template since the secondary structure identity between the template and Est3 was 66.7%.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "RB") (:stem . "successfully") (:form . "successfully") (:end . 23)\n  (:start . 11) (:id . 44))\n ((:tag . "VBD") (:stem . "recognize") (:form . "recognized") (:end . 34)\n  (:start . 24) (:id . 45))\n ((:tag . "NN") (:stem . "tpp1") (:form . "Tpp1") (:end . 39) (:start . 35)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 42) (:start . 40)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 48))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 55)\n  (:start . 47) (:id . 49))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 61) (:start . 56)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 75)\n  (:start . 66) (:id . 52))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 85)\n  (:start . 76) (:id . 53))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 94)\n  (:start . 86) (:id . 54))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 102)\n  (:start . 95) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 56))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 115)\n  (:start . 107) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 119) (:start . 116)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Est3") (:form . "Est3") (:end . 124) (:start . 120)\n  (:id . 59))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 128) (:start . 125)\n  (:id . 60))\n ((:tag . "CD") (:stem . "66.7") (:form . "66.7") (:end . 133) (:start . 129)\n  (:id . 61))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 134) (:start . 133)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 135) (:start . 134)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s15.132) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504871@unknown@formal@none@1@S@Our method could align together three conserved residues (i.e. Trp21/Trp98, Asp86/Asp148 and Leu155/Leu204, in Est3 versus Tpp1; green blocks in Figure 2C), which are primarily involved in protein folding and/or stability of the OB-fold.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VB") (:stem . "align") (:form . "align") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 31)\n  (:start . 23) (:id . 46))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 37) (:start . 32)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 47)\n  (:start . 38) (:id . 48))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 56)\n  (:start . 48) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 50))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 62) (:start . 58)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "Trp21/Trp98") (:form . "Trp21/Trp98") (:end . 74)\n  (:start . 63) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "NN") (:stem . "asp86/asp148") (:form . "Asp86/Asp148") (:end . 88)\n  (:start . 76) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 55))\n ((:tag . "NN") (:stem . "leu155/leu204") (:form . "Leu155/Leu204")\n  (:end . 106) (:start . 93) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 107) (:start . 106)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 110) (:start . 108)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Est3") (:form . "Est3") (:end . 115) (:start . 111)\n  (:id . 59))\n ((:tag . "CC") (:stem . "versus") (:form . "versus") (:end . 122)\n  (:start . 116) (:id . 60))\n ((:tag . "NNP") (:stem . "Tpp1") (:form . "Tpp1") (:end . 127) (:start . 123)\n  (:id . 61))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 128) (:start . 127)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 134)\n  (:start . 129) (:id . 63))\n ((:tag . "NNS") (:stem . "block") (:form . "blocks") (:end . 141)\n  (:start . 135) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 144) (:start . 142)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 151)\n  (:start . 145) (:id . 66))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 154) (:start . 152)\n  (:id . 67))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 155) (:start . 154)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 156) (:start . 155)\n  (:id . 69))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 162)\n  (:start . 157) (:id . 70))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 166) (:start . 163)\n  (:id . 71))\n ((:tag . "RB") (:stem . "primarily") (:form . "primarily") (:end . 176)\n  (:start . 167) (:id . 72))\n ((:tag . "VBN") (:stem . "involve") (:form . "involved") (:end . 185)\n  (:start . 177) (:id . 73))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 188) (:start . 186)\n  (:id . 74))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 196)\n  (:start . 189) (:id . 75))\n ((:tag . "NN") (:stem . "folding") (:form . "folding") (:end . 204)\n  (:start . 197) (:id . 76))\n ((:tag . "CC") (:stem . "and/or") (:form . "and/or") (:end . 211)\n  (:start . 205) (:id . 77))\n ((:tag . "NN") (:stem . "stability") (:form . "stability") (:end . 221)\n  (:start . 212) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 224) (:start . 222)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 228) (:start . 225)\n  (:id . 80))\n ((:tag . "NNP") (:stem . "OB-fold") (:form . "OB-fold") (:end . 236)\n  (:start . 229) (:id . 81))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 237) (:start . 236)\n  (:id . 82)))@@@1@41@((:identifiers (:sid . :s15.133) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504872@unknown@formal@none@1@S@Seven amino acid positions (yellow blocks in Figure 2C), which are structurally similar between the two protein families, were also aligned.@(((:tag . "CD") (:stem . "seven") (:form . "Seven") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "amino") (:form . "amino") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "position") (:form . "positions") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 34)\n  (:start . 28) (:id . 47))\n ((:tag . "NNS") (:stem . "block") (:form . "blocks") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "2c") (:form . "2C") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 55) (:start . 54)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 53))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 62) (:start . 57)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . "RB") (:stem . "structurally") (:form . "structurally") (:end . 79)\n  (:start . 67) (:id . 56))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 87)\n  (:start . 80) (:id . 57))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 95)\n  (:start . 88) (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 103) (:start . 100)\n  (:id . 60))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 111)\n  (:start . 104) (:id . 61))\n ((:tag . "NNS") (:stem . "family") (:form . "families") (:end . 120)\n  (:start . 112) (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 63))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 126) (:start . 122)\n  (:id . 64))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 131) (:start . 127)\n  (:id . 65))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 139)\n  (:start . 132) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 140) (:start . 139)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.134) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504873@unknown@formal@none@1@S@These 10 aligned residues, depicted in cyan, are clustered in the interior of the core of the OB-fold (Figure 2D).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "depict") (:form . "depicted") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "NN") (:stem . "cyan") (:form . "cyan") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 44) (:start . 43)\n  (:id . 50))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "cluster") (:form . "clustered") (:end . 58)\n  (:start . 49) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 61) (:start . 59)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 54))\n ((:tag . "NN") (:stem . "interior") (:form . "interior") (:end . 74)\n  (:start . 66) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 57))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 86) (:start . 82)\n  (:id . 58))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 89) (:start . 87)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "ob-fold") (:form . "OB-fold") (:end . 101)\n  (:start . 94) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 103) (:start . 102)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 109)\n  (:start . 103) (:id . 63))\n ((:tag . "NN") (:stem . "2d") (:form . "2D") (:end . 112) (:start . 110)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 114) (:start . 113)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s15.135) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504874@unknown@formal@none@1@S@Results and Discussion@(((:tag . "NNS") (:stem . "result") (:form . "Results") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 11) (:start . 8)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "Discussion") (:form . "Discussion") (:end . 22)\n  (:start . 12) (:id . 44)))@@@1@3@((:identifiers (:sid . :s15.136) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504875@unknown@formal@none@1@S@In the template-based protein structure prediction, the template selection and the target-template alignment are the two critical steps, since they will significantly affect the quality of the final model prediction.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "template-based") (:form . "template-based")\n  (:end . 21) (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 39)\n  (:start . 30) (:id . 46))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 50)\n  (:start . 40) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 51) (:start . 50)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 55) (:start . 52)\n  (:id . 49))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 64)\n  (:start . 56) (:id . 50))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 74)\n  (:start . 65) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 82) (:start . 79)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 98) (:start . 83) (:id . 54))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 108)\n  (:start . 99) (:id . 55))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 112) (:start . 109)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 57))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 120) (:start . 117)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "critical") (:form . "critical") (:end . 129)\n  (:start . 121) (:id . 59))\n ((:tag . "NNS") (:stem . "step") (:form . "steps") (:end . 135)\n  (:start . 130) (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 136) (:start . 135)\n  (:id . 61))\n ((:tag . "IN") (:stem . "since") (:form . "since") (:end . 142)\n  (:start . 137) (:id . 62))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 147) (:start . 143)\n  (:id . 63))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 152) (:start . 148)\n  (:id . 64))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 166) (:start . 153) (:id . 65))\n ((:tag . "VB") (:stem . "affect") (:form . "affect") (:end . 173)\n  (:start . 167) (:id . 66))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 177) (:start . 174)\n  (:id . 67))\n ((:tag . "NN") (:stem . "quality") (:form . "quality") (:end . 185)\n  (:start . 178) (:id . 68))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 188) (:start . 186)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 192) (:start . 189)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 198)\n  (:start . 193) (:id . 71))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 204)\n  (:start . 199) (:id . 72))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 215)\n  (:start . 205) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 216) (:start . 215)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s15.137) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504876@unknown@formal@none@1@S@The template selections and the sequence alignments of the proposed method with the S2A2 matrix were evaluated by the Lindahl benchmark [14] and ProSup benchmark [15], respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NNS") (:stem . "selection") (:form . "selections") (:end . 23)\n  (:start . 13) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 46))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 40)\n  (:start . 32) (:id . 47))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 51)\n  (:start . 41) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 54) (:start . 52)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 58) (:start . 55)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "propose") (:form . "proposed") (:end . 67)\n  (:start . 59) (:id . 51))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 74)\n  (:start . 68) (:id . 52))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 79) (:start . 75)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 54))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 88) (:start . 84)\n  (:id . 55))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 95)\n  (:start . 89) (:id . 56))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 100) (:start . 96)\n  (:id . 57))\n ((:tag . "VBN") (:stem . "evaluate") (:form . "evaluated") (:end . 110)\n  (:start . 101) (:id . 58))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 113) (:start . 111)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Lindahl") (:form . "Lindahl") (:end . 125)\n  (:start . 118) (:id . 61))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 135)\n  (:start . 126) (:id . 62))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 137) (:start . 136)\n  (:id . 63))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 139) (:start . 137)\n  (:id . 64))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 140) (:start . 139)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 144) (:start . 141)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "ProSup") (:form . "ProSup") (:end . 151)\n  (:start . 145) (:id . 67))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 161)\n  (:start . 152) (:id . 68))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 163) (:start . 162)\n  (:id . 69))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 165) (:start . 163)\n  (:id . 70))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 166) (:start . 165)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 167) (:start . 166)\n  (:id . 72))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 180)\n  (:start . 168) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 181) (:start . 180)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s15.138) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504877@unknown@formal@none@1@S@In general, it is neither straightforward nor completely fair to compare the results of different fold-recognition and alignment methods given that each employs different sequence databases for sequence profiles, structure databases for structure profiles and properties, release dates, and scoring functions.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "general") (:form . "general") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 44))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 14) (:start . 12)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 17) (:start . 15)\n  (:id . 46))\n ((:tag . "DT") (:stem . "neither") (:form . "neither") (:end . 25)\n  (:start . 18) (:id . 47))\n ((:tag . "RB") (:stem . "straightforward") (:form . "straightforward")\n  (:end . 41) (:start . 26) (:id . 48))\n ((:tag . "CC") (:stem . "nor") (:form . "nor") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "RB") (:stem . "completely") (:form . "completely") (:end . 56)\n  (:start . 46) (:id . 50))\n ((:tag . "JJ") (:stem . "fair") (:form . "fair") (:end . 61) (:start . 57)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 64) (:start . 62)\n  (:id . 52))\n ((:tag . "VB") (:stem . "compare") (:form . "compare") (:end . 72)\n  (:start . 65) (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 84)\n  (:start . 77) (:id . 55))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 87) (:start . 85)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 97)\n  (:start . 88) (:id . 57))\n ((:tag . "NN") (:stem . "fold-recognition") (:form . "fold-recognition")\n  (:end . 114) (:start . 98) (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 59))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 128)\n  (:start . 119) (:id . 60))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 136)\n  (:start . 129) (:id . 61))\n ((:tag . "VBN") (:stem . "give") (:form . "given") (:end . 142)\n  (:start . 137) (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 147) (:start . 143)\n  (:id . 63))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 152) (:start . 148)\n  (:id . 64))\n ((:tag . "VBZ") (:stem . "employ") (:form . "employs") (:end . 160)\n  (:start . 153) (:id . 65))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 170)\n  (:start . 161) (:id . 66))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 179)\n  (:start . 171) (:id . 67))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 189)\n  (:start . 180) (:id . 68))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 193) (:start . 190)\n  (:id . 69))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 202)\n  (:start . 194) (:id . 70))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 211)\n  (:start . 203) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 212) (:start . 211)\n  (:id . 72))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 222)\n  (:start . 213) (:id . 73))\n ((:tag . "NNS") (:stem . "database") (:form . "databases") (:end . 232)\n  (:start . 223) (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 236) (:start . 233)\n  (:id . 75))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 246)\n  (:start . 237) (:id . 76))\n ((:tag . "NNS") (:stem . "profile") (:form . "profiles") (:end . 255)\n  (:start . 247) (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 259) (:start . 256)\n  (:id . 78))\n ((:tag . "NNS") (:stem . "property") (:form . "properties") (:end . 270)\n  (:start . 260) (:id . 79))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 271) (:start . 270)\n  (:id . 80))\n ((:tag . "NN") (:stem . "release") (:form . "release") (:end . 279)\n  (:start . 272) (:id . 81))\n ((:tag . "NNS") (:stem . "date") (:form . "dates") (:end . 285)\n  (:start . 280) (:id . 82))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 286) (:start . 285)\n  (:id . 83))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 290) (:start . 287)\n  (:id . 84))\n ((:tag . "VBG") (:stem . "score") (:form . "scoring") (:end . 298)\n  (:start . 291) (:id . 85))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 308)\n  (:start . 299) (:id . 86))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 309) (:start . 308)\n  (:id . 87)))@@@1@46@((:identifiers (:sid . :s15.139) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504878@unknown@formal@none@1@S@Therefore, the comparisons between our methods and other published methods serve as an approximate guide.@(((:tag . "RB") (:stem . "therefore") (:form . "Therefore") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 10) (:start . 9)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "comparison") (:form . "comparisons") (:end . 26)\n  (:start . 15) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 56) (:start . 51)\n  (:id . 50))\n ((:tag . "VBN") (:stem . "publish") (:form . "published") (:end . 66)\n  (:start . 57) (:id . 51))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 74)\n  (:start . 67) (:id . 52))\n ((:tag . "VBP") (:stem . "serve") (:form . "serve") (:end . 80) (:start . 75)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 83) (:start . 81)\n  (:id . 54))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 86) (:start . 84)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "approximate") (:form . "approximate") (:end . 98)\n  (:start . 87) (:id . 56))\n ((:tag . "NN") (:stem . "guide") (:form . "guide") (:end . 104) (:start . 99)\n  (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 58)))@@@1@17@((:identifiers (:sid . :s15.140) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504879@unknown@formal@none@1@S@Here, we evaluated S2A2 matrix, PSI-BLAST and prof_sim using the same sequence database, UniRef90 [20], with the same parameters to generate a PSSM for fold recognitions (Lindahl benchmark) and sequence alignment (ProSup benchmark).@(((:tag . "RB") (:stem . "here") (:form . "Here") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 8) (:start . 6)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "evaluate") (:form . "evaluated") (:end . 18)\n  (:start . 9) (:id . 45))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 30)\n  (:start . 24) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 31) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 41)\n  (:start . 32) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "NN") (:stem . "prof_sim") (:form . "prof_sim") (:end . 54)\n  (:start . 46) (:id . 51))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 69) (:start . 65)\n  (:id . 54))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 78)\n  (:start . 70) (:id . 55))\n ((:tag . "NN") (:stem . "database") (:form . "database") (:end . 87)\n  (:start . 79) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "UniRef90") (:form . "UniRef90") (:end . 97)\n  (:start . 89) (:id . 58))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 99) (:start . 98)\n  (:id . 59))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 101) (:start . 99)\n  (:id . 60))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 62))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 108) (:start . 104)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 112) (:start . 109)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 117) (:start . 113)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "parameter") (:form . "parameters") (:end . 128)\n  (:start . 118) (:id . 66))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 131) (:start . 129)\n  (:id . 67))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 140)\n  (:start . 132) (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 142) (:start . 141)\n  (:id . 69))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 147) (:start . 143)\n  (:id . 70))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 151) (:start . 148)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 156) (:start . 152)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "recognition") (:form . "recognitions") (:end . 169)\n  (:start . 157) (:id . 73))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 171) (:start . 170)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "Lindahl") (:form . "Lindahl") (:end . 178)\n  (:start . 171) (:id . 75))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 188)\n  (:start . 179) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 189) (:start . 188)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 193) (:start . 190)\n  (:id . 78))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 202)\n  (:start . 194) (:id . 79))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 212)\n  (:start . 203) (:id . 80))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 214) (:start . 213)\n  (:id . 81))\n ((:tag . "NNP") (:stem . "ProSup") (:form . "ProSup") (:end . 220)\n  (:start . 214) (:id . 82))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 230)\n  (:start . 221) (:id . 83))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 231) (:start . 230)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s15.141) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504880@unknown@formal@none@1@S@Furthermore, (PS)2-v2 was assessed and compared with other 71 automatic servers on 154 TBM targets in CASP8.@(((:tag . "RB") (:stem . "furthermore") (:form . "Furthermore") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "assess") (:form . "assessed") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 47)\n  (:start . 39) (:id . 49))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 52) (:start . 48)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 58) (:start . 53)\n  (:id . 51))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 61) (:start . 59)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "automatic") (:form . "automatic") (:end . 71)\n  (:start . 62) (:id . 53))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 82) (:start . 80)\n  (:id . 55))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 86) (:start . 83)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "TBM") (:form . "TBM") (:end . 90) (:start . 87)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 98)\n  (:start . 91) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 101) (:start . 99)\n  (:id . 59))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 107)\n  (:start . 102) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s15.142) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504881@unknown@formal@none@1@S@Please note that (PS)2-v2 did not participate in the CASP8 experiment.@(((:tag . "NN") (:stem . "please") (:form . "Please") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "note") (:form . "note") (:end . 11) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 16) (:start . 12)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . "VBD") (:stem . "do") (:form . "did") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "VB") (:stem . "participate") (:form . "participate") (:end . 45)\n  (:start . 34) (:id . 49))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 58) (:start . 53)\n  (:id . 52))\n ((:tag . "NN") (:stem . "experiment") (:form . "experiment") (:end . 69)\n  (:start . 59) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s15.143) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504882@unknown@formal@none@1@S@Evaluation of S2A2 matrix@(((:tag . "NN") (:stem . "evaluation") (:form . "Evaluation") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 43))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 18) (:start . 14)\n  (:id . 44))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 25)\n  (:start . 19) (:id . 45)))@@@1@4@((:identifiers (:sid . :s15.144) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504883@unknown@formal@none@1@S@The S2A2 matrix (60 × 60) offers insights about substitution preferences of RS letters between homologous protein sequences (Figure 3 and Figure S1 in Additional file 2).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 17) (:start . 16)\n  (:id . 45))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 19) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 21) (:start . 20)\n  (:id . 47))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 24) (:start . 22)\n  (:id . 48))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 25) (:start . 24)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "offer") (:form . "offers") (:end . 32)\n  (:start . 26) (:id . 50))\n ((:tag . "NNS") (:stem . "insight") (:form . "insights") (:end . 41)\n  (:start . 33) (:id . 51))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 47) (:start . 42)\n  (:id . 52))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 60)\n  (:start . 48) (:id . 53))\n ((:tag . "NNS") (:stem . "preference") (:form . "preferences") (:end . 72)\n  (:start . 61) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "RS") (:form . "RS") (:end . 78) (:start . 76)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 86)\n  (:start . 79) (:id . 57))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 94)\n  (:start . 87) (:id . 58))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 105)\n  (:start . 95) (:id . 59))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 113)\n  (:start . 106) (:id . 60))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 123)\n  (:start . 114) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 131)\n  (:start . 125) (:id . 63))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 133) (:start . 132)\n  (:id . 64))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 144)\n  (:start . 138) (:id . 66))\n ((:tag . "NN") (:stem . "s1") (:form . "S1") (:end . 147) (:start . 145)\n  (:id . 67))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 150) (:start . 148)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 161)\n  (:start . 151) (:id . 69))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 166) (:start . 162)\n  (:id . 70))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 168) (:start . 167)\n  (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 169) (:start . 168)\n  (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s15.145) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504884@unknown@formal@none@1@S@The highest substitution score in this matrix is for the alignment of a RS letter 'Wß' with a RS letter 'Wß', where Wß is the residue Trp with the ß-strand structure (Figure S1 in Additional file 2).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 11) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 24)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 30) (:start . 25)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 46))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 38) (:start . 34)\n  (:id . 47))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 48) (:start . 46)\n  (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 66)\n  (:start . 57) (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 69) (:start . 67)\n  (:id . 53))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "RS") (:form . "RS") (:end . 74) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "letter") (:form . "letter") (:end . 81)\n  (:start . 75) (:id . 56))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "Wß") (:form . "Wß") (:end . 85) (:start . 83)\n  (:id . 58))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 86) (:start . 85)\n  (:id . 59))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 91) (:start . 87)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 93) (:start . 92)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "RS") (:form . "RS") (:end . 96) (:start . 94)\n  (:id . 62))\n ((:tag . "NN") (:stem . "letter") (:form . "letter") (:end . 103)\n  (:start . 97) (:id . 63))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 105) (:start . 104)\n  (:id . 64))\n ((:tag . "NNP") (:stem . "Wß") (:form . "Wß") (:end . 107) (:start . 105)\n  (:id . 65))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 108) (:start . 107)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 109) (:start . 108)\n  (:id . 67))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 115)\n  (:start . 110) (:id . 68))\n ((:tag . "NNP") (:stem . "Wß") (:form . "Wß") (:end . 118) (:start . 116)\n  (:id . 69))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 121) (:start . 119)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 71))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 133)\n  (:start . 126) (:id . 72))\n ((:tag . "NN") (:stem . "trp") (:form . "Trp") (:end . 137) (:start . 134)\n  (:id . 73))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 142) (:start . 138)\n  (:id . 74))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 146) (:start . 143)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "ß-strand") (:form . "ß-strand") (:end . 155)\n  (:start . 147) (:id . 76))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 165)\n  (:start . 156) (:id . 77))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 167) (:start . 166)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 173)\n  (:start . 167) (:id . 79))\n ((:tag . "NN") (:stem . "s1") (:form . "S1") (:end . 176) (:start . 174)\n  (:id . 80))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 179) (:start . 177)\n  (:id . 81))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 190)\n  (:start . 180) (:id . 82))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 195) (:start . 191)\n  (:id . 83))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 197) (:start . 196)\n  (:id . 84))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 198) (:start . 197)\n  (:id . 85))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 86)))@@@1@45@((:identifiers (:sid . :s15.146) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504885@unknown@formal@none@1@S@This substitution score is 6.2.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 17)\n  (:start . 5) (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 23) (:start . 18)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 26) (:start . 24)\n  (:id . 45))\n ((:tag . "CD") (:stem . "6.2") (:form . "6.2") (:end . 30) (:start . 27)\n  (:id . 46))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 31) (:start . 30)\n  (:id . 47)))@@@1@6@((:identifiers (:sid . :s15.147) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504886@unknown@formal@none@1@S@In addition, the substitution scores are also high when two identical structural letters (e.g., diagonal entries) are aligned.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 29)\n  (:start . 17) (:id . 46))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "high") (:form . "high") (:end . 50) (:start . 46)\n  (:id . 50))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "identical") (:form . "identical") (:end . 69)\n  (:start . 60) (:id . 53))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 80)\n  (:start . 70) (:id . 54))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 88)\n  (:start . 81) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 56))\n ((:tag . "FW") (:stem . "e.g.") (:form . "e.g.") (:end . 94) (:start . 90)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "diagonal") (:form . "diagonal") (:end . 104)\n  (:start . 96) (:id . 59))\n ((:tag . "NNS") (:stem . "entry") (:form . "entries") (:end . 112)\n  (:start . 105) (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 117) (:start . 114)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 125)\n  (:start . 118) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 126) (:start . 125)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s15.148) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504887@unknown@formal@none@1@S@For example, the alignment scores are 5.6 and 6.1 while 'Wα' and 'Cα' are aligned with 'Wα' and 'Cß', respectively; where Wα is the residue Trp with the α-helix structure and Cα represents the residue Cys with the α-helix structure.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 26)\n  (:start . 17) (:id . 46))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 33)\n  (:start . 27) (:id . 47))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "CD") (:stem . "5.6") (:form . "5.6") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 45) (:start . 42)\n  (:id . 50))\n ((:tag . "CD") (:stem . "6.1") (:form . "6.1") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "IN") (:stem . "while") (:form . "while") (:end . 55) (:start . 50)\n  (:id . 52))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "Wα") (:form . "Wα") (:end . 59) (:start . 57)\n  (:id . 54))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 60) (:start . 59)\n  (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 64) (:start . 61)\n  (:id . 56))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 66) (:start . 65)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "Cα") (:form . "Cα") (:end . 68) (:start . 66)\n  (:id . 58))\n ((:tag . "''") (:stem . "'") (:form . "’") (:end . 69) (:start . 68)\n  (:id . 59))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 73) (:start . 70)\n  (:id . 60))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 81)\n  (:start . 74) (:id . 61))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 86) (:start . 82)\n  (:id . 62))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 88) (:start . 87)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "Wα") (:form . "Wα") (:end . 90) (:start . 88)\n  (:id . 64))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 91) (:start . 90)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 66))\n ((:tag . "``") (:stem . "‘") (:form . "‘") (:end . 97) (:start . 96)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "Cß") (:form . "Cß") (:end . 99) (:start . 97)\n  (:id . 68))\n ((:tag . "POS") (:stem . "'") (:form . "’") (:end . 100) (:start . 99)\n  (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 70))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 114)\n  (:start . 102) (:id . 71))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 115) (:start . 114)\n  (:id . 72))\n ((:tag . "WRB") (:stem . "where") (:form . "where") (:end . 121)\n  (:start . 116) (:id . 73))\n ((:tag . "NNP") (:stem . "Wα") (:form . "Wα") (:end . 124) (:start . 122)\n  (:id . 74))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 127) (:start . 125)\n  (:id . 75))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 131) (:start . 128)\n  (:id . 76))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 139)\n  (:start . 132) (:id . 77))\n ((:tag . "NN") (:stem . "trp") (:form . "Trp") (:end . 143) (:start . 140)\n  (:id . 78))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 148) (:start . 144)\n  (:id . 79))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 80))\n ((:tag . "JJ") (:stem . "α-helix") (:form . "α-helix") (:end . 160)\n  (:start . 153) (:id . 81))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 170)\n  (:start . 161) (:id . 82))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 174) (:start . 171)\n  (:id . 83))\n ((:tag . "NN") (:stem . "cα") (:form . "Cα") (:end . 177) (:start . 175)\n  (:id . 84))\n ((:tag . "VBZ") (:stem . "represent") (:form . "represents") (:end . 188)\n  (:start . 178) (:id . 85))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 192) (:start . 189)\n  (:id . 86))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 200)\n  (:start . 193) (:id . 87))\n ((:tag . "NN") (:stem . "cys") (:form . "Cys") (:end . 204) (:start . 201)\n  (:id . 88))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 209) (:start . 205)\n  (:id . 89))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 213) (:start . 210)\n  (:id . 90))\n ((:tag . "JJ") (:stem . "α-helix") (:form . "α-helix") (:end . 221)\n  (:start . 214) (:id . 91))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 231)\n  (:start . 222) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 232) (:start . 231)\n  (:id . 93)))@@@1@52@((:identifiers (:sid . :s15.149) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504888@unknown@formal@none@1@S@Most of the substitution scores are positive if two RS letters in the same secondary structure are aligned.@(((:tag . "JJS") (:stem . "most") (:form . "Most") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 7) (:start . 5)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 24)\n  (:start . 12) (:id . 45))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 31)\n  (:start . 25) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "positive") (:form . "positive") (:end . 44)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "NN") (:stem . "rs") (:form . "RS") (:end . 54) (:start . 52)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 62)\n  (:start . 55) (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 74) (:start . 70)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 84)\n  (:start . 75) (:id . 56))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 94)\n  (:start . 85) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 98) (:start . 95)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 106)\n  (:start . 99) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 107) (:start . 106)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.150) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504889@unknown@formal@none@1@S@On the other hand, the lowest substitution score is -7.8 in this S2A2.@(((:tag . "IN") (:stem . "on") (:form . "On") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 12) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "hand") (:form . "hand") (:end . 17) (:start . 13)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "JJS") (:stem . "low") (:form . "lowest") (:end . 29) (:start . 23)\n  (:id . 48))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 42)\n  (:start . 30) (:id . 49))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 48) (:start . 43)\n  (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 51) (:start . 49)\n  (:id . 51))\n ((:tag . "CD") (:stem . "-7.8") (:form . "-7.8") (:end . 56) (:start . 52)\n  (:id . 52))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 64) (:start . 60)\n  (:id . 54))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 69) (:start . 65)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 70) (:start . 69)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s15.151) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504890@unknown@formal@none@1@S@All of the substitution scores are low when the helix RS letters are aligned with the strand RS letters.@(((:tag . "DT") (:stem . "all") (:form . "All") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 10) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 23)\n  (:start . 11) (:id . 45))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 34) (:start . 31)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "low") (:form . "low") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "helix") (:form . "helix") (:end . 53) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "rs") (:form . "RS") (:end . 56) (:start . 54)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 64)\n  (:start . 57) (:id . 53))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 68) (:start . 65)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 76)\n  (:start . 69) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 81) (:start . 77)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 85) (:start . 82)\n  (:id . 57))\n ((:tag . "NN") (:stem . "strand") (:form . "strand") (:end . 92)\n  (:start . 86) (:id . 58))\n ((:tag . "NN") (:stem . "rs") (:form . "RS") (:end . 95) (:start . 93)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 103)\n  (:start . 96) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s15.152) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504891@unknown@formal@none@1@S@The above relationships are in good agreement with biological functions of the relevant structures, showing that the matrix S2A2 embodies conventional knowledge about secondary structure conservation in proteins.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "above") (:form . "above") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "relationship") (:form . "relationships")\n  (:end . 23) (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 27) (:start . 24)\n  (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 30) (:start . 28)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "good") (:form . "good") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "agreement") (:form . "agreement") (:end . 45)\n  (:start . 36) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "biological") (:form . "biological") (:end . 61)\n  (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "function") (:form . "functions") (:end . 71)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 74) (:start . 72)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "relevant") (:form . "relevant") (:end . 87)\n  (:start . 79) (:id . 54))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 98)\n  (:start . 88) (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "show") (:form . "showing") (:end . 107)\n  (:start . 100) (:id . 57))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 112) (:start . 108)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 116) (:start . 113)\n  (:id . 59))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 123)\n  (:start . 117) (:id . 60))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 128) (:start . 124)\n  (:id . 61))\n ((:tag . "VBZ") (:stem . "embody") (:form . "embodies") (:end . 137)\n  (:start . 129) (:id . 62))\n ((:tag . "JJ") (:stem . "conventional") (:form . "conventional") (:end . 150)\n  (:start . 138) (:id . 63))\n ((:tag . "NN") (:stem . "knowledge") (:form . "knowledge") (:end . 160)\n  (:start . 151) (:id . 64))\n ((:tag . "IN") (:stem . "about") (:form . "about") (:end . 166)\n  (:start . 161) (:id . 65))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 176)\n  (:start . 167) (:id . 66))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 186)\n  (:start . 177) (:id . 67))\n ((:tag . "NN") (:stem . "conservation") (:form . "conservation") (:end . 199)\n  (:start . 187) (:id . 68))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 202) (:start . 200)\n  (:id . 69))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 211)\n  (:start . 203) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 212) (:start . 211)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s15.153) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504892@unknown@formal@none@1@S@We compared the S2A2 matrix with BLOSUM62.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "compare") (:form . "compared") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "blosum62") (:form . "BLOSUM62") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 42) (:start . 41)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s15.154) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504893@unknown@formal@none@1@S@The highest substitution scores are 6.2 (S2A2) and 11 (BLOSUM62).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 11) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "substitution") (:form . "substitution") (:end . 24)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 31)\n  (:start . 25) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "CD") (:stem . "6.2") (:form . "6.2") (:end . 39) (:start . 36)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 45) (:start . 41)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "CD") (:stem . "11") (:form . "11") (:end . 53) (:start . 51)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 55) (:start . 54)\n  (:id . 53))\n ((:tag . "NN") (:stem . "blosum62") (:form . "BLOSUM62") (:end . 63)\n  (:start . 55) (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 64) (:start . 63)\n  (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s15.155) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504894@unknown@formal@none@1@S@In contrast, the lowest score for S2A2 (-7.8) is much lower than that for BLOSUM62 (-4).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "contrast") (:form . "contrast") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "JJS") (:stem . "low") (:form . "lowest") (:end . 23) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "CD") (:stem . "-7.8") (:form . "-7.8") (:end . 44) (:start . 40)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 45) (:start . 44)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 48) (:start . 46)\n  (:id . 53))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 53) (:start . 49)\n  (:id . 54))\n ((:tag . "JJR") (:stem . "low") (:form . "lower") (:end . 59) (:start . 54)\n  (:id . 55))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 64) (:start . 60)\n  (:id . 56))\n ((:tag . "DT") (:stem . "that") (:form . "that") (:end . 69) (:start . 65)\n  (:id . 57))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 73) (:start . 70)\n  (:id . 58))\n ((:tag . "NN") (:stem . "blosum62") (:form . "BLOSUM62") (:end . 82)\n  (:start . 74) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 60))\n ((:tag . "CD") (:stem . "-4") (:form . "-4") (:end . 86) (:start . 84)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 87) (:start . 86)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 88) (:start . 87)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s15.156) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504895@unknown@formal@none@1@S@The main reasons for this large difference are that α-helices and ß-strands constitute very different protein secondary structures, and the RS letters pertaining to these two types of structure are more conserved than amino acid sequences.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "main") (:form . "main") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "reason") (:form . "reasons") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "large") (:form . "large") (:end . 31) (:start . 26)\n  (:id . 47))\n ((:tag . "NN") (:stem . "difference") (:form . "difference") (:end . 42)\n  (:start . 32) (:id . 48))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 46) (:start . 43)\n  (:id . 49))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 51) (:start . 47)\n  (:id . 50))\n ((:tag . "NNPS") (:stem . "α-helice") (:form . "α-helices") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 65) (:start . 62)\n  (:id . 52))\n ((:tag . "NNPS") (:stem . "ß-strand") (:form . "ß-strands") (:end . 75)\n  (:start . 66) (:id . 53))\n ((:tag . "VBP") (:stem . "constitute") (:form . "constitute") (:end . 86)\n  (:start . 76) (:id . 54))\n ((:tag . "RB") (:stem . "very") (:form . "very") (:end . 91) (:start . 87)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "different") (:form . "different") (:end . 101)\n  (:start . 92) (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 109)\n  (:start . 102) (:id . 57))\n ((:tag . "JJ") (:stem . "secondary") (:form . "secondary") (:end . 119)\n  (:start . 110) (:id . 58))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 130)\n  (:start . 120) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 131) (:start . 130)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 135) (:start . 132)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "RS") (:form . "RS") (:end . 142) (:start . 140)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 150)\n  (:start . 143) (:id . 64))\n ((:tag . "VBG") (:stem . "pertain") (:form . "pertaining") (:end . 161)\n  (:start . 151) (:id . 65))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 164) (:start . 162)\n  (:id . 66))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 170)\n  (:start . 165) (:id . 67))\n ((:tag . "CD") (:stem . "two") (:form . "two") (:end . 174) (:start . 171)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "type") (:form . "types") (:end . 180)\n  (:start . 175) (:id . 69))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 183) (:start . 181)\n  (:id . 70))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 193)\n  (:start . 184) (:id . 71))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 197) (:start . 194)\n  (:id . 72))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 202) (:start . 198)\n  (:id . 73))\n ((:tag . "VBN") (:stem . "conserve") (:form . "conserved") (:end . 212)\n  (:start . 203) (:id . 74))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 217) (:start . 213)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 223)\n  (:start . 218) (:id . 76))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 228) (:start . 224)\n  (:id . 77))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 238)\n  (:start . 229) (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s15.157) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504896@unknown@formal@none@1@S@These results demonstrate that the RS letters with the S2A2 matrix may be able to more accurately find remote homologous sequences than simple amino acid sequence analyses.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 13)\n  (:start . 6) (:id . 43))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 25)\n  (:start . 14) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 30) (:start . 26)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 34) (:start . 31)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "RS") (:form . "RS") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "letter") (:form . "letters") (:end . 45)\n  (:start . 38) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 50) (:start . 46)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 59) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 66)\n  (:start . 60) (:id . 52))\n ((:tag . "MD") (:stem . "may") (:form . "may") (:end . 70) (:start . 67)\n  (:id . 53))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 73) (:start . 71)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 78) (:start . 74)\n  (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 81) (:start . 79)\n  (:id . 56))\n ((:tag . "RBR") (:stem . "more") (:form . "more") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . "RB") (:stem . "accurately") (:form . "accurately") (:end . 97)\n  (:start . 87) (:id . 58))\n ((:tag . "VB") (:stem . "find") (:form . "find") (:end . 102) (:start . 98)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "remote") (:form . "remote") (:end . 109)\n  (:start . 103) (:id . 60))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 120)\n  (:start . 110) (:id . 61))\n ((:tag . "NNS") (:stem . "sequence") (:form . "sequences") (:end . 130)\n  (:start . 121) (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 135) (:start . 131)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "simple") (:form . "simple") (:end . 142)\n  (:start . 136) (:id . 64))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 148)\n  (:start . 143) (:id . 65))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 153) (:start . 149)\n  (:id . 66))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 162)\n  (:start . 154) (:id . 67))\n ((:tag . "NNS") (:stem . "analysis") (:form . "analyses") (:end . 171)\n  (:start . 163) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 172) (:start . 171)\n  (:id . 69)))@@@1@28@((:hcues ((:id . :x15.158.1) (:span 67 70)) ((:id . :x15.158.2) (:span 14 25)))\n (:hscopes ((:id . :x15.158.1) (:span 67 171))\n  ((:id . :x15.158.2) (:span 14 171)))\n (:identifiers (:sid . :s15.158) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504897@unknown@formal@none@1@S@Template selection@(((:tag . "NNP") (:stem . "Template") (:form . "Template") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 18)\n  (:start . 9) (:id . 43)))@@@1@2@((:identifiers (:sid . :s15.159) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504898@unknown@formal@none@1@S@For the template selection, our method with S2A2 matrix was compared to other methods on Lindahl benchmark [14], which consists of 976 proteins, for the fold recognition.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 16)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 26)\n  (:start . 17) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 31) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 38)\n  (:start . 32) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 43) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 48) (:start . 44)\n  (:id . 50))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 59) (:start . 56)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "compare") (:form . "compared") (:end . 68)\n  (:start . 60) (:id . 53))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 71) (:start . 69)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 77) (:start . 72)\n  (:id . 55))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 85)\n  (:start . 78) (:id . 56))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Lindahl") (:form . "Lindahl") (:end . 96)\n  (:start . 89) (:id . 58))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 106)\n  (:start . 97) (:id . 59))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 108) (:start . 107)\n  (:id . 60))\n ((:tag . "CD") (:stem . "14") (:form . "14") (:end . 110) (:start . 108)\n  (:id . 61))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 111) (:start . 110)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 112) (:start . 111)\n  (:id . 63))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 118)\n  (:start . 113) (:id . 64))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 127)\n  (:start . 119) (:id . 65))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 130) (:start . 128)\n  (:id . 66))\n ((:tag . "CD") (:stem . "976") (:form . "976") (:end . 134) (:start . 131)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "protein") (:form . "proteins") (:end . 143)\n  (:start . 135) (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 69))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 148) (:start . 145)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 152) (:start . 149)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 157) (:start . 153)\n  (:id . 72))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 169)\n  (:start . 158) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 170) (:start . 169)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s15.160) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504899@unknown@formal@none@1@S@This set included 555, 434 and 321 assignments for the family, superfamily and fold levels, respectively.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "include") (:form . "included") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "CD") (:stem . "555") (:form . "555") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "CD") (:stem . "434") (:form . "434") (:end . 26) (:start . 23)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 30) (:start . 27)\n  (:id . 48))\n ((:tag . "CD") (:stem . "321") (:form . "321") (:end . 34) (:start . 31)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 46)\n  (:start . 35) (:id . 50))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 50) (:start . 47)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "family") (:form . "family") (:end . 61)\n  (:start . 55) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 74)\n  (:start . 63) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 78) (:start . 75)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 83) (:start . 79)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 90)\n  (:start . 84) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 59))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 104)\n  (:start . 92) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s15.161) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504900@unknown@formal@none@1@S@The S2A2 matrix outperforms PSI-BLAST and is comparative to other methods on this set (Table 2).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "outperform") (:form . "outperforms") (:end . 27)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 41) (:start . 38)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "comparative") (:form . "comparative") (:end . 56)\n  (:start . 45) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 59) (:start . 57)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 65) (:start . 60)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 73)\n  (:start . 66) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 76) (:start . 74)\n  (:id . 53))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 81) (:start . 77)\n  (:id . 54))\n ((:tag . "NN") (:stem . "set") (:form . "set") (:end . 85) (:start . 82)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 87) (:start . 86)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 92) (:start . 87)\n  (:id . 57))\n ((:tag . "CD") (:stem . "2") (:form . "2") (:end . 94) (:start . 93)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 96) (:start . 95)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.162) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504901@unknown@formal@none@1@S@Our method (S2A2+PSSM), incorporating PSSM into S2A2, is the best for detecting similarity on the superfamily and fold levels for the top five ranks among the 10 comparative methods.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "S2A2+PSSM") (:form . "S2A2+PSSM") (:end . 21)\n  (:start . 12) (:id . 45))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 23) (:start . 22)\n  (:id . 47))\n ((:tag . "VBG") (:stem . "incorporate") (:form . "incorporating") (:end . 37)\n  (:start . 24) (:id . 48))\n ((:tag . "NNP") (:stem . "PSSM") (:form . "PSSM") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "S2A2") (:form . "S2A2") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 56) (:start . 54)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 54))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 65) (:start . 61)\n  (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 69) (:start . 66)\n  (:id . 56))\n ((:tag . "VBG") (:stem . "detect") (:form . "detecting") (:end . 79)\n  (:start . 70) (:id . 57))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 90)\n  (:start . 80) (:id . 58))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 93) (:start . 91)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 60))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 109)\n  (:start . 98) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 113) (:start . 110)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 118) (:start . 114)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "level") (:form . "levels") (:end . 125)\n  (:start . 119) (:id . 64))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 129) (:start . 126)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "top") (:form . "top") (:end . 137) (:start . 134)\n  (:id . 67))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 142) (:start . 138)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "rank") (:form . "ranks") (:end . 148)\n  (:start . 143) (:id . 69))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 154)\n  (:start . 149) (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 158) (:start . 155)\n  (:id . 71))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 161) (:start . 159)\n  (:id . 72))\n ((:tag . "JJ") (:stem . "comparative") (:form . "comparative") (:end . 173)\n  (:start . 162) (:id . 73))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 181)\n  (:start . 174) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s15.163) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504902@unknown@formal@none@1@S@At the superfamily level, the S2A2+PSSM, PSI-BLAST and prof_sim [36] identified 75.6%, 49.1% and 61.3% of assignments, respectively.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "NN") (:stem . "superfamily") (:form . "superfamily") (:end . 18)\n  (:start . 7) (:id . 44))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "S2A2+PSSM") (:form . "S2A2+PSSM") (:end . 39)\n  (:start . 30) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 40) (:start . 39)\n  (:id . 49))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 50)\n  (:start . 41) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "prof_sim") (:form . "prof_sim") (:end . 63)\n  (:start . 55) (:id . 52))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 65) (:start . 64)\n  (:id . 53))\n ((:tag . "CD") (:stem . "36") (:form . "36") (:end . 67) (:start . 65)\n  (:id . 54))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "VBD") (:stem . "identify") (:form . "identified") (:end . 79)\n  (:start . 69) (:id . 56))\n ((:tag . "CD") (:stem . "75.6") (:form . "75.6") (:end . 84) (:start . 80)\n  (:id . 57))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 85) (:start . 84)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 86) (:start . 85)\n  (:id . 59))\n ((:tag . "CD") (:stem . "49.1") (:form . "49.1") (:end . 91) (:start . 87)\n  (:id . 60))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 92) (:start . 91)\n  (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 96) (:start . 93)\n  (:id . 62))\n ((:tag . "CD") (:stem . "61.3") (:form . "61.3") (:end . 101) (:start . 97)\n  (:id . 63))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 102) (:start . 101)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 105) (:start . 103)\n  (:id . 65))\n ((:tag . "NNS") (:stem . "assignment") (:form . "assignments") (:end . 117)\n  (:start . 106) (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 67))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 131)\n  (:start . 119) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s15.164) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504903@unknown@formal@none@1@S@At the fold level, the S2A2+PSSM (54.5%) outperformed PSI-BLAST (14.6%) and prof_sim (39.6%) in identifying homologous pairs.@(((:tag . "IN") (:stem . "at") (:form . "At") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "level") (:form . "level") (:end . 17) (:start . 12)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 22) (:start . 19)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "S2A2+PSSM") (:form . "S2A2+PSSM") (:end . 32)\n  (:start . 23) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 34) (:start . 33)\n  (:id . 49))\n ((:tag . "CD") (:stem . "54.5") (:form . "54.5") (:end . 38) (:start . 34)\n  (:id . 50))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 39) (:start . 38)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 40) (:start . 39)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "outperformed") (:form . "outperformed") (:end . 53)\n  (:start . 41) (:id . 53))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 63)\n  (:start . 54) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 65) (:start . 64)\n  (:id . 55))\n ((:tag . "CD") (:stem . "14.6") (:form . "14.6") (:end . 69) (:start . 65)\n  (:id . 56))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 70) (:start . 69)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 71) (:start . 70)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 75) (:start . 72)\n  (:id . 59))\n ((:tag . "NN") (:stem . "prof_sim") (:form . "prof_sim") (:end . 84)\n  (:start . 76) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 86) (:start . 85)\n  (:id . 61))\n ((:tag . "CD") (:stem . "39.6") (:form . "39.6") (:end . 90) (:start . 86)\n  (:id . 62))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 91) (:start . 90)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 92) (:start . 91)\n  (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 95) (:start . 93)\n  (:id . 65))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 107)\n  (:start . 96) (:id . 66))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 118)\n  (:start . 108) (:id . 67))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 124)\n  (:start . 119) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 125) (:start . 124)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s15.165) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504904@unknown@formal@none@1@S@Comparing S2A2 matrix with other methods for fold recognition on the Lindahl benchmark@(((:tag . "VBG") (:stem . "compare") (:form . "Comparing") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "fold") (:form . "fold") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "NN") (:stem . "recognition") (:form . "recognition") (:end . 61)\n  (:start . 50) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 64) (:start . 62)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Lindahl") (:form . "Lindahl") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 86)\n  (:start . 77) (:id . 54)))@@@1@13@((:identifiers (:sid . :s15.166) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504905@unknown@formal@none@1@S@Target-template alignment@(((:tag . "JJ") (:stem . "target-template") (:form . "Target-template")\n  (:end . 15) (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 25)\n  (:start . 16) (:id . 43)))@@@1@2@((:identifiers (:sid . :s15.167) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504906@unknown@formal@none@1@S@For the alignment between the target and the template, our algorithm was evaluated based on the ProSup benchmark [15], which consists of 127 protein pairs with significant structural similarity but with sequence identity of no more than 30%.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 25)\n  (:start . 18) (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 36)\n  (:start . 30) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 53)\n  (:start . 45) (:id . 50))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 54) (:start . 53)\n  (:id . 51))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 58) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "algorithm") (:form . "algorithm") (:end . 68)\n  (:start . 59) (:id . 53))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 72) (:start . 69)\n  (:id . 54))\n ((:tag . "VBN") (:stem . "evaluate") (:form . "evaluated") (:end . 82)\n  (:start . 73) (:id . 55))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 88) (:start . 83)\n  (:id . 56))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 91) (:start . 89)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 95) (:start . 92)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "ProSup") (:form . "ProSup") (:end . 102)\n  (:start . 96) (:id . 59))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 112)\n  (:start . 103) (:id . 60))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 114) (:start . 113)\n  (:id . 61))\n ((:tag . "CD") (:stem . "15") (:form . "15") (:end . 116) (:start . 114)\n  (:id . 62))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 117) (:start . 116)\n  (:id . 63))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 118) (:start . 117)\n  (:id . 64))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 124)\n  (:start . 119) (:id . 65))\n ((:tag . "VBZ") (:stem . "consist") (:form . "consists") (:end . 133)\n  (:start . 125) (:id . 66))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 67))\n ((:tag . "CD") (:stem . "127") (:form . "127") (:end . 140) (:start . 137)\n  (:id . 68))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 148)\n  (:start . 141) (:id . 69))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 154)\n  (:start . 149) (:id . 70))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 159) (:start . 155)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "significant") (:form . "significant") (:end . 171)\n  (:start . 160) (:id . 72))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 182)\n  (:start . 172) (:id . 73))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 193)\n  (:start . 183) (:id . 74))\n ((:tag . "CC") (:stem . "but") (:form . "but") (:end . 197) (:start . 194)\n  (:id . 75))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 202) (:start . 198)\n  (:id . 76))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 211)\n  (:start . 203) (:id . 77))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 220)\n  (:start . 212) (:id . 78))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 223) (:start . 221)\n  (:id . 79))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 226) (:start . 224)\n  (:id . 80))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 231) (:start . 227)\n  (:id . 81))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 236) (:start . 232)\n  (:id . 82))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 239) (:start . 237)\n  (:id . 83))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 240) (:start . 239)\n  (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 241) (:start . 240)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s15.168) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504907@unknown@formal@none@1@S@The total numbers of correctly aligned residue pairs (Tc) of the S2A2, S2A2+PSSM, prof_sim and SSALN [10] were 8732, 9470, 8009 and 9256 pairs, respectively (Table 3).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "number") (:form . "numbers") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 20) (:start . 18)\n  (:id . 45))\n ((:tag . "RB") (:stem . "correctly") (:form . "correctly") (:end . 30)\n  (:start . 21) (:id . 46))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 46)\n  (:start . 39) (:id . 48))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 52) (:start . 47)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "Tc") (:form . "Tc") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 52))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 60) (:start . 58)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 64) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 69) (:start . 65)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 70) (:start . 69)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "S2A2+PSSM") (:form . "S2A2+PSSM") (:end . 80)\n  (:start . 71) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 81) (:start . 80)\n  (:id . 58))\n ((:tag . "NN") (:stem . "prof_sim") (:form . "prof_sim") (:end . 90)\n  (:start . 82) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "SSALN") (:form . "SSALN") (:end . 100)\n  (:start . 95) (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 102) (:start . 101)\n  (:id . 62))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 104) (:start . 102)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 105) (:start . 104)\n  (:id . 64))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 110) (:start . 106)\n  (:id . 65))\n ((:tag . "CD") (:stem . "8732") (:form . "8732") (:end . 115) (:start . 111)\n  (:id . 66))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 67))\n ((:tag . "CD") (:stem . "9470") (:form . "9470") (:end . 121) (:start . 117)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 122) (:start . 121)\n  (:id . 69))\n ((:tag . "CD") (:stem . "8009") (:form . "8009") (:end . 127) (:start . 123)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 131) (:start . 128)\n  (:id . 71))\n ((:tag . "CD") (:stem . "9256") (:form . "9256") (:end . 136) (:start . 132)\n  (:id . 72))\n ((:tag . "NNS") (:stem . "pair") (:form . "pairs") (:end . 142)\n  (:start . 137) (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 143) (:start . 142)\n  (:id . 74))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 156)\n  (:start . 144) (:id . 75))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 158) (:start . 157)\n  (:id . 76))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 163)\n  (:start . 158) (:id . 77))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 165) (:start . 164)\n  (:id . 78))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n  (:id . 79))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 80)))@@@1@39@((:identifiers (:sid . :s15.169) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504908@unknown@formal@none@1@S@The percentage σ0 (average percentage of correctly aligned residues, divided by the length of the structural alignment per protein pair) of the S2A2, S2A2+PSSM, PSI-BLAST, prof_sim and SSALN were 53.4%, 58.7%, 36.4%, 43.6% and 58.3%, respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "CD") (:stem . "σ0") (:form . "σ0") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 19) (:start . 18)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 26)\n  (:start . 19) (:id . 46))\n ((:tag . "NN") (:stem . "percentage") (:form . "percentage") (:end . 37)\n  (:start . 27) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 48))\n ((:tag . "RB") (:stem . "correctly") (:form . "correctly") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "VBN") (:stem . "align") (:form . "aligned") (:end . 58)\n  (:start . 51) (:id . 50))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 67)\n  (:start . 59) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 52))\n ((:tag . "VBN") (:stem . "divide") (:form . "divided") (:end . 76)\n  (:start . 69) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 79) (:start . 77)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "length") (:form . "length") (:end . 90)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 93) (:start . 91)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 108)\n  (:start . 98) (:id . 59))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 118)\n  (:start . 109) (:id . 60))\n ((:tag . "IN") (:stem . "per") (:form . "per") (:end . 122) (:start . 119)\n  (:id . 61))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 130)\n  (:start . 123) (:id . 62))\n ((:tag . "NN") (:stem . "pair") (:form . "pair") (:end . 135) (:start . 131)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 136) (:start . 135)\n  (:id . 64))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 139) (:start . 137)\n  (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 143) (:start . 140)\n  (:id . 66))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 148) (:start . 144)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 149) (:start . 148)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "S2A2+PSSM") (:form . "S2A2+PSSM") (:end . 159)\n  (:start . 150) (:id . 69))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 160) (:start . 159)\n  (:id . 70))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 170)\n  (:start . 161) (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 171) (:start . 170)\n  (:id . 72))\n ((:tag . "NN") (:stem . "prof_sim") (:form . "prof_sim") (:end . 180)\n  (:start . 172) (:id . 73))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 184) (:start . 181)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "SSALN") (:form . "SSALN") (:end . 190)\n  (:start . 185) (:id . 75))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 195) (:start . 191)\n  (:id . 76))\n ((:tag . "CD") (:stem . "53.4") (:form . "53.4") (:end . 200) (:start . 196)\n  (:id . 77))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 201) (:start . 200)\n  (:id . 78))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 202) (:start . 201)\n  (:id . 79))\n ((:tag . "CD") (:stem . "58.7") (:form . "58.7") (:end . 207) (:start . 203)\n  (:id . 80))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 208) (:start . 207)\n  (:id . 81))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 209) (:start . 208)\n  (:id . 82))\n ((:tag . "CD") (:stem . "36.4") (:form . "36.4") (:end . 214) (:start . 210)\n  (:id . 83))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 215) (:start . 214)\n  (:id . 84))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 216) (:start . 215)\n  (:id . 85))\n ((:tag . "CD") (:stem . "43.6") (:form . "43.6") (:end . 221) (:start . 217)\n  (:id . 86))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 222) (:start . 221)\n  (:id . 87))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 226) (:start . 223)\n  (:id . 88))\n ((:tag . "CD") (:stem . "58.3") (:form . "58.3") (:end . 231) (:start . 227)\n  (:id . 89))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 232) (:start . 231)\n  (:id . 90))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 233) (:start . 232)\n  (:id . 91))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 246)\n  (:start . 234) (:id . 92))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 247) (:start . 246)\n  (:id . 93)))@@@1@52@((:identifiers (:sid . :s15.170) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504909@unknown@formal@none@1@S@The S2A2 matrix is significantly better than those of sequence-based approaches, including FASTA, PSI-BLAST and prof_sim.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 32) (:start . 19) (:id . 46))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 39) (:start . 33)\n  (:id . 47))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 44) (:start . 40)\n  (:id . 48))\n ((:tag . "DT") (:stem . "those") (:form . "those") (:end . 50) (:start . 45)\n  (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "sequence-based") (:form . "sequence-based")\n  (:end . 68) (:start . 54) (:id . 51))\n ((:tag . "NNS") (:stem . "approach") (:form . "approaches") (:end . 79)\n  (:start . 69) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 80) (:start . 79)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "include") (:form . "including") (:end . 90)\n  (:start . 81) (:id . 54))\n ((:tag . "NNP") (:stem . "FASTA") (:form . "FASTA") (:end . 96) (:start . 91)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 56))\n ((:tag . "NN") (:stem . "psi-blast") (:form . "PSI-BLAST") (:end . 107)\n  (:start . 98) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 58))\n ((:tag . "NN") (:stem . "prof_sim") (:form . "prof_sim") (:end . 120)\n  (:start . 112) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 121) (:start . 120)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.171) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504910@unknown@formal@none@1@S@The S2A2+PSSM achieved the highest alignment accuracy with slightly better than SPARKS [9] and SSALN, and much better than the other comparative methods.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "S2A2+PSSM") (:form . "S2A2+PSSM") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "VBD") (:stem . "achieve") (:form . "achieved") (:end . 22)\n  (:start . 14) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 45))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 44)\n  (:start . 35) (:id . 47))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 53)\n  (:start . 45) (:id . 48))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 58) (:start . 54)\n  (:id . 49))\n ((:tag . "RB") (:stem . "slightly") (:form . "slightly") (:end . 67)\n  (:start . 59) (:id . 50))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 74) (:start . 68)\n  (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 79) (:start . 75)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "SPARKS") (:form . "SPARKS") (:end . 86)\n  (:start . 80) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 88) (:start . 87)\n  (:id . 54))\n ((:tag . "CD") (:stem . "9") (:form . "9") (:end . 89) (:start . 88)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 90) (:start . 89)\n  (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 94) (:start . 91)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "SSALN") (:form . "SSALN") (:end . 100)\n  (:start . 95) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 101) (:start . 100)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 110) (:start . 106)\n  (:id . 61))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 117)\n  (:start . 111) (:id . 62))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 122) (:start . 118)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 126) (:start . 123)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 132)\n  (:start . 127) (:id . 65))\n ((:tag . "JJ") (:stem . "comparative") (:form . "comparative") (:end . 144)\n  (:start . 133) (:id . 66))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 152)\n  (:start . 145) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s15.172) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504911@unknown@formal@none@1@S@Comparing S2A2 matrix with other methods for sequence alignment accuracies on the ProSup benchmark@(((:tag . "VBG") (:stem . "compare") (:form . "Comparing") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 14) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 26) (:start . 22)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 32) (:start . 27)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 40)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 53)\n  (:start . 45) (:id . 49))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 63)\n  (:start . 54) (:id . 50))\n ((:tag . "NNS") (:stem . "accuracy") (:form . "accuracies") (:end . 74)\n  (:start . 64) (:id . 51))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 77) (:start . 75)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "ProSup") (:form . "ProSup") (:end . 88)\n  (:start . 82) (:id . 54))\n ((:tag . "NN") (:stem . "benchmark") (:form . "benchmark") (:end . 98)\n  (:start . 89) (:id . 55)))@@@1@14@((:identifiers (:sid . :s15.173) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504912@unknown@formal@none@1@S@CASP8 structure prediction@(((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 15)\n  (:start . 6) (:id . 43))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 26)\n  (:start . 16) (:id . 44)))@@@1@3@((:identifiers (:sid . :s15.174) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504913@unknown@formal@none@1@S@Our previous server ((PS)2-CASP8) and other 70 servers participated in the CASP8 competition, involving 121 targets for tertiary structure prediction.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 19)\n  (:start . 13) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 21) (:start . 20)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 22) (:start . 21)\n  (:id . 46))\n ((:tag . "NN") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 32)\n  (:start . 22) (:id . 47))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 33) (:start . 32)\n  (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 37) (:start . 34)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 43) (:start . 38)\n  (:id . 50))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 46) (:start . 44)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 54)\n  (:start . 47) (:id . 52))\n ((:tag . "VBD") (:stem . "participate") (:form . "participated") (:end . 67)\n  (:start . 55) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 70) (:start . 68)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . "NN") (:stem . "competition") (:form . "competition") (:end . 92)\n  (:start . 81) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "involve") (:form . "involving") (:end . 103)\n  (:start . 94) (:id . 59))\n ((:tag . "CD") (:stem . "121") (:form . "121") (:end . 107) (:start . 104)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 115)\n  (:start . 108) (:id . 61))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 119) (:start . 116)\n  (:id . 62))\n ((:tag . "JJ") (:stem . "tertiary") (:form . "tertiary") (:end . 128)\n  (:start . 120) (:id . 63))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 138)\n  (:start . 129) (:id . 64))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 149)\n  (:start . 139) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s15.175) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504914@unknown@formal@none@1@S@These 121 targets are officially classified into 154 TBM domains (Table S1 in Additional file 3).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "121") (:form . "121") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 17)\n  (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "RB") (:stem . "officially") (:form . "officially") (:end . 32)\n  (:start . 22) (:id . 46))\n ((:tag . "VBN") (:stem . "classify") (:form . "classified") (:end . 43)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "into") (:form . "into") (:end . 48) (:start . 44)\n  (:id . 48))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 52) (:start . 49)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "TBM") (:form . "TBM") (:end . 56) (:start . 53)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 64)\n  (:start . 57) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 71) (:start . 66)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 77) (:start . 75)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 88)\n  (:start . 78) (:id . 56))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 93) (:start . 89)\n  (:id . 57))\n ((:tag . "CD") (:stem . "3") (:form . "3") (:end . 95) (:start . 94)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.176) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504915@unknown@formal@none@1@S@The accuracies of these 71 servers were evaluated based on the GDT_TS [37] scores directly summarized from the CASP8 website http://predictioncenter.org/casp8/.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "accuracy") (:form . "accuracies") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 23) (:start . 18)\n  (:id . 45))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 34)\n  (:start . 27) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 39) (:start . 35)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "evaluate") (:form . "evaluated") (:end . 49)\n  (:start . 40) (:id . 49))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 55) (:start . 50)\n  (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 58) (:start . 56)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 69)\n  (:start . 63) (:id . 53))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 71) (:start . 70)\n  (:id . 54))\n ((:tag . "CD") (:stem . "37") (:form . "37") (:end . 73) (:start . 71)\n  (:id . 55))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 74) (:start . 73)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 81)\n  (:start . 75) (:id . 57))\n ((:tag . "RB") (:stem . "directly") (:form . "directly") (:end . 90)\n  (:start . 82) (:id . 58))\n ((:tag . "VBN") (:stem . "summarize") (:form . "summarized") (:end . 101)\n  (:start . 91) (:id . 59))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 106) (:start . 102)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 110) (:start . 107)\n  (:id . 61))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 116)\n  (:start . 111) (:id . 62))\n ((:tag . "NN") (:stem . "website") (:form . "website") (:end . 124)\n  (:start . 117) (:id . 63))\n ((:tag . "NN") (:stem . "http://predictioncenter.org/casp8/")\n  (:form . "http://predictioncenter.org/casp8/") (:end . 159) (:start . 125)\n  (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s15.177) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504916@unknown@formal@none@1@S@(PS)2-v2, (PS)2-original and (PS)2-CASP8 servers were evaluated on these 154 TBM targets (Figure 4, Table 4 and Table S2 in Additional file 4).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 11) (:start . 10)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 24) (:start . 11) (:id . 46))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 28) (:start . 25)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 30) (:start . 29)\n  (:id . 48))\n ((:tag . "NN") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 40)\n  (:start . 30) (:id . 49))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "evaluate") (:form . "evaluated") (:end . 63)\n  (:start . 54) (:id . 52))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 66) (:start . 64)\n  (:id . 53))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 72) (:start . 67)\n  (:id . 54))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "TBM") (:form . "TBM") (:end . 80) (:start . 77)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 88)\n  (:start . 81) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 96)\n  (:start . 90) (:id . 59))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 98) (:start . 97)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 61))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 105)\n  (:start . 100) (:id . 62))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 107) (:start . 106)\n  (:id . 63))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 117)\n  (:start . 112) (:id . 65))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 120) (:start . 118)\n  (:id . 66))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 123) (:start . 121)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 134)\n  (:start . 124) (:id . 68))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 139) (:start . 135)\n  (:id . 69))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 141) (:start . 140)\n  (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 142) (:start . 141)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 143) (:start . 142)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s15.178) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504917@unknown@formal@none@1@S@The sum of GDT_TS scores were 10331.4 ((PS)2-v2), 9954.4 ((PS)2-CASP8) and 9447.5 ((PS)2-original), respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "sum") (:form . "sum") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 10) (:start . 8)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 17)\n  (:start . 11) (:id . 45))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 24)\n  (:start . 18) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "CD") (:stem . "10331.4") (:form . "10331.4") (:end . 37)\n  (:start . 30) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 40) (:start . 39)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 47)\n  (:start . 40) (:id . 51))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 49) (:start . 48)\n  (:id . 53))\n ((:tag . "CD") (:stem . "9954.4") (:form . "9954.4") (:end . 56)\n  (:start . 50) (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 59) (:start . 58)\n  (:id . 56))\n ((:tag . "NN") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 69)\n  (:start . 59) (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 70) (:start . 69)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 59))\n ((:tag . "CD") (:stem . "9447.5") (:form . "9447.5") (:end . 81)\n  (:start . 75) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 84) (:start . 83)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 97) (:start . 84) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 98) (:start . 97)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 99) (:start . 98)\n  (:id . 65))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 112)\n  (:start . 100) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.179) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504918@unknown@formal@none@1@S@(PS)2-v2 yielded 99 and 34 higher GDT_TS scores than (PS)2-original and (PS)2-CASP8, respectively, among 154 targets.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . "VBD") (:stem . "yield") (:form . "yielded") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "CD") (:stem . "99") (:form . "99") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 26) (:start . 24)\n  (:id . 47))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 33) (:start . 27)\n  (:id . 48))\n ((:tag . "NN") (:stem . "gdt_ts") (:form . "GDT_TS") (:end . 40)\n  (:start . 34) (:id . 49))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 47)\n  (:start . 41) (:id . 50))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 52) (:start . 48)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 67) (:start . 54) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 83)\n  (:start . 73) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 84) (:start . 83)\n  (:id . 57))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 97)\n  (:start . 85) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 98) (:start . 97)\n  (:id . 59))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 104) (:start . 99)\n  (:id . 60))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 116)\n  (:start . 109) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s15.180) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504919@unknown@formal@none@1@S@When the sequence identity between the target and template was more than 30%, these three servers achieved similar GDT_TS scores.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 34)\n  (:start . 27) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 47))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 45)\n  (:start . 39) (:id . 48))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 49))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 58)\n  (:start . 50) (:id . 50))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 62) (:start . 59)\n  (:id . 51))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 67) (:start . 63)\n  (:id . 52))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 72) (:start . 68)\n  (:id . 53))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 75) (:start . 73)\n  (:id . 54))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 76) (:start . 75)\n  (:id . 55))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 77) (:start . 76)\n  (:id . 56))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 83) (:start . 78)\n  (:id . 57))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 89) (:start . 84)\n  (:id . 58))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 97)\n  (:start . 90) (:id . 59))\n ((:tag . "VBD") (:stem . "achieve") (:form . "achieved") (:end . 106)\n  (:start . 98) (:id . 60))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 114)\n  (:start . 107) (:id . 61))\n ((:tag . "NN") (:stem . "gdt_ts") (:form . "GDT_TS") (:end . 121)\n  (:start . 115) (:id . 62))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 128)\n  (:start . 122) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s15.181) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504920@unknown@formal@none@1@S@However, if the sequence identity was less than 20%, the (PS)2-v2 server was significantly better than (PS)2-original server (p-value is 4.0E-7) and (PS)2-CASP8 (p-value is 6.6E-4) using the paired Student's t-test (Table 4).@(((:tag . "RB") (:stem . "however") (:form . "However") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 8) (:start . 7) (:id . 43))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 11) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 45))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 24)\n  (:start . 16) (:id . 46))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 33)\n  (:start . 25) (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 37) (:start . 34)\n  (:id . 48))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 50) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 51) (:start . 50)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 56) (:start . 53)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 58) (:start . 57)\n  (:id . 55))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 65)\n  (:start . 58) (:id . 56))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 72)\n  (:start . 66) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 76) (:start . 73)\n  (:id . 58))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 90) (:start . 77) (:id . 59))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 97) (:start . 91)\n  (:id . 60))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 102) (:start . 98)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 117) (:start . 104) (:id . 63))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 124)\n  (:start . 118) (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 126) (:start . 125)\n  (:id . 65))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 133)\n  (:start . 126) (:id . 66))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 136) (:start . 134)\n  (:id . 67))\n ((:tag . "NN") (:stem . "4.0e-7") (:form . "4.0E-7") (:end . 143)\n  (:start . 137) (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 144) (:start . 143)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n  (:id . 70))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 71))\n ((:tag . "NNP") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 160)\n  (:start . 150) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 162) (:start . 161)\n  (:id . 73))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 169)\n  (:start . 162) (:id . 74))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 172) (:start . 170)\n  (:id . 75))\n ((:tag . "NN") (:stem . "6.6e-4") (:form . "6.6E-4") (:end . 179)\n  (:start . 173) (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 180) (:start . 179)\n  (:id . 77))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 186) (:start . 181)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 190) (:start . 187)\n  (:id . 79))\n ((:tag . "JJ") (:stem . "paired") (:form . "paired") (:end . 197)\n  (:start . 191) (:id . 80))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 205)\n  (:start . 198) (:id . 81))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 207) (:start . 205)\n  (:id . 82))\n ((:tag . "NN") (:stem . "t-test") (:form . "t-test") (:end . 214)\n  (:start . 208) (:id . 83))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 216) (:start . 215)\n  (:id . 84))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 221)\n  (:start . 216) (:id . 85))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 223) (:start . 222)\n  (:id . 86))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 224) (:start . 223)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 225) (:start . 224)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s15.182) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504921@unknown@formal@none@1@S@For each target in CASP8, Table S2 (in Additional file 4) shows the GDT_TS score improvement with contributing components (i.e. multiple templates, multiple models, and template search method) between the (PS)2-v2 and our previous servers.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 25) (:start . 24)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 31) (:start . 26)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "S2") (:form . "S2") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 50))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 38) (:start . 36)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 49)\n  (:start . 39) (:id . 52))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 54) (:start . 50)\n  (:id . 53))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 56) (:start . 55)\n  (:id . 54))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 57) (:start . 56)\n  (:id . 55))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 63) (:start . 58)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 67) (:start . 64)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 74)\n  (:start . 68) (:id . 58))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 80) (:start . 75)\n  (:id . 59))\n ((:tag . "NN") (:stem . "improvement") (:form . "improvement") (:end . 92)\n  (:start . 81) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 97) (:start . 93)\n  (:id . 61))\n ((:tag . "VBG") (:stem . "contribute") (:form . "contributing") (:end . 110)\n  (:start . 98) (:id . 62))\n ((:tag . "NNS") (:stem . "component") (:form . "components") (:end . 121)\n  (:start . 111) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 123) (:start . 122)\n  (:id . 64))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 127) (:start . 123)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 136)\n  (:start . 128) (:id . 66))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 146)\n  (:start . 137) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 156)\n  (:start . 148) (:id . 69))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 163)\n  (:start . 157) (:id . 70))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 164) (:start . 163)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 168) (:start . 165)\n  (:id . 72))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 177)\n  (:start . 169) (:id . 73))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 184)\n  (:start . 178) (:id . 74))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 191)\n  (:start . 185) (:id . 75))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 192) (:start . 191)\n  (:id . 76))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 200)\n  (:start . 193) (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 204) (:start . 201)\n  (:id . 78))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 206) (:start . 205)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 213)\n  (:start . 206) (:id . 80))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 217) (:start . 214)\n  (:id . 81))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 221) (:start . 218)\n  (:id . 82))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 230)\n  (:start . 222) (:id . 83))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 238)\n  (:start . 231) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s15.183) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504922@unknown@formal@none@1@S@Comparison the (PS)2-v2 server with (A) (PS)2-original and (B) (PS)2-CASP8 servers on the 154 TBM targets in CASP8.@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "A") (:form . "A") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 39) (:start . 38)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 41) (:start . 40)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 54) (:start . 41) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 58) (:start . 55)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 60) (:start . 59)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 61) (:start . 60)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 62) (:start . 61)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 64) (:start . 63)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 74)\n  (:start . 64) (:id . 58))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 82)\n  (:start . 75) (:id . 59))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 85) (:start . 83)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 89) (:start . 86)\n  (:id . 61))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 93) (:start . 90)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "TBM") (:form . "TBM") (:end . 97) (:start . 94)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 105)\n  (:start . 98) (:id . 64))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 108) (:start . 106)\n  (:id . 65))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 114)\n  (:start . 109) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.184) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504923@unknown@formal@none@1@S@(PS)2-v2 yields 99 and 34 higher GDT_TS scores than (PS)2-original and (PS)2-CASP8, respectively, among these 154 targets.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . "NNS") (:stem . "yield") (:form . "yields") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "CD") (:stem . "99") (:form . "99") (:end . 18) (:start . 16)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "CD") (:stem . "34") (:form . "34") (:end . 25) (:start . 23)\n  (:id . 47))\n ((:tag . "JJR") (:stem . "high") (:form . "higher") (:end . 32) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "gdt_ts") (:form . "GDT_TS") (:end . 39)\n  (:start . 33) (:id . 49))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 46)\n  (:start . 40) (:id . 50))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 51) (:start . 47)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 53) (:start . 52)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 66) (:start . 53) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 72) (:start . 71)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 82)\n  (:start . 72) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 57))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 96)\n  (:start . 84) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 59))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 103) (:start . 98)\n  (:id . 60))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 109)\n  (:start . 104) (:id . 61))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 113) (:start . 110)\n  (:id . 62))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 121)\n  (:start . 114) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 122) (:start . 121)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s15.185) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504924@unknown@formal@none@1@S@These three servers have the similar GDT_TS scores when the sequence identity (SI) between the target and template is more than 30% (blue +).@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "three") (:form . "three") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 28) (:start . 25)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 43)\n  (:start . 37) (:id . 48))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 50)\n  (:start . 44) (:id . 49))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 55) (:start . 51)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 59) (:start . 56)\n  (:id . 51))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 68)\n  (:start . 60) (:id . 52))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 77)\n  (:start . 69) (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 79) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "SI") (:form . "SI") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 82) (:start . 81)\n  (:id . 56))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 90)\n  (:start . 83) (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 58))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 101)\n  (:start . 95) (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 114)\n  (:start . 106) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 117) (:start . 115)\n  (:id . 62))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 122) (:start . 118)\n  (:id . 63))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 127) (:start . 123)\n  (:id . 64))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 130) (:start . 128)\n  (:id . 65))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 131) (:start . 130)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 67))\n ((:tag . "JJ") (:stem . "blue") (:form . "blue") (:end . 137) (:start . 133)\n  (:id . 68))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 139) (:start . 138)\n  (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 140) (:start . 139)\n  (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 141) (:start . 140)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s15.186) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504925@unknown@formal@none@1@S@(PS)2-v2 outperforms our previous servers when SI is less than 20% (green ×).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . "VBZ") (:stem . "outperform") (:form . "outperforms") (:end . 20)\n  (:start . 9) (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 24) (:start . 21)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "previous") (:form . "previous") (:end . 33)\n  (:start . 25) (:id . 46))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 41)\n  (:start . 34) (:id . 47))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 46) (:start . 42)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "SI") (:form . "SI") (:end . 49) (:start . 47)\n  (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n  (:id . 50))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 57) (:start . 53)\n  (:id . 51))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 62) (:start . 58)\n  (:id . 52))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 65) (:start . 63)\n  (:id . 53))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 73) (:start . 68)\n  (:id . 56))\n ((:tag . "NN") (:stem . "×") (:form . "×") (:end . 75) (:start . 74)\n  (:id . 57))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n  (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 77) (:start . 76)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s15.187) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504926@unknown@formal@none@1@S@Comparison the (PS)2-v2 server with (PS)2-original and (PS)2-CASP8 servers on the 154 TBM targets in CASP8 based on GDT_TS scores@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 50) (:start . 37) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 66)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 74)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 85) (:start . 82)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "TBM") (:form . "TBM") (:end . 89) (:start . 86)\n  (:id . 57))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 97)\n  (:start . 90) (:id . 58))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 100) (:start . 98)\n  (:id . 59))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 106)\n  (:start . 101) (:id . 60))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 112)\n  (:start . 107) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 115) (:start . 113)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 122)\n  (:start . 116) (:id . 63))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 129)\n  (:start . 123) (:id . 64)))@@@1@23@((:identifiers (:sid . :s15.188) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504927@unknown@formal@none@1@S@These 154 TBM targets were also used to evaluate the automatic servers participating in CASP8.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NNP") (:stem . "TBM") (:form . "TBM") (:end . 13) (:start . 10)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 21)\n  (:start . 14) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 26) (:start . 22)\n  (:id . 46))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 36) (:start . 32)\n  (:id . 48))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "automatic") (:form . "automatic") (:end . 62)\n  (:start . 53) (:id . 52))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 70)\n  (:start . 63) (:id . 53))\n ((:tag . "VBG") (:stem . "participate") (:form . "participating") (:end . 84)\n  (:start . 71) (:id . 54))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 55))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 93) (:start . 88)\n  (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s15.189) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504928@unknown@formal@none@1@S@For the templates selection, the accuracy of identifying the best template of the target protein was used to evaluate the performance of these servers (Figure S2 in Additional file 5).@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 17)\n  (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 32) (:start . 29)\n  (:id . 47))\n ((:tag . "NN") (:stem . "accuracy") (:form . "accuracy") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 56)\n  (:start . 45) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 60) (:start . 57)\n  (:id . 51))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 65) (:start . 61)\n  (:id . 52))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 74)\n  (:start . 66) (:id . 53))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 88)\n  (:start . 82) (:id . 56))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 96)\n  (:start . 89) (:id . 57))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 100) (:start . 97)\n  (:id . 58))\n ((:tag . "VBN") (:stem . "use") (:form . "used") (:end . 105) (:start . 101)\n  (:id . 59))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 108) (:start . 106)\n  (:id . 60))\n ((:tag . "VB") (:stem . "evaluate") (:form . "evaluate") (:end . 117)\n  (:start . 109) (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 133)\n  (:start . 122) (:id . 63))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 136) (:start . 134)\n  (:id . 64))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 142)\n  (:start . 137) (:id . 65))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 150)\n  (:start . 143) (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 152) (:start . 151)\n  (:id . 67))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 158)\n  (:start . 152) (:id . 68))\n ((:tag . "NN") (:stem . "s2") (:form . "S2") (:end . 161) (:start . 159)\n  (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 164) (:start . 162)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 175)\n  (:start . 165) (:id . 71))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 180) (:start . 176)\n  (:id . 72))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 182) (:start . 181)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 183) (:start . 182)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 184) (:start . 183)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s15.190) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504929@unknown@formal@none@1@S@The accuracies of the (PS)2-v2 server were 54.1% and 75.0% for identifying the Top 1 templates and Top 10 templates, respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "accuracy") (:form . "accuracies") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 17) (:start . 15)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 23) (:start . 22)\n  (:id . 46))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 30)\n  (:start . 23) (:id . 47))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 42) (:start . 38)\n  (:id . 49))\n ((:tag . "CD") (:stem . "54.1") (:form . "54.1") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 52) (:start . 49)\n  (:id . 52))\n ((:tag . "CD") (:stem . "75.0") (:form . "75.0") (:end . 57) (:start . 53)\n  (:id . 53))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 58) (:start . 57)\n  (:id . 54))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 62) (:start . 59)\n  (:id . 55))\n ((:tag . "VBG") (:stem . "identify") (:form . "identifying") (:end . 74)\n  (:start . 63) (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 78) (:start . 75)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "Top") (:form . "Top") (:end . 82) (:start . 79)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 84) (:start . 83)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 94)\n  (:start . 85) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 98) (:start . 95)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "Top") (:form . "Top") (:end . 102) (:start . 99)\n  (:id . 62))\n ((:tag . "CD") (:stem . "10") (:form . "10") (:end . 105) (:start . 103)\n  (:id . 63))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 115)\n  (:start . 106) (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 129)\n  (:start . 117) (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 130) (:start . 129)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.191) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504930@unknown@formal@none@1@S@In addition, (PS)2-v2 was the rank 6th among these 72 severs based on GDT_TS scores (Table 5).@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 21)\n  (:start . 14) (:id . 46))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "rank") (:form . "rank") (:end . 34) (:start . 30)\n  (:id . 49))\n ((:tag . "NN") (:stem . "6th") (:form . "6th") (:end . 38) (:start . 35)\n  (:id . 50))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 44) (:start . 39)\n  (:id . 51))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 50) (:start . 45)\n  (:id . 52))\n ((:tag . "CD") (:stem . "72") (:form . "72") (:end . 53) (:start . 51)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "sever") (:form . "severs") (:end . 60)\n  (:start . 54) (:id . 54))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 66) (:start . 61)\n  (:id . 55))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 69) (:start . 67)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 76)\n  (:start . 70) (:id . 57))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 83)\n  (:start . 77) (:id . 58))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 85) (:start . 84)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 90) (:start . 85)\n  (:id . 60))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 92) (:start . 91)\n  (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 93) (:start . 92)\n  (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s15.192) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504931@unknown@formal@none@1@S@This server is often able to yield reliable predicted structures (i.e. GDT_TS score = 60%) if the E-value is less than 10-2 (Figure S3 in Additional file 6).@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 14) (:start . 12)\n  (:id . 44))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 25) (:start . 21)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 28) (:start . 26)\n  (:id . 47))\n ((:tag . "VB") (:stem . "yield") (:form . "yield") (:end . 34) (:start . 29)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "reliable") (:form . "reliable") (:end . 43)\n  (:start . 35) (:id . 49))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 64)\n  (:start . 54) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 66) (:start . 65)\n  (:id . 52))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 70) (:start . 66)\n  (:id . 53))\n ((:tag . "FW") (:stem . "gdt_ts") (:form . "GDT_TS") (:end . 77)\n  (:start . 71) (:id . 54))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 83) (:start . 78)\n  (:id . 55))\n ((:tag . "SYM") (:stem . "=") (:form . "=") (:end . 85) (:start . 84)\n  (:id . 56))\n ((:tag . "CD") (:stem . "60") (:form . "60") (:end . 88) (:start . 86)\n  (:id . 57))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 89) (:start . 88)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 90) (:start . 89)\n  (:id . 59))\n ((:tag . "IN") (:stem . "if") (:form . "if") (:end . 93) (:start . 91)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 97) (:start . 94)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 105)\n  (:start . 98) (:id . 62))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 108) (:start . 106)\n  (:id . 63))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 113) (:start . 109)\n  (:id . 64))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 118) (:start . 114)\n  (:id . 65))\n ((:tag . "CD") (:stem . "10-2") (:form . "10-2") (:end . 123) (:start . 119)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 125) (:start . 124)\n  (:id . 67))\n ((:tag . "NN") (:stem . "figure") (:form . "Figure") (:end . 131)\n  (:start . 125) (:id . 68))\n ((:tag . "NN") (:stem . "s3") (:form . "S3") (:end . 134) (:start . 132)\n  (:id . 69))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 137) (:start . 135)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 148)\n  (:start . 138) (:id . 71))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 153) (:start . 149)\n  (:id . 72))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 155) (:start . 154)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s15.193) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504932@unknown@formal@none@1@S@Comparing (PS)2-v2 with 71 automatic servers on 154 targets in CASP8@(((:tag . "NN") (:stem . "comparing") (:form . "Comparing") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 18)\n  (:start . 11) (:id . 44))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "CD") (:stem . "71") (:form . "71") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "automatic") (:form . "automatic") (:end . 36)\n  (:start . 27) (:id . 47))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 44)\n  (:start . 37) (:id . 48))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 47) (:start . 45)\n  (:id . 49))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 51) (:start . 48)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 59)\n  (:start . 52) (:id . 51))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 62) (:start . 60)\n  (:id . 52))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 68) (:start . 63)\n  (:id . 53)))@@@1@12@((:identifiers (:sid . :s15.194) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|TableLegend|)))@oe@9-2-2011
5504933@unknown@formal@none@1@S@The top-rank five serves (Zhang-Server, RAPTOR, pro-sp3-TASSER, Phyre_de_novo and BAKER-ROBETTA) are better than (PS)2-v2 on 40 hard targets (i.e., LGA_S score < 70%) (Table S3 in Additional file 7).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "top-rank") (:form . "top-rank") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "NNS") (:stem . "serve") (:form . "serves") (:end . 24)\n  (:start . 18) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 26) (:start . 25)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Zhang-Server") (:form . "Zhang-Server") (:end . 38)\n  (:start . 26) (:id . 47))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 39) (:start . 38)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "RAPTOR") (:form . "RAPTOR") (:end . 46)\n  (:start . 40) (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 47) (:start . 46)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "pro-sp3-TASSER") (:form . "pro-sp3-TASSER")\n  (:end . 62) (:start . 48) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 63) (:start . 62)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "Phyre_de_novo") (:form . "Phyre_de_novo")\n  (:end . 77) (:start . 64) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 81) (:start . 78)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "BAKER-ROBETTA") (:form . "BAKER-ROBETTA")\n  (:end . 95) (:start . 82) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 56))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 100) (:start . 97)\n  (:id . 57))\n ((:tag . "JJR") (:stem . "good") (:form . "better") (:end . 107)\n  (:start . 101) (:id . 58))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 112) (:start . 108)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 114) (:start . 113)\n  (:id . 60))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 121)\n  (:start . 114) (:id . 61))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 124) (:start . 122)\n  (:id . 62))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 127) (:start . 125)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "hard") (:form . "hard") (:end . 132) (:start . 128)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 140)\n  (:start . 133) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 142) (:start . 141)\n  (:id . 66))\n ((:tag . "FW") (:stem . "i.e.") (:form . "i.e.") (:end . 146) (:start . 142)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 147) (:start . 146)\n  (:id . 68))\n ((:tag . "NN") (:stem . "lga_s") (:form . "LGA_S") (:end . 153)\n  (:start . 148) (:id . 69))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 159)\n  (:start . 154) (:id . 70))\n ((:tag . "SYM") (:stem . "<") (:form . "<") (:end . 161) (:start . 160)\n  (:id . 71))\n ((:tag . "CD") (:stem . "70") (:form . "70") (:end . 164) (:start . 162)\n  (:id . 72))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 165) (:start . 164)\n  (:id . 73))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 166) (:start . 165)\n  (:id . 74))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 168) (:start . 167)\n  (:id . 75))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 173)\n  (:start . 168) (:id . 76))\n ((:tag . "NNP") (:stem . "S3") (:form . "S3") (:end . 176) (:start . 174)\n  (:id . 77))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 179) (:start . 177)\n  (:id . 78))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 190)\n  (:start . 180) (:id . 79))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 195) (:start . 191)\n  (:id . 80))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 197) (:start . 196)\n  (:id . 81))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 198) (:start . 197)\n  (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 199) (:start . 198)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s15.195) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504934@unknown@formal@none@1@S@These serves were much slower than (PS)2-v2 because they often utilized ab initio methods to build the unaligned loop regions and to generate the models, such as the Poing folding system for Phyre_de_novo server, the chunk-TASSER [38] for pro-sp3-TASSER server, and the Rosetta fragment-assembly methodology [39] for BAKER-ROBETTA server.@(((:tag . "DT") (:stem . "these") (:form . "These") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "serve") (:form . "serves") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "be") (:form . "were") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . "RB") (:stem . "much") (:form . "much") (:end . 22) (:start . 18)\n  (:id . 45))\n ((:tag . "JJR") (:stem . "slow") (:form . "slower") (:end . 29) (:start . 23)\n  (:id . 46))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 43)\n  (:start . 36) (:id . 49))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 51)\n  (:start . 44) (:id . 50))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 56) (:start . 52)\n  (:id . 51))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 62) (:start . 57)\n  (:id . 52))\n ((:tag . "VBD") (:stem . "utilize") (:form . "utilized") (:end . 71)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "ab") (:form . "ab") (:end . 74) (:start . 72)\n  (:id . 54))\n ((:tag . "NN") (:stem . "initio") (:form . "initio") (:end . 81)\n  (:start . 75) (:id . 55))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 89)\n  (:start . 82) (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 92) (:start . 90)\n  (:id . 57))\n ((:tag . "VB") (:stem . "build") (:form . "build") (:end . 98) (:start . 93)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "unaligned") (:form . "unaligned") (:end . 112)\n  (:start . 103) (:id . 60))\n ((:tag . "NN") (:stem . "loop") (:form . "loop") (:end . 117) (:start . 113)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 125)\n  (:start . 118) (:id . 62))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 63))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 132) (:start . 130)\n  (:id . 64))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 141)\n  (:start . 133) (:id . 65))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 145) (:start . 142)\n  (:id . 66))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 152)\n  (:start . 146) (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 68))\n ((:tag . "JJ") (:stem . "such") (:form . "such") (:end . 158) (:start . 154)\n  (:id . 69))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 161) (:start . 159)\n  (:id . 70))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 165) (:start . 162)\n  (:id . 71))\n ((:tag . "NN") (:stem . "poing") (:form . "Poing") (:end . 171)\n  (:start . 166) (:id . 72))\n ((:tag . "NN") (:stem . "folding") (:form . "folding") (:end . 179)\n  (:start . 172) (:id . 73))\n ((:tag . "NN") (:stem . "system") (:form . "system") (:end . 186)\n  (:start . 180) (:id . 74))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 190) (:start . 187)\n  (:id . 75))\n ((:tag . "NNP") (:stem . "Phyre_de_novo") (:form . "Phyre_de_novo")\n  (:end . 204) (:start . 191) (:id . 76))\n ((:tag . "NNP") (:stem . "server") (:form . "server") (:end . 211)\n  (:start . 205) (:id . 77))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 212) (:start . 211)\n  (:id . 78))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 216) (:start . 213)\n  (:id . 79))\n ((:tag . "NNP") (:stem . "chunk-TASSER") (:form . "chunk-TASSER")\n  (:end . 229) (:start . 217) (:id . 80))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 231) (:start . 230)\n  (:id . 81))\n ((:tag . "CD") (:stem . "38") (:form . "38") (:end . 233) (:start . 231)\n  (:id . 82))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 234) (:start . 233)\n  (:id . 83))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 238) (:start . 235)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "pro-sp3-TASSER") (:form . "pro-sp3-TASSER")\n  (:end . 253) (:start . 239) (:id . 85))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 260)\n  (:start . 254) (:id . 86))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 261) (:start . 260)\n  (:id . 87))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 265) (:start . 262)\n  (:id . 88))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 269) (:start . 266)\n  (:id . 89))\n ((:tag . "NNP") (:stem . "Rosetta") (:form . "Rosetta") (:end . 277)\n  (:start . 270) (:id . 90))\n ((:tag . "NN") (:stem . "fragment-assembly") (:form . "fragment-assembly")\n  (:end . 295) (:start . 278) (:id . 91))\n ((:tag . "NN") (:stem . "methodology") (:form . "methodology") (:end . 307)\n  (:start . 296) (:id . 92))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 309) (:start . 308)\n  (:id . 93))\n ((:tag . "CD") (:stem . "39") (:form . "39") (:end . 311) (:start . 309)\n  (:id . 94))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 312) (:start . 311)\n  (:id . 95))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 316) (:start . 313)\n  (:id . 96))\n ((:tag . "NNP") (:stem . "BAKER-ROBETTA") (:form . "BAKER-ROBETTA")\n  (:end . 330) (:start . 317) (:id . 97))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 337)\n  (:start . 331) (:id . 98))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 338) (:start . 337)\n  (:id . 99)))@@@1@58@((:identifiers (:sid . :s15.196) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504935@unknown@formal@none@1@S@In the near future, our (PS)2-v2 server will incorporate ab initio methods to model long-length loops and hard targets.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 6) (:start . 3)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "near") (:form . "near") (:end . 11) (:start . 7)\n  (:id . 44))\n ((:tag . "NN") (:stem . "future") (:form . "future") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 19) (:start . 18)\n  (:id . 46))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 23) (:start . 20)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 25) (:start . 24)\n  (:id . 48))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 32)\n  (:start . 25) (:id . 49))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 39)\n  (:start . 33) (:id . 50))\n ((:tag . "MD") (:stem . "will") (:form . "will") (:end . 44) (:start . 40)\n  (:id . 51))\n ((:tag . "VB") (:stem . "incorporate") (:form . "incorporate") (:end . 56)\n  (:start . 45) (:id . 52))\n ((:tag . "NN") (:stem . "ab") (:form . "ab") (:end . 59) (:start . 57)\n  (:id . 53))\n ((:tag . "NN") (:stem . "initio") (:form . "initio") (:end . 66)\n  (:start . 60) (:id . 54))\n ((:tag . "NNS") (:stem . "method") (:form . "methods") (:end . 74)\n  (:start . 67) (:id . 55))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "VB") (:stem . "model") (:form . "model") (:end . 83) (:start . 78)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "long-length") (:form . "long-length") (:end . 95)\n  (:start . 84) (:id . 58))\n ((:tag . "NNS") (:stem . "loop") (:form . "loops") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 105) (:start . 102)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "hard") (:form . "hard") (:end . 110) (:start . 106)\n  (:id . 61))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 118)\n  (:start . 111) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 119) (:start . 118)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s15.197) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504936@unknown@formal@none@1@S@Multiple templates for multiple domains@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 18)\n  (:start . 9) (:id . 43))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 22) (:start . 19)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 31)\n  (:start . 23) (:id . 45))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 39)\n  (:start . 32) (:id . 46)))@@@1@5@((:identifiers (:sid . :s15.198) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504937@unknown@formal@none@1@S@We used the target T0504 as an example to describe (PS)2-v2 for selecting multiple templates to model protein structures (Figure 5).@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 7) (:start . 3)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 11) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 18)\n  (:start . 12) (:id . 45))\n ((:tag . "NN") (:stem . "t0504") (:form . "T0504") (:end . 24) (:start . 19)\n  (:id . 46))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 27) (:start . 25)\n  (:id . 47))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 30) (:start . 28)\n  (:id . 48))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 38)\n  (:start . 31) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 50))\n ((:tag . "NN") (:stem . "describe") (:form . "describe") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 52))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 59)\n  (:start . 52) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 63) (:start . 60)\n  (:id . 54))\n ((:tag . "VBG") (:stem . "select") (:form . "selecting") (:end . 73)\n  (:start . 64) (:id . 55))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 82)\n  (:start . 74) (:id . 56))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 92)\n  (:start . 83) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 101) (:start . 96)\n  (:id . 59))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 109)\n  (:start . 102) (:id . 60))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 120)\n  (:start . 110) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 122) (:start . 121)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 128)\n  (:start . 122) (:id . 63))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 130) (:start . 129)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 131) (:start . 130)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 132) (:start . 131)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s15.199) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504938@unknown@formal@none@1@S@The (PS)2-v2 server first selected the 53BP1 tandem tudor domains (PDB code 2g3r) as the best template.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "RB") (:stem . "first") (:form . "first") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 48))\n ((:tag . "NN") (:stem . "53bp1") (:form . "53BP1") (:end . 44) (:start . 39)\n  (:id . 49))\n ((:tag . "JJ") (:stem . "tandem") (:form . "tandem") (:end . 51)\n  (:start . 45) (:id . 50))\n ((:tag . "NN") (:stem . "tudor") (:form . "tudor") (:end . 57) (:start . 52)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 65)\n  (:start . 58) (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 70) (:start . 67)\n  (:id . 54))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 75) (:start . 71)\n  (:id . 55))\n ((:tag . "NN") (:stem . "2g3r") (:form . "2g3r") (:end . 80) (:start . 76)\n  (:id . 56))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 57))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 84) (:start . 82)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 59))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 93) (:start . 89)\n  (:id . 60))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 102)\n  (:start . 94) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 103) (:start . 102)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s15.200) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504939@unknown@formal@none@1@S@The template 2g3rA aligned a part of regions (138 residues, residues 10-147) to the target, and the model yielded the GDT_TS scores of 74.2 and 32.2 for the target T0504-D1 and T0504-D2.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "2g3ra") (:form . "2g3rA") (:end . 18) (:start . 13)\n  (:id . 44))\n ((:tag . "VBD") (:stem . "align") (:form . "aligned") (:end . 26)\n  (:start . 19) (:id . 45))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 28) (:start . 27)\n  (:id . 46))\n ((:tag . "NN") (:stem . "part") (:form . "part") (:end . 33) (:start . 29)\n  (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 44)\n  (:start . 37) (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 46) (:start . 45)\n  (:id . 50))\n ((:tag . "CD") (:stem . "138") (:form . "138") (:end . 49) (:start . 46)\n  (:id . 51))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 58)\n  (:start . 50) (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 68)\n  (:start . 60) (:id . 54))\n ((:tag . "CD") (:stem . "10-147") (:form . "10-147") (:end . 75)\n  (:start . 69) (:id . 55))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 76) (:start . 75)\n  (:id . 56))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 79) (:start . 77)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 58))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 90)\n  (:start . 84) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 91) (:start . 90)\n  (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 95) (:start . 92)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 99) (:start . 96)\n  (:id . 62))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 105)\n  (:start . 100) (:id . 63))\n ((:tag . "VBD") (:stem . "yield") (:form . "yielded") (:end . 113)\n  (:start . 106) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 117) (:start . 114)\n  (:id . 65))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 124)\n  (:start . 118) (:id . 66))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 131)\n  (:start . 125) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 134) (:start . 132)\n  (:id . 68))\n ((:tag . "CD") (:stem . "74.2") (:form . "74.2") (:end . 139) (:start . 135)\n  (:id . 69))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 143) (:start . 140)\n  (:id . 70))\n ((:tag . "CD") (:stem . "32.2") (:form . "32.2") (:end . 148) (:start . 144)\n  (:id . 71))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 152) (:start . 149)\n  (:id . 72))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 156) (:start . 153)\n  (:id . 73))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 163)\n  (:start . 157) (:id . 74))\n ((:tag . "NN") (:stem . "t0504-d1") (:form . "T0504-D1") (:end . 172)\n  (:start . 164) (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 176) (:start . 173)\n  (:id . 76))\n ((:tag . "NN") (:stem . "t0504-d2") (:form . "T0504-D2") (:end . 185)\n  (:start . 177) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 186) (:start . 185)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s15.201) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504940@unknown@formal@none@1@S@Since the number of the unaligned residues is 61 (residue 148-208), the (PS)2-v2 server used unaligned residues to search the new template for modeling this segment.@(((:tag . "IN") (:stem . "since") (:form . "Since") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 9) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "number") (:form . "number") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "unaligned") (:form . "unaligned") (:end . 33)\n  (:start . 24) (:id . 47))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 42)\n  (:start . 34) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 45) (:start . 43)\n  (:id . 49))\n ((:tag . "CD") (:stem . "61") (:form . "61") (:end . 48) (:start . 46)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 50) (:start . 49)\n  (:id . 51))\n ((:tag . "NN") (:stem . "residue") (:form . "residue") (:end . 57)\n  (:start . 50) (:id . 52))\n ((:tag . "CD") (:stem . "148-208") (:form . "148-208") (:end . 65)\n  (:start . 58) (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 66) (:start . 65)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 67) (:start . 66)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 71) (:start . 68)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 73) (:start . 72)\n  (:id . 57))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 80)\n  (:start . 73) (:id . 58))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 87)\n  (:start . 81) (:id . 59))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 92) (:start . 88)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "unaligned") (:form . "unaligned") (:end . 102)\n  (:start . 93) (:id . 61))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 111)\n  (:start . 103) (:id . 62))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 114) (:start . 112)\n  (:id . 63))\n ((:tag . "VB") (:stem . "search") (:form . "search") (:end . 121)\n  (:start . 115) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 125) (:start . 122)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "new") (:form . "new") (:end . 129) (:start . 126)\n  (:id . 66))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 138)\n  (:start . 130) (:id . 67))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 142) (:start . 139)\n  (:id . 68))\n ((:tag . "VBG") (:stem . "model") (:form . "modeling") (:end . 151)\n  (:start . 143) (:id . 69))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 156) (:start . 152)\n  (:id . 70))\n ((:tag . "NN") (:stem . "segment") (:form . "segment") (:end . 164)\n  (:start . 157) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 165) (:start . 164)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s15.202) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504941@unknown@formal@none@1@S@After search template library, (PS)2-v2 selected the PHD finger protein 20-like 1 (PDB code 2eqm) as the template for modeling this unmodeling residues (T0504-D3).@(((:tag . "IN") (:stem . "after") (:form . "After") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "search") (:form . "search") (:end . 12) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "NN") (:stem . "library") (:form . "library") (:end . 29)\n  (:start . 22) (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 39)\n  (:start . 32) (:id . 48))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 48)\n  (:start . 40) (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 52) (:start . 49)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PHD") (:form . "PHD") (:end . 56) (:start . 53)\n  (:id . 51))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 63)\n  (:start . 57) (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 71)\n  (:start . 64) (:id . 53))\n ((:tag . "JJ") (:stem . "20-like") (:form . "20-like") (:end . 79)\n  (:start . 72) (:id . 54))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 81) (:start . 80)\n  (:id . 55))\n ((:tag . "NN") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 86) (:start . 83)\n  (:id . 57))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 91) (:start . 87)\n  (:id . 58))\n ((:tag . "NN") (:stem . "2eqm") (:form . "2eqm") (:end . 96) (:start . 92)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 100) (:start . 98)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 104) (:start . 101)\n  (:id . 62))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 113)\n  (:start . 105) (:id . 63))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 117) (:start . 114)\n  (:id . 64))\n ((:tag . "VBG") (:stem . "model") (:form . "modeling") (:end . 126)\n  (:start . 118) (:id . 65))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 131) (:start . 127)\n  (:id . 66))\n ((:tag . "JJ") (:stem . "unmodeling") (:form . "unmodeling") (:end . 142)\n  (:start . 132) (:id . 67))\n ((:tag . "NNS") (:stem . "residue") (:form . "residues") (:end . 151)\n  (:start . 143) (:id . 68))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 153) (:start . 152)\n  (:id . 69))\n ((:tag . "NNP") (:stem . "T0504-D3") (:form . "T0504-D3") (:end . 161)\n  (:start . 153) (:id . 70))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 162) (:start . 161)\n  (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 163) (:start . 162)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s15.203) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504942@unknown@formal@none@1@S@The GDT_TS score of this model is 80.7 for the target T0504-D3.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 10)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 33) (:start . 31)\n  (:id . 48))\n ((:tag . "CD") (:stem . "80.7") (:form . "80.7") (:end . 38) (:start . 34)\n  (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 42) (:start . 39)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 51))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 53)\n  (:start . 47) (:id . 52))\n ((:tag . "NN") (:stem . "t0504-d3") (:form . "T0504-D3") (:end . 62)\n  (:start . 54) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 63) (:start . 62)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s15.204) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504943@unknown@formal@none@1@S@The total GDT_TS score improvement is 136.42 when (PS)2-v2 utilizes a multiple-template strategy.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "gdt_ts") (:form . "GDT_TS") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "improvement") (:form . "improvement") (:end . 34)\n  (:start . 23) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 37) (:start . 35)\n  (:id . 47))\n ((:tag . "CD") (:stem . "136.42") (:form . "136.42") (:end . 44)\n  (:start . 38) (:id . 48))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 51) (:start . 50)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 58)\n  (:start . 51) (:id . 51))\n ((:tag . "VBZ") (:stem . "utilize") (:form . "utilizes") (:end . 67)\n  (:start . 59) (:id . 52))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 69) (:start . 68)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "multiple-template") (:form . "multiple-template")\n  (:end . 87) (:start . 70) (:id . 54))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 96)\n  (:start . 88) (:id . 55))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 56)))@@@1@15@((:identifiers (:sid . :s15.205) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504944@unknown@formal@none@1@S@Conversely, the GDT-TS scores of the (PS)2-original server, using PDB code 2g3r as the template, are 17.3 (T0504-D1), 48.9 (T0504-D2) and 56.1 (T0504-D3), respectively.@(((:tag . "RB") (:stem . "conversely") (:form . "Conversely") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 11) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "gdt-ts") (:form . "GDT-TS") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 29)\n  (:start . 23) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 32) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 36) (:start . 33)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 38) (:start . 37)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 51) (:start . 38) (:id . 50))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 58)\n  (:start . 52) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 59) (:start . 58)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 69) (:start . 66)\n  (:id . 54))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 74) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "2g3r") (:form . "2g3r") (:end . 79) (:start . 75)\n  (:id . 56))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 82) (:start . 80)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 86) (:start . 83)\n  (:id . 58))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 95)\n  (:start . 87) (:id . 59))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 100) (:start . 97)\n  (:id . 61))\n ((:tag . "CD") (:stem . "17.3") (:form . "17.3") (:end . 105) (:start . 101)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 107) (:start . 106)\n  (:id . 63))\n ((:tag . "NNP") (:stem . "T0504-D1") (:form . "T0504-D1") (:end . 115)\n  (:start . 107) (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 116) (:start . 115)\n  (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 117) (:start . 116)\n  (:id . 66))\n ((:tag . "CD") (:stem . "48.9") (:form . "48.9") (:end . 122) (:start . 118)\n  (:id . 67))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 124) (:start . 123)\n  (:id . 68))\n ((:tag . "NN") (:stem . "t0504-d2") (:form . "T0504-D2") (:end . 132)\n  (:start . 124) (:id . 69))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 133) (:start . 132)\n  (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 137) (:start . 134)\n  (:id . 71))\n ((:tag . "CD") (:stem . "56.1") (:form . "56.1") (:end . 142) (:start . 138)\n  (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 144) (:start . 143)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "T0504-D3") (:form . "T0504-D3") (:end . 152)\n  (:start . 144) (:id . 74))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 153) (:start . 152)\n  (:id . 75))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 154) (:start . 153)\n  (:id . 76))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 167)\n  (:start . 155) (:id . 77))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 168) (:start . 167)\n  (:id . 78)))@@@1@37@((:identifiers (:sid . :s15.206) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504945@unknown@formal@none@1@S@For the (PS)2-CASP8 server, the GDT-TS scores using PDB code 2ns2 as the template are 44.4 (T0504-D1), 25.6 (T0504-D2) and 41.0 (T0504-D3), respectively.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 9) (:start . 8) (:id . 44))\n ((:tag . "NN") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 19)\n  (:start . 9) (:id . 45))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 27) (:start . 26)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 31) (:start . 28)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "GDT-TS") (:form . "GDT-TS") (:end . 38)\n  (:start . 32) (:id . 49))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 45)\n  (:start . 39) (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 51) (:start . 46)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 55) (:start . 52)\n  (:id . 52))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 60) (:start . 56)\n  (:id . 53))\n ((:tag . "CD") (:stem . "2ns2") (:form . "2ns2") (:end . 65) (:start . 61)\n  (:id . 54))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 68) (:start . 66)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 72) (:start . 69)\n  (:id . 56))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 81)\n  (:start . 73) (:id . 57))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 85) (:start . 82)\n  (:id . 58))\n ((:tag . "CD") (:stem . "44.4") (:form . "44.4") (:end . 90) (:start . 86)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 92) (:start . 91)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "T0504-D1") (:form . "T0504-D1") (:end . 100)\n  (:start . 92) (:id . 61))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 101) (:start . 100)\n  (:id . 62))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 102) (:start . 101)\n  (:id . 63))\n ((:tag . "CD") (:stem . "25.6") (:form . "25.6") (:end . 107) (:start . 103)\n  (:id . 64))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 109) (:start . 108)\n  (:id . 65))\n ((:tag . "NN") (:stem . "t0504-d2") (:form . "T0504-D2") (:end . 117)\n  (:start . 109) (:id . 66))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 118) (:start . 117)\n  (:id . 67))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 122) (:start . 119)\n  (:id . 68))\n ((:tag . "CD") (:stem . "41.0") (:form . "41.0") (:end . 127) (:start . 123)\n  (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 129) (:start . 128)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "T0504-D3") (:form . "T0504-D3") (:end . 137)\n  (:start . 129) (:id . 71))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 138) (:start . 137)\n  (:id . 72))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 139) (:start . 138)\n  (:id . 73))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 152)\n  (:start . 140) (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 153) (:start . 152)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s15.207) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504946@unknown@formal@none@1@S@Comparison the (PS)2-v2 server with (PS)2-original and (PS)2-CASP8 servers on the target T0504 in CASP8.@(((:tag . "NN") (:stem . "comparison") (:form . "Comparison") (:end . 10)\n  (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 14) (:start . 11)\n  (:id . 43))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 16) (:start . 15)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 23)\n  (:start . 16) (:id . 45))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 30)\n  (:start . 24) (:id . 46))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 35) (:start . 31)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 37) (:start . 36)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PS)2-original") (:form . "PS)2-original")\n  (:end . 50) (:start . 37) (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 51))\n ((:tag . "NN") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 66)\n  (:start . 56) (:id . 52))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 74)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 81) (:start . 78)\n  (:id . 55))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 88)\n  (:start . 82) (:id . 56))\n ((:tag . "NN") (:stem . "t0504") (:form . "T0504") (:end . 94) (:start . 89)\n  (:id . 57))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 97) (:start . 95)\n  (:id . 58))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 103) (:start . 98)\n  (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 104) (:start . 103)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.208) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504947@unknown@formal@none@1@S@The (PS)2-CASP8 server uses human spindlin1 (PDB code 2ns2) as the template, conversely, (PS)2-v2 utilizes a multiple-template strategy and selects both 53BP1 tandem tudor domains (PDB code 2g3r) and PHD finger protein 20-like 1 (PDB code 2eqm) as templates.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 15)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 22)\n  (:start . 16) (:id . 45))\n ((:tag . "VBZ") (:stem . "use") (:form . "uses") (:end . 27) (:start . 23)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "human") (:form . "human") (:end . 33) (:start . 28)\n  (:id . 47))\n ((:tag . "NN") (:stem . "spindlin1") (:form . "spindlin1") (:end . 43)\n  (:start . 34) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 45) (:start . 44)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 48) (:start . 45)\n  (:id . 50))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 53) (:start . 49)\n  (:id . 51))\n ((:tag . "CD") (:stem . "2ns2") (:form . "2ns2") (:end . 58) (:start . 54)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 59) (:start . 58)\n  (:id . 53))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 62) (:start . 60)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 66) (:start . 63)\n  (:id . 55))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 75)\n  (:start . 67) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 76) (:start . 75)\n  (:id . 57))\n ((:tag . "RB") (:stem . "conversely") (:form . "conversely") (:end . 87)\n  (:start . 77) (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 88) (:start . 87)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 97)\n  (:start . 90) (:id . 61))\n ((:tag . "VBZ") (:stem . "utilize") (:form . "utilizes") (:end . 106)\n  (:start . 98) (:id . 62))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 108) (:start . 107)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "multiple-template") (:form . "multiple-template")\n  (:end . 126) (:start . 109) (:id . 64))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 135)\n  (:start . 127) (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 139) (:start . 136)\n  (:id . 66))\n ((:tag . "VBZ") (:stem . "select") (:form . "selects") (:end . 147)\n  (:start . 140) (:id . 67))\n ((:tag . "CC") (:stem . "both") (:form . "both") (:end . 152) (:start . 148)\n  (:id . 68))\n ((:tag . "NN") (:stem . "53bp1") (:form . "53BP1") (:end . 158)\n  (:start . 153) (:id . 69))\n ((:tag . "JJ") (:stem . "tandem") (:form . "tandem") (:end . 165)\n  (:start . 159) (:id . 70))\n ((:tag . "NN") (:stem . "tudor") (:form . "tudor") (:end . 171)\n  (:start . 166) (:id . 71))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 179)\n  (:start . 172) (:id . 72))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 181) (:start . 180)\n  (:id . 73))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 184) (:start . 181)\n  (:id . 74))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 189) (:start . 185)\n  (:id . 75))\n ((:tag . "NN") (:stem . "2g3r") (:form . "2g3r") (:end . 194) (:start . 190)\n  (:id . 76))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 195) (:start . 194)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 199) (:start . 196)\n  (:id . 78))\n ((:tag . "NNP") (:stem . "PHD") (:form . "PHD") (:end . 203) (:start . 200)\n  (:id . 79))\n ((:tag . "NN") (:stem . "finger") (:form . "finger") (:end . 210)\n  (:start . 204) (:id . 80))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 218)\n  (:start . 211) (:id . 81))\n ((:tag . "JJ") (:stem . "20-like") (:form . "20-like") (:end . 226)\n  (:start . 219) (:id . 82))\n ((:tag . "CD") (:stem . "1") (:form . "1") (:end . 228) (:start . 227)\n  (:id . 83))\n ((:tag . "NN") (:stem . "(") (:form . "(") (:end . 230) (:start . 229)\n  (:id . 84))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 233) (:start . 230)\n  (:id . 85))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 238) (:start . 234)\n  (:id . 86))\n ((:tag . "NN") (:stem . "2eqm") (:form . "2eqm") (:end . 243) (:start . 239)\n  (:id . 87))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 244) (:start . 243)\n  (:id . 88))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 247) (:start . 245)\n  (:id . 89))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 257)\n  (:start . 248) (:id . 90))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 258) (:start . 257)\n  (:id . 91)))@@@1@50@((:identifiers (:sid . :s15.209) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504948@unknown@formal@none@1@S@(PS)2-v2 significantly outperforms (PS)2-CASP8 on the T0504-D1 and T0504-D3 domains.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 22) (:start . 9) (:id . 44))\n ((:tag . "NNS") (:stem . "outperform") (:form . "outperforms") (:end . 34)\n  (:start . 23) (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 36) (:start . 35)\n  (:id . 46))\n ((:tag . "NN") (:stem . "PS)2-CASP8") (:form . "PS)2-CASP8") (:end . 46)\n  (:start . 36) (:id . 47))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 49) (:start . 47)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "t0504-d1") (:form . "T0504-D1") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 66) (:start . 63)\n  (:id . 51))\n ((:tag . "NN") (:stem . "t0504-d3") (:form . "T0504-D3") (:end . 75)\n  (:start . 67) (:id . 52))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 83)\n  (:start . 76) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 84) (:start . 83)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s15.210) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504949@unknown@formal@none@1@S@Multiple models and model selection@(((:tag . "JJ") (:stem . "multiple") (:form . "Multiple") (:end . 8)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 15) (:start . 9)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 19) (:start . 16)\n  (:id . 44))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 25) (:start . 20)\n  (:id . 45))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 35)\n  (:start . 26) (:id . 46)))@@@1@5@((:identifiers (:sid . :s15.211) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504950@unknown@formal@none@1@S@Figure 6 shows the improvement in GDT_TS scores of (PS)2-v2 by applying a multiple-model strategy and using the program ProQ for the final model selection.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "NN") (:stem . "improvement") (:form . "improvement") (:end . 30)\n  (:start . 19) (:id . 46))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 47)\n  (:start . 41) (:id . 49))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 52) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 59)\n  (:start . 52) (:id . 52))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 62) (:start . 60)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "apply") (:form . "applying") (:end . 71)\n  (:start . 63) (:id . 54))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 73) (:start . 72)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "multiple-model") (:form . "multiple-model")\n  (:end . 88) (:start . 74) (:id . 56))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 97)\n  (:start . 89) (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 101) (:start . 98)\n  (:id . 58))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 107) (:start . 102)\n  (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 111) (:start . 108)\n  (:id . 60))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 119)\n  (:start . 112) (:id . 61))\n ((:tag . "NNP") (:stem . "ProQ") (:form . "ProQ") (:end . 124) (:start . 120)\n  (:id . 62))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 128) (:start . 125)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 64))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 138)\n  (:start . 133) (:id . 65))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 144)\n  (:start . 139) (:id . 66))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 154)\n  (:start . 145) (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 155) (:start . 154)\n  (:id . 68)))@@@1@27@((:identifiers (:sid . :s15.212) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504951@unknown@formal@none@1@S@Among these 154 CASP8 targets, (PS)2-v2 improved GDT_TS scores for 23 targets; conversely, only 4 targets are lightly worse when (PS)2-v2 used a multiple-model strategy.@(((:tag . "IN") (:stem . "among") (:form . "Among") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 11) (:start . 6)\n  (:id . 43))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 15) (:start . 12)\n  (:id . 44))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 21) (:start . 16)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 29)\n  (:start . 22) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 30) (:start . 29)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 32) (:start . 31)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 39)\n  (:start . 32) (:id . 49))\n ((:tag . "VBD") (:stem . "improve") (:form . "improved") (:end . 48)\n  (:start . 40) (:id . 50))\n ((:tag . "NN") (:stem . "gdt_ts") (:form . "GDT_TS") (:end . 55)\n  (:start . 49) (:id . 51))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 62)\n  (:start . 56) (:id . 52))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 66) (:start . 63)\n  (:id . 53))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 77)\n  (:start . 70) (:id . 55))\n ((:tag . ":") (:stem . ";") (:form . ";") (:end . 78) (:start . 77)\n  (:id . 56))\n ((:tag . "RB") (:stem . "conversely") (:form . "conversely") (:end . 89)\n  (:start . 79) (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "RB") (:stem . "only") (:form . "only") (:end . 95) (:start . 91)\n  (:id . 59))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 97) (:start . 96)\n  (:id . 60))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 105)\n  (:start . 98) (:id . 61))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 109) (:start . 106)\n  (:id . 62))\n ((:tag . "RB") (:stem . "lightly") (:form . "lightly") (:end . 117)\n  (:start . 110) (:id . 63))\n ((:tag . "JJR") (:stem . "worse") (:form . "worse") (:end . 123)\n  (:start . 118) (:id . 64))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 128) (:start . 124)\n  (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 130) (:start . 129)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 137)\n  (:start . 130) (:id . 67))\n ((:tag . "VBD") (:stem . "use") (:form . "used") (:end . 142) (:start . 138)\n  (:id . 68))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 144) (:start . 143)\n  (:id . 69))\n ((:tag . "JJ") (:stem . "multiple-model") (:form . "multiple-model")\n  (:end . 159) (:start . 145) (:id . 70))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 168)\n  (:start . 160) (:id . 71))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 169) (:start . 168)\n  (:id . 72)))@@@1@31@((:identifiers (:sid . :s15.213) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504952@unknown@formal@none@1@S@For the other 127 targets, (PS)2-v2 obtained the same GDT_TS scores and the total GDT_TS improvement is 145.3.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "CD") (:stem . "127") (:form . "127") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 35)\n  (:start . 28) (:id . 49))\n ((:tag . "VBD") (:stem . "obtain") (:form . "obtained") (:end . 44)\n  (:start . 36) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 48) (:start . 45)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 53) (:start . 49)\n  (:id . 52))\n ((:tag . "NN") (:stem . "gdt_ts") (:form . "GDT_TS") (:end . 60)\n  (:start . 54) (:id . 53))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 67)\n  (:start . 61) (:id . 54))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "total") (:form . "total") (:end . 81) (:start . 76)\n  (:id . 57))\n ((:tag . "NN") (:stem . "gdt_ts") (:form . "GDT_TS") (:end . 88)\n  (:start . 82) (:id . 58))\n ((:tag . "NN") (:stem . "improvement") (:form . "improvement") (:end . 100)\n  (:start . 89) (:id . 59))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 103) (:start . 101)\n  (:id . 60))\n ((:tag . "CD") (:stem . "145.3") (:form . "145.3") (:end . 109)\n  (:start . 104) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 110) (:start . 109)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s15.214) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504953@unknown@formal@none@1@S@According to the paired Student's t-test (p-value is 0.0045 shown in Table S4 Additional file 8), (PS)2-v2 applying the multiple-model strategy significantly improved the GDT_TS scores when the sequence identity between the target and the template is less than 20%.@(((:tag . "VBG") (:stem . "accord") (:form . "According") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 12) (:start . 10)\n  (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 16) (:start . 13)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "paired") (:form . "paired") (:end . 23)\n  (:start . 17) (:id . 45))\n ((:tag . "NNP") (:stem . "Student") (:form . "Student") (:end . 31)\n  (:start . 24) (:id . 46))\n ((:tag . "POS") (:stem . "'s") (:form . "'s") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "NN") (:stem . "t-test") (:form . "t-test") (:end . 40)\n  (:start . 34) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "NN") (:stem . "p-value") (:form . "p-value") (:end . 49)\n  (:start . 42) (:id . 50))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "CD") (:stem . "0.0045") (:form . "0.0045") (:end . 59)\n  (:start . 53) (:id . 52))\n ((:tag . "VBN") (:stem . "show") (:form . "shown") (:end . 65) (:start . 60)\n  (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 68) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "table") (:form . "Table") (:end . 74) (:start . 69)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "S4") (:form . "S4") (:end . 77) (:start . 75)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "additional") (:form . "Additional") (:end . 88)\n  (:start . 78) (:id . 57))\n ((:tag . "NN") (:stem . "file") (:form . "file") (:end . 93) (:start . 89)\n  (:id . 58))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 95) (:start . 94)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 96) (:start . 95)\n  (:id . 60))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 99) (:start . 98)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 106)\n  (:start . 99) (:id . 63))\n ((:tag . "VBG") (:stem . "apply") (:form . "applying") (:end . 115)\n  (:start . 107) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 119) (:start . 116)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "multiple-model") (:form . "multiple-model")\n  (:end . 134) (:start . 120) (:id . 66))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 143)\n  (:start . 135) (:id . 67))\n ((:tag . "RB") (:stem . "significantly") (:form . "significantly")\n  (:end . 157) (:start . 144) (:id . 68))\n ((:tag . "VBD") (:stem . "improve") (:form . "improved") (:end . 166)\n  (:start . 158) (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 170) (:start . 167)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 177)\n  (:start . 171) (:id . 71))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 184)\n  (:start . 178) (:id . 72))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 189) (:start . 185)\n  (:id . 73))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 193) (:start . 190)\n  (:id . 74))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 202)\n  (:start . 194) (:id . 75))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 211)\n  (:start . 203) (:id . 76))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 219)\n  (:start . 212) (:id . 77))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 223) (:start . 220)\n  (:id . 78))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 230)\n  (:start . 224) (:id . 79))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 234) (:start . 231)\n  (:id . 80))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 238) (:start . 235)\n  (:id . 81))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 247)\n  (:start . 239) (:id . 82))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 250) (:start . 248)\n  (:id . 83))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 255) (:start . 251)\n  (:id . 84))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 260) (:start . 256)\n  (:id . 85))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 263) (:start . 261)\n  (:id . 86))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 264) (:start . 263)\n  (:id . 87))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 265) (:start . 264)\n  (:id . 88)))@@@1@47@((:identifiers (:sid . :s15.215) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504954@unknown@formal@none@1@S@(PS)2-v2 results for using single-model and multiple-model strategies on 154 targets in CASP8 based on GDT_TS scores.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 16)\n  (:start . 9) (:id . 44))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "single-model") (:form . "single-model") (:end . 39)\n  (:start . 27) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "multiple-model") (:form . "multiple-model")\n  (:end . 58) (:start . 44) (:id . 49))\n ((:tag . "NNS") (:stem . "strategy") (:form . "strategies") (:end . 69)\n  (:start . 59) (:id . 50))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 72) (:start . 70)\n  (:id . 51))\n ((:tag . "CD") (:stem . "154") (:form . "154") (:end . 76) (:start . 73)\n  (:id . 52))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 84)\n  (:start . 77) (:id . 53))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 87) (:start . 85)\n  (:id . 54))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 93) (:start . 88)\n  (:id . 55))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 99) (:start . 94)\n  (:id . 56))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 102) (:start . 100)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 109)\n  (:start . 103) (:id . 58))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 116)\n  (:start . 110) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 117) (:start . 116)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.216) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504955@unknown@formal@none@1@S@(PS)2-v2 improves and decreases the GDT_TS scores for 23 and 4 targets, respectively, when the multiple-model method is utilized.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . "VBZ") (:stem . "improve") (:form . "improves") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 21) (:start . 18)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "decrease") (:form . "decreases") (:end . 31)\n  (:start . 22) (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 35) (:start . 32)\n  (:id . 47))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 42)\n  (:start . 36) (:id . 48))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 49)\n  (:start . 43) (:id . 49))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 53) (:start . 50)\n  (:id . 50))\n ((:tag . "CD") (:stem . "23") (:form . "23") (:end . 56) (:start . 54)\n  (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 60) (:start . 57)\n  (:id . 52))\n ((:tag . "CD") (:stem . "4") (:form . "4") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 70)\n  (:start . 63) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 71) (:start . 70)\n  (:id . 55))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 84)\n  (:start . 72) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 85) (:start . 84)\n  (:id . 57))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 90) (:start . 86)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 94) (:start . 91)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "multiple-model") (:form . "multiple-model")\n  (:end . 109) (:start . 95) (:id . 60))\n ((:tag . "NN") (:stem . "method") (:form . "method") (:end . 116)\n  (:start . 110) (:id . 61))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 119) (:start . 117)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "utilize") (:form . "utilized") (:end . 128)\n  (:start . 120) (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 129) (:start . 128)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s15.217) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504956@unknown@formal@none@1@S@For the other 127 targets, (PS)2-v2 obtains the same GDT_TS scores.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "other") (:form . "other") (:end . 13) (:start . 8)\n  (:id . 44))\n ((:tag . "CD") (:stem . "127") (:form . "127") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NNS") (:stem . "target") (:form . "targets") (:end . 25)\n  (:start . 18) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 26) (:start . 25)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 28) (:start . 27)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 35)\n  (:start . 28) (:id . 49))\n ((:tag . "VBZ") (:stem . "obtain") (:form . "obtains") (:end . 43)\n  (:start . 36) (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 47) (:start . 44)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "same") (:form . "same") (:end . 52) (:start . 48)\n  (:id . 52))\n ((:tag . "NN") (:stem . "gdt_ts") (:form . "GDT_TS") (:end . 59)\n  (:start . 53) (:id . 53))\n ((:tag . "NNS") (:stem . "score") (:form . "scores") (:end . 66)\n  (:start . 60) (:id . 54))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 67) (:start . 66)\n  (:id . 55)))@@@1@14@((:identifiers (:sid . :s15.218) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504957@unknown@formal@none@1@S@The symbols "+", "▫" and "×" represent the performance when the sequence identity (SI) ≥ 30%, between 30% and 20%, and less than 20%, respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "symbol") (:form . "symbols") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 13) (:start . 12)\n  (:id . 44))\n ((:tag . "SYM") (:stem . "+") (:form . "+") (:end . 14) (:start . 13)\n  (:id . 45))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 15) (:start . 14)\n  (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 16) (:start . 15)\n  (:id . 47))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 18) (:start . 17)\n  (:id . 48))\n ((:tag . "UH") (:stem . "▫") (:form . "▫") (:end . 19) (:start . 18)\n  (:id . 49))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 20) (:start . 19)\n  (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 24) (:start . 21)\n  (:id . 51))\n ((:tag . "``") (:stem . "``") (:form . "“") (:end . 26) (:start . 25)\n  (:id . 52))\n ((:tag . ",") (:stem . "×") (:form . "×") (:end . 27) (:start . 26)\n  (:id . 53))\n ((:tag . "''") (:stem . "''") (:form . "”") (:end . 28) (:start . 27)\n  (:id . 54))\n ((:tag . "VBP") (:stem . "represent") (:form . "represent") (:end . 38)\n  (:start . 29) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 42) (:start . 39)\n  (:id . 56))\n ((:tag . "NN") (:stem . "performance") (:form . "performance") (:end . 54)\n  (:start . 43) (:id . 57))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 59) (:start . 55)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 63) (:start . 60)\n  (:id . 59))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 72)\n  (:start . 64) (:id . 60))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 81)\n  (:start . 73) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 83) (:start . 82)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "SI") (:form . "SI") (:end . 85) (:start . 83)\n  (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 86) (:start . 85)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "≥") (:form . "≥") (:end . 88) (:start . 87)\n  (:id . 65))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 91) (:start . 89)\n  (:id . 66))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 92) (:start . 91)\n  (:id . 67))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 93) (:start . 92)\n  (:id . 68))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 101)\n  (:start . 94) (:id . 69))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 104) (:start . 102)\n  (:id . 70))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 105) (:start . 104)\n  (:id . 71))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 109) (:start . 106)\n  (:id . 72))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 112) (:start . 110)\n  (:id . 73))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 113) (:start . 112)\n  (:id . 74))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 114) (:start . 113)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 118) (:start . 115)\n  (:id . 76))\n ((:tag . "JJR") (:stem . "less") (:form . "less") (:end . 123) (:start . 119)\n  (:id . 77))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 128) (:start . 124)\n  (:id . 78))\n ((:tag . "CD") (:stem . "20") (:form . "20") (:end . 131) (:start . 129)\n  (:id . 79))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 132) (:start . 131)\n  (:id . 80))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 133) (:start . 132)\n  (:id . 81))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 146)\n  (:start . 134) (:id . 82))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 147) (:start . 146)\n  (:id . 83)))@@@1@42@((:identifiers (:sid . :s15.219) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504958@unknown@formal@none@1@S@The target T0471 selected from CASP8 was taken as an example to describe the structure modeling of the (PS)2-v2 server using multiple-model strategy (Figure 7).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "t0471") (:form . "T0471") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 52) (:start . 50)\n  (:id . 51))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 60)\n  (:start . 53) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 63) (:start . 61)\n  (:id . 53))\n ((:tag . "VB") (:stem . "describe") (:form . "describe") (:end . 72)\n  (:start . 64) (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 86)\n  (:start . 77) (:id . 56))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 95)\n  (:start . 87) (:id . 57))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 98) (:start . 96)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 104) (:start . 103)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 111)\n  (:start . 104) (:id . 61))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 118)\n  (:start . 112) (:id . 62))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 124) (:start . 119)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "multiple-model") (:form . "multiple-model")\n  (:end . 139) (:start . 125) (:id . 64))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 148)\n  (:start . 140) (:id . 65))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 150) (:start . 149)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 156)\n  (:start . 150) (:id . 67))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 158) (:start . 157)\n  (:id . 68))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 159) (:start . 158)\n  (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 160) (:start . 159)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s15.220) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504959@unknown@formal@none@1@S@When the multiple-model strategy was not considered, (PS)2-v2 selected the 2-dehydro-3-deoxyphosphooctonate aldolase (PDB code 2nwr) as the best template with an E-value of 0.055.@(((:tag . "WRB") (:stem . "when") (:form . "When") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 8) (:start . 5)\n  (:id . 43))\n ((:tag . "JJ") (:stem . "multiple-model") (:form . "multiple-model")\n  (:end . 23) (:start . 9) (:id . 44))\n ((:tag . "NN") (:stem . "strategy") (:form . "strategy") (:end . 32)\n  (:start . 24) (:id . 45))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 36) (:start . 33)\n  (:id . 46))\n ((:tag . "RB") (:stem . "not") (:form . "not") (:end . 40) (:start . 37)\n  (:id . 47))\n ((:tag . "VBN") (:stem . "consider") (:form . "considered") (:end . 51)\n  (:start . 41) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 52) (:start . 51)\n  (:id . 49))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 50))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 61)\n  (:start . 54) (:id . 51))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 70)\n  (:start . 62) (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 74) (:start . 71)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "2-dehydro-3-deoxyphosphooctonate")\n  (:form . "2-dehydro-3-deoxyphosphooctonate") (:end . 107) (:start . 75)\n  (:id . 54))\n ((:tag . "NN") (:stem . "aldolase") (:form . "aldolase") (:end . 116)\n  (:start . 108) (:id . 55))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 121) (:start . 118)\n  (:id . 57))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 126) (:start . 122)\n  (:id . 58))\n ((:tag . "NN") (:stem . "2nwr") (:form . "2nwr") (:end . 131) (:start . 127)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 60))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 135) (:start . 133)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 139) (:start . 136)\n  (:id . 62))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 144) (:start . 140)\n  (:id . 63))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 153)\n  (:start . 145) (:id . 64))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 158) (:start . 154)\n  (:id . 65))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 161) (:start . 159)\n  (:id . 66))\n ((:tag . "NN") (:stem . "e-value") (:form . "E-value") (:end . 169)\n  (:start . 162) (:id . 67))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 172) (:start . 170)\n  (:id . 68))\n ((:tag . "CD") (:stem . "0.055") (:form . "0.055") (:end . 178)\n  (:start . 173) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 179) (:start . 178)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s15.221) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504960@unknown@formal@none@1@S@GDT_TS score of this model is 32.67.@(((:tag . "NN") (:stem . "gdt_ts") (:form . "GDT_TS") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 12) (:start . 7)\n  (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 15) (:start . 13)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 26) (:start . 21)\n  (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 29) (:start . 27)\n  (:id . 47))\n ((:tag . "CD") (:stem . "32.67") (:form . "32.67") (:end . 35) (:start . 30)\n  (:id . 48))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 36) (:start . 35)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s15.222) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504961@unknown@formal@none@1@S@If we considered the top-ranking 5 structures (PDB codes 2nwr, 1pea, 1nv8, 1ufr and 1v2d) as the modeling templates, (PS)2-v2 generated 6 alternative target-template alignments for each template, and obtained 30 alignments for this target.@(((:tag . "IN") (:stem . "if") (:form . "If") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "PRP") (:stem . "we") (:form . "we") (:end . 5) (:start . 3)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "consider") (:form . "considered") (:end . 16)\n  (:start . 6) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "top-ranking") (:form . "top-ranking") (:end . 32)\n  (:start . 21) (:id . 46))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 34) (:start . 33)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 45)\n  (:start . 35) (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 50) (:start . 47)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "code") (:form . "codes") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "2nwr") (:form . "2nwr") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 53))\n ((:tag . "NN") (:stem . "1pea") (:form . "1pea") (:end . 67) (:start . 63)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 68) (:start . 67)\n  (:id . 55))\n ((:tag . "CD") (:stem . "1nv8") (:form . "1nv8") (:end . 73) (:start . 69)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 57))\n ((:tag . "CD") (:stem . "1ufr") (:form . "1ufr") (:end . 79) (:start . 75)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 83) (:start . 80)\n  (:id . 59))\n ((:tag . "CD") (:stem . "1v2d") (:form . "1v2d") (:end . 88) (:start . 84)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 89) (:start . 88)\n  (:id . 61))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 92) (:start . 90)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 96) (:start . 93)\n  (:id . 63))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 105)\n  (:start . 97) (:id . 64))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 115)\n  (:start . 106) (:id . 65))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 116) (:start . 115)\n  (:id . 66))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n  (:id . 67))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 125)\n  (:start . 118) (:id . 68))\n ((:tag . "VBD") (:stem . "generate") (:form . "generated") (:end . 135)\n  (:start . 126) (:id . 69))\n ((:tag . "CD") (:stem . "6") (:form . "6") (:end . 137) (:start . 136)\n  (:id . 70))\n ((:tag . "JJ") (:stem . "alternative") (:form . "alternative") (:end . 149)\n  (:start . 138) (:id . 71))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 165) (:start . 150) (:id . 72))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 176)\n  (:start . 166) (:id . 73))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 180) (:start . 177)\n  (:id . 74))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 185) (:start . 181)\n  (:id . 75))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 194)\n  (:start . 186) (:id . 76))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 195) (:start . 194)\n  (:id . 77))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 199) (:start . 196)\n  (:id . 78))\n ((:tag . "VBN") (:stem . "obtain") (:form . "obtained") (:end . 208)\n  (:start . 200) (:id . 79))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 211) (:start . 209)\n  (:id . 80))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 222)\n  (:start . 212) (:id . 81))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 226) (:start . 223)\n  (:id . 82))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 231) (:start . 227)\n  (:id . 83))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 238)\n  (:start . 232) (:id . 84))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 239) (:start . 238)\n  (:id . 85)))@@@1@44@((:identifiers (:sid . :s15.223) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504962@unknown@formal@none@1@S@The software MODELLER was then applied to generate 30 structures for these 30 target-template alignments.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "software") (:form . "software") (:end . 12)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "modeller") (:form . "MODELLER") (:end . 21)\n  (:start . 13) (:id . 44))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 25) (:start . 22)\n  (:id . 45))\n ((:tag . "RB") (:stem . "then") (:form . "then") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "VBN") (:stem . "apply") (:form . "applied") (:end . 38)\n  (:start . 31) (:id . 47))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 41) (:start . 39)\n  (:id . 48))\n ((:tag . "VB") (:stem . "generate") (:form . "generate") (:end . 50)\n  (:start . 42) (:id . 49))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 53) (:start . 51)\n  (:id . 50))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 64)\n  (:start . 54) (:id . 51))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 68) (:start . 65)\n  (:id . 52))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 74) (:start . 69)\n  (:id . 53))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 77) (:start . 75)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 93) (:start . 78) (:id . 55))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 104)\n  (:start . 94) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 105) (:start . 104)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s15.224) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504963@unknown@formal@none@1@S@Figure 7 shows the best model with the highest LGscores, assessing by the program ProQ, for each template.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "CD") (:stem . "7") (:form . "7") (:end . 8) (:start . 7)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "show") (:form . "shows") (:end . 14) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 45))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 23) (:start . 19)\n  (:id . 46))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 29) (:start . 24)\n  (:id . 47))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 34) (:start . 30)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 38) (:start . 35)\n  (:id . 49))\n ((:tag . "JJS") (:stem . "high") (:form . "highest") (:end . 46)\n  (:start . 39) (:id . 50))\n ((:tag . "NNS") (:stem . "lgscore") (:form . "LGscores") (:end . 55)\n  (:start . 47) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "assess") (:form . "assessing") (:end . 66)\n  (:start . 57) (:id . 53))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 69) (:start . 67)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 55))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 81)\n  (:start . 74) (:id . 56))\n ((:tag . "NNP") (:stem . "ProQ") (:form . "ProQ") (:end . 86) (:start . 82)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 87) (:start . 86)\n  (:id . 58))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 91) (:start . 88)\n  (:id . 59))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 96) (:start . 92)\n  (:id . 60))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 105)\n  (:start . 97) (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 106) (:start . 105)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s15.225) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504964@unknown@formal@none@1@S@The model generated by the template 1nv8A was selected as the final model, because it had the best LGscore (2.838) among these 30 models.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "VBN") (:stem . "generate") (:form . "generated") (:end . 19)\n  (:start . 10) (:id . 44))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 35)\n  (:start . 27) (:id . 47))\n ((:tag . "NNP") (:stem . "1nv8A") (:form . "1nv8A") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 45) (:start . 42)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 54)\n  (:start . 46) (:id . 50))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 57) (:start . 55)\n  (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 61) (:start . 58)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 67) (:start . 62)\n  (:id . 53))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 73) (:start . 68)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "IN") (:stem . "because") (:form . "because") (:end . 82)\n  (:start . 75) (:id . 56))\n ((:tag . "PRP") (:stem . "it") (:form . "it") (:end . 85) (:start . 83)\n  (:id . 57))\n ((:tag . "VBD") (:stem . "have") (:form . "had") (:end . 89) (:start . 86)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 93) (:start . 90)\n  (:id . 59))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 98) (:start . 94)\n  (:id . 60))\n ((:tag . "NN") (:stem . "lgscore") (:form . "LGscore") (:end . 106)\n  (:start . 99) (:id . 61))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 108) (:start . 107)\n  (:id . 62))\n ((:tag . "CD") (:stem . "2.838") (:form . "2.838") (:end . 113)\n  (:start . 108) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 114) (:start . 113)\n  (:id . 64))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 120)\n  (:start . 115) (:id . 65))\n ((:tag . "DT") (:stem . "these") (:form . "these") (:end . 126)\n  (:start . 121) (:id . 66))\n ((:tag . "CD") (:stem . "30") (:form . "30") (:end . 129) (:start . 127)\n  (:id . 67))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 136)\n  (:start . 130) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 137) (:start . 136)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s15.226) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504965@unknown@formal@none@1@S@The GDT_TS score of this final model is 61.65.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 10)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 19) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 24) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 30) (:start . 25)\n  (:id . 47))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 36) (:start . 31)\n  (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 39) (:start . 37)\n  (:id . 49))\n ((:tag . "CD") (:stem . "61.65") (:form . "61.65") (:end . 45) (:start . 40)\n  (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 46) (:start . 45)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s15.227) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504966@unknown@formal@none@1@S@The (PS)2-v2 server using multiple models is often able to effectively improve accuracies when the E-value between the target and the template is more than 0.01.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 5) (:start . 4) (:id . 43))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 12)\n  (:start . 5) (:id . 44))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 19)\n  (:start . 13) (:id . 45))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 25) (:start . 20)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 34)\n  (:start . 26) (:id . 47))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 41)\n  (:start . 35) (:id . 48))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 44) (:start . 42)\n  (:id . 49))\n ((:tag . "RB") (:stem . "often") (:form . "often") (:end . 50) (:start . 45)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "able") (:form . "able") (:end . 55) (:start . 51)\n  (:id . 51))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 58) (:start . 56)\n  (:id . 52))\n ((:tag . "RB") (:stem . "effectively") (:form . "effectively") (:end . 70)\n  (:start . 59) (:id . 53))\n ((:tag . "VB") (:stem . "improve") (:form . "improve") (:end . 78)\n  (:start . 71) (:id . 54))\n ((:tag . "NNS") (:stem . "accuracy") (:form . "accuracies") (:end . 89)\n  (:start . 79) (:id . 55))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 94) (:start . 90)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 98) (:start . 95)\n  (:id . 57))\n ((:tag . "NN") (:stem . "e-value") (:form . "E-value") (:end . 106)\n  (:start . 99) (:id . 58))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 114)\n  (:start . 107) (:id . 59))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 118) (:start . 115)\n  (:id . 60))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 125)\n  (:start . 119) (:id . 61))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 129) (:start . 126)\n  (:id . 62))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 133) (:start . 130)\n  (:id . 63))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 142)\n  (:start . 134) (:id . 64))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 145) (:start . 143)\n  (:id . 65))\n ((:tag . "JJR") (:stem . "more") (:form . "more") (:end . 150) (:start . 146)\n  (:id . 66))\n ((:tag . "IN") (:stem . "than") (:form . "than") (:end . 155) (:start . 151)\n  (:id . 67))\n ((:tag . "CD") (:stem . "0.01") (:form . "0.01") (:end . 160) (:start . 156)\n  (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 161) (:start . 160)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s15.228) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504967@unknown@formal@none@1@S@The average GDT_TS improvements are 8.53 and 2.23, respectively, when the E-value ≥ 0.01 and E-value ≤ 1e-6.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "average") (:form . "average") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "NNP") (:stem . "GDT_TS") (:form . "GDT_TS") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "NNS") (:stem . "improvement") (:form . "improvements") (:end . 31)\n  (:start . 19) (:id . 45))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 35) (:start . 32)\n  (:id . 46))\n ((:tag . "CD") (:stem . "8.53") (:form . "8.53") (:end . 40) (:start . 36)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "CD") (:stem . "2.23") (:form . "2.23") (:end . 49) (:start . 45)\n  (:id . 49))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 50) (:start . 49)\n  (:id . 50))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 63)\n  (:start . 51) (:id . 51))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 64) (:start . 63)\n  (:id . 52))\n ((:tag . "WRB") (:stem . "when") (:form . "when") (:end . 69) (:start . 65)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 73) (:start . 70)\n  (:id . 54))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 81)\n  (:start . 74) (:id . 55))\n ((:tag . "NNP") (:stem . "≥") (:form . "≥") (:end . 83) (:start . 82)\n  (:id . 56))\n ((:tag . "CD") (:stem . "0.01") (:form . "0.01") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 92) (:start . 89)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "E-value") (:form . "E-value") (:end . 100)\n  (:start . 93) (:id . 59))\n ((:tag . "NNP") (:stem . "≤") (:form . "≤") (:end . 102) (:start . 101)\n  (:id . 60))\n ((:tag . "CD") (:stem . "1e-6") (:form . "1e-6") (:end . 107) (:start . 103)\n  (:id . 61))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 108) (:start . 107)\n  (:id . 62)))@@@1@21@((:identifiers (:sid . :s15.229) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504968@unknown@formal@none@1@S@(PS)2-v2 models the target T0471 in CASP 8 using multiple models.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 8)\n  (:start . 1) (:id . 43))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 15) (:start . 9)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 26)\n  (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "t0471") (:form . "T0471") (:end . 32) (:start . 27)\n  (:id . 47))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 35) (:start . 33)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "CASP") (:form . "CASP") (:end . 40) (:start . 36)\n  (:id . 49))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 42) (:start . 41)\n  (:id . 50))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 48) (:start . 43)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 57)\n  (:start . 49) (:id . 52))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 64)\n  (:start . 58) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s15.230) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504969@unknown@formal@none@1@S@This server models T0471 by selecting top-ranking five structures (PDB code 2nwrA, 1peaA, 1nv8A, 1ufrA and 1v2dA) as templates using S2A2 matrix and PSSM scoring matrices.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 18)\n  (:start . 12) (:id . 44))\n ((:tag . "NN") (:stem . "t0471") (:form . "T0471") (:end . 24) (:start . 19)\n  (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 27) (:start . 25)\n  (:id . 46))\n ((:tag . "VBG") (:stem . "select") (:form . "selecting") (:end . 37)\n  (:start . 28) (:id . 47))\n ((:tag . "JJ") (:stem . "top-ranking") (:form . "top-ranking") (:end . 49)\n  (:start . 38) (:id . 48))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 54) (:start . 50)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 65)\n  (:start . 55) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 70) (:start . 67)\n  (:id . 52))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 75) (:start . 71)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "2nwrA") (:form . "2nwrA") (:end . 81) (:start . 76)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 82) (:start . 81)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "1peaA") (:form . "1peaA") (:end . 88) (:start . 83)\n  (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 89) (:start . 88)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "1nv8A") (:form . "1nv8A") (:end . 95) (:start . 90)\n  (:id . 58))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 96) (:start . 95)\n  (:id . 59))\n ((:tag . "NNP") (:stem . "1ufrA") (:form . "1ufrA") (:end . 102)\n  (:start . 97) (:id . 60))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 106) (:start . 103)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "1v2dA") (:form . "1v2dA") (:end . 112)\n  (:start . 107) (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 113) (:start . 112)\n  (:id . 63))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 116) (:start . 114)\n  (:id . 64))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 126)\n  (:start . 117) (:id . 65))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 132) (:start . 127)\n  (:id . 66))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 137) (:start . 133)\n  (:id . 67))\n ((:tag . "NN") (:stem . "matrix") (:form . "matrix") (:end . 144)\n  (:start . 138) (:id . 68))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 148) (:start . 145)\n  (:id . 69))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 153) (:start . 149)\n  (:id . 70))\n ((:tag . "NN") (:stem . "scoring") (:form . "scoring") (:end . 161)\n  (:start . 154) (:id . 71))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrices") (:end . 170)\n  (:start . 162) (:id . 72))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 73)))@@@1@32@((:identifiers (:sid . :s15.231) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504970@unknown@formal@none@1@S@For each template, (PS)2-v2 generates 5 structures and (D) the final model (1nv8) is identified by the program ProQ based on LGscore.@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "each") (:form . "each") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 20) (:start . 19)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 27)\n  (:start . 20) (:id . 47))\n ((:tag . "VBZ") (:stem . "generate") (:form . "generates") (:end . 37)\n  (:start . 28) (:id . 48))\n ((:tag . "CD") (:stem . "5") (:form . "5") (:end . 39) (:start . 38)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "structure") (:form . "structures") (:end . 50)\n  (:start . 40) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 56) (:start . 55)\n  (:id . 52))\n ((:tag . "NNP") (:stem . "D") (:form . "D") (:end . 57) (:start . 56)\n  (:id . 53))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 58) (:start . 57)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 55))\n ((:tag . "JJ") (:stem . "final") (:form . "final") (:end . 68) (:start . 63)\n  (:id . 56))\n ((:tag . "NN") (:stem . "model") (:form . "model") (:end . 74) (:start . 69)\n  (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 76) (:start . 75)\n  (:id . 58))\n ((:tag . "CD") (:stem . "1nv8") (:form . "1nv8") (:end . 80) (:start . 76)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 81) (:start . 80)\n  (:id . 60))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 84) (:start . 82)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "identify") (:form . "identified") (:end . 95)\n  (:start . 85) (:id . 62))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 98) (:start . 96)\n  (:id . 63))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 64))\n ((:tag . "NN") (:stem . "program") (:form . "program") (:end . 110)\n  (:start . 103) (:id . 65))\n ((:tag . "NNP") (:stem . "ProQ") (:form . "ProQ") (:end . 115) (:start . 111)\n  (:id . 66))\n ((:tag . "VBN") (:stem . "base") (:form . "based") (:end . 121)\n  (:start . 116) (:id . 67))\n ((:tag . "IN") (:stem . "on") (:form . "on") (:end . 124) (:start . 122)\n  (:id . 68))\n ((:tag . "NNP") (:stem . "LGscore") (:form . "LGscore") (:end . 132)\n  (:start . 125) (:id . 69))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 133) (:start . 132)\n  (:id . 70)))@@@1@29@((:identifiers (:sid . :s15.232) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504971@unknown@formal@none@1@S@T0409 in CASP8@(((:tag . "NNP") (:stem . "T0409") (:form . "T0409") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 8) (:start . 6)\n  (:id . 43))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 14) (:start . 9)\n  (:id . 44)))@@@1@3@((:identifiers (:sid . :s15.233) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SubSectionTitle|)))@oe@9-2-2011
5504972@unknown@formal@none@1@S@The target T0409 selected from CASP8 was taken to describe the structure modeling of the (PS)2-v2 server (Figure 8).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "t0409") (:form . "T0409") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 25)\n  (:start . 17) (:id . 45))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 30) (:start . 26)\n  (:id . 46))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 36) (:start . 31)\n  (:id . 47))\n ((:tag . "VBD") (:stem . "be") (:form . "was") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "take") (:form . "taken") (:end . 46) (:start . 41)\n  (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 49) (:start . 47)\n  (:id . 50))\n ((:tag . "VB") (:stem . "describe") (:form . "describe") (:end . 58)\n  (:start . 50) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 62) (:start . 59)\n  (:id . 52))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 72)\n  (:start . 63) (:id . 53))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 81)\n  (:start . 73) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 84) (:start . 82)\n  (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 88) (:start . 85)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 90) (:start . 89)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 97)\n  (:start . 90) (:id . 58))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 104)\n  (:start . 98) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 106) (:start . 105)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 112)\n  (:start . 106) (:id . 61))\n ((:tag . "CD") (:stem . "8") (:form . "8") (:end . 114) (:start . 113)\n  (:id . 62))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 115) (:start . 114)\n  (:id . 63))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 116) (:start . 115)\n  (:id . 64)))@@@1@23@((:identifiers (:sid . :s15.234) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504973@unknown@formal@none@1@S@The target is the BIG_1156.2 domain of putative penicillin-binding protein MrcA from Nitrosomonas europaea ATCC 19718.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "big_1156.2") (:form . "BIG_1156.2") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 38) (:start . 36)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 47)\n  (:start . 39) (:id . 49))\n ((:tag . "JJ") (:stem . "penicillin-binding") (:form . "penicillin-binding")\n  (:end . 66) (:start . 48) (:id . 50))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 74)\n  (:start . 67) (:id . 51))\n ((:tag . "NNP") (:stem . "MrcA") (:form . "MrcA") (:end . 79) (:start . 75)\n  (:id . 52))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 84) (:start . 80)\n  (:id . 53))\n ((:tag . "NNP") (:stem . "Nitrosomonas") (:form . "Nitrosomonas") (:end . 97)\n  (:start . 85) (:id . 54))\n ((:tag . "NN") (:stem . "europaea") (:form . "europaea") (:end . 106)\n  (:start . 98) (:id . 55))\n ((:tag . "NNP") (:stem . "ATCC") (:form . "ATCC") (:end . 111) (:start . 107)\n  (:id . 56))\n ((:tag . "CD") (:stem . "19718") (:form . "19718") (:end . 117)\n  (:start . 112) (:id . 57))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 58)))@@@1@17@((:hcues ((:id . :x15.235.1) (:span 39 47)))\n (:hscopes ((:id . :x15.235.1) (:span 39 117)))\n (:identifiers (:sid . :s15.235) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504974@unknown@formal@none@1@S@This server yielded the best GDT_TS score (77.8) among all participating servers for this target.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 11) (:start . 5)\n  (:id . 43))\n ((:tag . "VBD") (:stem . "yield") (:form . "yielded") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 28) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "gdt_ts") (:form . "GDT_TS") (:end . 35)\n  (:start . 29) (:id . 47))\n ((:tag . "NN") (:stem . "score") (:form . "score") (:end . 41) (:start . 36)\n  (:id . 48))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 49))\n ((:tag . "CD") (:stem . "77.8") (:form . "77.8") (:end . 47) (:start . 43)\n  (:id . 50))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "IN") (:stem . "among") (:form . "among") (:end . 54) (:start . 49)\n  (:id . 52))\n ((:tag . "DT") (:stem . "all") (:form . "all") (:end . 58) (:start . 55)\n  (:id . 53))\n ((:tag . "VBG") (:stem . "participate") (:form . "participating") (:end . 72)\n  (:start . 59) (:id . 54))\n ((:tag . "NNS") (:stem . "server") (:form . "servers") (:end . 80)\n  (:start . 73) (:id . 55))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 89) (:start . 85)\n  (:id . 57))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 96)\n  (:start . 90) (:id . 58))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 97) (:start . 96)\n  (:id . 59)))@@@1@18@((:identifiers (:sid . :s15.236) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504975@unknown@formal@none@1@S@An example of the prediction results of the target T0409 from the (PS)2-v2 server.@(((:tag . "DT") (:stem . "an") (:form . "An") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "example") (:form . "example") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 13) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 28)\n  (:start . 18) (:id . 46))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 36)\n  (:start . 29) (:id . 47))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 39) (:start . 37)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 49))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 50)\n  (:start . 44) (:id . 50))\n ((:tag . "NN") (:stem . "t0409") (:form . "T0409") (:end . 56) (:start . 51)\n  (:id . 51))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 61) (:start . 57)\n  (:id . 52))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 65) (:start . 62)\n  (:id . 53))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 67) (:start . 66)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 74)\n  (:start . 67) (:id . 55))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 81)\n  (:start . 75) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 82) (:start . 81)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s15.237) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504976@unknown@formal@none@1@S@The alignment and predicted structure of the BIG_1156.2 domain of putative penicillin-binding protein MrcA from Nitrosomonas europaea ATCC 19718 using the (PS)2-v2 server.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 13)\n  (:start . 4) (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 17) (:start . 14)\n  (:id . 44))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 27)\n  (:start . 18) (:id . 45))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 37)\n  (:start . 28) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 40) (:start . 38)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 44) (:start . 41)\n  (:id . 48))\n ((:tag . "NN") (:stem . "big_1156.2") (:form . "BIG_1156.2") (:end . 55)\n  (:start . 45) (:id . 49))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 62)\n  (:start . 56) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 65) (:start . 63)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "putative") (:form . "putative") (:end . 74)\n  (:start . 66) (:id . 52))\n ((:tag . "JJ") (:stem . "penicillin-binding") (:form . "penicillin-binding")\n  (:end . 93) (:start . 75) (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 101)\n  (:start . 94) (:id . 54))\n ((:tag . "NNP") (:stem . "MrcA") (:form . "MrcA") (:end . 106) (:start . 102)\n  (:id . 55))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 111) (:start . 107)\n  (:id . 56))\n ((:tag . "NNP") (:stem . "Nitrosomonas") (:form . "Nitrosomonas")\n  (:end . 124) (:start . 112) (:id . 57))\n ((:tag . "NN") (:stem . "europaea") (:form . "europaea") (:end . 133)\n  (:start . 125) (:id . 58))\n ((:tag . "NNP") (:stem . "ATCC") (:form . "ATCC") (:end . 138) (:start . 134)\n  (:id . 59))\n ((:tag . "CD") (:stem . "19718") (:form . "19718") (:end . 144)\n  (:start . 139) (:id . 60))\n ((:tag . "VBG") (:stem . "use") (:form . "using") (:end . 150) (:start . 145)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 154) (:start . 151)\n  (:id . 62))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 156) (:start . 155)\n  (:id . 63))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 163)\n  (:start . 156) (:id . 64))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 170)\n  (:start . 164) (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 171) (:start . 170)\n  (:id . 66)))@@@1@25@((:hcues ((:id . :x15.238.1) (:span 66 74)))\n (:hscopes ((:id . :x15.238.1) (:span 66 106)))\n (:identifiers (:sid . :s15.238) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504977@unknown@formal@none@1@S@(A) The alignment between the query and the selected template, translation initiation factor 5A protein (PDB code 1bkbA), from Pyrobaculum aerophilum.@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "DT") (:stem . "a") (:form . "A") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 17)\n  (:start . 8) (:id . 46))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 25)\n  (:start . 18) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 29) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 35) (:start . 30)\n  (:id . 49))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 39) (:start . 36)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 43) (:start . 40)\n  (:id . 51))\n ((:tag . "VBN") (:stem . "select") (:form . "selected") (:end . 52)\n  (:start . 44) (:id . 52))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 61)\n  (:start . 53) (:id . 53))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 62) (:start . 61)\n  (:id . 54))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 74)\n  (:start . 63) (:id . 55))\n ((:tag . "NN") (:stem . "initiation") (:form . "initiation") (:end . 85)\n  (:start . 75) (:id . 56))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 92)\n  (:start . 86) (:id . 57))\n ((:tag . "NN") (:stem . "5a") (:form . "5A") (:end . 95) (:start . 93)\n  (:id . 58))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 103)\n  (:start . 96) (:id . 59))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n  (:id . 60))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 108) (:start . 105)\n  (:id . 61))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 113) (:start . 109)\n  (:id . 62))\n ((:tag . "NNP") (:stem . "1bkbA") (:form . "1bkbA") (:end . 119)\n  (:start . 114) (:id . 63))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 120) (:start . 119)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 121) (:start . 120)\n  (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 126) (:start . 122)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Pyrobaculum") (:form . "Pyrobaculum") (:end . 138)\n  (:start . 127) (:id . 67))\n ((:tag . "NN") (:stem . "aerophilum") (:form . "aerophilum") (:end . 149)\n  (:start . 139) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 150) (:start . 149)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s15.239) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504978@unknown@formal@none@1@S@(B) The superposition, the native structure of T0409 (broad, PDB code 3d0f) and the predicted structure (thin).@(((:tag . "(") (:stem . "(") (:form . "(") (:end . 1) (:start . 0) (:id . 42))\n ((:tag . "NNP") (:stem . "B") (:form . "B") (:end . 2) (:start . 1)\n  (:id . 43))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 3) (:start . 2) (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "The") (:end . 7) (:start . 4)\n  (:id . 45))\n ((:tag . "NN") (:stem . "superposition") (:form . "superposition")\n  (:end . 21) (:start . 8) (:id . 46))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 22) (:start . 21)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 33)\n  (:start . 27) (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 43)\n  (:start . 34) (:id . 50))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 46) (:start . 44)\n  (:id . 51))\n ((:tag . "NNP") (:stem . "T0409") (:form . "T0409") (:end . 52) (:start . 47)\n  (:id . 52))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 54) (:start . 53)\n  (:id . 53))\n ((:tag . "JJ") (:stem . "broad") (:form . "broad") (:end . 59) (:start . 54)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 60) (:start . 59)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 64) (:start . 61)\n  (:id . 56))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 69) (:start . 65)\n  (:id . 57))\n ((:tag . "NN") (:stem . "3d0f") (:form . "3d0f") (:end . 74) (:start . 70)\n  (:id . 58))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 75) (:start . 74)\n  (:id . 59))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 79) (:start . 76)\n  (:id . 60))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 83) (:start . 80)\n  (:id . 61))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 93)\n  (:start . 84) (:id . 62))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 103)\n  (:start . 94) (:id . 63))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 105) (:start . 104)\n  (:id . 64))\n ((:tag . "NN") (:stem . "thin") (:form . "thin") (:end . 109) (:start . 105)\n  (:id . 65))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 110) (:start . 109)\n  (:id . 66))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 111) (:start . 110)\n  (:id . 67)))@@@1@26@((:identifiers (:sid . :s15.240) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504979@unknown@formal@none@1@S@The green blocks are the regions that the predicted structure matches to the native structure.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "green") (:form . "green") (:end . 9) (:start . 4)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "block") (:form . "blocks") (:end . 16)\n  (:start . 10) (:id . 44))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 20) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 24) (:start . 21)\n  (:id . 46))\n ((:tag . "NNS") (:stem . "region") (:form . "regions") (:end . 32)\n  (:start . 25) (:id . 47))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 49))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 51)\n  (:start . 42) (:id . 50))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 61)\n  (:start . 52) (:id . 51))\n ((:tag . "VBZ") (:stem . "match") (:form . "matches") (:end . 69)\n  (:start . 62) (:id . 52))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 72) (:start . 70)\n  (:id . 53))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 76) (:start . 73)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 83)\n  (:start . 77) (:id . 55))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 93)\n  (:start . 84) (:id . 56))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 94) (:start . 93)\n  (:id . 57)))@@@1@16@((:identifiers (:sid . :s15.241) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504980@unknown@formal@none@1@S@The yellow and purple blocks indicate the shift errors between predicted structure and native structure, the Cα distances between them are <5 A and >5 A, respectively.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "yellow") (:form . "yellow") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 14) (:start . 11)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "purple") (:form . "purple") (:end . 21)\n  (:start . 15) (:id . 45))\n ((:tag . "NNS") (:stem . "block") (:form . "blocks") (:end . 28)\n  (:start . 22) (:id . 46))\n ((:tag . "VBP") (:stem . "indicate") (:form . "indicate") (:end . 37)\n  (:start . 29) (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 48))\n ((:tag . "NN") (:stem . "shift") (:form . "shift") (:end . 47) (:start . 42)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "error") (:form . "errors") (:end . 54)\n  (:start . 48) (:id . 50))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 62)\n  (:start . 55) (:id . 51))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 72)\n  (:start . 63) (:id . 52))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 82)\n  (:start . 73) (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 86) (:start . 83)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "native") (:form . "native") (:end . 93)\n  (:start . 87) (:id . 55))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 103)\n  (:start . 94) (:id . 56))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 104) (:start . 103)\n  (:id . 57))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 108) (:start . 105)\n  (:id . 58))\n ((:tag . "NNP") (:stem . "Cα") (:form . "Cα") (:end . 111) (:start . 109)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "distance") (:form . "distances") (:end . 121)\n  (:start . 112) (:id . 60))\n ((:tag . "IN") (:stem . "between") (:form . "between") (:end . 129)\n  (:start . 122) (:id . 61))\n ((:tag . "PRP") (:stem . "them") (:form . "them") (:end . 134) (:start . 130)\n  (:id . 62))\n ((:tag . "VBP") (:stem . "be") (:form . "are") (:end . 138) (:start . 135)\n  (:id . 63))\n ((:tag . "CD") (:stem . "<5") (:form . "<5") (:end . 141) (:start . 139)\n  (:id . 64))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 143) (:start . 142)\n  (:id . 65))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 147) (:start . 144)\n  (:id . 66))\n ((:tag . "CD") (:stem . ">5") (:form . ">5") (:end . 150) (:start . 148)\n  (:id . 67))\n ((:tag . "NN") (:stem . "a") (:form . "A") (:end . 152) (:start . 151)\n  (:id . 68))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 153) (:start . 152)\n  (:id . 69))\n ((:tag . "RB") (:stem . "respectively") (:form . "respectively") (:end . 166)\n  (:start . 154) (:id . 70))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 71)))@@@1@30@((:identifiers (:sid . :s15.242) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|FigureLegend|)))@oe@9-2-2011
5504981@unknown@formal@none@1@S@For the target T0409, the (PS)2-v2 server selected the C-terminal domain of translation initiation factor 5A protein (PDB code 1bkb) from Pyrobaculum aerophilum as the template [40].@(((:tag . "IN") (:stem . "for") (:form . "For") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 7) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 14) (:start . 8)\n  (:id . 44))\n ((:tag . "NN") (:stem . "t0409") (:form . "T0409") (:end . 20) (:start . 15)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 21) (:start . 20)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 25) (:start . 22)\n  (:id . 47))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 27) (:start . 26)\n  (:id . 48))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 34)\n  (:start . 27) (:id . 49))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 41)\n  (:start . 35) (:id . 50))\n ((:tag . "VBD") (:stem . "select") (:form . "selected") (:end . 50)\n  (:start . 42) (:id . 51))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 65)\n  (:start . 55) (:id . 53))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 72)\n  (:start . 66) (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 75) (:start . 73)\n  (:id . 55))\n ((:tag . "NN") (:stem . "translation") (:form . "translation") (:end . 87)\n  (:start . 76) (:id . 56))\n ((:tag . "NN") (:stem . "initiation") (:form . "initiation") (:end . 98)\n  (:start . 88) (:id . 57))\n ((:tag . "NN") (:stem . "factor") (:form . "factor") (:end . 105)\n  (:start . 99) (:id . 58))\n ((:tag . "NN") (:stem . "5a") (:form . "5A") (:end . 108) (:start . 106)\n  (:id . 59))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 116)\n  (:start . 109) (:id . 60))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 118) (:start . 117)\n  (:id . 61))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 121) (:start . 118)\n  (:id . 62))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 126) (:start . 122)\n  (:id . 63))\n ((:tag . "NN") (:stem . "1bkb") (:form . "1bkb") (:end . 131) (:start . 127)\n  (:id . 64))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 132) (:start . 131)\n  (:id . 65))\n ((:tag . "IN") (:stem . "from") (:form . "from") (:end . 137) (:start . 133)\n  (:id . 66))\n ((:tag . "NNP") (:stem . "Pyrobaculum") (:form . "Pyrobaculum") (:end . 149)\n  (:start . 138) (:id . 67))\n ((:tag . "NN") (:stem . "aerophilum") (:form . "aerophilum") (:end . 160)\n  (:start . 150) (:id . 68))\n ((:tag . "IN") (:stem . "as") (:form . "as") (:end . 163) (:start . 161)\n  (:id . 69))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 167) (:start . 164)\n  (:id . 70))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 176)\n  (:start . 168) (:id . 71))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 178) (:start . 177)\n  (:id . 72))\n ((:tag . "CD") (:stem . "40") (:form . "40") (:end . 180) (:start . 178)\n  (:id . 73))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 181) (:start . 180)\n  (:id . 74))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 182) (:start . 181)\n  (:id . 75)))@@@1@34@((:identifiers (:sid . :s15.243) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504982@unknown@formal@none@1@S@The C-terminal domain is found to be homologous to the cold-shock protein CspA of E. coli, which has a well characterized RNA-binding fold.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJ") (:stem . "c-terminal") (:form . "C-terminal") (:end . 14)\n  (:start . 4) (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 21)\n  (:start . 15) (:id . 44))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 24) (:start . 22)\n  (:id . 45))\n ((:tag . "VBN") (:stem . "find") (:form . "found") (:end . 30) (:start . 25)\n  (:id . 46))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 33) (:start . 31)\n  (:id . 47))\n ((:tag . "VB") (:stem . "be") (:form . "be") (:end . 36) (:start . 34)\n  (:id . 48))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 47)\n  (:start . 37) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "cold-shock") (:form . "cold-shock") (:end . 65)\n  (:start . 55) (:id . 52))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 73)\n  (:start . 66) (:id . 53))\n ((:tag . "NNP") (:stem . "CspA") (:form . "CspA") (:end . 78) (:start . 74)\n  (:id . 54))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 81) (:start . 79)\n  (:id . 55))\n ((:tag . "FW") (:stem . "e.") (:form . "E.") (:end . 84) (:start . 82)\n  (:id . 56))\n ((:tag . "FW") (:stem . "coli") (:form . "coli") (:end . 89) (:start . 85)\n  (:id . 57))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 90) (:start . 89)\n  (:id . 58))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 96) (:start . 91)\n  (:id . 59))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 100) (:start . 97)\n  (:id . 60))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 102) (:start . 101)\n  (:id . 61))\n ((:tag . "RB") (:stem . "well") (:form . "well") (:end . 107) (:start . 103)\n  (:id . 62))\n ((:tag . "VBN") (:stem . "characterize") (:form . "characterized")\n  (:end . 121) (:start . 108) (:id . 63))\n ((:tag . "JJ") (:stem . "rna-binding") (:form . "RNA-binding") (:end . 133)\n  (:start . 122) (:id . 64))\n ((:tag . "RB") (:stem . "fold") (:form . "fold") (:end . 138) (:start . 134)\n  (:id . 65))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 139) (:start . 138)\n  (:id . 66)))@@@1@25@((:identifiers (:sid . :s15.244) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504983@unknown@formal@none@1@S@The best template reported in the CASP8 website is the yeast exosome core, Rrp44 (PDB code 2vnvD) [41], which contains four domains (CSD1, CSD2, RNB and S1).@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "JJS") (:stem . "good") (:form . "best") (:end . 8) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 17)\n  (:start . 9) (:id . 44))\n ((:tag . "VBN") (:stem . "report") (:form . "reported") (:end . 26)\n  (:start . 18) (:id . 45))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 29) (:start . 27)\n  (:id . 46))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 33) (:start . 30)\n  (:id . 47))\n ((:tag . "NN") (:stem . "casp8") (:form . "CASP8") (:end . 39) (:start . 34)\n  (:id . 48))\n ((:tag . "NN") (:stem . "website") (:form . "website") (:end . 47)\n  (:start . 40) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 50) (:start . 48)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 54) (:start . 51)\n  (:id . 51))\n ((:tag . "NN") (:stem . "yeast") (:form . "yeast") (:end . 60) (:start . 55)\n  (:id . 52))\n ((:tag . "NN") (:stem . "exosome") (:form . "exosome") (:end . 68)\n  (:start . 61) (:id . 53))\n ((:tag . "NN") (:stem . "core") (:form . "core") (:end . 73) (:start . 69)\n  (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 74) (:start . 73)\n  (:id . 55))\n ((:tag . "NNP") (:stem . "Rrp44") (:form . "Rrp44") (:end . 80) (:start . 75)\n  (:id . 56))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 82) (:start . 81)\n  (:id . 57))\n ((:tag . "NNP") (:stem . "PDB") (:form . "PDB") (:end . 85) (:start . 82)\n  (:id . 58))\n ((:tag . "NN") (:stem . "code") (:form . "code") (:end . 90) (:start . 86)\n  (:id . 59))\n ((:tag . "NN") (:stem . "2vnvd") (:form . "2vnvD") (:end . 96) (:start . 91)\n  (:id . 60))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 97) (:start . 96)\n  (:id . 61))\n ((:tag . "(") (:stem . "[") (:form . "[") (:end . 99) (:start . 98)\n  (:id . 62))\n ((:tag . "CD") (:stem . "41") (:form . "41") (:end . 101) (:start . 99)\n  (:id . 63))\n ((:tag . ")") (:stem . "]") (:form . "]") (:end . 102) (:start . 101)\n  (:id . 64))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 103) (:start . 102)\n  (:id . 65))\n ((:tag . "WDT") (:stem . "which") (:form . "which") (:end . 109)\n  (:start . 104) (:id . 66))\n ((:tag . "VBZ") (:stem . "contain") (:form . "contains") (:end . 118)\n  (:start . 110) (:id . 67))\n ((:tag . "CD") (:stem . "four") (:form . "four") (:end . 123) (:start . 119)\n  (:id . 68))\n ((:tag . "NNS") (:stem . "domain") (:form . "domains") (:end . 131)\n  (:start . 124) (:id . 69))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 133) (:start . 132)\n  (:id . 70))\n ((:tag . "NNP") (:stem . "CSD1") (:form . "CSD1") (:end . 137) (:start . 133)\n  (:id . 71))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 138) (:start . 137)\n  (:id . 72))\n ((:tag . "NNP") (:stem . "CSD2") (:form . "CSD2") (:end . 143) (:start . 139)\n  (:id . 73))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 144) (:start . 143)\n  (:id . 74))\n ((:tag . "NNP") (:stem . "RNB") (:form . "RNB") (:end . 148) (:start . 145)\n  (:id . 75))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 152) (:start . 149)\n  (:id . 76))\n ((:tag . "NNP") (:stem . "S1") (:form . "S1") (:end . 155) (:start . 153)\n  (:id . 77))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 156) (:start . 155)\n  (:id . 78))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 157) (:start . 156)\n  (:id . 79)))@@@1@38@((:identifiers (:sid . :s15.245) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504984@unknown@formal@none@1@S@The S1 domain has the most similar structure to the target T0409-D1.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "s1") (:form . "S1") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 17) (:start . 14)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 21) (:start . 18)\n  (:id . 46))\n ((:tag . "RBS") (:stem . "most") (:form . "most") (:end . 26) (:start . 22)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "similar") (:form . "similar") (:end . 34)\n  (:start . 27) (:id . 48))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 44)\n  (:start . 35) (:id . 49))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 47) (:start . 45)\n  (:id . 50))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 51) (:start . 48)\n  (:id . 51))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 58)\n  (:start . 52) (:id . 52))\n ((:tag . "NN") (:stem . "t0409-d1") (:form . "T0409-D1") (:end . 67)\n  (:start . 59) (:id . 53))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 68) (:start . 67)\n  (:id . 54)))@@@1@13@((:identifiers (:sid . :s15.246) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504985@unknown@formal@none@1@S@The S1 domain also has a common OB fold characteristic of RNA-binding protein, with five anti-parallel ß strands.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "s1") (:form . "S1") (:end . 6) (:start . 4)\n  (:id . 43))\n ((:tag . "NN") (:stem . "domain") (:form . "domain") (:end . 13) (:start . 7)\n  (:id . 44))\n ((:tag . "RB") (:stem . "also") (:form . "also") (:end . 18) (:start . 14)\n  (:id . 45))\n ((:tag . "VBZ") (:stem . "have") (:form . "has") (:end . 22) (:start . 19)\n  (:id . 46))\n ((:tag . "DT") (:stem . "a") (:form . "a") (:end . 24) (:start . 23)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "common") (:form . "common") (:end . 31)\n  (:start . 25) (:id . 48))\n ((:tag . "NN") (:stem . "ob") (:form . "OB") (:end . 34) (:start . 32)\n  (:id . 49))\n ((:tag . "RB") (:stem . "fold") (:form . "fold") (:end . 39) (:start . 35)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "characteristic") (:form . "characteristic")\n  (:end . 54) (:start . 40) (:id . 51))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 57) (:start . 55)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "rna-binding") (:form . "RNA-binding") (:end . 69)\n  (:start . 58) (:id . 53))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 77)\n  (:start . 70) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 78) (:start . 77)\n  (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 83) (:start . 79)\n  (:id . 56))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 88) (:start . 84)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "anti-parallel") (:form . "anti-parallel")\n  (:end . 102) (:start . 89) (:id . 58))\n ((:tag . "NN") (:stem . "ß") (:form . "ß") (:end . 104) (:start . 103)\n  (:id . 59))\n ((:tag . "NNS") (:stem . "strand") (:form . "strands") (:end . 112)\n  (:start . 105) (:id . 60))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 113) (:start . 112)\n  (:id . 61)))@@@1@20@((:identifiers (:sid . :s15.247) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504986@unknown@formal@none@1@S@Figure 8A shows the target-template alignment and the template shares 17.0% sequence identity with the query sequence.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "8a") (:form . "8A") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 35) (:start . 20) (:id . 46))\n ((:tag . "NN") (:stem . "alignment") (:form . "alignment") (:end . 45)\n  (:start . 36) (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 49) (:start . 46)\n  (:id . 48))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 53) (:start . 50)\n  (:id . 49))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 62)\n  (:start . 54) (:id . 50))\n ((:tag . "NNS") (:stem . "share") (:form . "shares") (:end . 69)\n  (:start . 63) (:id . 51))\n ((:tag . "CD") (:stem . "17.0") (:form . "17.0") (:end . 74) (:start . 70)\n  (:id . 52))\n ((:tag . "NN") (:stem . "%") (:form . "%") (:end . 75) (:start . 74)\n  (:id . 53))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 84)\n  (:start . 76) (:id . 54))\n ((:tag . "NN") (:stem . "identity") (:form . "identity") (:end . 93)\n  (:start . 85) (:id . 55))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 98) (:start . 94)\n  (:id . 56))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 102) (:start . 99)\n  (:id . 57))\n ((:tag . "NN") (:stem . "query") (:form . "query") (:end . 108)\n  (:start . 103) (:id . 58))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 117)\n  (:start . 109) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 118) (:start . 117)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.248) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504987@unknown@formal@none@1@S@Our server could align the five anti-parallel ß strands together.@(((:tag . "PRP$") (:stem . "our") (:form . "Our") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 10) (:start . 4)\n  (:id . 43))\n ((:tag . "MD") (:stem . "could") (:form . "could") (:end . 16) (:start . 11)\n  (:id . 44))\n ((:tag . "VB") (:stem . "align") (:form . "align") (:end . 22) (:start . 17)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 26) (:start . 23)\n  (:id . 46))\n ((:tag . "CD") (:stem . "five") (:form . "five") (:end . 31) (:start . 27)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "anti-parallel") (:form . "anti-parallel")\n  (:end . 45) (:start . 32) (:id . 48))\n ((:tag . "NN") (:stem . "ß") (:form . "ß") (:end . 47) (:start . 46)\n  (:id . 49))\n ((:tag . "NNS") (:stem . "strand") (:form . "strands") (:end . 55)\n  (:start . 48) (:id . 50))\n ((:tag . "RB") (:stem . "together") (:form . "together") (:end . 64)\n  (:start . 56) (:id . 51))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 65) (:start . 64)\n  (:id . 52)))@@@1@11@((:identifiers (:sid . :s15.249) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504988@unknown@formal@none@1@S@Figure 8B shows the superposition of the predicted structure (thin) and the X-ray structure (broad) of the target T0409.@(((:tag . "NNP") (:stem . "Figure") (:form . "Figure") (:end . 6) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "8b") (:form . "8B") (:end . 9) (:start . 7)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "show") (:form . "shows") (:end . 15) (:start . 10)\n  (:id . 44))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 19) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "superposition") (:form . "superposition")\n  (:end . 33) (:start . 20) (:id . 46))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 36) (:start . 34)\n  (:id . 47))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 40) (:start . 37)\n  (:id . 48))\n ((:tag . "VBN") (:stem . "predict") (:form . "predicted") (:end . 50)\n  (:start . 41) (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 60)\n  (:start . 51) (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 62) (:start . 61)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "thin") (:form . "thin") (:end . 66) (:start . 62)\n  (:id . 52))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 67) (:start . 66)\n  (:id . 53))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 71) (:start . 68)\n  (:id . 54))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 75) (:start . 72)\n  (:id . 55))\n ((:tag . "NN") (:stem . "x-ray") (:form . "X-ray") (:end . 81) (:start . 76)\n  (:id . 56))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 91)\n  (:start . 82) (:id . 57))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 93) (:start . 92)\n  (:id . 58))\n ((:tag . "JJ") (:stem . "broad") (:form . "broad") (:end . 98) (:start . 93)\n  (:id . 59))\n ((:tag . ")") (:stem . ")") (:form . ")") (:end . 99) (:start . 98)\n  (:id . 60))\n ((:tag . "IN") (:stem . "of") (:form . "of") (:end . 102) (:start . 100)\n  (:id . 61))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 106) (:start . 103)\n  (:id . 62))\n ((:tag . "NN") (:stem . "target") (:form . "target") (:end . 113)\n  (:start . 107) (:id . 63))\n ((:tag . "NN") (:stem . "t0409") (:form . "T0409") (:end . 119)\n  (:start . 114) (:id . 64))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 120) (:start . 119)\n  (:id . 65)))@@@1@24@((:identifiers (:sid . :s15.250) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504989@unknown@formal@none@1@S@Conclusion@(((:tag . "NN") (:stem . "conclusion") (:form . "Conclusion") (:end . 10)\n  (:start . 0) (:id . 42)))@@@1@1@((:identifiers (:sid . :s15.251) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504990@unknown@formal@none@1@S@This study presents an automatic server for protein structure predictions by applying numerous enhancements and modifications to the original technique, thereby improving the reliability and applicability.@(((:tag . "DT") (:stem . "this") (:form . "This") (:end . 4) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "study") (:form . "study") (:end . 10) (:start . 5)\n  (:id . 43))\n ((:tag . "VBZ") (:stem . "present") (:form . "presents") (:end . 19)\n  (:start . 11) (:id . 44))\n ((:tag . "DT") (:stem . "an") (:form . "an") (:end . 22) (:start . 20)\n  (:id . 45))\n ((:tag . "JJ") (:stem . "automatic") (:form . "automatic") (:end . 32)\n  (:start . 23) (:id . 46))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 39)\n  (:start . 33) (:id . 47))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 43) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 51)\n  (:start . 44) (:id . 49))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 61)\n  (:start . 52) (:id . 50))\n ((:tag . "NNS") (:stem . "prediction") (:form . "predictions") (:end . 73)\n  (:start . 62) (:id . 51))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 76) (:start . 74)\n  (:id . 52))\n ((:tag . "VBG") (:stem . "apply") (:form . "applying") (:end . 85)\n  (:start . 77) (:id . 53))\n ((:tag . "JJ") (:stem . "numerous") (:form . "numerous") (:end . 94)\n  (:start . 86) (:id . 54))\n ((:tag . "NNS") (:stem . "enhancement") (:form . "enhancements") (:end . 107)\n  (:start . 95) (:id . 55))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 111) (:start . 108)\n  (:id . 56))\n ((:tag . "NNS") (:stem . "modification") (:form . "modifications")\n  (:end . 125) (:start . 112) (:id . 57))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 128) (:start . 126)\n  (:id . 58))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 132) (:start . 129)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "original") (:form . "original") (:end . 141)\n  (:start . 133) (:id . 60))\n ((:tag . "NN") (:stem . "technique") (:form . "technique") (:end . 151)\n  (:start . 142) (:id . 61))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 152) (:start . 151)\n  (:id . 62))\n ((:tag . "RB") (:stem . "thereby") (:form . "thereby") (:end . 160)\n  (:start . 153) (:id . 63))\n ((:tag . "VBG") (:stem . "improve") (:form . "improving") (:end . 170)\n  (:start . 161) (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 174) (:start . 171)\n  (:id . 65))\n ((:tag . "NN") (:stem . "reliability") (:form . "reliability") (:end . 186)\n  (:start . 175) (:id . 66))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 190) (:start . 187)\n  (:id . 67))\n ((:tag . "NN") (:stem . "applicability") (:form . "applicability")\n  (:end . 204) (:start . 191) (:id . 68))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 205) (:start . 204)\n  (:id . 69)))@@@1@28@((:identifiers (:sid . :s15.252) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504991@unknown@formal@none@1@S@By integrating the S2A2 and PSSM matrixes, the (PS)2-v2 server seamlessly blends the amino acid and structural propensities so that they work cooperatively for the template selection and target-template alignments.@(((:tag . "IN") (:stem . "by") (:form . "By") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBG") (:stem . "integrate") (:form . "integrating") (:end . 14)\n  (:start . 3) (:id . 43))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 18) (:start . 15)\n  (:id . 44))\n ((:tag . "NN") (:stem . "s2a2") (:form . "S2A2") (:end . 23) (:start . 19)\n  (:id . 45))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 27) (:start . 24)\n  (:id . 46))\n ((:tag . "NN") (:stem . "pssm") (:form . "PSSM") (:end . 32) (:start . 28)\n  (:id . 47))\n ((:tag . "NNS") (:stem . "matrix") (:form . "matrixes") (:end . 41)\n  (:start . 33) (:id . 48))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 42) (:start . 41)\n  (:id . 49))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 46) (:start . 43)\n  (:id . 50))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 48) (:start . 47)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 55)\n  (:start . 48) (:id . 52))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 62)\n  (:start . 56) (:id . 53))\n ((:tag . "RB") (:stem . "seamlessly") (:form . "seamlessly") (:end . 73)\n  (:start . 63) (:id . 54))\n ((:tag . "VBZ") (:stem . "blend") (:form . "blends") (:end . 80)\n  (:start . 74) (:id . 55))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 84) (:start . 81)\n  (:id . 56))\n ((:tag . "JJ") (:stem . "amino") (:form . "amino") (:end . 90) (:start . 85)\n  (:id . 57))\n ((:tag . "NN") (:stem . "acid") (:form . "acid") (:end . 95) (:start . 91)\n  (:id . 58))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 99) (:start . 96)\n  (:id . 59))\n ((:tag . "JJ") (:stem . "structural") (:form . "structural") (:end . 110)\n  (:start . 100) (:id . 60))\n ((:tag . "NNS") (:stem . "propensity") (:form . "propensities") (:end . 123)\n  (:start . 111) (:id . 61))\n ((:tag . "IN") (:stem . "so") (:form . "so") (:end . 126) (:start . 124)\n  (:id . 62))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 131) (:start . 127)\n  (:id . 63))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 136) (:start . 132)\n  (:id . 64))\n ((:tag . "VBP") (:stem . "work") (:form . "work") (:end . 141) (:start . 137)\n  (:id . 65))\n ((:tag . "RB") (:stem . "cooperatively") (:form . "cooperatively")\n  (:end . 155) (:start . 142) (:id . 66))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 159) (:start . 156)\n  (:id . 67))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 163) (:start . 160)\n  (:id . 68))\n ((:tag . "NN") (:stem . "template") (:form . "template") (:end . 172)\n  (:start . 164) (:id . 69))\n ((:tag . "NN") (:stem . "selection") (:form . "selection") (:end . 182)\n  (:start . 173) (:id . 70))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 186) (:start . 183)\n  (:id . 71))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 202) (:start . 187) (:id . 72))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 213)\n  (:start . 203) (:id . 73))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 214) (:start . 213)\n  (:id . 74)))@@@1@33@((:identifiers (:sid . :s15.253) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504992@unknown@formal@none@1@S@In addition, our (PS)2-v2 utilizes multiple templates and multiple models for building models and assessing models.@(((:tag . "IN") (:stem . "in") (:form . "In") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "NN") (:stem . "addition") (:form . "addition") (:end . 11)\n  (:start . 3) (:id . 43))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 12) (:start . 11)\n  (:id . 44))\n ((:tag . "PRP$") (:stem . "our") (:form . "our") (:end . 16) (:start . 13)\n  (:id . 45))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 18) (:start . 17)\n  (:id . 46))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 25)\n  (:start . 18) (:id . 47))\n ((:tag . "VBZ") (:stem . "utilize") (:form . "utilizes") (:end . 34)\n  (:start . 26) (:id . 48))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 43)\n  (:start . 35) (:id . 49))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 53)\n  (:start . 44) (:id . 50))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 57) (:start . 54)\n  (:id . 51))\n ((:tag . "JJ") (:stem . "multiple") (:form . "multiple") (:end . 66)\n  (:start . 58) (:id . 52))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 73)\n  (:start . 67) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 77) (:start . 74)\n  (:id . 54))\n ((:tag . "NN") (:stem . "building") (:form . "building") (:end . 86)\n  (:start . 78) (:id . 55))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 93)\n  (:start . 87) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 97) (:start . 94)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "assess") (:form . "assessing") (:end . 107)\n  (:start . 98) (:id . 58))\n ((:tag . "NNS") (:stem . "model") (:form . "models") (:end . 114)\n  (:start . 108) (:id . 59))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 115) (:start . 114)\n  (:id . 60)))@@@1@19@((:identifiers (:sid . :s15.254) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504993@unknown@formal@none@1@S@Experimental results demonstrate that the (PS)2-v2 server is efficient and effective for template selections and target-template alignments in template-based modeling.@(((:tag . "JJ") (:stem . "experimental") (:form . "Experimental") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "result") (:form . "results") (:end . 20)\n  (:start . 13) (:id . 43))\n ((:tag . "VBP") (:stem . "demonstrate") (:form . "demonstrate") (:end . 32)\n  (:start . 21) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 37) (:start . 33)\n  (:id . 45))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 41) (:start . 38)\n  (:id . 46))\n ((:tag . "(") (:stem . "(") (:form . "(") (:end . 43) (:start . 42)\n  (:id . 47))\n ((:tag . "NN") (:stem . "PS)2-v2") (:form . "PS)2-v2") (:end . 50)\n  (:start . 43) (:id . 48))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 57)\n  (:start . 51) (:id . 49))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 60) (:start . 58)\n  (:id . 50))\n ((:tag . "JJ") (:stem . "efficient") (:form . "efficient") (:end . 70)\n  (:start . 61) (:id . 51))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 74) (:start . 71)\n  (:id . 52))\n ((:tag . "JJ") (:stem . "effective") (:form . "effective") (:end . 84)\n  (:start . 75) (:id . 53))\n ((:tag . "IN") (:stem . "for") (:form . "for") (:end . 88) (:start . 85)\n  (:id . 54))\n ((:tag . "JJ") (:stem . "template") (:form . "template") (:end . 97)\n  (:start . 89) (:id . 55))\n ((:tag . "NNS") (:stem . "selection") (:form . "selections") (:end . 108)\n  (:start . 98) (:id . 56))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 112) (:start . 109)\n  (:id . 57))\n ((:tag . "JJ") (:stem . "target-template") (:form . "target-template")\n  (:end . 128) (:start . 113) (:id . 58))\n ((:tag . "NNS") (:stem . "alignment") (:form . "alignments") (:end . 139)\n  (:start . 129) (:id . 59))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 142) (:start . 140)\n  (:id . 60))\n ((:tag . "JJ") (:stem . "template-based") (:form . "template-based")\n  (:end . 157) (:start . 143) (:id . 61))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 166)\n  (:start . 158) (:id . 62))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 167) (:start . 166)\n  (:id . 63)))@@@1@22@((:identifiers (:sid . :s15.255) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504994@unknown@formal@none@1@S@We believe that this server is useful in protein structure prediction and modeling, especially in detecting homologous templates with sequence similarity in the twilight zone.@(((:tag . "PRP") (:stem . "we") (:form . "We") (:end . 2) (:start . 0)\n  (:id . 42))\n ((:tag . "VBP") (:stem . "believe") (:form . "believe") (:end . 10)\n  (:start . 3) (:id . 43))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 15) (:start . 11)\n  (:id . 44))\n ((:tag . "DT") (:stem . "this") (:form . "this") (:end . 20) (:start . 16)\n  (:id . 45))\n ((:tag . "NN") (:stem . "server") (:form . "server") (:end . 27)\n  (:start . 21) (:id . 46))\n ((:tag . "VBZ") (:stem . "be") (:form . "is") (:end . 30) (:start . 28)\n  (:id . 47))\n ((:tag . "JJ") (:stem . "useful") (:form . "useful") (:end . 37)\n  (:start . 31) (:id . 48))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 40) (:start . 38)\n  (:id . 49))\n ((:tag . "NN") (:stem . "protein") (:form . "protein") (:end . 48)\n  (:start . 41) (:id . 50))\n ((:tag . "NN") (:stem . "structure") (:form . "structure") (:end . 58)\n  (:start . 49) (:id . 51))\n ((:tag . "NN") (:stem . "prediction") (:form . "prediction") (:end . 69)\n  (:start . 59) (:id . 52))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 73) (:start . 70)\n  (:id . 53))\n ((:tag . "NN") (:stem . "modeling") (:form . "modeling") (:end . 82)\n  (:start . 74) (:id . 54))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 83) (:start . 82)\n  (:id . 55))\n ((:tag . "RB") (:stem . "especially") (:form . "especially") (:end . 94)\n  (:start . 84) (:id . 56))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 97) (:start . 95)\n  (:id . 57))\n ((:tag . "VBG") (:stem . "detect") (:form . "detecting") (:end . 107)\n  (:start . 98) (:id . 58))\n ((:tag . "JJ") (:stem . "homologous") (:form . "homologous") (:end . 118)\n  (:start . 108) (:id . 59))\n ((:tag . "NNS") (:stem . "template") (:form . "templates") (:end . 128)\n  (:start . 119) (:id . 60))\n ((:tag . "IN") (:stem . "with") (:form . "with") (:end . 133) (:start . 129)\n  (:id . 61))\n ((:tag . "NN") (:stem . "sequence") (:form . "sequence") (:end . 142)\n  (:start . 134) (:id . 62))\n ((:tag . "NN") (:stem . "similarity") (:form . "similarity") (:end . 153)\n  (:start . 143) (:id . 63))\n ((:tag . "IN") (:stem . "in") (:form . "in") (:end . 156) (:start . 154)\n  (:id . 64))\n ((:tag . "DT") (:stem . "the") (:form . "the") (:end . 160) (:start . 157)\n  (:id . 65))\n ((:tag . "JJ") (:stem . "twilight") (:form . "twilight") (:end . 169)\n  (:start . 161) (:id . 66))\n ((:tag . "NN") (:stem . "zone") (:form . "zone") (:end . 174) (:start . 170)\n  (:id . 67))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 175) (:start . 174)\n  (:id . 68)))@@@1@27@((:hcues ((:id . :x15.256.1) (:span 3 10)))\n (:hscopes ((:id . :x15.256.1) (:span 3 174)))\n (:identifiers (:sid . :s15.256) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504995@unknown@formal@none@1@S@Availability and requirements@(((:tag . "NN") (:stem . "availability") (:form . "Availability") (:end . 12)\n  (:start . 0) (:id . 42))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 16) (:start . 13)\n  (:id . 43))\n ((:tag . "NNS") (:stem . "requirement") (:form . "requirements") (:end . 29)\n  (:start . 17) (:id . 44)))@@@1@3@((:identifiers (:sid . :s15.257) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5504996@unknown@formal@none@1@S@Project home page: http://ps2v2.life.nctu.edu.tw@(((:tag . "NNP") (:stem . "Project") (:form . "Project") (:end . 7)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "home") (:form . "home") (:end . 12) (:start . 8)\n  (:id . 43))\n ((:tag . "NN") (:stem . "page") (:form . "page") (:end . 17) (:start . 13)\n  (:id . 44))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 18) (:start . 17)\n  (:id . 45))\n ((:tag . "NN") (:stem . "http://ps2v2.life.nctu.edu.tw")\n  (:form . "http://ps2v2.life.nctu.edu.tw") (:end . 48) (:start . 19)\n  (:id . 46)))@@@1@5@((:identifiers (:sid . :s15.258) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504997@unknown@formal@none@1@S@Operating system(s): Platform independent@(((:tag . "NN") (:stem . "operating") (:form . "Operating") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "system(s)") (:form . "system(s)") (:end . 19)\n  (:start . 10) (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 20) (:start . 19)\n  (:id . 44))\n ((:tag . "NN") (:stem . "platform") (:form . "Platform") (:end . 29)\n  (:start . 21) (:id . 45))\n ((:tag . "JJ") (:stem . "independent") (:form . "independent") (:end . 41)\n  (:start . 30) (:id . 46)))@@@1@5@((:identifiers (:sid . :s15.259) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504998@unknown@formal@none@1@S@Programming language: C, Perl and PHP@(((:tag . "VBG") (:stem . "program") (:form . "Programming") (:end . 11)\n  (:start . 0) (:id . 42))\n ((:tag . "NN") (:stem . "language") (:form . "language") (:end . 20)\n  (:start . 12) (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 21) (:start . 20)\n  (:id . 44))\n ((:tag . "NNP") (:stem . "C") (:form . "C") (:end . 23) (:start . 22)\n  (:id . 45))\n ((:tag . ",") (:stem . ",") (:form . ",") (:end . 24) (:start . 23)\n  (:id . 46))\n ((:tag . "NNP") (:stem . "Perl") (:form . "Perl") (:end . 29) (:start . 25)\n  (:id . 47))\n ((:tag . "CC") (:stem . "and") (:form . "and") (:end . 33) (:start . 30)\n  (:id . 48))\n ((:tag . "NNP") (:stem . "PHP") (:form . "PHP") (:end . 37) (:start . 34)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s15.260) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5504999@unknown@formal@none@1@S@Other requirements: JavaScript-enabled web browser@(((:tag . "JJ") (:stem . "other") (:form . "Other") (:end . 5) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "requirement") (:form . "requirements") (:end . 18)\n  (:start . 6) (:id . 43))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 19) (:start . 18)\n  (:id . 44))\n ((:tag . "JJ") (:stem . "javascript-enabled") (:form . "JavaScript-enabled")\n  (:end . 38) (:start . 20) (:id . 45))\n ((:tag . "NN") (:stem . "web") (:form . "web") (:end . 42) (:start . 39)\n  (:id . 46))\n ((:tag . "NN") (:stem . "browser") (:form . "browser") (:end . 50)\n  (:start . 43) (:id . 47)))@@@1@6@((:identifiers (:sid . :s15.261) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5505000@unknown@formal@none@1@S@Any restrictions to use by non-academics: None@(((:tag . "DT") (:stem . "any") (:form . "Any") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "restriction") (:form . "restrictions") (:end . 16)\n  (:start . 4) (:id . 43))\n ((:tag . "TO") (:stem . "to") (:form . "to") (:end . 19) (:start . 17)\n  (:id . 44))\n ((:tag . "VB") (:stem . "use") (:form . "use") (:end . 23) (:start . 20)\n  (:id . 45))\n ((:tag . "IN") (:stem . "by") (:form . "by") (:end . 26) (:start . 24)\n  (:id . 46))\n ((:tag . "JJ") (:stem . "non-academics") (:form . "non-academics")\n  (:end . 40) (:start . 27) (:id . 47))\n ((:tag . ":") (:stem . ":") (:form . ":") (:end . 41) (:start . 40)\n  (:id . 48))\n ((:tag . "NN") (:stem . "none") (:form . "None") (:end . 46) (:start . 42)\n  (:id . 49)))@@@1@8@((:identifiers (:sid . :s15.262) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011
5505001@unknown@formal@none@1@S@Competing interests@(((:tag . "VBG") (:stem . "compete") (:form . "Competing") (:end . 9)\n  (:start . 0) (:id . 42))\n ((:tag . "NNS") (:stem . "interest") (:form . "interests") (:end . 19)\n  (:start . 10) (:id . 43)))@@@1@2@((:identifiers (:sid . :s15.263) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|SectionTitle|)))@oe@9-2-2011
5505002@unknown@formal@none@1@S@The authors declare that they have no competing interests.@(((:tag . "DT") (:stem . "the") (:form . "The") (:end . 3) (:start . 0)\n  (:id . 42))\n ((:tag . "NNS") (:stem . "author") (:form . "authors") (:end . 11)\n  (:start . 4) (:id . 43))\n ((:tag . "VBP") (:stem . "declare") (:form . "declare") (:end . 19)\n  (:start . 12) (:id . 44))\n ((:tag . "IN") (:stem . "that") (:form . "that") (:end . 24) (:start . 20)\n  (:id . 45))\n ((:tag . "PRP") (:stem . "they") (:form . "they") (:end . 29) (:start . 25)\n  (:id . 46))\n ((:tag . "VBP") (:stem . "have") (:form . "have") (:end . 34) (:start . 30)\n  (:id . 47))\n ((:tag . "DT") (:stem . "no") (:form . "no") (:end . 37) (:start . 35)\n  (:id . 48))\n ((:tag . "VBG") (:stem . "compete") (:form . "competing") (:end . 47)\n  (:start . 38) (:id . 49))\n ((:tag . "NNS") (:stem . "interest") (:form . "interests") (:end . 57)\n  (:start . 48) (:id . 50))\n ((:tag . ".") (:stem . ".") (:form . ".") (:end . 58) (:start . 57)\n  (:id . 51)))@@@1@10@((:identifiers (:sid . :s15.264) (:did . :pmc2775752) (:did-type . :pmcid)\n  (:dtype . :|Biological_full_article|) (:dpart . :|Text|)))@oe@9-2-2011